Publications

Antimicrobial resistance and serotype distribution of Salmonella spp. isolated from fresh foods in Cambodia.

Huoy L, Nasirzadeh L, Phan K, ..., Rudloff EB, Boqvist S

J Appl Microbiol - (-) - [2025-06-03; online 2025-06-03]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]

Fin Whale as a Sink of Legacy and Emerging Contaminants: First Integrated Chemical Exposomics and Gene Expression Analysis in Cetaceans.

Fossi MC, Limonta G, Baini M, ..., Rosso M, Panti C

Environ. Sci. Technol. - (-) - [2025-06-02; online 2025-06-02]

Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer.

Sur I, Zhao W, Zhang J, ..., de la Roche M, Taipale J

Life Sci. Alliance 8 (6) - [2025-06-00; online 2025-04-03]

NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.

Thörn F, Müller IA, Soares AER, ..., Blom MPK, Irestedt M

Mol. Ecol. 34 (11) e17780 [2025-06-00; online 2025-04-29]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diffuse large B cell lymphoma in rheumatoid arthritis patients is associated with elevated B-cell driving factors including CXCL13.

Euler N, Hellbacher E, Klint EA, ..., Grönwall C, AUTO-LYMPHOMA study group

Clin. Immunol. 275 (-) 110476 [2025-06-00; online 2025-03-19]

Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes.

Papadopoulou S, Linkhorst A, Balmonte JP, ..., Bertilsson S, Székely AJ

Environ Microbiol Rep 17 (3) e70099 [2025-06-00; online 2025-05-09]

NGI Short read [Service] NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma membrane labelling efficiency, internalization and partitioning of functionalized fluorescent lipids as a function of lipid structure

Sezgin E

- - (-) - [2025-05-13; online 2025-05-13]

Integrated Microscopy Technologies Stockholm [Service]

Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.

An Y, Garcia SL, Hambäck PA

mSystems - (-) e0172324 [2025-05-13; online 2025-05-13]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

CpG island methylator phenotype classification improves risk assessment in pediatric T-cell acute lymphoblastic leukemia.

Schäfer Hackenhaar F, Refhagen N, Hagleitner M, ..., Hultdin M, Degerman S

Blood 145 (19) 2161-2178 [2025-05-08; online 2025-01-22]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gut microbiota mediates SREBP-1c-driven hepatic lipogenesis and steatosis in response to zero-fat high-sucrose diet.

Bergentall M, Tremaroli V, Sun C, ..., Nieuwdorp M, Bäckhed F

Mol Metab 97 (-) 102162 [2025-05-07; online 2025-05-07]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Green Listed v2.0: A Web Application for Streamlined Design of Custom CRISPR Screens.

Henkel E, Li Z, Uvehag D, ..., Henkel M, Wermeling F

CRISPR J - (-) - [2025-05-07; online 2025-05-07]

CRISPR Functional Genomics [Technology development] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity.

Xu Y, Lou D, Chen P, ..., Hu Y, Wang J

Dev. Cell - (-) - [2025-05-06; online 2025-05-06]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

External validation of plasma CSF1 as a preoperative prognostic marker in patients with resectable intrahepatic cholangiocarcinoma.

Akiki A, Jacobsson H, Nouairia G, ..., Taflin H, Jansson H

Eur J Surg Oncol 51 (8) 110123 [2025-05-04; online 2025-05-04]

Ancient DNA [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Museum Ecologies

Fredengren C, Ewing A, Owman C, Holmstedt J

Mus. Soc. 23 (1) - [2025-05-01; online 2025-05-01]

High Content Imaging in Drug Discovery

- - (-) - [2025-04-30; online 2025-04-30]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis.

Sreenivasan AP, Vaivade A, Noui Y, ..., Spjuth O, Kultima K

NPJ Digit Med 8 (1) 224 [2025-04-24; online 2025-04-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

Dussex N, Jansson I, van der Valk T, ..., E Mjingo E, Spong G

Commun Biol 8 (1) 640 [2025-04-21; online 2025-04-21]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis.

González-López A, Ge X, Larsson DSD, ..., Sanyal S, Selmer M

Nat Commun 16 (1) 3693 [2025-04-18; online 2025-04-18]

Challenging the "Undruggable"─Targeting STAT3 but Identifying Potent TrkA-Targeted Inhibitors.

Iliev P, McCutcheon C, Admas TH, ..., Frank DA, Page BDG

J. Med. Chem. - (-) - [2025-04-17; online 2025-04-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

In vivo composition of the mitochondrial nucleoid in mice.

García-Villegas R, Odenthal F, Giannoula Y, ..., Levander F, Larsson NG

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research - (-) 119955 [2025-04-15; online 2025-04-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Choline levels in the pregenual anterior cingulate cortex associated with unpleasant pain experience and anxiety.

Hudhud L, Hauksson J, Haney M, ..., Eriksson J, Lindgren L

Neuroimage 310 (-) 121153 [2025-04-15; online 2025-03-16]

Cytoskeletal alterations in neuronal cells implicate Toxoplasma gondii secretory machinery and host microRNA-containing extracellular vesicles.

Mazza T, Aslanzadeh M, Berentsen L, ..., Friedländer MR, Barragan A

Sci Rep 15 (1) 12606 [2025-04-12; online 2025-04-12]

NGI Other [Collaborative] NGI Short read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Collaborative]

Antibacterial compounds against non-growing and intracellular bacteria

Kaldalu N, Bērziņš N, Berglund Fick S, ..., Hauryliuk V, Tenson T

npj Antimicrob Resist 3 (1) - [2025-04-11; online 2025-04-11]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A red fluorescent lifeact marker to study actin morphology in podocytes.

Wiesner E, Binz-Lotter J, Tröder SE, ..., Wedlich-Söldner R, Hackl MJ

Sci Rep 15 (1) 12386 [2025-04-11; online 2025-04-11]

Integrated Microscopy Technologies Stockholm [Service]

Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation.

Huang H, Fong M, Nowak I, ..., Angeletti D, Sarshad AA

Nucleic Acids Res. 53 (7) - [2025-04-10; online 2025-04-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dual GSK-3β/HDAC Inhibitors Enhance the Efficacy of Macrophages to Control Mycobacterium tuberculosis Infection.

Kalsum S, Xu R, Akber M, ..., Zhou Y, Brighenti S

Biomolecules 15 (4) 550 [2025-04-09; online 2025-04-09]

Chemical Biology Consortium Sweden (CBCS) [Service]

Design, Synthesis, and Biophysical Characterization of Pyridine Bis‐Quinazoline Derivatives as Selective G‐Quadruplex DNA Stabilizers

Nath Das R, Chorell E

Chem. Eur. J. 31 (21) - [2025-04-09; online 2025-03-05]

Chemical Biology Consortium Sweden (CBCS) [Service]

Metabolic readouts of tumor instructed normal tissues (TINT) identify aggressive prostate cancer subgroups for tailored therapy.

Dudka I, Figueira J, Wikström P, Bergh A, Gröbner G

Front Mol Biosci 12 (-) 1426949 [2025-04-07; online 2025-04-07]

Ectoderm barcoding reveals neural and cochlear compartmentalization.

de Haan S, He J, Corbat AA, ..., Kelley MW, Andersson ER

Science 388 (6742) 60-68 [2025-04-04; online 2025-04-03]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Million Years of Mammoth Mitogenome Evolution.

Chacón-Duque JC, Thomas Thorpe JA, Li W, ..., Heintzman PD, Dalén L

Mol. Biol. Evol. 42 (4) - [2025-04-01; online 2025-04-09]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Development of Selective Chemical Probes for Serine Arginine Protein Kinase 3

Hanke D, McCutcheon C, Page BDG

Chem Biol Drug Des 105 (4) - [2025-04-00; online 2025-04-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Non‐Native Earthworms Alter Carbon Sequestration in Arctic Tundra Ecosystems

Jonsson H, Blume‐Werry G, Wackett AA, ..., Sparrman T, Klaminder J

JGR Biogeosciences 130 (4) - [2025-04-00; online 2025-04-14]

Centennial-scale atmospheric CO2 rise increased photosynthetic efficiency in a tropical tree species.

Zwartsenberg SA, Sterck FJ, Haddad L, ..., Heinrich I, Zuidema PA

New Phytol. 246 (1) 131-143 [2025-04-00; online 2025-02-12]

A genome-wide association study of imaging-defined atherosclerosis.

Gummesson A, Lundmark P, Chen QS, ..., Fall T, Gigante B

Nat Commun 16 (1) 2266 [2025-03-31; online 2025-03-31]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sex pheromone biosynthesis in the Oriental fruit moth Grapholita molesta involves Δ8 desaturation.

Dam MI, Ding BJ, Brauburger K, ..., Heckel DG, Löfstedt C

Insect Biochem. Mol. Biol. - (-) 104307 [2025-03-30; online 2025-03-30]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The DNA methylation landscape of primary triple-negative breast cancer.

Aine M, Nacer DF, Arbajian E, ..., Borg Å, Staaf J

Nat Commun 16 (1) 3041 [2025-03-28; online 2025-03-28]

Clinical Genomics Lund [Service]

Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes - With particular focus on Hymenocoleus Robbr.

Thilén L, Lachenaud O, Thureborn O, Razafimandimbison SG, Rydin C

Mol. Phylogenet. Evol. - (-) 108338 [2025-03-28; online 2025-03-28]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.

Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I

Cell - (-) - [2025-03-26; online 2025-03-26]

Integrated Microscopy Technologies Stockholm [Service]

Blood-based biomarkers of Alzheimer's disease and incident dementia in the community.

Grande G, Valletta M, Rizzuto D, ..., Fratiglioni L, Vetrano DL

Nat. Med. - (-) - [2025-03-26; online 2025-03-26]

Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity.

Fan C, Wang Q, Krijger PHL, ..., de Laat W, Ten Dijke P

Nat Commun 16 (1) 2890 [2025-03-25; online 2025-03-25]

CRISPR Functional Genomics [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord.

Zhang MD, Kupari J, Su J, ..., Lagerström MC, Ernfors P

Nat. Neurosci. - (-) - [2025-03-24; online 2025-03-24]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness.

Schlesinger D, Dirks C, Navarro C, ..., Martinez TF, Elsässer SJ

iScience 28 (3) 111884 [2025-03-21; online 2025-01-23]

Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment.

Birgersson M, Holm M, Gallardo-Dodd CJ, ..., Archer A, Williams C

Cancer Lett. - (-) 217661 [2025-03-20; online 2025-03-20]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Computational drug repurposing: approaches, evaluation of in silico resources and case studies.

Tanoli Z, Fernández-Torras A, Özcan UO, ..., Carreras-Puigvert J, Aittokallio T

Nat Rev Drug Discov - (-) - [2025-03-18; online 2025-03-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Targeting TUBG1 in RB1‐negative tumors

Lindström L, Zhou J, Villoutreix BO, ..., Olsson R, Alvarado‐Kristensson M

The FASEB Journal 39 (5) - [2025-03-15; online 2025-02-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Sox9 and nuclear factor I transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors.

Lahti L, Volakakis N, Gillberg L, ..., Gronostajski R, Perlmann T

Development 152 (6) - [2025-03-15; online 2025-03-26]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dietary patterns and blood-based biomarkers of Alzheimer's disease in cognitively intact older adults: Findings from a population-based study.

Mrhar A, Carballo-Casla A, Grande G, ..., Calderón-Larrañaga A, Vetrano DL

J Prev Alzheimers Dis - (-) 100124 [2025-03-14; online 2025-03-14]

Genetic liability for anxiety and treatment response to the monoamine stabilizer OSU6162 in alcohol dependence: a retrospective secondary analysis.

Hong MG, Khemiri L, Guterstam J, ..., Jayaram-Lindström N, Melas PA

Pharmacol Rep - (-) - [2025-03-12; online 2025-03-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.

Kistler L, de Oliveira Freitas F, Gutaker RM, ..., Capriles JM, Allaby RG

Science 387 (6738) eadq0018 [2025-03-07; online 2025-03-07]

Ancient DNA [Collaborative]

Continuous map of early hematopoietic stem cell differentiation across human lifetime.

Komic H, Schmachtel T, Simoes C, ..., Thorén FB, Rieger MA

Nat Commun 16 (1) 2287 [2025-03-07; online 2025-03-07]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Antisense-mediated regulation of exon usage in the elastic spring region of Titin modulates sarcomere function.

Celik S, Hyrefelt L, Czuba T, ..., Smith JG, Gidlöf O

Cardiovasc. Res. - (-) - [2025-03-05; online 2025-03-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Decreased levels and function of dendritic cells in blood and airways predict COVID-19 severity.

Österberg B, Falck-Jones S, Vangeti S, ..., Färnert A, Smed-Sörensen A

Clin Transl Immunology 14 (3) e70026 [2025-03-03; online 2025-03-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Time-Resolved Hierarchical Modeling Highlights Metabolites Influencing Productivity and Cell Death in Chinese Hamster Ovary Cells.

Eriksson A, Richelle A, Trygg J, ..., Surowiec I, Jonsson P

Biotechnol J 20 (3) e202400624 [2025-03-00; online 2025-03-11]

Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening.

Vaivade A, Erngren I, Carlsson H, ..., Burman J, Kultima K

Nat Commun 16 (1) 2014 [2025-02-27; online 2025-02-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Lithography-Free Water Stable Conductive Polymer Nanowires

Hughes D, Mousa AH, Musumeci C, ..., Olsson R, Hjort M

Nano Lett. 25 (8) 3059-3065 [2025-02-26; online 2025-02-13]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Duplexed CeTEAM drug biosensors reveal determinants of PARP inhibitor selectivity in cells.

Pires MJ, Alam S, Lovric A, ..., Altun M, Valerie NCK

J. Biol. Chem. - (-) 108361 [2025-02-26; online 2025-02-26]

Chemical Biology Consortium Sweden (CBCS) [Service]

Dissecting the properties of circulating IgG against streptococcal pathogens through a combined systems antigenomics-serology workflow

Gomez Toledo A, Chowdhury S, Hjortswang E, ..., Rasmussen M, Malmström J

Nat Commun 16 (1) - [2025-02-24; online 2025-02-24]

Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures

Hawgood M, Urién González B, Agostinho A, ..., Blom H, Lemmens B

- - (-) - [2025-02-23; online 2025-02-23]

Integrated Microscopy Technologies Stockholm [Collaborative]

Comprehensive Gene Expression Analysis in Papillary Thyroid Carcinoma Reveals a Transcriptional Profile Associated with Reduced Radioiodine Avidity.

Condello V, Marchettini C, Ihre-Lundgren C, Nilsson JN, Juhlin CC

Endocr. Pathol. 36 (1) 4 [2025-02-21; online 2025-02-21]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open.

Tredup C, Ackloo S, Beck H, ..., Arrowsmith CH, Knapp S

RSC Med Chem 16 (2) 457-464 [2025-02-19; online 2024-11-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Temporal dynamics of airborne fungi in Swedish forest nurseries.

Larsson R, Menkis A, Olson Å

Appl. Environ. Microbiol. 91 (2) e0130624 [2025-02-19; online 2025-01-16]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Measuring plasma membrane fluidity using confocal microscopy.

Carravilla P, Andronico L, Schlegel J, ..., Lorent J, Sezgin E

Nat Protoc - (-) - [2025-02-19; online 2025-02-19]

Integrated Microscopy Technologies Stockholm [Service]

A chromosome-level genome assembly of the European green toad (Bufotes viridis).

Rödin-Mörch P, Bunikis I, Choi E, ..., Proux-Wéra E, Höglund J

G3 (Bethesda) - (-) - [2025-02-19; online 2025-02-19]

NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing.

Wang Q, Niu G, Liu Z, ..., Sommar P, Xu Landén N

Br J Dermatol 192 (3) 468-480 [2025-02-18; online 2024-10-18]

Bioinformatics Support for Computational Resources [Service]

Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.

Rosenqvist T, Hilding J, Suarez C, Paul CJ

Water Res. 270 (-) 122843 [2025-02-15; online 2024-11-23]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Methodological aspects of investigating the resistome in pig farm environments.

Ladyhina V, Rajala E, Sternberg-Lewerin S, ..., Bongcam-Rudloff E, Dicksved J

J Microbiol Methods 230-231 (-) 107103 [2025-02-13; online 2025-02-13]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Imaging Single Particle Profiler to Study Nanoscale Bioparticles Using Conventional Confocal Microscopy.

Sych T, Görgens A, Steiner L, ..., El Andaloussi S, Sezgin E

Nano Lett. 25 (6) 2173-2180 [2025-02-12; online 2025-01-29]

Integrated Microscopy Technologies Stockholm [Service]

Rare and common single nucleotide variants in childhood-onset systemic lupus erythematosus.

Sayadi A, Sandling JK, Eloranta ML, ..., Rönnblom L, DISSECT Consortium

Lupus Sci Med 12 (1) - [2025-02-11; online 2025-02-11]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High-content morphological profiling by Cell Painting in 3D spheroids

Ringers C, Holmberg D, Flobak Å, ..., Carreras Puigvert J, Spjuth O

- - (-) - [2025-02-08; online 2025-02-08]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Whole genome sequencing in early onset advanced heart failure.

Linnér E, Czuba T, Gidlöf O, ..., Ehrencrona H, Smith JG

Sci Rep 15 (1) 4306 [2025-02-05; online 2025-02-05]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The expanded genome of Hexamita inflata, a free-living diplomonad.

Akdeniz Z, Havelka M, Stoklasa M, ..., Andersson JO, Tachezy J

Sci Data 12 (1) 192 [2025-02-01; online 2025-02-01]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Single cell sequencing reveals shared clonal signatures in non-malignant B- and tumor cells in T-prolymphocytic leukemia

Hesselager C, Thörn I, Marincevic M, ..., Baliakas P, Amini RM

Blood Neoplasia - (-) 100076 [2025-02-00; online 2025-02-00]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Robust approach for production of the human oncology target Aurora kinase B in complex with its binding partner INCENP.

Mattsson J, Rogne P, Landström M, Wolf-Watz M

Biochimie 229 (-) 129-140 [2025-02-00; online 2024-10-18]

Modelling age at death reveals Nordic Corded Ware paleodemography

Tornberg A, Vandkilde H

Archaeol Anthropol Sci 17 (2) - [2025-02-00; online 2025-01-20]

Ancient DNA [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Impact of plant diversity in potato-ley strip-cropping systems on soil microbial communities

Riggi LGA, Ranheim Sveen T, Castaño C, ..., Clemmensen KE, Bahram M

Applied Soil Ecology 206 (-) 105777 [2025-02-00; online 2025-02-00]

Bioinformatics Support for Computational Resources [Service]

Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.

Jönsson J, Perfilyev A, Kugelberg U, ..., Öst A, Ling C

Epigenomics 17 (2) 89-104 [2025-02-00; online 2024-12-20]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche.

Steward RA, Ortega Giménez J, Choudhary S, ..., Van Aken O, Runemark A

Mol. Ecol. 34 (4) e17653 [2025-02-00; online 2025-01-09]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Earliest modern human genomes constrain timing of Neanderthal admixture.

Sümer AP, Rougier H, Villalba-Mouco V, ..., Prüfer K, Krause J

Nature 638 (8051) 711-717 [2025-02-00; online 2024-12-12]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity.

Cougnoux A, Mahmoud L, Johnsson PA, ..., Sandberg R, Hausser J

Sci Rep 15 (1) 3811 [2025-01-30; online 2025-01-30]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Modulation of biological activities in adipose derived stem cells by histone deacetylation.

Abdallah S, Tabebi M, Qanadilo S, ..., Elmasry M, El-Serafi A

Sci Rep 15 (1) 3629 [2025-01-29; online 2025-01-29]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]

The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.

Rekha RS, Padhi A, Frengen N, ..., Guðmundsson GH, Bergman P

Cell Rep 44 (1) 115031 [2025-01-28; online 2024-12-20]

Bioinformatics Support for Computational Resources [Service]

Association between alcohol consumption and peripheral artery disease: two de novo prospective cohorts and a systematic review with meta-analysis.

Yuan S, Wu J, Chen J, ..., Åkesson A, Larsson SC

Eur J Prev Cardiol 32 (2) 149-155 [2025-01-27; online 2024-04-16]

Bioinformatics Support for Computational Resources [Service]

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells.

Fegraeus K, Riihimäki M, Nordlund J, ..., Wernersson S, Raine A

PLoS ONE 20 (1) e0317343 [2025-01-24; online 2025-01-24]

NGI Short read [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Ultra-Sensitive Detection of Bacterial Spores via SERS.

Segervald J, Malyshev D, Öberg R, ..., Wågberg T, Andersson M

ACS Sens. - (-) - [2025-01-23; online 2025-01-23]

A de novo, mosaic and complex chromosome 21 rearrangement causes APP triplication and familial autosomal dominant early onset Alzheimer disease.

Ehn E, Eisfeldt J, Laffita-Mesa JM, ..., Nennesemo I, Graff C

Sci Rep 15 (1) 2912 [2025-01-23; online 2025-01-23]

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Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.

Brown T, Mishra K, Elewa A, ..., Yun MH, Simon A

Cell Genomics - (-) 100761 [2025-01-22; online 2025-01-22]

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Visualization using NIPTviewer support the clinical interpretation of noninvasive prenatal testing results.

Smeds P, Baranowska Körberg I, Melin M, Ladenvall C

BMC Med Genomics 18 (1) 15 [2025-01-20; online 2025-01-20]

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Systems-level immunomonitoring in children with solid tumors to enable precision medicine.

Chen Q, Zhao B, Tan Z, ..., Ljungblad L, Brodin P

Cell - (-) - [2025-01-17; online 2025-01-17]

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Somatic CAG repeat expansion in blood associates with biomarkers of neurodegeneration in Huntington's disease decades before clinical motor diagnosis.

Scahill RI, Farag M, Murphy MJ, ..., Langbehn DR, Tabrizi SJ

Nat. Med. - (-) - [2025-01-17; online 2025-01-17]

Structure of the T=13 capsid of infectious pancreatic necrosis virus (IPNV)-a salmonid birnavirus.

Munke A, Ahmed Abdelrahim Gamil A, Mikalsen AB, ..., Evensen Ø, Okamoto K

J. Virol. - (-) e0145424 [2025-01-16; online 2025-01-16]

A thermoplastic chip for 2D and 3D correlative assays combining screening and high-resolution imaging of immune cell responses.

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Cell Reports Methods - (-) 100965 [2025-01-16; online 2025-01-16]

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The Progression of Mycosis Fungoides During Treatment with Mogamulizumab: A BIO-MUSE Case Study of the Tumor and Immune Response in Peripheral Blood and Tissue.

Johansson A, Kalliara E, Belfrage E, ..., Drott K, Ek S

Biomedicines 13 (1) - [2025-01-14; online 2025-01-14]

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Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.

Kaldhusdal V, Boger MF, Tjernlund A, ..., Czarnewski P, Broliden K

Sci Rep 15 (1) 1014 [2025-01-06; online 2025-01-06]

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Model-informed drug development for antimicrobials: translational pharmacokinetic-pharmacodynamic modelling of apramycin to facilitate prediction of efficacious dose in complicated urinary tract infections.

Hernández-Lozano I, Aranzana-Climent V, Cao S, ..., Vingsbo Lundberg C, Friberg LE

J. Antimicrob. Chemother. 80 (1) 301-310 [2025-01-03; online 2024-11-16]

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Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

Hank EC, D'Arcy-Evans N, Scaletti ER, ..., Helleday T, Michel M

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A Rationally Designed Azobenzene Photoswitch for DNA G-Quadruplex Regulation in Live Cells.

Dudek M, López-Pacios L, Sabouri N, ..., Martinez-Fernandez L, Deiana M

Angew. Chem. Int. Ed. Engl. 64 (1) e202413000 [2025-01-02; online 2024-11-06]

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Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia.

Komic H, Nilsson MS, Wennström L, ..., Thorén FB, Martner A

Haematologica 110 (1) 117-128 [2025-01-01; online 2025-01-01]

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Dark carbon fixation is a common process in the water column of stratified boreal lakes.

Martin G, Rissanen AJ, Garcia SL, Peura S

Sci. Total Environ. 958 (-) 177433 [2025-01-01; online 2024-12-10]

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Trees First Inhibit Then Promote Litter Decomposition in the Subarctic.

Jonsson M, Clemmensen KE, Castaño C, Parker TC

Ecol. Lett. 28 (1) e70063 [2025-01-00; online 2025-01-20]

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Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.

Tång Hallbäck E, Björkman JT, Dyrkell F, ..., Sikora P, Mölling P

Microb Genom 11 (1) - [2025-01-00; online 2025-01-27]

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Chemogenomic Screening in a Patient‐Derived 3D Fatty Liver Disease Model Reveals the CHRM1‐TRPM8 Axis as a Novel Module for Targeted Intervention

Youhanna S, Kemas AM, Wright SC, ..., Sundström M, Lauschke VM

Adv Sci (Weinh) 12 (3) - [2025-01-00; online 2024-11-28]

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Producing dissolving pulp from agricultural waste

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RSC Sustain. 3 (5) 2210-2220 [2025-00-00; online 2025-00-00]

Sulfidic mine waste rock alkaliphilic microbial communities rapidly replaced by aerobic acidophiles following deposition

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Biogeochemistry 168 (1) - [2024-12-31; online 2024-12-31]

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Life Science 2.0: reframing the life science sector for 'the benefit on mankind'.

Vallin M, Tomson G, Kampmann B, ..., Wanyenze RK, Ottersen OP

Glob Health Action 17 (1) 2330758 [2024-12-31; online 2024-04-05]

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Identification of novel FosX family determinants from diverse environmental samples.

Kieffer N, Böhm ME, Berglund F, ..., Gillings MR, Larsson DGJ

J Glob Antimicrob Resist 41 (-) 8-14 [2024-12-24; online 2024-12-24]

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VLDLR mediates Semliki Forest virus neuroinvasion through the blood-cerebrospinal fluid barrier.

Martikainen M, Lugano R, Pietilä I, ..., Dimberg A, Essand M

Nat Commun 15 (1) 10718 [2024-12-23; online 2024-12-23]

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MARC1 downregulation reduces hepatocyte lipid content by increasing beta-oxidation.

Ciociola E, Dutta T, Sasidharan K, ..., Mancina RM, Romeo S

Clin Mol Hepatol - (-) - [2024-12-23; online 2024-12-23]

Evolution of fast-growing piscivorous herring in the young Baltic Sea.

Goodall J, Pettersson ME, Bergström U, ..., Wennerström L, Andersson L

Nat Commun 15 (1) 10707 [2024-12-23; online 2024-12-23]

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Phthalate esters in baltic lagoons: Spatial distribution, ecological risks, and novel insights into their fate using transcriptomics.

Lorre E, Bianchi F, Broman E, ..., Woźniczka A, Zilius M

Sci. Total Environ. 957 (-) 177526 [2024-12-20; online 2024-11-18]

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MUC17 is an essential small intestinal glycocalyx component that is disrupted in Crohn's disease.

Layunta E, Jäverfelt S, van de Koolwijk FC, ..., Vallance BA, Pelaseyed T

JCI Insight 10 (3) - [2024-12-19; online 2024-12-19]

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Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens.

de Haas EN, Pértille F, Kjaer JB, Jensen P, Guerrero-Bosagna C

BMC Genomics 25 (1) 1219 [2024-12-19; online 2024-12-19]

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Treatment of Periprosthetic Joint Infection with Intravenous Vancomycin: Do We Hit the Target?

Haglund R, Tornberg U, Claesson AC, Freyhult E, Hailer NP

Antibiotics (Basel) 13 (12) - [2024-12-18; online 2024-12-18]

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Transcriptome analysis of sugar beet in response to the pathogenic oomycete Aphanomyces cochlioides.

Rossi V, Holmquist L, Alexandersson E, Grenville-Briggs L

BMC Plant Biol. 24 (1) 1177 [2024-12-18; online 2024-12-18]

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The AxBioTick study - immune gene expression signatures in human skin bitten by Borrelia-infected versus non-infected ticks.

Berthén NC, Cronhjort S, Nordberg M, ..., Wilhelmsson P, Sjöwall J

BMC Infect. Dis. 24 (1) 1422 [2024-12-18; online 2024-12-18]

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Spatiotemporal single-cell roadmap of human skin wound healing.

Liu Z, Bian X, Luo L, ..., Li D, Landén NX

Cell Stem Cell - (-) - [2024-12-18; online 2024-12-18]

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ABHD2 activity is not required for the non-genomic action of progesterone on human sperm

Arnolds O, Carter EM, Edwards M, ..., Tredup C, Gileadi O

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Complete genome sequences of the prosthecate dimorphic bacteria Brevundimonas intermedia CB63T and Brevundimonas staleyi FWC43T.

Hallgren J, Daneby F, Jonas K

Microbiol Resour Announc 13 (12) e0105024 [2024-12-12; online 2024-11-20]

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Stem Cell-Associated Proteins and Extracellular Matrix Composition of the Human Atrioventricular Junction.

Thorsell A, Sjölin L, Berger E, ..., Rotter Sopasakis V, Vukusic K

Cells 13 (24) - [2024-12-11; online 2024-12-11]

Naturally acquired IgG responses to Plasmodium falciparum do not target the conserved termini of the malaria vaccine candidate Merozoite Surface Protein 2.

Zerebinski J, Margerie L, Han NS, ..., Färnert A, Plaza DF

Front Immunol 15 (-) 1501700 [2024-12-09; online 2024-12-09]

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Sex-Specific Dominance of Gene Expression in Seed Beetles.

Kaufmann P, Rönn JL, Immonen E, Arnqvist G

Mol. Biol. Evol. 41 (12) - [2024-12-06; online 2024-12-18]

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Coupling cellular drug-target engagement to downstream pharmacology with CeTEAM.

Valerie NCK, Sanjiv K, Mortusewicz O, ..., Page BDG, Altun M

Nat Commun 15 (1) 10347 [2024-12-06; online 2024-12-06]

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Chemical exposomics in biobanked plasma samples and associations with breast cancer risk factors.

Edlund J, Sdougkou K, Papazian S, ..., Martin JW, Harlid S

J Expo Sci Environ Epidemiol - (-) - [2024-12-06; online 2024-12-06]

Multi-omics analysis detail a submicroscopic inv(15)(q14q15) generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency.

Ek M, Kvarnung M, Pettersson M, ..., Eisfeldt J, Lindstrand A

Sci Rep 14 (1) 30343 [2024-12-05; online 2024-12-05]

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Dynamics of the blood plasma proteome during hyperacute HIV-1 infection.

Nazziwa J, Freyhult E, Hong MG, ..., Hassan AS, Esbjörnsson J

Nat Commun 15 (1) 10593 [2024-12-05; online 2024-12-05]

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A landscape of X-inactivation during human T cell development.

Gylemo B, Bensberg M, Hennings V, ..., Ekwall O, Nestor CE

Nat Commun 15 (1) 10527 [2024-12-04; online 2024-12-04]

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High-solid digestion - A comparison of completely stirred and plug-flow reactor systems.

Perman E, Karlsson A, Westerholm M, Isaksson S, Schnürer A

Waste Management 189 (-) 265-275 [2024-12-01; online 2024-08-31]

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The evolutionary history of metastatic pancreatic neuroendocrine tumours reveals a therapy driven route to high-grade transformation.

Backman S, Botling J, Nord H, ..., Åkerström T, Crona J

J. Pathol. 264 (4) 357-370 [2024-12-00; online 2024-10-03]

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Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells

Arcoverde Cerveira R, Lenart K, Martin M, ..., Ols S, Loré K

Immunoinformatics (Amst) 16 (-) 100046 [2024-12-00; online 2024-12-00]

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Quantitative Comparisons of Progressive Supranuclear Palsy Rating Scale Versions Using Item Response Theory.

Gewily M, Plan EL, Yousefi E, ..., Höglinger G, Karlsson MO

Mov Disord 39 (12) 2181-2189 [2024-12-00; online 2024-08-29]

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Occurrence of cancer in Marfan syndrome: Report of two patients with neuroblastoma and review of the literature.

Maya-González C, Delgado-Vega AM, Taylan F, ..., Martinsson T, Nordgren A

Am. J. Med. Genet. A 194 (12) e63812 [2024-12-00; online 2024-07-11]

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Longitudinal Analysis of Natural History Progression of Rare and Ultra-Rare Cerebellar Ataxias Using Item Response Theory.

Hamdan A, Hendrickx N, Hooker AC, ..., Synofzik M, Karlsson MO

Clin. Pharmacol. Ther. 116 (6) 1593-1605 [2024-12-00; online 2024-10-15]

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Lifestyle, biological, and genetic factors related to brain iron accumulation across adulthood.

Gustavsson J, Ištvánfyová Z, Papenberg G, ..., Mangialasche F, Kalpouzos G

Neurobiol. Aging 144 (-) 56-67 [2024-12-00; online 2024-09-10]

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Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation.

Yu H, Nagi SS, Usoskin D, ..., Ernfors P, Luo W

Nat. Neurosci. 27 (12) 2326-2340 [2024-12-00; online 2024-11-04]

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Genomics of severe and treatment-resistant obsessive-compulsive disorder treated with deep brain stimulation: A preliminary investigation.

Chen LL, Naesström M, Halvorsen M, ..., Crowley JJ, Pascal D

Am. J. Med. Genet. B Neuropsychiatr. Genet. 195 (8) e32983 [2024-12-00; online 2024-04-22]

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Genomic signals of adaptation to a natural CO2 gradient over a striking microgeographic scale

González-Delgado S, Pérez-Portela R, Ortega-Martínez O, ..., Pereyra RT, Hernández JC

Marine Pollution Bulletin 209 (-) 117225 [2024-12-00; online 2024-12-00]

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Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations

Palaiokostas C, Kurta K, Pappas F, ..., Janhunen M, Kause A

Aquaculture Reports 39 (-) 102495 [2024-12-00; online 2024-12-00]

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Genetic analysis and family screening for dilated cardiomyopathy: a retrospective analysis of the stepwise pedigree approach.

Ylipää J, Andersson T

Scand Cardiovasc J 58 (1) 2379356 [2024-12-00; online 2024-07-24]

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Different gene expression patterns between mouse and human brain pericytes revealed by single-cell/nucleus RNA sequencing.

Miao Y, Li W, Jeansson M, ..., Muhl L, He L

Vascul Pharmacol 157 (-) 107434 [2024-12-00; online 2024-10-17]

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Applications of NMR based methodologies investigating the behavior of lignin and cellulose towards bio-based carbon fibers production.

Guerroudj F, Fliri L, Bengtsson J, ..., Hummel M, Bernin D

Solid State Nucl Magn Reson 134 (-) 101977 [2024-12-00; online 2024-11-21]

Achieving optically selective coatings of silica fixated carbon nanotubes for solar energy applications

Zäll E, Segervald J, Mahmoodi H, ..., Edman L, Wågberg T

Solar Energy Materials and Solar Cells 278 (-) 113202 [2024-12-00; online 2024-12-00]

A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce.

Stojkovič K, Canovi C, Le KC, ..., Egertsdotter U, Street NR

Plant J. 120 (5) 2238-2252 [2024-12-00; online 2024-10-27]

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A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera.

Cangren P, Bertrand YJK, Braverman JM, ..., Hamilton MB, Oxelman B

Data Brief 57 (-) 111094 [2024-12-00; online 2024-11-01]

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Spatial profiling of the mouse colonic immune landscape associated with colitis and sex.

Holm M, Stepanauskaitė L, Bäckström A, ..., Stadler C, Williams C

Commun Biol 7 (1) 1595 [2024-11-29; online 2024-11-29] Open Access

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Closed and open structures of the eukaryotic magnesium channel Mrs2 reveal the auto-ligand-gating regulation mechanism.

Li P, Liu S, Wallerstein J, ..., Liin SI, Gourdon P

Nat. Struct. Mol. Biol. - (-) - [2024-11-28; online 2024-11-28]

Preanalytical (Mis)Handling of Plasma Investigated by 1H NMR Metabolomics

Malmodin D, Bay Nord A, Zafar H, ..., Karlsson BG, Naluai ÅT

ACS Omega - (-) - [2024-11-27; online 2024-11-27]

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Streptolysin O accelerates the conversion of plasminogen to plasmin

Tang D, Khakzad H, Hjortswang E, ..., Happonen L, Malmström J

Nat Commun 15 (1) 10212 [2024-11-25; online 2024-11-25]

In-situ X-ray analysis of cold alkali dissolution of cellulose pulps of various origin

Wojtasz J, Bengtsson J, Ulmefors H, ..., Östlund Å, Yu S

Cellulose - (-) - [2024-11-25; online 2024-11-25]

Candidate serum protein biomarkers for active pulmonary tuberculosis diagnosis in tuberculosis endemic settings.

Ayalew S, Wegayehu T, Wondale B, ..., Fredolini C, Mihret A

BMC Infect. Dis. 24 (1) 1329 [2024-11-21; online 2024-11-21]

Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR.

De Coster W, Höijer I, Bruggeman I, ..., Ameur A, Rademakers R

Genome Res. 34 (11) 2074-2080 [2024-11-20; online 2024-11-20]

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Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote.

Sayers C, Pandey V, Balakrishnan A, ..., Berntsson R, Billker O

Cell Syst 15 (11) 1075-1091.e6 [2024-11-20; online 2024-11-13]

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SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion.

Christ W, Kapell S, Sobkowiak MJ, ..., El Andaloussi S, Ezzat K

ACS Chem Neurosci 15 (22) 4095-4104 [2024-11-20; online 2024-11-07]

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Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing.

Eisfeldt J, Higginbotham EJ, Lenner F, ..., Scherer SW, Feuk L

Genome Res. 34 (11) 1763-1773 [2024-11-20; online 2024-11-20]

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One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification.

Meng Z, Saei AA, Lyu H, Gaetani M, Zubarev RA

Anal. Chem. - (-) - [2024-11-20; online 2024-11-20]

Liver X receptor unlinks intestinal regeneration and tumorigenesis.

Das S, Parigi SM, Luo X, ..., Katajisto P, Villablanca EJ

Nature - (-) - [2024-11-20; online 2024-11-20]

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Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps.

Bilgrav Saether K, Eisfeldt J, Bengtsson JD, ..., Carvalho CMB, Lindstrand A

Genome Res. 34 (11) 1785-1797 [2024-11-20; online 2024-11-20]

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A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.

Eisfeldt J, Ameur A, Lenner F, ..., Feuk L, Lindstrand A

Genome Res. 34 (11) 1774-1784 [2024-11-20; online 2024-11-20]

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Unraveling the dynamics of lignin chemistry on decomposition to understand its contribution to soil organic matter accumulation

Thirunavukkarasu A, Hedenström M, Sparrman T, ..., Schleucher J, Öquist M

Plant Soil - (-) - [2024-11-19; online 2024-11-19]

Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide.

Kovalova T, Król S, Gamiz-Hernandez AP, ..., Brzezinski P, Högbom M

Proc. Natl. Acad. Sci. U.S.A. 121 (47) e2412780121 [2024-11-19; online 2024-11-12]

Detecting transposable elements in long read genomes using sTELLeR.

Bilgrav Saether K, Eisfeldt J

Bioinformatics - (-) - [2024-11-18; online 2024-11-18]

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Combining live cell fluorescence imaging within situcryo electron tomography sheds light on the septation process inDeinococcus radiodurans

Gaifas L, Kleman JP, Lacroix F, ..., Gutsche I, Timmins J

- - (-) - [2024-11-18; online 2024-11-18]

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Autoantibodies against a subunit of mitochondrial respiratory chain complex I in inclusion body myositis.

Notarnicola A, Hellstrom C, Horuluoglu B, ..., Nilsson P, Lundberg IE

J. Autoimmun. 149 (-) 103332 [2024-11-18; online 2024-11-18]

Autoimmunity and Serology Profiling [Collaborative]

Whole-Genome Sequencing of Invasive Neonatal Escherichia coli From Uppsala County, Sweden.

Heydecke A, Myrelid Å, Normann E, ..., Tano E, Sütterlin S

J. Infect. Dis. 230 (5) e1136-e1145 [2024-11-15; online 2024-06-13]

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Tau processing and tau-mediated inflammation differ in human APOEε2 and APOEε4 astrocytes.

Mothes T, Konstantinidis E, Eltom K, ..., Rostami J, Erlandsson A

iScience 27 (11) 111163 [2024-11-15; online 2024-10-11]

Sirtuin inhibitors reduce intracellular growth of M. tuberculosis in human macrophages via modulation of host cell immunity.

Kalsum S, Akber M, Loreti MG, ..., Lerm M, Brighenti S

Sci Rep 14 (1) 28150 [2024-11-15; online 2024-11-15]

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Järn och gravar i Våmb

Gustafsson J, Nordman A, Hjärthner-Holdar E, Stilborg O

Jönköping läns museum arkeologisk rapport 2024:07 - (-) - [2024-11-15]

Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors.

Benediktsdottir A, Sooriyaarachchi S, Cao S, ..., Sandström A, Karlén A

Eur J Med Chem 278 (-) 116790 [2024-11-15; online 2024-08-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Plasma proteome and incident myocardial infarction: sex-specific differences.

Titova OE, Yuan S, Byberg L, ..., Michaëlsson K, Larsson SC

Eur. Heart J. 45 (43) 4647-4657 [2024-11-14; online 2024-10-14]

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A genome-wide association study in Swedish colorectal cancer patients with gastric- and prostate cancer in relatives.

Samola Winnberg J, Vermani L, Liu W, ..., Lindblad M, Lindblom A

Hered Cancer Clin Pract 22 (1) 25 [2024-11-14; online 2024-11-14]

Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A comprehensive human embryo reference tool using single-cell RNA-sequencing data

Zhao C, Plaza Reyes A, Schell JP, ..., Petropoulos S, Lanner F

Nat Methods - (-) - [2024-11-14; online 2024-11-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Prospective Screening of Cancer Syndromes in Patients with Mesenchymal Tumors.

Öfverholm I, Lin Y, Mondini J, ..., Haglund de Flon F, Wallander K

Cancers (Basel) 16 (22) 3816 [2024-11-13; online 2024-11-13]

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ATP1A3 dysfunction causes motor hyperexcitability and afterhyperpolarization loss in a dystonia model.

Akkuratov EE, Sorrell F, Picton L, ..., Miles GB, Aperia A

Brain - (-) - [2024-11-13; online 2024-11-13]

Integrated Microscopy Technologies Stockholm [Service]

Simultaneous detection of membrane contact dynamics and associated Ca2+ signals by reversible chemogenetic reporters.

García Casas P, Rossini M, Påvénius L, ..., Pizzo P, Filadi R

Nat Commun 15 (1) 9775 [2024-11-12; online 2024-11-12]

Integrated Microscopy Technologies Stockholm [Collaborative]

MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling.

Raouraoua N, Mirabello C, Véry T, ..., Lensink MF, Brysbaert G

Nat Comput Sci - (-) - [2024-11-11; online 2024-11-11]

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Equid-human interactions in Medieval Rome: exploring the role and management of equids through an interdisciplinary approach

Claudia Minniti CCAMaDC

30th conference of the European Association of Archaeologists, session 3893 - (-) - [2024-11-11; online 2024-08-27]

A unique symbiosome in an anaerobic single-celled eukaryote.

Jerlström-Hultqvist J, Gallot-Lavallée L, Salas-Leiva DE, ..., Archibald JM, Roger AJ

Nat Commun 15 (1) 9726 [2024-11-09; online 2024-11-09]

Structural Variants in COL1A1 and COL1A2 in Osteogenesis Imperfecta.

Batkovskyte D, Swolin-Eide D, Hammarsjö A, ..., Åström E, Grigelioniene G

Am. J. Med. Genet. A - (-) e63935 [2024-11-08; online 2024-11-08]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Patient-derived organoids in precision cancer medicine.

Tong L, Cui W, Zhang B, ..., Si L, Lundqvist A

Med 5 (11) 1351-1377 [2024-11-08; online 2024-09-27]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Non-fermented and fermented milk intake in relation to risk of ischemic heart disease and to circulating cardiometabolic proteins in swedish women and men: Two prospective longitudinal cohort studies with 100,775 participants.

Michaëlsson K, Lemming EW, Larsson SC, ..., Wolk A, Byberg L

BMC Med 22 (1) 483 [2024-11-08; online 2024-11-08]

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Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat.

Karlsson ME, Forsberg G, Rosberg AK, Thaning C, Alsanius B

Sci Rep 14 (1) 27197 [2024-11-08; online 2024-11-08]

Cancer-associated fibroblast subtypes modulate the tumor-immune microenvironment and are associated with skin cancer malignancy.

Forsthuber A, Aschenbrenner B, Korosec A, ..., Kasper M, Lichtenberger BM

Nat Commun 15 (1) 9678 [2024-11-08; online 2024-11-08]

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Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism.

Bódizs S, Mészáros P, Grunewald L, Takala H, Westenhoff S

Structure 32 (11) 1952-1962.e3 [2024-11-07; online 2024-08-30]

Transmembrane peptide-loaded ionic liquid nanocarriers for targeting ErbB2-positive cancer

Abujubara H, Bharmoria P, Alvarez S, ..., Sayin V, Tietze A

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Integrated Microscopy Technologies Gothenburg [Service]

The structure and function of P5A-ATPases.

Li P, Bågenholm V, Hägglund P, ..., Wang K, Gourdon P

Nat Commun 15 (1) 9605 [2024-11-06; online 2024-11-06]

Postprandial Effects of Four Test Meals Containing Wholegrain Rye or Refined Wheat Foods on Circulating Incretins, Ghrelin, Glucose, and Inflammatory Markers.

Åberg S, Webb DL, Nordin E, Hellström PM, Landberg R

J. Nutr. - (-) - [2024-11-06; online 2024-11-06]

DMI fungicide resistance in Zymoseptoria tritici is unlinked to geographical origin and genetic background: a case study in Europe.

Oreiro EG, Samils B, Kildea S, ..., Zhan J, Andersson B

Pest Manag Sci - (-) - [2024-11-06; online 2024-11-06]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle.

Karempudi P, Gras K, Amselem E, ..., Schirman D, Elf J

Commun Biol 7 (1) 1443 [2024-11-05; online 2024-11-05]

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Pasteurella multocida from deep nasal swabs and tracheobronchial lavage in bovine calves from Sweden.

Myrenås M, Pringle M, Harbom B, Bengtsson B

Acta Vet. Scand. 66 (1) 58 [2024-11-05; online 2024-11-05]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

A bispecific CD40 agonistic antibody allowing for antibody-peptide conjugate formation to enable cancer-specific peptide delivery, resulting in improved T proliferation and anti-tumor immunity in mice.

Mebrahtu A, Laurén I, Veerman R, ..., Rockberg J, Mangsbo S

Nat Commun 15 (1) 9542 [2024-11-05; online 2024-11-05]

Affinity Proteomics Uppsala [Service] Drug Discovery and Development (DDD) [Service]

Urban Pigeons as Reservoirs of Critical Pathogens: Improved protocol for sequencing pigeon faeces in disease monitoring

Hermann E, Van Damme R, Bongcam-Rudloff E, Nasirzadeh L

EMBnet j. 30 (-) e1059 [2024-11-04; online 2024-11-04]

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Population pharmacokinetic modelling of cetirizine concentrations in human breast milk-A contribution from the ConcePTION project.

Melander E, Nielsen EI, Lindqvist A, ..., Spigset O, Nordeng H

Basic Clin Pharmacol Toxicol - (-) - [2024-11-04; online 2024-11-04]

Drug Discovery and Development (DDD) [Collaborative]

Incontinentia pigmenti underlies thymic dysplasia, autoantibodies to type I IFNs, and viral diseases.

Rosain J, Le Voyer T, Liu X, ..., Anderson MS, Casanova JL

J. Exp. Med. 221 (11) - [2024-11-04; online 2024-10-01]

Characterisation of IBD heterogeneity using serum proteomics: A multicentre study.

Salomon B, Sudhakar P, Bergemalm D, ..., Vermeire S, Halfvarson J

J Crohns Colitis - (-) - [2024-11-04; online 2024-11-04]

Revised diffusion law permits quantitative nanoscale characterization of membrane organization

Svobodová B, Šťastný D, Blom H, ..., Hof M, Šachl R

- - (-) - [2024-11-03; online 2024-11-03]

Integrated Microscopy Technologies Stockholm [Service]

Spatial Multiomics Reveals Intratumoral Immune Heterogeneity with Distinct Cytokine Networks in Lung Cancer Brain Metastases.

Christensson G, Bocci M, Kazi JU, ..., Gonzalez Velozo H, Hagerling C

Cancer Res Commun 4 (11) 2888-2902 [2024-11-01; online 2024-10-14]

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Perfluorooctanesulfonic acid (PFOS) induced cancer related DNA methylation alterations in human breast cells: A whole genome methylome study.

Pierozan P, Höglund A, Theodoropoulou E, Karlsson O

Sci. Total Environ. 949 (-) 174864 [2024-11-01; online 2024-07-20]

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Transcriptomic profiles of myxofibrosarcoma and undifferentiated pleomorphic sarcoma correlate with clinical and genomic features.

Mitra S, Farswan A, Piccinelli P, ..., Pillay N, Mertens F

J. Pathol. 264 (3) 293-304 [2024-11-00; online 2024-09-11]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia.

Hägerstrand D, Oder B, Cortese D, ..., Sutton LA, Rosenquist R

Leukemia 38 (11) 2429-2442 [2024-11-00; online 2024-09-11]

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The TβRI promotes migration and metastasis through thrombospondin 1 and ITGAV in prostate cancer cells.

Mu Y, Wallenius A, Zang G, ..., Mateus A, Landström M

Oncogene 43 (45) 3321-3334 [2024-11-00; online 2024-09-20]

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The Arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance.

El Arbi N, Nardeli SM, Šimura J, Ljung K, Schmid M

New Phytol. 244 (4) 1408-1421 [2024-11-00; online 2024-09-27]

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Sustained immune activation and impaired epithelial barrier integrity in the ectocervix of women with chronic HIV infection.

Franzén Boger M, Hasselrot T, Kaldhusdal V, ..., Broliden K, Tjernlund A

PLoS Pathog. 20 (11) e1012709 [2024-11-00; online 2024-11-19]

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Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers.

Qvick A, Andersson E, Oldaeus Almerén A, ..., Karlsson MG, Helenius G

Mol Diagn Ther 28 (6) 835-845 [2024-11-00; online 2024-09-26]

Clinical Genomics [Technology development] Clinical Genomics Örebro [Technology development]

Real-world assessment of immunogenicity in immunocompromised individuals following SARS-CoV-2 mRNA vaccination: a two-year follow-up of the prospective clinical trial COVAXID.

Chen P, Bergman P, Blennow O, ..., Aleman S, Ljunggren HG

EBioMedicine 109 (-) 105385 [2024-11-00; online 2024-10-11]

Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon.

Delgado-Vega AM, Cederroth H, Taylan F, ..., Cederroth M, Nordgren A

Nat. Genet. 56 (11) 2287-2294 [2024-11-00; online 2024-10-22]

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Pisolithus microcarpus isolates with contrasting abilities to colonise Eucalyptus grandis exhibit significant differences in metabolic signalling.

Vishwakarma K, Buckley S, Plett JM, ..., Jämtgård S, Plett KL

Fungal Biol 128 (7) 2157-2166 [2024-11-00; online 2024-09-10]

Network analysis reveals age- and virus-specific circuits in nasal epithelial cells of extremely premature infants.

Wisgrill L, Martens A, Kasbauer R, ..., Fyhrquist N, Alenius H

Allergy 79 (11) 3062-3081 [2024-11-00; online 2024-06-19]

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Molecular Profiling Defines Three Subtypes of Synovial Sarcoma.

Chen Y, Su Y, Cao X, ..., Li X, de Flon FH

Adv Sci (Weinh) 11 (41) e2404510 [2024-11-00; online 2024-09-10]

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Loss of heterozygosity of CYP2D6 enhances the sensitivity of hepatocellular carcinomas to talazoparib.

Zhang X, Rameika N, Zhong L, ..., Globisch D, Sjöblom T

EBioMedicine 109 (-) 105368 [2024-11-00; online 2024-10-04]

Chemical Biology Consortium Sweden (CBCS) [Service]

Local climate, air quality and leaf litter cover shape foliar fungal communities on an urban tree.

Faticov M, Amorim JH, Abdelfattah A, ..., Laforest-Lapointe I, Tack AJM

Ambio 53 (11) 1673-1685 [2024-11-00; online 2024-06-13]

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Jag1 insufficiency alters liver fibrosis via T cell and hepatocyte differentiation defects.

Mašek J, Filipovic I, Van Hul N, ..., Dobeš J, Andersson ER

EMBO Mol Med 16 (11) 2946-2975 [2024-11-00; online 2024-10-02]

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Heart failure treatment in the last years of life: A nationwide study of 364 000 individuals.

Sundström J, Gustafsson S, Cars T, Lindholm D

Eur. J. Heart Fail. 26 (11) 2443-2450 [2024-11-00; online 2024-08-31]

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Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.

Vera-Ponce de León A, Hensen T, Hoetzinger M, ..., Pope PB, La Rosa SL

Nat Microbiol 9 (11) 3059-3074 [2024-11-00; online 2024-10-14]

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Genomic analyses of Streptococcus uberis reveal high diversity but few antibiotic resistance genes

Myrenås M, Fasth C, Waller KP, Pedersen K

Vet. Microbiol. - (-) 110319 [2024-11-00; online 2024-11-00]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Examining the liver-pancreas crosstalk reveals a role for the molybdenum cofactor in β-cell regeneration.

Karampelias C, Băloiu B, Rathkolb B, ..., Hrabě de Angelis M, Andersson O

Life Sci. Alliance 7 (11) e202402771 [2024-11-00; online 2024-08-19]

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Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N).

Sipes K, Buongiorno J, Steen AD, ..., Vishnivetskaya TA, Lloyd KG

Syst. Appl. Microbiol. 47 (6) 126544 [2024-11-00; online 2024-08-28]

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Characterization of Pediatric Acute Myeloid Leukemia With t(7;12)(q36;p13)

Östlund A, Waraky A, Staffas A, ..., Abrahamsson J, Palmqvist L

Genes Chromosomes Cancer 63 (11) - [2024-11-00; online 2024-11-07]

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Androgen receptor pathway inhibitors and taxanes in metastatic prostate cancer: an outcome-adaptive randomized platform trial.

De Laere B, Crippa A, Discacciati A, ..., Grönberg H, Lindberg J

Nat. Med. 30 (11) 3291-3302 [2024-11-00; online 2024-08-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An ancient ecospecies of Helicobacter pylori.

Tourrette E, Torres RC, Svensson SL, ..., Thorell K, Falush D

Nature 635 (8037) 178-185 [2024-11-00; online 2024-10-16]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

A new species of Erinaceusyllis (Annelida: Syllidae) discovered at a wood-fall in the eastern Clarion-Clipperton Zone, central Pacific Ocean.

Nilsson CL, Wiklund H, Glover AG, Bribiesca-Contreras G, Dahlgren TG

Deep Sea Research Part I: Oceanographic Research Papers - (-) 104415 [2024-11-00; online 2024-11-00]

Integrated Microscopy Technologies Gothenburg [Service]

Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.

Jayaprasad S, Peona V, Ellerstrand SJ, ..., Schielzeth H, Palacios-Gimenez OM

Mol. Ecol. - (-) e17567 [2024-10-30; online 2024-10-30]

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High-parametric protein maps reveal the spatial organization in early-developing human lung.

Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B

Nat Commun 15 (1) 9381 [2024-10-30; online 2024-10-30]

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Explorative study of stimulated saliva proteome in head and neck cancer patients pre- and post-treatment.

Almhöjd U, Fisic A, Cevik-Aras H, ..., Finizia C, Almståhl A

Heliyon 10 (20) e39033 [2024-10-30; online 2024-10-09]

Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.

Shafighi S, Geras A, Jurzysta B, ..., Lagergren J, Szczurek E

Nat Commun 15 (1) 9343 [2024-10-29; online 2024-10-29]

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Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors.

Bian X, Piipponen M, Liu Z, ..., Halle M, Xu Landén N

Nat Commun 15 (1) 9286 [2024-10-28; online 2024-10-28]

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Elucidating microRNA-34a organisation within human Argonaute-2 by dynamic nuclear polarisation-enhanced magic angle spinning NMR.

Dasgupta R, Becker W, Petzold K

Nucleic Acids Res. 52 (19) 11995-12004 [2024-10-28; online 2024-09-04]

Dynamic nuclear polarization solid-state NMR spectroscopy as a tool to rapidly determine degree of modification in dialcohol cellulose

Karlsson H, Svenningsson L, Storm R, ..., Larsson PA, Evenäs L

Cellulose - (-) - [2024-10-28; online 2024-10-28]

ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation.

Karlström V, Sagredo EA, Planells J, ..., Visa N, Öhman M

Nucleic Acids Res. 52 (19) 12021-12038 [2024-10-28; online 2024-09-01]

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Highly Active and Durable Nanostructured Nickel-Molybdenum Coatings as Hydrogen Electrocatalysts via Solution Precursor Plasma Spraying.

Wu X, Piñeiro-García A, Rafei M, ..., Canto-Aguilar EJ, Gracia-Espino E

ChemistryOpen - (-) e202400069 [2024-10-25; online 2024-10-25]

A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data.

Abalde S, Jondelius U

Syst. Biol. - (-) - [2024-10-25; online 2024-10-25]

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Surface microlayer-mediated virome dissemination in the Central Arctic.

Rahlff J, Westmeijer G, Weissenbach J, Antson A, Holmfeldt K

Microbiome 12 (1) 218 [2024-10-24; online 2024-10-24]

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Comparative Analysis of Plasma Protein Dynamics in Women with ST-Elevation Myocardial Infarction and Takotsubo Syndrome.

Hussain S, Jha S, Berger E, ..., Omerovic E, Redfors B

Cells 13 (21) 1764 [2024-10-24; online 2024-10-24]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service] Glycoproteomics and MS Proteomics [Collaborative]

Normalized Interferon Signatures and Clinical Improvements by IFNAR1 Blocking Antibody (Anifrolumab) in Patients with Type I Interferonopathies.

Kretzschmar G, Páez LP, Tan Z, ..., Horne A, Brodin P

J Clin Immunol 45 (1) 31 [2024-10-23; online 2024-10-23]

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Epigenome-wide analysis across the development span of pediatric acute lymphoblastic leukemia: backtracking to birth.

Ghantous A, Nusslé SG, Nassar FJ, ..., Munthe-Kaas MC, Herceg Z

Mol. Cancer 23 (1) 238 [2024-10-23; online 2024-10-23]

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Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae).

Schöneberg Y, Audisio TL, Ben Hamadou A, ..., Prost S, Kennedy S

Mol Ecol Resour - (-) e14038 [2024-10-22; online 2024-10-22]

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Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease.

Correia SP, Moedas MF, Taylor LS, ..., Wedell A, Wredenberg A

JCI Insight 9 (20) - [2024-10-22; online 2024-10-22]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial.

Lee S, Arefaine B, Begum N, ..., Shoaie S, Patel VC

J Hepatol - (-) - [2024-10-22; online 2024-10-22]

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Oral biofilm composition and phenotype in caries-active and caries-free children.

Boisen G, Brogårdh-Roth S, Neilands J, ..., Carda-Diéguez M, Davies JR

Front Oral Health 5 (-) 1475361 [2024-10-22; online 2024-10-22]

Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs and improves saccharification.

Sivan P, Urbancsok J, Donev EN, ..., Vilaplana F, Mellerowicz EJ

Plant Biotechnol. J. - (-) - [2024-10-22; online 2024-10-22]

Cryo-EM [Service] Swedish Metabolomics Centre (SMC) [Service]

Cancer Risk in Patients With Muscular Dystrophy and Myotonic Dystrophy: A Register-Based Cohort Study.

Maya-González C, Tettamanti G, Taylan F, ..., Sejersen T, Nordgren A

Neurology 103 (8) e209883 [2024-10-22; online 2024-09-19]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

The DoGA consortium expression atlas of promoters and genes in 100 canine tissues.

Hörtenhuber M, Hytönen MK, Mukarram AK, ..., Kere J, Lohi H

Nat Commun 15 (1) 9082 [2024-10-21; online 2024-10-21]

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Persistent effects of di-n-butyl phthalate on liver transcriptome: impaired energy and lipid metabolic pathways.

Theodoropoulou E, Pierozan P, Marabita F, Höglund A, Karlsson O

Chemosphere - (-) 143605 [2024-10-21; online 2024-10-21]

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Building pangenome graphs.

Garrison E, Guarracino A, Heumos S, ..., Williams RW, Prins P

Nat. Methods - (-) - [2024-10-21; online 2024-10-21]

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Phase-separated polymer blends for controlled drug delivery by tuning morphology

Olsson M, Storm R, Björn L, ..., Liebi M, Matic A

Commun Mater 5 (1) - [2024-10-18; online 2024-10-18]

In vivo dendritic cell reprogramming for cancer immunotherapy.

Ascic E, Åkerström F, Sreekumar Nair M, ..., Rosa FF, Pereira CF

Science 386 (6719) eadn9083 [2024-10-18; online 2024-10-18]

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Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.

Karlsson J, Yasui H, Mañas A, ..., Bexell D, Gisselsson D

Nat Commun 15 (1) 8992 [2024-10-18; online 2024-10-18]

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Changes in circulating extracellular vesicle cargo are associated with cognitive decline after major surgery: an observational case-control study.

Mkrtchian S, Eldh M, Ebberyd A, ..., Eriksson LI, Gómez-Galán M

Br J Anaesth - (-) - [2024-10-18; online 2024-10-18]

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Autoantibodies to protein S may explain rare cases of coagulopathy following COVID-19 vaccination.

Yalcinkaya A, Cavalli M, Aranda-Guillén M, ..., Hallberg P, Landegren N

Sci Rep 14 (1) 24512 [2024-10-18; online 2024-10-18]

Prevalent and persistent new-onset autoantibodies in mild to severe COVID-19.

Jernbom AF, Skoglund L, Pin E, ..., Månberg A, Nilsson P

Nat Commun 15 (1) 8941 [2024-10-17; online 2024-10-17]

Autoimmunity and Serology Profiling [Collaborative]

Parvimonas micra forms a distinct bacterial network with oral pathobionts in colorectal cancer patients.

Löwenmark T, Köhn L, Kellgren T, ..., Edin S, Palmqvist R

J Transl Med 22 (1) 947 [2024-10-17; online 2024-10-17]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

Temperature, sediment resuspension, and salinity drive the prevalence of Vibrio vulnificus in the coastal Baltic Sea.

Fernández-Juárez V, Riedinger DJ, Gusmao JB, ..., Labrenz M, Riemann L

MBio 15 (10) e0156924 [2024-10-16; online 2024-09-19]

Bioinformatics Support for Computational Resources [Service]

SARS-CoV-2 infection induces hyaluronan production in vitro and hyaluronan levels in COVID-19 patients relate to morbidity and long-term lung impairment: a prospective cohort study.

Hellman U, Rosendal E, Lehrstrand J, ..., Överby AK, Lenman A

MBio 15 (10) e0130324 [2024-10-16; online 2024-09-20]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service]

Uranium Repartitioning during Microbial Driven Reductive Transformation of U(VI)-Sorbed Schwertmannite and Jarosite.

Yu C, Johnson A, Karlsson A, ..., Dopson M, Åström ME

Environ. Sci. Technol. 58 (41) 18324-18334 [2024-10-15; online 2024-10-03]

Bioinformatics Support for Computational Resources [Service]

The crucial role of bioimage analysts in scientific research and publication.

Cimini BA, Bankhead P, D'Antuono R, ..., Wiggins L, Eliceiri KW

J. Cell. Sci. 137 (20) - [2024-10-15; online 2024-10-30]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

Modulating protein unfolding and refolding via the synergistic association of an anionic and a nonionic surfactant.

Hjalte J, Diehl C, Leung AE, ..., Wahlgren M, Sanchez-Fernandez A

Journal of Colloid and Interface Science 672 (-) 244-255 [2024-10-15; online 2024-05-22]

Defective ribosome assembly impairs leukemia progression in a murine model of acute myeloid leukemia.

Sjövall D, Ghosh S, Fernandez-Fuentes N, ..., Guibentif C, Jaako P

Cell Rep 43 (11) 114864 [2024-10-15; online 2024-10-15]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.

Westmeijer G, van Dam F, Kietäväinen R, ..., Drake H, Dopson M

Commun Biol 7 (1) 1332 [2024-10-15; online 2024-10-15]

Bioinformatics Support for Computational Resources [Service]

Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

Mc Cartney AM, Formenti G, Mouton A, ..., Waterhouse RM, Mazzoni CJ

NPJ Biodivers 3 (1) 31 [2024-10-15; online 2024-10-15]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Resilience of genetic diversity in forest trees over the Quaternary.

Milesi P, Kastally C, Dauphin B, ..., Pyhäjärvi T, GenTree Consortium

Nat Commun 15 (1) 8538 [2024-10-14; online 2024-10-14]

Bioinformatics Support for Computational Resources [Service]

LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.

Rubalcava-Gracia D, Bubb K, Levander F, ..., Koolmeister C, Larsson NG

Nucleic Acids Res. 52 (18) 11266-11282 [2024-10-14; online 2024-08-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] CRISPR Functional Genomics [Service]

Fabrication and Electrocatalytic Evolution of Alkali-Free CoNb2O6 Thin Films for Water Oxidation via Polyoxoniobates

De A, Rambaran MA, Ohlin CA

ACS Appl. Energy Mater. 7 (19) 8333-8341 [2024-10-14; online 2024-09-22]

Autoantibodies towards HFE and SYT5 in anti-neutrophil cytoplasm antibody-associated vasculitis relapse.

Bayati S, Nazeer J, Ng J, ..., Nilsson P, Pin E

Rheumatology (Oxford) - (-) - [2024-10-14; online 2024-10-14]

Autoimmunity and Serology Profiling [Collaborative]

Quaternary Mixed Oxides of Non-Noble Metals with Enhanced Stability during the Oxygen Evolution Reaction.

Piñeiro-García A, Wu X, Canto-Aguilar EJ, ..., Rafei M, Gracia-Espino E

ACS Appl Mater Interfaces - (-) - [2024-10-13; online 2024-10-13]

Smart variant filtering - A blueprint solution for massively parallel sequencing-based variant analysis.

Brahimllari O, Eloranta S, Georgii-Hemming P, ..., Wästerlid T, Boman M

Health Informatics J 30 (4) 14604582241290725 [2024-10-12; online 2024-10-12]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Limosilactobacillus reuteri DSM 17938 Produce Bioactive Components during Formulation in Sucrose.

Ermann Lundberg L, Mata Forsberg M, Lemanczyk J, ..., Roos S, Håkansson S

Microorganisms 12 (10) - [2024-10-12; online 2024-10-12]

Genomic Analyses of Methicillin-Resistant Staphylococcus pseudintermedius from Companion Animals Reveal Changing Clonal Populations, Multidrug Resistance, and Virulence

Myrenås M, Pedersen K, Windahl U

Antibiotics (Basel) 13 (10) 962 [2024-10-12; online 2024-10-12]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

The power of hybridization capture - Illustrated using an expanded gene panel on 100 post mortem samples, focusing on sudden unexplained death.

Kling D, Adolfsson E, Gréen H, Gréen A

Forensic Sci Int Genet 74 (-) 103160 [2024-10-11; online 2024-10-11]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Dephosphorylation and ion binding in prokaryotic calcium transport.

Prabudiansyah I, Orädd F, Magkakis K, ..., Levantino M, Andersson M

Sci Adv 10 (41) eadp2916 [2024-10-11; online 2024-10-11]

Chemical Biology Consortium Sweden (CBCS) [Service] Cryo-EM [Service]

GCKIII Kinases Control Hepatocellular Lipid Homeostasis via Shared Mode of Action.

Cansby E, Caputo M, Andersson E, ..., Hoy AJ, Mahlapuu M

J. Lipid Res. - (-) 100669 [2024-10-10; online 2024-10-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.

Mirabello C, Wallner B, Nystedt B, Azinas S, Carroni M

Nat Commun 15 (1) 8724 [2024-10-09; online 2024-10-09]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Cryo-EM [Service]

The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758).

Pálsson S, Skarphéðinsson KH, Heintz J, ..., Tree of Life Core Informatics collective , Darwin Tree of Life Consortium

Wellcome Open Res 9 (-) 575 [2024-10-09; online 2024-10-09]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

De novo production of protoberberine and benzophenanthridine alkaloids through metabolic engineering of yeast.

Jiao X, Fu X, Li Q, ..., Nielsen J, Chen Y

Nat Commun 15 (1) 8759 [2024-10-09; online 2024-10-09]

Chalmers Mass Spectrometry Infrastructure [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

Estradiol-mediated enhancement of the human ectocervical epithelial barrier correlates with desmoglein-1 expression in the follicular menstrual phase.

Bradley F, Stern A, Franzén Boger M, ..., Fowke KR, Broliden K

Front Endocrinol (Lausanne) 15 (-) 1454006 [2024-10-08; online 2024-10-08]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Chemical Exposomics in Human Plasma by Lipid Removal and Large-Volume Injection Gas Chromatography–High-Resolution Mass Spectrometry

Xie H, Sdougkou K, Bonnefille B, ..., Rantakokko P, Martin JW

Environ. Sci. Technol. 58 (40) 17592-17605 [2024-10-08; online 2024-09-24]

Orthogonal Phase Transfer of Oppositely Charged FeII 4L6 Cages.

Matic ES, Bernard M, Jernstedt AJ, Grommet AB

Chemistry - (-) e202403411 [2024-10-07; online 2024-10-07]

Chalmers Mass Spectrometry Infrastructure [Collaborative] Swedish NMR Centre (SNC) [Service]

Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting.

Frisk C, Ekström M, Eriksson MJ, ..., Linde C, Persson B

BMC Genomics 25 (1) 938 [2024-10-07; online 2024-10-07]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A topographic lung cell atlas reveals regional variation in cell-type specific gene programs and identifies healthy and diseased cellular neighborhoods

Samakovlis C, Firsova A, Salas SM, ..., Nilsson M, Nawijn M

- - (-) - [2024-10-07; online 2024-10-07]

Metagenomic characterization of viruses in the serum of children with newly diagnosed cancer.

Leijonhufvud G, Soratto TAT, Matos GM, ..., Ljungman G, Andersson B

J. Clin. Virol. 175 (-) 105736 [2024-10-06; online 2024-10-06]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.

Li D, Liu Z, Zhang L, ..., Sommar P, Xu Landén N

Nat Commun 15 (1) 8637 [2024-10-05; online 2024-10-05]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Pesticide-induced transgenerational alterations of genome-wide DNA methylation patterns in the pancreas of Xenopus tropicalis correlate with metabolic phenotypes.

Roza M, Eriksson ANM, Svanholm S, Berg C, Karlsson O

J Hazard Mater 478 (-) 135455 [2024-10-05; online 2024-08-09]

Bioinformatics Support for Computational Resources [Service]

Genomic tumor evolution dictates human medulloblastoma progression.

Ruchiy Y, Tsea I, Preka E, ..., Johnsen JI, Baryawno N

Neurooncol Adv 6 (1) vdae172 [2024-10-05; online 2024-10-05]

Bioinformatics Support for Computational Resources [Service]

Elucidating Thermothielavioides terrestris secretome changes for improved saccharification of mild steam-pretreated spruce.

Caputo F, Siaperas R, Dias C, Nikolaivits E, Olsson L

Biotechnol Biofuels Bioprod 17 (1) 127 [2024-10-05; online 2024-10-05]

The single-cell transcriptomic atlas iPain identifies senescence of nociceptors as a therapeutical target for chronic pain treatment.

Techameena P, Feng X, Zhang K, Hadjab S

Nat Commun 15 (1) 8585 [2024-10-04; online 2024-10-04]

Bioinformatics Support for Computational Resources [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Population History of Domestic Sheep Revealed by Paleogenomes.

Kaptan D, Atağ G, Vural KB, ..., Somel M, Özer F

Mol. Biol. Evol. 41 (10) - [2024-10-04; online 2024-10-23]

Ancient DNA [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Inflammatory and cardiovascular markers in placenta following SARS-CoV-2 infection during pregnancy: A Swedish prospective cohort study.

Östling H, Lodefalk M, Bergman L, ..., Backman H, Kruse R

Placenta 158 (-) 78-88 [2024-10-04; online 2024-10-04]

Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.

Kumar B, Navarro C, Yung PYK, ..., Martin M, Elsässer SJ

Nat Protoc - (-) - [2024-10-03; online 2024-10-03]

Bioinformatics Support for Computational Resources [Service]

Estrogen-stimulated uropathogenic E. coli mediate enhanced neutrophil responses.

Pettersson C, Wu R, Demirel I

Sci Rep 14 (1) 23030 [2024-10-03; online 2024-10-03]

Early-Life Hygiene-Related Factors and Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study.

Guo A, Östensson M, Størdal K, Ludvigsson J, Mårild K

Inflamm Bowel Dis 30 (10) 1820-1830 [2024-10-03; online 2023-11-03]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Childhood Socioeconomic Characteristics and Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study.

Sigvardsson I, Størdal K, Östensson M, ..., Ludvigsson J, Mårild K

Inflamm Bowel Dis 30 (10) 1801-1811 [2024-10-03; online 2023-09-23]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material.

Liu L, Hakhverdyan M, Wallgren P, ..., Hulst M, Van Borm S

Microbiol Spectr 12 (10) e0420823 [2024-10-03; online 2024-08-20]

Bioinformatics Support for Computational Resources [Service]

Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.

Meng L, Jin H, Yulug B, ..., Uhlén M, Mardinoglu A

Alzheimers Res Ther 16 (1) 213 [2024-10-02; online 2024-10-02]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] NGI Short read NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Spatial multiomic insights into acute cocaine exposure

Nezhyva M, Shahen-Zoabi S, Kabirova M, ..., Margulis K, Jansson ET

- 3 (10) - [2024-10-01; online 2024-10-10]

Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim.

Andersson A, Escriva Conde M, Surova O, ..., Nilsson M, Nyström H

Clin. Cancer Res. 30 (19) 4517-4529 [2024-10-01; online 2024-07-26]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service] In Situ Sequencing (ISS) [Service]

IL-7-dependent and -independent lineages of IL-7R-dependent human T cells.

Arango-Franco CA, Ogishi M, Unger S, ..., Casanova JL, Puel A

J. Clin. Invest. 134 (19) - [2024-10-01; online 2024-10-01]

Ebullition dominates methane emissions in stratified coastal waters.

Hermans M, Stranne C, Broman E, ..., Jilbert T, Humborg C

Sci. Total Environ. 945 (-) 174183 [2024-10-01; online 2024-06-21]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.

Mirabello C, Wallner B

Bioinformatics 40 (10) - [2024-10-01; online 2024-09-30]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Determining Marine Biodegradation Kinetics of Chemicals Discharged from Offshore Oil Platforms─Whole Mixture Testing at High Dilutions Increases Environmental Relevance

Møller MT, Birch H, Sjøholm KK, ..., Papazian S, Mayer P

Environ. Sci. Technol. 58 (39) 17454-17463 [2024-10-01; online 2024-09-18]

A novel SARS-CoV-2 recombinant transmitted from a patient with an acute co-infection.

Dyrdak R, Stamouli S, Ganeshappa Aralaguppe S, ..., Murrell B, Albert J

Lancet Microbe - (-) 100998 [2024-10-01; online 2024-10-01]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Unraveling GRIA1 neurodevelopmental disorders: Lessons learned from the p.(Ala636Thr) variant.

Tvergaard NK, Tkemaladze T, Stödberg T, ..., Tümer Z, Bayat A

Clin. Genet. 106 (4) 427-436 [2024-10-00; online 2024-06-18]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Sex estimation using long bones in the largest burial site of the Copper Age: Linear discriminant analysis and random forest

Díaz-Navarro S, Díez-Hermano S, Rojo-Guerra MA, ..., Gunther T, Uriarte MH

Journal of Archaeological Science: Reports 58 (-) 104730 [2024-10-00; online 2024-10-00]

Seasonal nitrogen removal in an outdoor microalgal polyculture at Nordic conditions.

Mattsson L, Farnelid H, Hirwa M, ..., Legrand C, Lindehoff E

Water Environ Res 96 (10) e11142 [2024-10-00; online 2024-10-17]

Bioinformatics Support for Computational Resources [Service]

Personalized mixture toxicity testing: A proof-of-principle in vitro study evaluating the steroidogenic effects of reconstructed contaminant mixtures measured in blood of individual adults.

Strand D, Lundgren B, Bergdahl IA, Martin JW, Karlsson O

Environ Int 192 (-) 108991 [2024-10-00; online 2024-08-30]

Drug Discovery and Development (DDD) [Collaborative]

Multi-omics profiling to identify early plasma biomarkers in pre-diagnostic pancreatic ductal adenocarcinoma: a nested case-control study.

Borgmästars E, Ulfenborg B, Johansson M, ..., Lubovac-Pilav Z, Sund M

Transl Oncol 48 (-) 102059 [2024-10-00; online 2024-07-16]

Affinity Proteomics Uppsala [Service] Swedish Metabolomics Centre (SMC) [Service]

Molecular Subtypes Are Associated With Clinical Benefit in Cisplatin-Treated Metastatic Urothelial Cancer Patients.

Holmsten K, Sjödahl G, Abrahamsson J, ..., Liedberg F, Ullén A

JCO Precision Oncology 8 (-) e2400209 [2024-10-00; online 2024-10-02]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.

Horváth V, Garza R, Jönsson ME, ..., Douse CH, Jakobsson J

Nat. Struct. Mol. Biol. 31 (10) 1543-1556 [2024-10-00; online 2024-06-04]

Clinical Genomics [Service] Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Liquefaction of lignocellulosic biomass into phenolic monomers and dimers over multifunctional Pd/NbOPO4 catalyst

Jogi R, Samikannu A, Mäki-Arvela P, ..., Xu C, Mikkola JP

Renewable Energy 233 (-) 121148 [2024-10-00; online 2024-10-00]

Increased CSF DOPA Decarboxylase Correlates with Lower DaT-SPECT Binding: Analyses in Biopark and PPMI Cohorts.

Khosousi S, Sturchio A, Appleton E, ..., Iwaki H, Svenningsson P

Mov Disord 39 (10) 1881-1885 [2024-10-00; online 2024-05-26]

High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae.

Khan FK, Sánchez-García M, Johannesson H, Ryberg M

New Phytol. 244 (1) 219-234 [2024-10-00; online 2024-08-07]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gilthead seabream mucus glycosylation is complex, differs between epithelial sites and carries unusual poly N-acetylhexosamine motifs.

Thomsson KA, Benktander J, Toxqui-Rodríguez S, Piazzon MC, Linden SK

Fish Shellfish Immunol. 153 (-) 109864 [2024-10-00; online 2024-08-30]

Epidemiology and ecology of the sylvatic cycle of African Swine Fever Virus in Kenya.

Obanda V, Akinyi M, King'ori E, ..., Stenberg-Lewerin S, Lwande OW

Virus Res. 348 (-) 199434 [2024-10-00; online 2024-07-19]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

Elucidation of cellulose phosphorylation with phytic acid

Orzan E, Barrio A, Spirk S, Nypelö T

Industrial Crops and Products 218 (-) 118858 [2024-10-00; online 2024-10-00]

Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020.

Dyrdak R, Hodcroft EB, Broddesson S, ..., Neher RA, Albert J

Euro Surveill. 29 (41) - [2024-10-00; online 2024-10-11]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service] Clinical Genomics Örebro [Collaborative]

Duloxetine enhances PAX6 expression and suppresses innate immune responses in murine LPS-induced corneal inflammation.

Moustardas P, Abbasi M, Javidjam D, ..., Aberdam D, Lagali N

Ocul Surf 34 (-) 225-234 [2024-10-00; online 2024-08-08]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days.

Resjö S, Willforss J, Large A, ..., Levander F, Andreasson E

Plant Physiol Biochem 215 (-) 109032 [2024-10-00; online 2024-08-10]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.

Overgaard CK, Jamy M, Radutoiu S, Burki F, Dueholm MKD

Mol Ecol Resour 24 (7) e13991 [2024-10-00; online 2024-07-09]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Associations between epigenetic aging and diabetes mellitus in a Swedish longitudinal study.

Wikström Shemer D, Mostafaei S, Tang B, ..., Fall T, Hägg S

Geroscience 46 (5) 5003-5014 [2024-10-00; online 2024-06-27]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A randomized controlled cross-over trial investigating the acute inflammatory and metabolic response after meals based on red meat, fatty fish, or soy protein: the postprandial inflammation in rheumatoid arthritis (PIRA) trial.

Hulander E, Bärebring L, Winkvist A, Gjertsson I, Lindqvist HM

Eur J Nutr 63 (7) 2631-2642 [2024-10-00; online 2024-06-27]

"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".

Zheng D, Wilén BM, Öberg O, Wik T, Modin O

Environ. Microbiol. 26 (10) e16696 [2024-10-00; online 2024-10-09]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions.

Piombo E, Vetukuri RR, Konakalla NC, ..., Karlsson M, Dubey M

BMC Biol. 22 (1) 219 [2024-09-30; online 2024-09-30]

Bioinformatics Support for Computational Resources [Service]

BPP43_05035 is a Brachyspira pilosicoli cell surface adhesin that weakens the integrity of the epithelial barrier during infection.

Rajan A, Gallego P, Dolan B, ..., Simrén M, Pelaseyed T

Gut Microbes 16 (1) 2409247 [2024-09-30; online 2024-09-30]

A research data management (RDM) community for ELIXIR.

D'Anna F, Jareborg N, Jetten M, ..., Vondrasek J, Andrabi M

F1000Res 13 (-) - [2024-09-30; online 2024-09-30]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis.

Murga M, Lopez-Pernas G, Soliva R, ..., Orozco M, Fernández-Capetillo O

Cell Death Dis 15 (9) 694 [2024-09-28; online 2024-09-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Global Proteomics and Proteogenomics [Service]

NiO thin films fabricated using spray-pyrolysis technique: structural and optical characterization and ultrafast charge dynamics studies

Das L, Canto-Aguilar EJ, Tapani T, ..., Gracia-Espino E, Maccaferri N

J. Phys. D: Appl. Phys. 57 (38) 385303 [2024-09-27; online 2024-07-02]

Multiomic biomarkers after cardiac arrest.

Stopa V, Lileikyte G, Bakochi A, ..., Nielsen N, Devaux Y

Intensive Care Med Exp 12 (1) 83 [2024-09-27; online 2024-09-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action.

Maity R, Zhang X, Liberati FR, ..., Aínsa JA, Sancho J

Elife 13 (-) - [2024-09-27; online 2024-09-27]

Single-cell genomics details the maturation block in BCP-ALL and identifies therapeutic vulnerabilities in DUX4-r cases.

Thorsson H, Henningsson R, Puente-Moncada N, ..., Lilljebjörn H, Fioretos T

Blood 144 (13) 1399-1411 [2024-09-26; online 2024-07-05]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Harnessing Light for G-Quadruplex Modulation: Dual Isomeric Effects of an Ortho-Fluoroazobenzene Derivative.

Dudek M, López-Pacios L, Sabouri N, ..., Martinez-Fernandez L, Deiana M

J Phys Chem Lett 15 (38) 9757-9765 [2024-09-26; online 2024-09-17]

Chemical Biology Consortium Sweden (CBCS) [Service]

CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma.

Saba KH, Difilippo V, Styring E, ..., Baumhoer D, Nord KH

npj Genom. Med. 9 (1) 42 [2024-09-25; online 2024-09-25]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analyzing Fusion Pore Dynamics and Counting the Number of Acetylcholine Molecules Released by Exocytosis.

Wang Y, Pradhan A, Gupta P, ..., Zetterberg H, Cans AS

J. Am. Chem. Soc. 146 (38) 25902-25906 [2024-09-25; online 2024-09-11]

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J. Biol. Chem. 300 (11) 107815 [2024-09-24; online 2024-09-24]

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A Versatile and Upgraded Version of the LundTax Classification Algorithm Applied to Independent Cohorts.

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J Mol Diagn - (-) - [2024-09-24; online 2024-09-24]

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Ringlander J, Strömberg LG, Stenbäck JB, ..., Rydell GE, Lindh M

J. Infect. Dis. 230 (3) e684-e693 [2024-09-23; online 2024-01-25]

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PITAR, a DNA damage-inducible cancer/testis long noncoding RNA, inactivates p53 by binding and stabilizing TRIM28 mRNA.

Jana S, Mondal M, Mahale S, ..., Kanduri C, Somasundaram K

Elife 12 (-) - [2024-09-20; online 2024-09-20]

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iScience 27 (9) 110659 [2024-09-20; online 2024-08-03]

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Cancer associated variant enrichment CAVE, a gene agnostic approach to identify low burden variants in chronic lymphocytic leukemia.

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Sci Rep 14 (1) 21962 [2024-09-20; online 2024-09-20]

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Faraday Discuss. - (-) - [2024-09-19; online 2024-09-19]

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J. Biol. Chem. 300 (11) 107795 [2024-09-19; online 2024-09-19]

Metabolic Phenotyping from Whole-Blood Responses to a Standardized Exercise Test May Discriminate for Physiological, Performance, and Illness Outcomes: A Pilot Study in Highly-Trained Cross-Country Skiers.

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Sports Med Open 10 (1) 99 [2024-09-18; online 2024-09-18]

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Nat Commun 15 (1) 8176 [2024-09-18; online 2024-09-18]

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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

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NPJ Biodivers 3 (1) 28 [2024-09-17; online 2024-09-17]

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Wang M, Kamali-Moghaddam M, Löf L, ..., Landegren U, Zhao H

Sci Rep 14 (1) 21655 [2024-09-17; online 2024-09-17]

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Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood.

Sdougkou K, Papazian S, Bonnefille B, ..., Martin LJ, Martin JW

Environ. Sci. Technol. 58 (37) 16302-16315 [2024-09-17; online 2024-09-05]

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Conserv Genet - (-) - [2024-09-17; online 2024-09-17]

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Unraveling the Genetics of Shared Clinical and Serological Manifestations in Patients With Systemic Inflammatory Autoimmune Diseases.

Bianchi M, Kozyrev SV, Notarnicola A, ..., Lindblad-Toh K, with the DISSECT consortium and the ImmunoArray consortium

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Hozakowska-Roszkowska DM, Mengel-From J, Hristozova TK, ..., Röttger R, Nygaard M

Mech Ageing Dev 222 (-) 111979 [2024-09-16; online 2024-09-16]

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Robinson KM, Schiffthaler B, Liu H, ..., Ingvarsson PK, Street NR

Physiol Plantarum 176 (5) e14511 [2024-09-16; online 2024-09-16]

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The CHCHD2-CHCHD10 protein complex is modulated by mitochondrial dysfunction and alters lipid homeostasis in the mouse brain

Gerlach J, Pireddu P, Zhang X, ..., Svenningsson P, Filograna R

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Solution-Processable Bismuthene Nanosheets for Ultrasensitive Sensing of Heavy Metal Ions via Anodic Stripping Voltammetry

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ACS Appl. Nano Mater. 7 (17) 20217-20228 [2024-09-13; online 2024-08-30]

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Int J Mol Sci 25 (18) - [2024-09-13; online 2024-09-13]

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Early-Life Diet Diversity and the Subsequent Risk of Inflammatory Bowel Disease: Findings From Two Scandinavian Birth Cohorts.

Guo A, Ludvigsson J, Hård Af Segerstad EM, ..., Størdal K, Mårild K

Inflamm Bowel Dis - (-) - [2024-09-13; online 2024-09-13]

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Sci Data 11 (1) 997 [2024-09-12; online 2024-09-12]

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LoRicco JG, Malone S, Becker A, ..., Epstein R, Domozych DS

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Verma A, Amnebrink D, Lee CC, ..., Pinhassi J, Wikner J

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Probing erythrocytes as sensitive and reliable sensors of metabolic disturbances in the crosstalk between childhood obesity and insulin resistance: findings from an observational study, in vivo challenge tests, and ex vivo incubation assays.

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Cardiovasc Diabetol 23 (1) 336 [2024-09-11; online 2024-09-11]

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Jhamat N, Guo Y, Han J, ..., Andersson G, Niazi A

Int J Mol Sci 25 (18) - [2024-09-11; online 2024-09-11]

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Aging is associated with functional and molecular changes in distinct hematopoietic stem cell subsets.

Su TY, Hauenstein J, Somuncular E, ..., Månsson R, Luc S

Nat Commun 15 (1) 7966 [2024-09-11; online 2024-09-11]

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Le Voyer T, Maglorius Renkilaraj MRL, Moriya K, ..., Tangye SG, Puel A

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Nagarajan D, Parracho RT, Corujo D, ..., Buschbeck M, Mao Y

J. Clin. Invest. 134 (21) - [2024-09-10; online 2024-09-10]

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Lobo V, Nowak I, Fernandez C, ..., Angeletti D, Sarshad AA

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Transient colonizing microbes promote gut dysbiosis and functional impairment.

Lee S, Meslier V, Bidkhori G, ..., Uhlen M, Shoaie S

NPJ Biofilms Microbiomes 10 (1) 80 [2024-09-08; online 2024-09-08]

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Kammann T, Cai C, Sekine T, ..., Buggert M, Sandberg JK

Sci Immunol 9 (99) eadn2362 [2024-09-06; online 2024-09-06]

Defining the Soluble and Extracellular Vesicle Protein Compartments of Plasma Using In-Depth Mass Spectrometry-Based Proteomics.

Sharma N, Angori S, Sandberg A, ..., Eriksson H, Pernemalm M

J. Proteome Res. 23 (9) 4114-4127 [2024-09-06; online 2024-08-14]

Compound heterozygosity for two variants in BMP5 in human skeletal dysostosis with atrioventricular septal defect.

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The Influence of Disulfide, Thioacetal and Lanthionine-Bridges on the Conformation of a Macrocyclic Peptide.

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Chemistry 30 (50) e202401654 [2024-09-05; online 2024-08-20]

Structure of the iminium reaction intermediate in an engineered aldolase explains the carboligation activity toward arylated ketones and aldehydes.

Hebert H, Sönmez E, Purhonen P, Widersten M

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Blood based metabolic markers of glioma from pre-diagnosis to surgery.

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Sci Rep 14 (1) 20680 [2024-09-05; online 2024-09-05]

Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.

Zhang H, Lundberg M, Ponnikas S, Hasselquist D, Hansson B

G3 (Bethesda) 14 (9) - [2024-09-04; online 2024-07-10]

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Immune system adaptation during gender-affirming testosterone treatment

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Nature 633 (-) 155-164 [2024-09-04]

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Urine metabolomic profiles of autism and autistic traits-A twin study.

Arora A, Mastropasqua F, Bölte S, Tammimies K

PLoS ONE 19 (9) e0308224 [2024-09-03; online 2024-09-03]

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Evolution 78 (9) 1554-1567 [2024-09-03; online 2024-05-30]

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In silico gepotidacin target mining among 33 213 global Neisseria gonorrhoeae genomes from 1928 to 2023 combined with gepotidacin MIC testing of 22 gonococcal isolates with different GyrA and ParC substitutions.

David A, Golparian D, Jacobsson S, ..., Davies C, Unemo M

J. Antimicrob. Chemother. 79 (9) 2221-2226 [2024-09-03; online 2024-07-15]

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Strålfors A, Lagerstedt-Robinson K, Landin B

Clin. Chem. 70 (9) 1185-1187 [2024-09-03; online 2024-07-03]

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Gene-based association analysis of a large patient cohort provides insights into genetics of atypical femur fractures.

Zhou W, Ås J, Shore-Lorenti C, ..., Ebeling PR, Zillikens MC

J. Bone Miner. Res. 39 (9) 1315-1326 [2024-09-02; online 2024-08-10]

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Protective Non-neutralizing anti-N-terminal Domain mAb Maintains Fc-mediated Function against SARS-COV-2 Variants up to BA.2.86-JN.1 with Superfluous In Vivo Protection against JN.1 Due to Attenuated Virulence.

Izadi A, Godzwon M, Söderlund Strand A, ..., Ohlin M, Nordenfelt P

J. Immunol. 213 (5) 678-689 [2024-09-01; online 2024-07-17]

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Pacoste L, Ignat'ev VM, Dominiak PM, Zou X

Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ 11 (Pt 5) 878-890 [2024-09-01; online 2024-09-01]

Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly.

Li Y, Pacoste LC, Gu W, ..., Xu H, Nanson JD

Acta Crystallogr D Struct Biol 80 (Pt 9) 699-712 [2024-09-01; online 2024-09-04]

Elevated carbohydrate antigen 125 (CA125) is associated with incident heart failure and mortality in acute coronary syndrome.

Yndigegn T, Gu T, Grufman H, ..., Goncalves I, Schiopu A

ESC Heart Failure - (-) - [2024-09-01; online 2024-09-01]

A Drug Discovery Pipeline for MAPK/ERK Pathway Inhibitors in Caenorhabditis elegans.

Gorgoń S, Billing O, Eriksson AU, Hemmingsson O

Cancer Res Commun 4 (9) 2454-2462 [2024-09-01; online 2024-08-31]

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pH‐Responsive Virus‐Based Colloidal Crystals for Advanced Material Platforms

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Adv Funct Materials 34 (37) - [2024-09-00; online 2024-04-26]

Transcriptomic and functional analyses on a Botrytis cinerea multidrug-resistant (MDR) strain provides new insights into the potential molecular mechanisms of MDR and fitness.

Sofianos G, Piombo E, Dubey M, ..., Karaoglanidis G, Tzelepis G

Mol. Plant Pathol. 25 (9) e70004 [2024-09-00; online 2024-09-08]

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The PerioGene North Study Uncovers Serum Proteins Related to Periodontitis.

Wänman M, Betnér S, Esberg A, ..., Kindstedt E, Lundberg P

J Dent Res 103 (10) 999-1007 [2024-09-00; online 2024-08-05]

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Córdoba-Beldad CM, Grantham J

Eur J Cell Biol 103 (3) 151430 [2024-09-00; online 2024-06-15]

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Luomaranta M, Grones C, Choudhary S, ..., Street NR, Tuominen H

New Phytol. 243 (6) 2157-2174 [2024-09-00; online 2024-07-28]

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Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs.

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J. Intern. Med. 296 (3) 234-248 [2024-09-00; online 2024-07-07]

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Species-genetic diversity correlation in a metacommunity of urban pond invertebrates

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Basic and Applied Ecology 79 (-) 114-122 [2024-09-00; online 2024-09-00]

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Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon.

Fernandes AM, Cohn-Haft M, Fábio Silveira L, ..., Nascimento N, Olsson U

Mol. Phylogenet. Evol. 198 (-) 108117 [2024-09-00; online 2024-06-07]

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Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data.

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Cytometry A 105 (9) 677-687 [2024-09-00; online 2024-07-03]

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Plasma Protein Profiling to Discern Indolent from Advanced Systemic Mastocytosis.

Iribarren C, Levedahl KH, Atanasoai I, ..., Carlson M, Nilsson GP

J Mol Diagn 26 (9) 792-804 [2024-09-00; online 2024-06-24]

New finds of European bison identified through the systematic DNA-based species identification of archaeological remains of large bovines from Scandinavia

Rosengren E, Rossi C, Heino MT, Sinding MHS

Journal of Archaeological Science: Reports 57 (-) 104668 [2024-09-00; online 2024-09-00]

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Marina H, Nielsen PP, Fikse WF, Rönnegård L

Applied Animal Behaviour Science 278 (-) 106366 [2024-09-00; online 2024-09-00]

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Metagenomic identification of bull semen microbiota in different seasons.

Cojkic A, Niazi A, Morrell JM

Animal Reproduction Science 268 (-) 107569 [2024-09-00; online 2024-07-30]

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Longitudinal changes in cardiovascular disease-related proteins in welders.

Dauter UM, Gliga AR, Albin M, Broberg K

Int Arch Occup Environ Health 97 (7) 803-812 [2024-09-00; online 2024-07-03]

Immune system adaptation during gender-affirming testosterone treatment.

Lakshmikanth T, Consiglio C, Sardh F, ..., Landegren N, Brodin P

Nature 633 (8028) 155-164 [2024-09-00; online 2024-09-04]

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Hop stunt viroid infection induces heterochromatin reorganization.

Marquez-Molins J, Cheng J, Corell-Sierra J, ..., Gomez G, Martinez G

New Phytol. 243 (6) 2351-2367 [2024-09-00; online 2024-07-18]

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Genome-Wide Association Study of Obsessive-Compulsive Symptoms including 33,943 individuals from the general population.

Strom NI, Burton CL, Iyegbe C, ..., Smit DJA, Arnold PD

Mol. Psychiatry 29 (9) 2714-2723 [2024-09-00; online 2024-03-28]

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Dantrolene corrects cellular disease features of Darier disease and may be a novel treatment.

Hunt M, Wang N, Pupinyo N, ..., Bachar-Wikstrom E, Wikstrom JD

EMBO Mol Med 16 (9) 1986-2001 [2024-09-00; online 2024-07-26]

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Contemporary intergeneric hybridization and backcrossing among birds-of-paradise.

Thörn F, Soares AER, Müller IA, ..., Blom MPK, Irestedt M

Evolution Letters 8 (5) 680-694 [2024-09-00; online 2024-06-08]

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Associations between sickness behavior, but not inflammatory cytokines, and psychiatric comorbidity in chronic pain.

Åström Reitan JLM, Karshikoff B, Holmström L, ..., Kemani MK, Wicksell RK

Psychoneuroendocrinology 167 (-) 107094 [2024-09-00; online 2024-06-13]

Activating mutations remodel the chromatin accessibility landscape to drive distinct regulatory networks in KMT2A-rearranged acute leukemia.

Zhang Q, Falqués-Costa T, Pilheden M, ..., Hyrenius-Wittsten A, Hagström-Andersson AK

Hemasphere 8 (9) e70006 [2024-09-00; online 2024-09-26]

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Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels.

Deen AJ, Thorsson J, O'Roberts EM, ..., Oses C, Stadler C

J. Histochem. Cytochem. 72 (8-9) 517-544 [2024-08-31; online 2024-08-31]

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Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma.

Olsen TK, Otte J, Mei S, ..., Kharchenko PV, Baryawno N

Mol. Cancer 23 (1) 180 [2024-08-31; online 2024-08-31]

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Soft Tissue Tumor with PAK2::RAF1 Kinase Fusion: An Emerging Sarcoma Entity.

Haglund C, Behrendtz M, Hesla A, Haglund de Flon F

Case Rep Oncol 17 (1) 960-965 [2024-08-30; online 2024-08-30]

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Rapid and robust isolation of microglia and vascular cells from brain subregions for integrative single-cell analyses.

Preka E, Lastra Romero A, Sun Y, ..., Osman AM, Blomgren K

Heliyon 10 (16) e35838 [2024-08-30; online 2024-08-05]

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Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells

Kee N, Leboeuf M, Gómez S, ..., Ericson J, Hedlund E

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Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat.

Edlund M, Anderson BM, Su H, ..., Nickrent DL, Petersen G

Ann. Bot. - (-) - [2024-08-30; online 2024-08-30]

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Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.

Rodríguez-Varela R, Yaka R, Pochon Z, ..., Azkarate A, Götherström A

Sci Adv 10 (35) eadp8625 [2024-08-30; online 2024-08-28]

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DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor.

Pandiloski N, Horváth V, Karlsson O, ..., Jakobsson J, Douse CH

Nat Commun 15 (1) 7534 [2024-08-30; online 2024-08-30]

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Conference report: the first bacterial genome sequencing pan-European network conference.

Germuskova Z, Sosa E, Lagos AC, ..., Mölling P, Egli A

Microbes Infect - (-) 105410 [2024-08-30; online 2024-08-30]

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The Crosstalk Analysis between mPSCs and Panc1 Cells Identifies CCN1 as a Positive Regulator of Gemcitabine Sensitivity in Pancreatic Cancer Cells.

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Int J Mol Sci 25 (17) - [2024-08-29; online 2024-08-29]

Expression of inducible nitric oxide synthase, nitrotyrosine, eosinophilic peroxidase, eotaxin-3, and galectin-3 in patients with gastroesophageal reflux disease, eosinophilic esophagitis, and in healthy controls: a semiquantitative image analysis of 3,3'-diaminobenzidine-stained esophageal biopsies.

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Dis Esophagus 37 (9) - [2024-08-29; online 2024-04-29]

Integrated Microscopy Technologies Gothenburg [Service]

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Nat Commun 15 (1) 7510 [2024-08-29; online 2024-08-29]

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PLoS ONE 19 (8) e0308521 [2024-08-29; online 2024-08-29]

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Nat Commun 15 (1) 7422 [2024-08-28; online 2024-08-28]

Polygenic Risk Scores and Twin Concordance for Schizophrenia and Bipolar Disorder.

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JAMA Psychiatry - (-) - [2024-08-28; online 2024-08-28]

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Antimicrob Agents Chemother - (-) - [2024-08-28; online 2024-08-28]

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Cardiovasc Diabetol 23 (1) 315 [2024-08-27; online 2024-08-27]

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Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis.

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Nat Commun 15 (1) 7177 [2024-08-26; online 2024-08-26]

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Intensified, Kilogram-Scaled, and Environment-Friendly: Chemoenzymatic Synthesis of Bio-Based Acylated Hydroxystyrenes.

Petermeier P, Domínguez de María P, Byström E, Kara S

ACS Sustainable Chem. Eng. 12 (34) 12869-12878 [2024-08-26; online 2024-08-15]

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JOSS 9 (100) 6869 [2024-08-26; online 2024-08-26]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

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Nat Commun 15 (1) 7307 [2024-08-24; online 2024-08-24]

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Cell Commun Signal 22 (1) 411 [2024-08-23; online 2024-08-23]

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Acta Neuropathol Commun 12 (1) 137 [2024-08-23; online 2024-08-23]

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Science 385 (6711) 892-898 [2024-08-23; online 2024-08-22]

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Chem. Commun. (Camb.) 60 (69) 9238-9241 [2024-08-22; online 2024-08-22]

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J Mater Chem B 12 (33) 8107-8121 [2024-08-22; online 2024-08-22]

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Blood 144 (8) 873-887 [2024-08-22; online 2024-07-03]

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Sci Rep 14 (1) 19306 [2024-08-20; online 2024-08-20]

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Nat Commun 15 (1) 7065 [2024-08-16; online 2024-08-16]

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MBio 15 (8) e0003924 [2024-08-14; online 2024-07-08]

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Front Immunol 15 (-) 1442749 [2024-08-14; online 2024-08-14]

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FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]

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Sun W, Torrens G, Ter Beek J, Cava F, Berntsson RP

MBio 15 (8) e0048824 [2024-08-14; online 2024-06-28]

Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service]

Screening persistent organic pollutants for effects on testosterone and estrogen synthesis at human-relevant concentrations using H295R cells in 96-well plates.

Strand D, Nylander E, Höglund A, ..., Martin JW, Karlsson O

Cell Biol. Toxicol. 40 (1) 69 [2024-08-13; online 2024-08-13]

Drug Discovery and Development (DDD) [Collaborative]

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Sci Rep 14 (1) 18806 [2024-08-13; online 2024-08-13]

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Blending Samples to Increase Accuracy and Precision of 1H NMR Urine Metabolomics.

Bay Nord A, Lindqvist H, Rådjursöga M, ..., Karlsson BG, Malmodin D

Anal. Chem. 96 (32) 13078-13085 [2024-08-13; online 2024-07-31]

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Martínez-Carranza M, Škerlová J, Lee PG, ..., Dong M, Stenmark P

Commun Chem 7 (1) 179 [2024-08-13; online 2024-08-13]

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Fu J, Zaghen S, Lu H, ..., Di Bartolomeo F, Kerkhoven EJ

Sci Adv 10 (32) eadn0414 [2024-08-09; online 2024-08-09]

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Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification.

Saei AA, Lundin A, Lyu H, ..., Gygi SP, Zubarev RA

Adv Sci (Weinh) - (-) e2401502 [2024-08-09; online 2024-08-09]

Magnesium induced structural reorganization in the active site of adenylate kinase.

Nam K, Thodika ARA, Tischlik S, ..., Sauer-Eriksson AE, Wolf-Watz M

Sci Adv 10 (32) eado5504 [2024-08-09; online 2024-08-09]

Long-term ambient air pollution exposure and renal function and biomarkers of renal disease.

Kilbo Edlund K, Xu Y, Andersson EM, ..., Ljungman P, Stockfelt L

Environ Health 23 (1) 67 [2024-08-09; online 2024-08-09]

AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1.

Díaz-Holguín A, Saarinen M, Vo DD, ..., Carlsson J, Svenningsson P

Sci Adv 10 (32) eadn1524 [2024-08-09; online 2024-08-07]

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Micro-costing of genetic diagnostics in acute leukemia in Sweden: from standard-of-care to whole-genome sequencing.

Thangavelu T, Wirta V, Orsmark-Pietras C, ..., Rosenquist R, Levin LÅ

J Med Econ 27 (1) 1053-1060 [2024-08-08; online 2024-08-08]

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JAK inhibition decreases the autoimmune burden in Down syndrome

Rachubinski AL, Wallace E, Gurnee E, ..., Norris DA, Espinosa JM

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Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.

Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S

BMC Genomics 25 (1) 772 [2024-08-08; online 2024-08-08]

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The genetic architecture of dog ownership: large-scale genome-wide association study in 97,552 European-ancestry individuals.

Gong T, Karlsson R, Yao S, ..., Fall T, Almqvist C

G3 (Bethesda) 14 (8) - [2024-08-07; online 2024-05-31]

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Hypoxic-Ischemic Insult Alters Polyamine and Neurotransmitter Abundance in the Specific Neonatal Rat Brain Subregions.

Mácha H, Luptáková D, Juránek I, Andrén PE, Havlíček V

ACS Chem Neurosci 15 (15) 2811-2821 [2024-08-07; online 2024-07-26]

History of childhood maltreatment associated with hospitalization or death due to COVID-19: a cohort study.

Wang Y, Ge F, Aspelund T, ..., Song H, Valdimarsdóttir UA

BMC Med 22 (1) 319 [2024-08-07; online 2024-08-07]

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Applying Spatial Metabolomics To Investigate Age- and Drug-Induced Neurochemical Changes.

Vallianatou T, Angerer TB, Kaya I, ..., Svenningsson P, Andrén PE

ACS Chem Neurosci 15 (15) 2822-2829 [2024-08-07; online 2024-07-29]

Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.

Salgkamis D, Sifakis EG, Agartz S, ..., Matikas A, Zerdes I

Sci Rep 14 (1) 18275 [2024-08-06; online 2024-08-06]

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Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.

Biswas T, Vogel H, Biedermann PHW, ..., Yuvaraj JK, Andersson MN

BMC Genomics 25 (1) 764 [2024-08-06; online 2024-08-06]

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AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.

Rashid U, Wu C, Shiller J, ..., Thomson S, Deng CH

Bioinformatics 40 (8) - [2024-08-02; online 2024-07-30]

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A genome-wide genetic screen identified targets for destabilizing the parasitophorous vacuole ofChlamydia trachomatis

Babu Sait MR, Jachmann LH, Milivojevic M, ..., Schmierer B, Sixt BS

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A genome-wide genetic screen identified targets for destabilizing the parasitophorous vacuole ofChlamydia trachomatis

Babu Sait MR, Jachmann LH, Milivojevic M, ..., Schmierer B, Sixt BS

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The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization.

Unemo M, Sánchez-Busó L, Golparian D, ..., Wi T, Lahra MM

J. Antimicrob. Chemother. 79 (8) 1885-1899 [2024-08-01; online 2024-06-18]

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The interaction of genetics and physical activity in the pathogenesis of metabolic dysfunction associated liver disease.

Frostdahl H, Ahmad N, Hammar U, ..., Brooke HL, Ahmad S

Sci Rep 14 (1) 17817 [2024-08-01; online 2024-08-01]

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Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV.

Narayanan A, Kieri O, Vesterbacka J, ..., Ray S, Nowak P

Sci Rep 14 (1) 17820 [2024-08-01; online 2024-08-01]

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Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.

Unneberg P, Larsson M, Olsson A, ..., Meyer B, Wallberg A

Nat Commun 15 (1) 6297 [2024-08-01; online 2024-08-01]

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Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.

Skytte Af Sätra J, Garkava-Gustavsson L, Ingvarsson PK

Heredity (Edinb) 133 (2) 67-77 [2024-08-00; online 2024-06-04]

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Species-specific erosion of genetic diversity in grassland butterflies depends on landscape land cover

Nolen ZJ, Rundlöf M, Runemark A

Biological Conservation 296 (-) 110694 [2024-08-00; online 2024-08-00]

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Spatiotemporal Release of Singlet Oxygen in Low Molecular Weight Organo-Gels Upon Thermal or Photochemical External Stimuli.

Sandelin E, Schilling L, Saha E, ..., Sundén H, Wallentin CJ

Small 20 (35) e2400827 [2024-08-00; online 2024-04-25]

Soluble and hydrolyzable phenolic compounds in date fruits (Phoenix dactylifera L.) by UPLC-QTOF-MS/MS and UPLC-DAD

Alam MZ, Fristedt R, Landberg R, Kamal-Eldin A

Journal of Food Composition and Analysis 132 (-) 106354 [2024-08-00; online 2024-08-00]

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Andrade P, Alves JM, Pereira P, ..., Andersson L, Carneiro M

Nat Ecol Evol 8 (8) 1543-1555 [2024-08-00; online 2024-06-21]

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PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.

Breidenstein A, Lamy A, Bader CP, ..., Wanrooij PH, Berntsson RP

Life Sci. Alliance 7 (8) - [2024-08-00; online 2024-05-29]

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Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album).

Schneider K, Steward RA, Celorio-Mancera MdlP, ..., Wheat CW, Nylin S

Mol. Ecol. 33 (16) e17479 [2024-08-00; online 2024-07-22]

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One-year longitudinal changes of peripheral CD4+ T-lymphocyte counts, gut microbiome, and plaque vulnerability after an acute coronary syndrome.

I Fernández-Avila A, Gutiérrez-Ibanes E, Martín de Miguel I, ..., Correa R, Bermejo J

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Multi-parametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer.

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Nat. Med. 30 (8) 2170-2180 [2024-08-00; online 2024-06-28]

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Migratory CD103+CD11b+ cDC2s in Peyer's patches are critical for gut IgA responses following oral immunization.

Gribonika I, Strömberg A, Chandode RK, ..., Bemark M, Lycke N

Mucosal Immunol 17 (4) 509-523 [2024-08-00; online 2024-03-15]

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Fryk E, Rodrigues Silva VR, Strindberg L, ..., Lind L, Jansson PA

Int J Obes (Lond) 48 (8) 1180-1189 [2024-08-00; online 2024-05-22]

Meat consumption and the risk of hip fracture in women and men: two prospective Swedish cohort studies.

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Eur J Nutr 63 (5) 1819-1833 [2024-08-00; online 2024-04-17]

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Acta Obstet Gynecol Scand 103 (8) 1564-1569 [2024-08-00; online 2024-06-14]

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Fungal communities associated with Picea abiesPinus sylvestris and Larix sp. seeds of different geographic origin: Implications for disease management

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For. Path. 54 (4) - [2024-08-00; online 2024-08-05]

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Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding.

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J Environ Manage 365 (-) 121619 [2024-08-00; online 2024-07-03]

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Evolution Letters 8 (4) 550-560 [2024-08-00; online 2024-03-17]

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Nat. Biotechnol. 42 (8) 1296-1302 [2024-08-00; online 2023-09-21]

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Evolution Letters 8 (4) 575-586 [2024-08-00; online 2024-04-23]

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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.

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Life Sci. Alliance 7 (8) - [2024-08-00; online 2024-05-22]

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FASEB J. 38 (14) e23815 [2024-07-31; online 2024-07-11]

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Plant Physiol. 195 (4) 2877-2890 [2024-07-31; online 2024-04-17]

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Gene-environment interaction in expertise acquisition: Practice effects on musical expertise vary by polygenic scores for cognitive performance.

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Heliyon 10 (14) e34264 [2024-07-30; online 2024-07-06]

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Enhancers regulate genes linked to severe and mild childhood asthma.

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Heliyon 10 (14) e34386 [2024-07-30; online 2024-07-09]

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Front. Biomater. Sci. 3 (-) - [2024-07-30; online 2024-07-30]

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Nat Commun 15 (1) 6419 [2024-07-30; online 2024-07-30]

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Ichthyosporea: a window into the origin of animals.

Shabardina V, Dharamshi JE, Ara PS, ..., Casacuberta E, Ruiz-Trillo I

Commun Biol 7 (1) 915 [2024-07-29; online 2024-07-29]

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Mandolesi M, Das H, de Vries L, ..., Murrell B, Karlsson Hedestam GB

Nat Commun 15 (1) 6338 [2024-07-27; online 2024-07-27]

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Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.

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Bifidobacterium longum subsp. longum BG-L47 boosts growth and activity of Limosilactobacillus reuteri DSM 17938 and its extracellular membrane vesicles.

Ermann Lundberg L, Pallabi Mishra P, Liu P, ..., Linninge C, Roos S

Appl. Environ. Microbiol. 90 (7) e0024724 [2024-07-24; online 2024-06-18]

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Genome Res. 34 (6) 967-978 [2024-07-23; online 2024-07-23]

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Elevated cytokine levels in the central nervous system of cluster headache patients in bout and in remission.

Ran C, Olofsgård FJ, Wellfelt K, Steinberg A, Belin AC

J Headache Pain 25 (1) 121 [2024-07-23; online 2024-07-23]

Nematocida displodere mechanosensitive ion channel of small conductance 2 assembles into a unique 6-channel super-structure in vitro.

Berg A, Berntsson RP, Barandun J

PLoS ONE 19 (7) e0301951 [2024-07-22; online 2024-07-22]

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Nat Commun 15 (1) 6164 [2024-07-22; online 2024-07-22]

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A single-cell pan-cancer analysis to show the variability of tumor-infiltrating myeloid cells in immune checkpoint blockade.

Li W, Pan L, Hong W, ..., Xiao C, Li X

Nat Commun 15 (1) 6142 [2024-07-21; online 2024-07-21]

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Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system.

Blom MPK, Peona V, Prost S, ..., Suh A, Irestedt M

iScience 27 (7) 110300 [2024-07-19; online 2024-06-19]

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Normoglycemia and physiological cortisone level maintain glucose homeostasis in a pancreas-liver microphysiological system.

Rigal S, Casas B, Kanebratt KP, ..., Andersson TB, Vilén LK

Commun Biol 7 (1) 877 [2024-07-18; online 2024-07-18]

The rate of W chromosome degeneration across multiple avian neo-sex chromosomes.

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Sci Rep 14 (1) 16548 [2024-07-17; online 2024-07-17]

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The Escherichia coli chromosome moves to the replisome.

Gras K, Fange D, Elf J

Nat Commun 15 (1) 6018 [2024-07-17; online 2024-07-17]

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Separate hydrolysis and fermentation of softwood bark pretreated with 2-naphthol by steam explosion.

Averheim A, Stagge S, Jönsson LJ, Larsson SH, Thyrel M

Biotechnol Biofuels Bioprod 17 (1) 102 [2024-07-17; online 2024-07-17]

Salivary Proteins and Metabolites as Caries Biomarkers in Adolescents.

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Suppression of the Escherichia coli rnpA49 conditionally lethal phenotype by different compensatory mutations.

Babina AM, Kirsebom LA, Andersson DI

RNA 30 (8) 977-991 [2024-07-16; online 2024-07-16]

Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.

Wallerstein J, Han X, Levkovets M, ..., Agback T, Orekhov V

Commun Biol 7 (1) 868 [2024-07-16; online 2024-07-16]

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Enhancing Molecular Characterization of Dissolved Organic Matter by Integrative Direct Infusion and Liquid Chromatography Nontargeted Workflows.

Patrone J, Vila-Costa M, Dachs J, ..., Gago-Ferrero P, Gil-Solsona R

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Front Immunol 15 (-) 1415016 [2024-07-15; online 2024-07-15]

Maturation of Human Intestinal Epithelial Cell Layers Fortifies the Apical Surface againstSalmonellaAttack

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UniCarb-DB: An MS/MS Experimental Glycomic Fragmentation Database.

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FEMS Microbiol. Ecol. 100 (8) - [2024-07-12; online 2024-07-14]

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Cell 187 (14) 3531-3540.e13 [2024-07-11; online 2024-06-27]

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Seroepidemiological assessment of the spread of SARS-CoV-2 among 25 and 28 year-old adult women in Finland between March 2020-June 2022.

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PLoS ONE 19 (7) e0305285 [2024-07-11; online 2024-07-11]

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A cancer immunotherapy modality based on dendritic cell reprogrammingin vivo

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Regional Changes in Brain Biomolecular Markers in a Collagen-Induced Arthritis Rat Model.

Millen AME, Maluleke TT, Pienaar L, ..., Andrén PE, Baijnath S

Biology (Basel) 13 (7) - [2024-07-10; online 2024-07-10]

Obscurity of chlorophyll tails - Is chlorophyll with farnesyl tail incorporated into PSII complexes?

Graça AT, Lihavainen J, Hussein R, Schröder WP

Physiol Plantarum 176 (4) e14428 [2024-07-10; online 2024-07-10]

Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.

Grochowski CM, Bengtsson JD, Du H, ..., Lupski JR, Carvalho CMB

Cell Genomics 4 (7) 100590 [2024-07-10; online 2024-06-21]

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Bimai O, Banerjee I, Rozman Grinberg I, ..., Sjöberg BM, Logan DT

Elife 12 (-) - [2024-07-05; online 2024-07-05]

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Johansson Å, Subramani MV, Yilmaz B, ..., Johansson MEV, Birchenough GMH

bioRxiv - (-) - [2024-07-05; online 2024-07-05]

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Evaluating Bacterial Spore Preparation Methods for Scanning Electron Microscopy

Malyshev D, Lee CC, Andersson M

Microsc Microanal 30 (3) 564-573 [2024-07-04; online 2024-05-03]

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DNA methylation of exercise-responsive genes differs between trained and untrained men.

Geiger C, Needhamsen M, Emanuelsson EB, ..., Reitzner SM, Lindholm ME

BMC Biol. 22 (1) 147 [2024-07-04; online 2024-07-04]

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A DNA Methylation Signature from Buccal Swabs to Identify Tuberculosis Infection.

Karlsson L, Öhrnberg I, Sayyab S, ..., Paues J, Lerm M

J. Infect. Dis. - (-) - [2024-07-04; online 2024-07-04]

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Thalén NB, Karlander M, Lundqvist M, ..., Ohlin M, Rockberg J

Commun Biol 7 (1) 805 [2024-07-03; online 2024-07-03]

Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.

Pettersson ME, Quintela M, Besnier F, ..., Glover KA, Andersson L

Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-26]

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Evaluating regression and probabilistic methods for ECG-based electrolyte prediction.

von Bachmann P, Gedon D, Gustafsson FK, ..., Sundström J, Schön TB

Sci Rep 14 (1) 15273 [2024-07-03; online 2024-07-03]

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Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.

Papachristos K, Sayadi A, Arnqvist G

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Discovery of a novel inhibitor of macropinocytosis with antiviral activity.

Porebski B, Christ W, Corman A, ..., Hühn D, Fernandez-Capetillo O

Mol Ther - (-) - [2024-07-02; online 2024-07-02]

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CRISPR-Cas9 Knockout Screens Identify DNA Damage Response Pathways and BTK as Essential for Cisplatin Response in Diffuse Large B-Cell Lymphoma.

Issa II, Due H, Brøndum RF, ..., Schmierer B, Dybkær K

Cancers (Basel) 16 (13) 2437 [2024-07-02; online 2024-07-02]

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Unravelling reference bias in ancient DNA datasets.

Dolenz S, van der Valk T, Jin C, ..., Dalén L, Heintzman PD

Bioinformatics 40 (7) - [2024-07-01; online 2024-07-04]

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Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer.

Hammarström K, Nunes L, Mathot L, ..., Sjöblom T, Glimelius B

Int. J. Cancer 155 (1) 40-53 [2024-07-01; online 2024-02-20]

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Carboxyl-group compounds activate voltage-gated potassium channels via a distinct mechanism.

Rönnelid O, Elinder F

J. Gen. Physiol. 156 (7) - [2024-07-01; online 2024-06-04]

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Cancer Core Europe: Leveraging Institutional Synergies to Advance Oncology Research and Care Globally.

Carmona J, Chavarria E, Donoghue K, ..., Zwart W, Tabernero J

Cancer Discov 14 (7) 1147-1153 [2024-07-01; online 2024-06-13]

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BirthSeq, a new method to isolate and analyze dated cells in different vertebrates.

Rueda-Alaña E, Grillo M, Vázquez E, ..., Nilsson M, García-Moreno F

Development 151 (13) - [2024-07-01; online 2024-07-10]

Utilising ancient DNA to understand crop population dynamics across a millennium: A case study of archaeological barley (Hordeum vulgare L.) from Gran Canaria, Spain

Hagenblad J, Morales J, Leino MW, ..., Rodríguez-Rodríguez AC, Santana J

Journal of Archaeological Science 167 (-) 106001 [2024-07-00; online 2024-07-00]

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Uncommon Variants in FLG2 and NOD2 Are Associated with Atopic Dermatitis in the Ethiopian Population.

Wang S, Elmgren JK, Eisfeldt J, ..., Tapia-Paez I, Bradley M

JID Innov 4 (4) 100284 [2024-07-00; online 2024-04-29]

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The WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP) identifies high levels of ceftriaxone resistance across Vietnam, 2023.

Lan PT, Nguyen HT, Golparian D, ..., Unemo M, EGASP-Vietnam WGS study group

Lancet Reg Health West Pac 48 (-) 101125 [2024-07-00; online 2024-06-27]

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Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health.

Lecoutre S, Maqdasy S, Rizo-Roca D, ..., Mejhert N, Rydén M

Nat Metab 6 (7) 1329-1346 [2024-07-00; online 2024-07-15]

Predicting glycan structure from tandem mass spectrometry via deep learning.

Urban J, Jin C, Thomsson KA, ..., Fadda E, Bojar D

Nat. Methods 21 (7) 1206-1215 [2024-07-00; online 2024-07-01]

Precision Diagnostics in Myeloid Malignancies: Development and Validation of a National Capture-Based Gene Panel.

Orsmark-Pietras C, Lyander A, Ladenvall C, ..., Fioretos T, SciLifeLab Clinical Genomics Platform and Genomic Medicine Sweden

Genes Chromosomes Cancer 63 (7) e23257 [2024-07-00; online 2024-07-20]

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Multiarray screening identifies plasma proteins associated with Th17 cell differentiation and viral defense in coincident asthma and obesity.

Manell H, Tsolakis N, Janson C, Malinovschi A, Alving K

Pediatr Allergy Immunol 35 (7) e14187 [2024-07-00; online 2024-07-05]

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Chen G, Wang Y, Zheng Z, ..., Knight SD, Johansson J

Protein Sci. 33 (7) e5063 [2024-07-00; online 2024-06-12]

LIGHT protein: A novel gingival crevicular fluid biomarker associated with increased probing depth after periodontal surgery.

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J Clin Periodontol 51 (7) 852-862 [2024-07-00; online 2024-02-23]

Genomic insights into the evolutionary and demographic histories of the extinct Hoopoe Starling (Fregilupus varius)

Fuchs J, Ericson PGP, Irestedt M

Ibis 166 (3) 1073-1080 [2024-07-00; online 2024-01-03]

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GABA-mediated inhibition of human CD4+ T cell functions is enhanced by insulin but impaired by high glucose levels.

Jin Z, Hammoud H, Bhandage AK, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 105 (-) 105217 [2024-07-00; online 2024-06-28]

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Facilitated introgression from domestic goat into Alpine ibex at immune loci.

Münger X, Robin M, Dalén L, Grossen C

Mol. Ecol. 33 (14) e17429 [2024-07-00; online 2024-06-07]

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Drug solubilization in dog intestinal fluids with and without administration of lipid-based formulations.

Parrow A, Kabedev A, Larsson P, ..., Abrahamsson B, Bergström CAS

Journal of Controlled Release 371 (-) 555-569 [2024-07-00; online 2024-06-13]

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Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice.

Holl D, Hau WF, Julien A, ..., Dias DO, Göritz C

Nat. Neurosci. 27 (7) 1285-1298 [2024-07-00; online 2024-06-07]

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Diagnostic patterns of serum inflammatory protein markers in children with Lyme neuroborreliosis.

Fredriksson T, Brudin L, Henningsson AJ, Skogman BH, Tjernberg I

Ticks Tick Borne Dis 15 (4) 102349 [2024-07-00; online 2024-05-08]

Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing.

Widén J, Morén J, Mölling P, ..., Sundqvist M, Westman G

Infect Dis (Lond) 56 (7) 521-530 [2024-07-00; online 2024-03-26]

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Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.

Nordahl L, Akkuratov EE, Heimgärtner J, ..., Wennmalm S, Brismar H

Biochimica et Biophysica Acta (BBA) - General Subjects 1868 (7) 130619 [2024-07-00; online 2024-04-20]

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Box-Behnken design for the synthesis optimization of mesoporous sulfur-doped carbon-based materials from birch waste: Promising candidates for environmental and energy storage application

Laisné E, Thivet J, Manavalan G, ..., Lassi U, dos Reis GS

Colloids and Surfaces A: Physicochemical and Engineering Aspects 692 (-) 133899 [2024-07-00; online 2024-07-00]

Bacterial community characterization by deep learning aided image analysis in soil chips

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Ecological Informatics 81 (-) 102562 [2024-07-00; online 2024-07-00]

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A community effort to track commercial single-cell and spatial 'omic technologies and business trends.

De Jonghe J, Opzoomer JW, Vilas-Zornoza A, ..., Cribbs AP, Taylor-King JP

Nat. Biotechnol. 42 (7) 1017-1023 [2024-07-00; online 2024-07-18]

Myofiber-specific lipidomics unveil differential contributions to insulin sensitivity in individuals of African and European ancestry.

Eurén T, Gower B, Steneberg P, ..., Edlund H, Chorell E

Heliyon 10 (12) e32456 [2024-06-30; online 2024-06-05]

Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy – identification and correction

Adler J, Bernhem K, Parmryd I

Commun Biol 7 (1) - [2024-06-29; online 2024-06-29]

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The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1.

Gustavsson EK, Sethi S, Gao Y, ..., Hardy J, Ryten M

Sci Adv 10 (26) eadk1296 [2024-06-28; online 2024-06-26]

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NOS2-derived low levels of NO drive psoriasis pathogenesis.

Köhler I, Bivik Eding C, Kasic NK, Verma D, Enerbäck C

Cell Death Dis 15 (6) 449 [2024-06-26; online 2024-06-26]

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Small molecules dominate organic phosphorus in NaOH-EDTA extracts of soils as determined by 31P NMR.

Haddad L, Vincent AG, Giesler R, Schleucher J

Sci. Total Environ. 931 (-) 172496 [2024-06-25; online 2024-04-16]

Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.

Rönn T, Perfilyev A, Oskolkov N, Ling C

Sci Rep 14 (1) 14637 [2024-06-25; online 2024-06-25]

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Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis.

Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F

Sci Data 11 (1) 678 [2024-06-22; online 2024-06-22]

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Quantification and Profiling of Early and Late Differentiation Stage T Cells in Mantle Cell Lymphoma Reveals Immunotherapeutic Targets in Subsets of Patients.

Lokhande L, Nilsson D, de Matos Rodrigues J, ..., Jerkeman M, Ek S

Cancers (Basel) 16 (13) - [2024-06-21; online 2024-06-21]

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Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota.

Raba G, Luis AS, Schneider H, ..., Adamberg K, Arike L

iScience 27 (6) 110093 [2024-06-21; online 2024-05-23]

MOXD1 is a lineage-specific gene and a tumor suppressor in neuroblastoma

Fredlund E, Andersson S, Hilgert E, ..., van Nes J, Mohlin S

Sci Adv 10 (25) - [2024-06-21; online 2024-06-21]

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Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II.

Hussein R, Graça A, Forsman J, ..., Zouni A, Schröder WP

Science 384 (6702) 1349-1355 [2024-06-21; online 2024-06-20]

Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane.

González-López A, Larsson DSD, Koripella RK, ..., Sanyal S, Selmer M

Sci Rep 14 (1) 14253 [2024-06-20; online 2024-06-20]

Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex.

Riepl D, Gamiz-Hernandez AP, Kovalova T, ..., Brzezinski P, Kaila VRI

Nat Commun 15 (1) 5276 [2024-06-20; online 2024-06-20]

LAPTM4B counteracts ferroptosis via suppressing the ubiquitin-proteasome degradation of SLC7A11 in non-small cell lung cancer.

Yan R, Liu D, Guo H, ..., Blom T, Zhou K

Cell Death Dis 15 (6) 436 [2024-06-20; online 2024-06-20]

Hearing loss and its association with the proteome of perilymph, cerebrospinal fluid, and tumor tissue in patients with vestibular schwannoma.

Edvardsson Rasmussen J, Li P, Laurell G, Bergquist J, Eriksson PO

Sci Rep 14 (1) 14118 [2024-06-19; online 2024-06-19]

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Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.

Kellgren T, Dwibedi C, Widerström M, ..., Rydén P, Johansson A

BMC Microbiol. 24 (1) 215 [2024-06-19; online 2024-06-19]

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Pyrene Functionalized Norbornadiene-Quadricyclane Fluorescent Photoswitches: Characterization of their Spectral Properties and Application in Imaging of Amyloid Beta Plaques.

Ghasemi S, Shamsabadi M, Olesund A, ..., Dreos A, Moth-Poulsen K

Chemistry 30 (34) e202400322 [2024-06-17; online 2024-05-22]

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From SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance.

Cumlin T, Karlsson I, Haars J, ..., Ladenvall C, Kaden R

Int J Mol Sci 25 (12) - [2024-06-17; online 2024-06-17]

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Distinct biological signature and modifiable risk factors underlie the comorbidity between major depressive disorder and cardiovascular disease

Bergstedt J, Pasman JA, Ma Z, ..., Lu Y, Fang F

Nat Cardiovasc Res 3 (6) 754-769 [2024-06-17; online 2024-06-17]

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Convergence and molecular evolution of floral fragrance after independent transitions to self-fertilization.

Woźniak NJ, Sartori K, Kappel C, ..., Kopka J, Sicard A

Curr. Biol. 34 (12) 2702-2711.e6 [2024-06-17; online 2024-05-21]

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Metabolomics profiling reveals the detoxification and tolerance behavior of two bread wheat (Triticum aestivum L.) varieties under arsenate stress.

Saeed M, Masood Quraishi U, Mustafa G, ..., Greger M, Naseem Malik R

Food Chem 443 (-) 138612 [2024-06-15; online 2024-01-28]

Intra-Individual Variations in How Insulin Sensitivity Responds to Long-Term Exercise: Predictions by Machine Learning Based on Large-Scale Serum Proteomics.

Viken JK, Olsen T, Drevon CA, ..., Norheim F, Lee-Ødegård S

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Exposing kinetic disparities between inflammasome readouts using time-resolved analysis.

Herring M, Persson A, Potter R, ..., Särndahl E, Ejdebäck M

Heliyon 10 (11) e32023 [2024-06-15; online 2024-05-29]

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Intestinal Ketogenesis and Permeability.

Casselbrant A, Elias E, Hallersund P, ..., Fändriks L, Wallenius V

Int J Mol Sci 25 (12) - [2024-06-14; online 2024-06-14]

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Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma.

Öfverholm I, Wallander K, Haglund C, ..., Lin Y, Haglund de Flon F

Clin. Cancer Res. 30 (12) 2647-2658 [2024-06-14; online 2024-04-04]

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Characterization of Limestone Surface Impurities and Resulting Quicklime Quality

Sandström K, Carlborg M, Eriksson M, Broström M

Minerals 14 (6) 608 [2024-06-13; online 2024-06-13]

descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.

Otomo K, Omura T, Nozawa Y, ..., Brismar H, Susaki EA

Nat Commun 15 (1) 4941 [2024-06-12; online 2024-06-12]

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Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.

Lobo V, Shcherbinina E, Westholm JO, ..., Anastasakis DG, Sarshad AA

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Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice.

Masarapu Y, Cekanaviciute E, Andrusivova Z, ..., Costes SV, Giacomello S

Nat Commun 15 (1) 4778 [2024-06-11; online 2024-06-11]

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DOPA-decarboxylase is elevated in CSF, but not plasma, in prodromal and de novo Parkinson's disease.

Appleton E, Khosousi S, Ta M, ..., Iwaki H, Svenningsson P

Transl Neurodegener 13 (1) 31 [2024-06-11; online 2024-06-11]

Climate change induces shifts in coastal Baltic Sea surface water microorganism stress and photosynthesis gene expression.

Seidel L, Broman E, Ståhle M, ..., Ketzer M, Dopson M

Front Microbiol 15 (-) 1393538 [2024-06-07; online 2024-06-07]

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ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers.

Zhang Y, Xie G, Lee JE, ..., Ge K, Kutateladze TG

Nat Commun 15 (1) 4883 [2024-06-07; online 2024-06-07]

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Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures.

John EA, Riel AMS, Wieske LHE, ..., Bryantsev VS, Berryman OB

J. Am. Chem. Soc. - (-) - [2024-06-06; online 2024-06-06]

Structural diversity of Arc oligomers within the excitatory synapse

Damenti M, Coceano G, Mendes Silva M, ..., Jungmann R, Testa I

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MLL4 binds TET3.

Becht DC, Mohid SA, Lee JE, ..., Zhang Y, Kutateladze TG

Structure 32 (6) 706-714.e3 [2024-06-06; online 2024-04-04]

Long-term impact of digital media on brain development in children.

Nivins S, Sauce B, Liebherr M, Judd N, Klingberg T

Sci Rep 14 (1) 13030 [2024-06-06; online 2024-06-06]

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Effect of an endothelial regulatory module on plasma proteomics in exercising horses.

Amiri Roudbar M, Rosengren MK, Mousavi SF, ..., Meadows JRS, Lindgren G

Comp Biochem Physiol Part D Genomics Proteomics 52 (-) 101265 [2024-06-06; online 2024-06-06]

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

Wernersson E, Gelali E, Girelli G, ..., Crosetto N, Bienko M

Nat. Methods - (-) - [2024-06-06; online 2024-06-06]

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Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198.

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Aβ Oligomer Dissociation Is Catalyzed by Fibril Surfaces.

Dear AJ, Thacker D, Wennmalm S, ..., Linse S, Knowles TPJ

ACS Chem Neurosci 15 (11) 2296-2307 [2024-06-05; online 2024-05-24]

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Structure and mechanism of the K+/H+ exchanger KefC.

Gulati A, Kokane S, Perez-Boerema A, ..., Matsuoka R, Drew D

Nat Commun 15 (1) 4751 [2024-06-04; online 2024-06-04]

Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O

Tang D, Gueto-Tettay C, Hjortswang E, ..., Malmström L, Malmström J

Anal. Chem. 96 (22) 9060-9068 [2024-06-04; online 2024-05-03]

Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.

Larsson MNA, Morell Miranda P, Pan L, ..., Storå J, Günther T

Genome Biol Evol 16 (6) - [2024-06-04; online 2024-05-25]

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Balthazar JT, Golparian D, Unemo M, ..., Vassylyev DG, Shafer WM

Microbiol Spectr 12 (6) e0056024 [2024-06-04; online 2024-04-22]

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Chemical signatures delineate heterogeneous amyloid plaque populations across the Alzheimer's disease spectrum.

Koutarapu S, Ge J, Dulewicz M, ..., Schöll M, Hanrieder J

bioRxiv - (-) - [2024-06-03; online 2024-06-03]

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A CRISPR homing screen finds a chloroquine resistance transporter-like protein of thePlasmodiumoocyst essential for mosquito transmission of malaria

Balakrishnan A, Hunziker M, Tiwary P, ..., Drew D, Billker O

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Towards identification of new genetic determinants for post-weaning diarrhea in piglets.

Ibragimov E, Eriksen EØ, Nielsen JP, ..., Fredholm M, Karlskov-Mortensen P

Anim Genet 55 (3) 387-395 [2024-06-00; online 2024-02-11]

Structure and interactions of the endogenous human Commander complex.

Laulumaa S, Kumpula EP, Huiskonen JT, Varjosalo M

Nat. Struct. Mol. Biol. 31 (6) 925-938 [2024-06-00; online 2024-03-08]

Spatial Transcriptomics in a Case of Follicular Thyroid Carcinoma Reveals Clone-Specific Dysregulation of Genes Regulating Extracellular Matrix in the Invading Front.

Condello V, Paulsson JO, Zedenius J, Näsman A, Juhlin CC

Endocr. Pathol. 35 (2) 122-133 [2024-06-00; online 2024-01-27]

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Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities.

Wright GD, Thompson KA, Reis Y, ..., Vasconcelos ADS, Keppler A

J Microsc 294 (3) 397-410 [2024-06-00; online 2024-05-01]

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Proteomics of cell-free breast cancer scaffolds identify clinically relevant imprinted proteins and cancer-progressing properties.

Gustafsson A, Jonasson E, Ståhlberg A, Landberg G

Cancer Commun (Lond) 44 (6) 695-699 [2024-06-00; online 2024-04-04]

Proteomic profiling of polyglucosan bodies associated with glycogenin-1 deficiency in skeletal muscle.

Visuttijai K, Hedberg-Oldfors C, Costello DJ, Bermingham N, Oldfors A

Neuropathol Appl Neurobiol 50 (3) e12995 [2024-06-00; online 2024-06-26]

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Polygenic liability for anxiety in association with comorbid anxiety in multiple sclerosis.

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Ann Clin Transl Neurol 11 (6) 1393-1404 [2024-06-00; online 2024-05-07]

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Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees.

Lähteenaro M, Benda D, Straka J, Nylander JAA, Bergsten J

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Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model.

Enström A, Carlsson R, Buizza C, Lewi M, Paul G

Mol. Cell Proteomics 23 (6) 100782 [2024-06-00; online 2024-05-04]

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Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support.

Amoedo-Leite C, Parv K, Testini C, ..., Christoffersson G, Phillipson M

Nat Cardiovasc Res 3 (6) 685-700 [2024-06-00; online 2024-06-06]

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Hybrid capture-based next-generation sequencing of new and old world Orthohantavirus strains and wild-type Puumala isolates from humans and bank voles.

Rosenbaum W, Bovinder Ylitalo E, Castel G, ..., Pettersson L, Tuiskunen Bäck A

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Fine-Tuning Amyloid Precursor Protein Expression through Nonsense-Mediated mRNA Decay.

Rahmati M, Chebli J, Kumar Banote R, ..., Zetterberg H, Abramsson A

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Expedient Bayesian prediction of subfossil bone protein content using portable ATR-FTIR data

Hixon S, Roberts P, Rodríguez-Varela R, ..., Lagia A, Fernandes R

Quaternary International 694 (-) 1-12 [2024-06-00; online 2024-06-00]

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Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci.

Wu PC, McGowan EC, Lee YQ, ..., Hansson J, Olsson ML

Transfusion 64 (6) 1083-1096 [2024-06-00; online 2024-04-21]

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Childhood screening for type 1 diabetes comparing automated multiplex Antibody Detection by Agglutination-PCR (ADAP) with single plex islet autoantibody radiobinding assays.

Lind A, Freyhult E, de Jesus Cortez F, ..., Lernmark Å, Better Diabetes Diagnosis (BDD) study group

EBioMedicine 104 (-) 105144 [2024-06-00; online 2024-05-08]

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Cellulose gelation in aqueous hydroxide solutions by CO2(g): Fact and theory

Naserifar S, Karna NK, Kozlowski AM, Bernin D, Hasani M

Carbohydrate Polymer Technologies and Applications 7 (-) 100514 [2024-06-00; online 2024-06-00]

Blood biomarkers of Alzheimer's disease in the community: Variation by chronic diseases and inflammatory status.

Valletta M, Vetrano DL, Rizzuto D, ..., Fratiglioni L, Grande G

Alzheimers Dement 20 (6) 4115-4125 [2024-06-00; online 2024-05-08]

Bacterial diversity in semen from stallions in three European countries evaluated by 16S sequencing.

Malaluang P, Niazi A, Guo Y, ..., Aurich C, Morrell JM

Vet Res Commun 48 (3) 1409-1421 [2024-06-00; online 2024-02-02]

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An endothelial regulatory module links blood pressure regulation with elite athletic performance.

Fegraeus K, Rosengren MK, Naboulsi R, ..., Meadows JRS, Lindgren G

PLoS Genet. 20 (6) e1011285 [2024-06-00; online 2024-06-17]

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A monoallelic UXS1 variant associated with short-limbed short stature.

Rustad CF, Backe PH, Jin C, ..., Elgstøen KBP, Holla ØL

Mol Genet Genomic Med 12 (6) e2472 [2024-06-00; online 2024-06-11]

Tumor-matched and unmatched cancer associated fibroblasts exhibit differential effect on proliferation and FMOD and MMP9 gene expression in head and neck squamous cell carcinoma cells when cocultured in spheroids.

Rademaekers M, Johansson EO, Johansson E, Roberg K, Wiechec E

Cancer Cell Int 24 (1) 190 [2024-05-31; online 2024-05-31]

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Tobacco Smoke Exposure in Early Childhood and Later Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study.

Sigvardsson I, Ludvigsson J, Andersson B, Størdal K, Mårild K

J Crohns Colitis 18 (5) 661-670 [2024-05-31; online 2024-02-08]

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Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers.

De Oliveira DH, Gowda V, Sparrman T, ..., Lendel C, Hedhammar M

Nat Commun 15 (1) 4670 [2024-05-31; online 2024-05-31]

Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia.

Malyukova A, Lahnalampi M, Falqués-Costa T, ..., Heinäniemi M, Sangfelt O

Genome Biol. 25 (1) 143 [2024-05-31; online 2024-05-31]

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PIK3CA mutations in endocrine-resistant breast cancer.

Schagerholm C, Robertson S, Toosi H, Sifakis EG, Hartman J

Sci Rep 14 (1) 12542 [2024-05-31; online 2024-05-31]

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Overexpression of the plastidial pseudo-protease AtFtsHi3 enhances drought tolerance while sustaining plant growth.

Mishra LS, Cook SD, Kushwah S, ..., Libby E, Funk C

Physiol Plantarum 176 (3) e14370 [2024-05-31; online 2024-05-31]

Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids.

Boman J, Qvarnström A, Mugal CF

BMC Biol. 22 (1) 124 [2024-05-29; online 2024-05-29]

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NGS method for parallel processing of high quality, damaged or fragmented input material using target enrichment.

Lyander A, Gellerbring A, Hägglund M, Elhami K, Wirta V

PLoS ONE 19 (5) e0304411 [2024-05-29; online 2024-05-29]

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Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis.

Rosling A, Eshghi Sahraei S, Kalsoom Khan F, ..., Bonito G, Sánchez-García M

BMC Genomics 25 (1) 529 [2024-05-29; online 2024-05-29]

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The structure of the second CysD domain of MUC2 and role in mucin organization by transglutaminase-based cross-linking.

Recktenwald CV, Karlsson G, Garcia-Bonete MJ, ..., Hansson GC, Trillo-Muyo S

Cell Rep 43 (5) 114207 [2024-05-28; online 2024-05-09]

Distinct Infiltration of T Cell Populations in Bladder Cancer Molecular Subtypes.

Sincic V, Arlenhold KF, Richtmann S, ..., Liedberg F, Lundberg K

Cells 13 (11) - [2024-05-28; online 2024-05-28]

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The Metabolomic Profile of Microscopic Colitis Is Affected by Smoking but Not Histopathological Diagnosis, Clinical Course, Symptoms, or Treatment.

Ström A, Stenlund H, Ohlsson B

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Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).

Müller IA, Thörn F, Rajan S, ..., Jønsson KA, Irestedt M

PLoS ONE 19 (5) e0293715 [2024-05-23; online 2024-05-23]

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Quantifying combined effects of colistin and ciprofloxacin against Escherichia coli in an in silico pharmacokinetic-pharmacodynamic model.

Zhao C, Kristoffersson AN, Khan DD, ..., Nielsen EI, Friberg LE

Sci Rep 14 (1) 11706 [2024-05-22; online 2024-05-22]

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The Gly82Ser polymorphism in the receptor for advanced glycation endproducts increases the risk for coronary events in the general population.

Grauen Larsen H, Sun J, Sjögren M, ..., Melander O, Schiopu A

Sci Rep 14 (1) 11567 [2024-05-21; online 2024-05-21]

Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.

Cámara E, Mormino M, Siewers V, Nygård Y

Appl. Environ. Microbiol. 90 (5) e0233023 [2024-05-21; online 2024-04-08]

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Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae.

Thureborn O, Wikström N, Razafimandimbison SG, Rydin C

PLoS ONE 19 (5) e0302365 [2024-05-20; online 2024-05-20]

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MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.

Sydow S, Piccinelli P, Mitra S, ..., Spierings D, Mertens F

Commun Biol 7 (1) 606 [2024-05-20; online 2024-05-20]

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Defining the contribution of Troy-positive progenitor cells to the mouse esophageal epithelium.

Grommisch D, Wang M, Eenjes E, ..., Giselsson P, Genander M

Dev. Cell 59 (10) 1269-1283.e6 [2024-05-20; online 2024-04-01]

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Retron-Eco1 assembles NAD+-hydrolyzing filaments that provide immunity against bacteriophages.

Carabias A, Camara-Wilpert S, Mestre MR, ..., Pinilla-Redondo R, Montoya G

Mol. Cell - (-) - [2024-05-18; online 2024-05-18]

Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing.

Engvall K, Uvdal H, Björn N, Åvall-Lundqvist E, Gréen H

NPJ Precis Oncol 8 (1) 102 [2024-05-16; online 2024-05-16]

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Exploring carbon source related localization and phosphorylation in the Snf1/Mig1 network using population and single cell-based approaches.

Braam S, Tripodi F, Österberg L, ..., Coccetti P, Cvijovic M

Microb Cell 11 (-) 143-154 [2024-05-16; online 2024-05-16]

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Quantitation of circulating short-chain fatty acids in small volume blood samples from animals and humans.

Fristedt R, Ruppert V, Trower T, Cooney J, Landberg R

Talanta 272 (-) 125743 [2024-05-15; online 2024-02-03]

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Novel findings in a Swedish primary familial brain calcification cohort.

Sennfält S, Gustavsson P, Malmgren H, ..., Svenningsson P, Paucar M

J. Neurol. Sci. 460 (-) 123020 [2024-05-15; online 2024-04-18]

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Depression proteomic profiling in adolescents with transcriptome analyses in independent cohorts.

Sokolov AV, Lafta MS, Nordberg DOT, Jonsson J, Schiöth HB

Front Psychiatry 15 (-) 1372106 [2024-05-15; online 2024-05-15]

Complex genetic architecture of the chicken Growth1 QTL region.

Ou JH, Rönneburg T, Carlborg Ö, ..., Siegel PB, Rubin CJ

PLoS ONE 19 (5) e0295109 [2024-05-13; online 2024-05-13]

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Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.

Mohamadnejad Sangdehi F, Jamsandekar MS, Enbody ED, Pettersson ME, Andersson L

BMC Genomics 25 (1) 459 [2024-05-10; online 2024-05-10]

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Control of Vibrio vulnificus proliferation in the Baltic Sea through eutrophication and algal bloom management

Riedinger DJ, Fernández-Juárez V, Delgado LF, ..., Riemann L, Labrenz M

Commun Earth Environ 5 (1) - [2024-05-09; online 2024-05-09]

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Modulation of innate immune response to mRNA vaccination after SARS-CoV-2 infection or sequential vaccination in humans.

Hellgren F, Rosdahl A, Arcoverde Cerveira R, ..., Cajander S, Loré K

JCI Insight 9 (9) - [2024-05-08; online 2024-05-08]

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All-photonic kinase inhibitors: light-controlled release-and-report inhibition.

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Chem. Sci. 15 (18) 6897-6905 [2024-05-08; online 2024-04-12]

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Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer.

Wang K, Zerdes I, Johansson HJ, ..., Matikas A, Foukakis T

Nat Commun 15 (1) 3837 [2024-05-07; online 2024-05-07]

Global Proteomics and Proteogenomics [Collaborative]

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Mol Plant 17 (5) 725-746 [2024-05-06; online 2024-03-13]

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Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

Peona V, Martelossi J, Almojil D, ..., Pecoraro C, Suh A

Mob DNA 15 (1) 10 [2024-05-06; online 2024-05-06]

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Hempel E, Faith JT, Preick M, ..., Westbury MV, Hofreiter M

Curr. Biol. 34 (9) 2020-2029.e6 [2024-05-06; online 2024-04-12]

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Meiotic drive against chromosome fusions in butterfly hybrids.

Boman J, Wiklund C, Vila R, Backström N

Chromosome Res. 32 (2) 7 [2024-05-04; online 2024-05-04]

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Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.

Gutiérrez-Valencia J, Zervakis P, Postel Z, ..., Arroyo J, Slotte T

Mol. Biol. Evol. 41 (5) - [2024-05-03; online 2024-05-06]

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Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria.

Hiltunen Thorén M, Onuț-Brännström I, Alfjorden A, ..., Bass D, Burki F

BMC Biol. 22 (1) 103 [2024-05-03; online 2024-05-03]

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Recent dynamics in Neisseria gonorrhoeae genomic epidemiology in Brazil: antimicrobial resistance and genomic lineages in 2017-20 compared to 2015-16.

Golparian D, Bazzo ML, Ahlstrand J, ..., Unemo M, Brazilian-GASP Network

J. Antimicrob. Chemother. 79 (5) 1081-1092 [2024-05-02; online 2024-03-22]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Pharmacodynamic evaluation of ceftriaxone single-dose therapy (0.125-1 g) to eradicate ceftriaxone-susceptible and ceftriaxone-resistant Neisseria gonorrhoeae strains in a hollow fibre infection model for gonorrhoea.

Unemo M, Golparian D, Oxelbark J, ..., Drusano G, Jacobsson S

J. Antimicrob. Chemother. 79 (5) 1006-1013 [2024-05-02; online 2024-03-18]

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Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque.

Castro Dopico X, Guryleva M, Mandolesi M, ..., Murrell B, Karlsson Hedestam GB

Clin Transl Immunology 13 (5) e1508 [2024-05-02; online 2024-05-02]

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Growth and mortality rates of picophytoplankton in the Baltic Sea Proper

Alegria Zufia J, Laber C, Legrand C, Lindehoff E, Farnelid H

Mar. Ecol. Prog. Ser. 735 (-) 63-76 [2024-05-02; online 2024-05-02]

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Genomic alterations in ovarian endometriosis and subsequently diagnosed ovarian carcinoma.

Linder A, Westbom-Fremer S, Mateoiu C, ..., Hedenfalk I, Sundfeldt K

Hum. Reprod. 39 (5) 1141-1154 [2024-05-02; online 2024-03-09]

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Experimental Evaluation of a Direct Fitness Effect of the De Novo Evolved Mouse Gene Pldi.

Linnenbrink M, Breton G, Misra P, ..., Dutheil JY, Tautz D

Genome Biol Evol 16 (5) - [2024-05-02; online 2024-05-14]

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Evolutionary convergence of sensory circuits in the pallium of amniotes

Rueda-Alaña E, Senovilla-Ganzo R, Grillo M, ..., De Pitta M, García-Moreno F

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Sex-biased gene expression during neural differentiation of human embryonic stem cells

Pottmeier P, Nikolantonaki D, Lanner F, Peuckert C, Jazin E

Front Cell Dev Biol 12 (-) - [2024-05-01; online 2024-05-01]

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Multiple cis-regulatory elements control prox1a expression in distinct lymphatic vascular beds.

Panara V, Yu H, Peng D, ..., Hogan BM, Koltowska K

Development 151 (9) - [2024-05-01; online 2024-05-09]

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Male-transmitted transgenerational effects of the herbicide linuron on DNA methylation profiles in Xenopus tropicalis brain and testis.

Roza M, Eriksson ANM, Svanholm S, Berg C, Karlsson O

Sci. Total Environ. 923 (-) 170949 [2024-05-01; online 2024-02-15]

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Excitatory Spinal Lhx9-Derived Interneurons Modulate Locomotor Frequency in Mice.

Bertho M, Caldeira V, Hsu LJ, ..., Borgius L, Kiehn O

J. Neurosci. 44 (18) - [2024-05-01; online 2024-05-01]

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Chromatin accessibility during human first-trimester neurodevelopment.

Mannens CCA, Hu L, Lönnerberg P, ..., Posthuma D, Linnarsson S

Nature - (-) - [2024-05-01; online 2024-05-01]

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Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting.

Westenius E, Conner P, Pettersson M, ..., Lindstrand A, Iwarsson E

Ultrasound Obstet Gynecol 63 (5) 658-663 [2024-05-00; online 2024-04-14]

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Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics.

Gustafsson M, Strand Å, Laugen AT, ..., Wrange AL, De Wit P

Evol Appl 17 (5) e13704 [2024-05-00; online 2024-05-20]

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The anti-leprosy drug clofazimine reduces polyQ toxicity through activation of PPARγ.

Li X, Hernandez I, Koyuncu S, ..., Vilchez D, Fernandez-Capetillo O

EBioMedicine 103 (-) 105124 [2024-05-00; online 2024-05-02]

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Ruxolitinib: A new hope for ventilator-induced diaphragm dysfunction.

Addinsall AB, Cacciani N, Moruzzi N, ..., Kirkland JL, Larsson L

Acta Physiol (Oxf) 240 (5) e14128 [2024-05-00; online 2024-03-29]

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Plasma proteomics for prediction of subclinical coronary artery calcifications in primary prevention.

Royer P, Björnson E, Adiels M, ..., Gummesson A, Bergström G

Am. Heart J. 271 (-) 55-67 [2024-05-00; online 2024-02-05]

Novel Associations Between Mid-Pregnancy Cardiovascular Biomarkers and Preeclampsia: An Explorative Nested Case-Control Study.

Callbo PN, Junus K, Gabrysch K, ..., Lager S, Wikström AK

Reprod Sci 31 (5) 1391-1400 [2024-05-00; online 2024-01-22]

Low birthweight and overweight during childhood and young adulthood and the risk of type 2 diabetes in men: a population-based cohort study.

Célind J, Bygdell M, Bramsved R, ..., Ohlsson C, Kindblom JM

Diabetologia 67 (5) 874-884 [2024-05-00; online 2024-02-22]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Item response theory analysis of daytime sleepiness as a symptom of obstructive sleep apnea.

Wellhagen GJ, Karlsson MO, Kjellsson MC, ..., Weimann G, Yassen A

CPT Pharmacometrics Syst Pharmacol 13 (5) 880-890 [2024-05-00; online 2024-03-12]

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In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge.

Blume-Werry G, Semenchuk P, Ljung K, ..., Olofsson J, Brunoni F

New Phytol. 242 (3) 988-999 [2024-05-00; online 2024-02-20]

Impact of the neurotoxin β-N-methylamino-L-alanine on the diatom Thalassiosira pseudonana using metabolomics.

Kim SY, Rasmussen U, Rydberg S

Mar Pollut Bull 202 (-) 116299 [2024-05-00; online 2024-04-06]

Head-to-head comparison of relevant cell sources of small extracellular vesicles for cardiac repair: Superiority of embryonic stem cells.

González-King H, Rodrigues PG, Albery T, ..., Wang QD, Jennbacken K

J Extracell Vesicles 13 (5) e12445 [2024-05-00; online 2024-05-07]

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Fluorescently labeled prey surrogates in combination with fluorescence‐activated cell sorting successfully discriminate actively feeding mixotrophs in a lake water sample

Florenza J, Divne A, Bertilsson S

Limnol Oceanogr 69 (5) 1030-1044 [2024-05-00; online 2024-03-13]

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Fasting plasma metabolites reflecting meat consumption and their associations with incident type 2 diabetes in two Swedish cohorts.

Noerman S, Johansson A, Shi L, ..., Brunius C, Landberg R

Am. J. Clin. Nutr. 119 (5) 1280-1292 [2024-05-00; online 2024-02-23]

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Evaluation of covariate effects in item response theory models.

Wellhagen GJ, Yassen A, Garmann D, ..., Kjellsson MC, Karlsson MO

CPT Pharmacometrics Syst Pharmacol 13 (5) 812-822 [2024-05-00; online 2024-03-04]

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Ectomycorrhizal fungi are more sensitive to high soil nitrogen levels in forests exposed to nitrogen deposition.

Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD

New Phytol. 242 (4) 1725-1738 [2024-05-00; online 2024-01-11]

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Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.

Yaka R, Lagerholm VK, Linderholm A, ..., Somel M, Götherström A

BioTechniques 76 (5) 216-223 [2024-05-00; online 2024-03-26]

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Antimicrobial-resistant Neisseria gonorrhoeae in Europe in 2020 compared with in 2013 and 2018: a retrospective genomic surveillance study.

Golparian D, Cole MJ, Sánchez-Busó L, ..., Unemo M, Euro-GASP study group

Lancet Microbe 5 (5) e478-e488 [2024-05-00; online 2024-04-10]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Metabolomics for early pancreatic cancer detection in plasma samples from a Swedish prospective population-based biobank.

Borgmästars E, Jacobson S, Simm M, ..., Franklin O, Sund M

J Gastrointest Oncol 15 (2) 755-767 [2024-04-30; online 2024-04-28]

PARKIN is not required to sustain OXPHOS function in adult mammalian tissues.

Filograna R, Gerlach J, Choi H, ..., Svenningsson P, Larsson N

NPJ Parkinsons Dis 10 (1) 93 [2024-04-29; online 2024-04-29]

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Local Immune Activation and Age Impact on Humoral Immunity in Mice, with a Focus on IgG Sialylation.

Gupta P, Sághy T, Bollmann M, ..., Corciulo C, Engdahl C

Vaccines (Basel) 12 (5) - [2024-04-29; online 2024-04-29]

Biomarker Candidates of Habitual Food Intake in a Swedish Cohort of Pregnant and Lactating Women and Their Infants.

Stråvik M, Hartvigsson O, Noerman S, ..., Barman M, Sandberg AS

Metabolites 14 (5) - [2024-04-29; online 2024-04-29]

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The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies.

Izadi A, Karami Y, Bratanis E, ..., Malmström L, Nordenfelt P

Nat Commun 15 (1) 3600 [2024-04-27; online 2024-04-27]

Population genomic history of the endangered Anatolian and Cyprian mouflons in relation to worldwide wild, feral and domestic sheep lineages.

Atağ G, Kaptan D, Yüncü E, ..., Hadjisterkotis E, Somel M

Genome Biol Evol - (-) - [2024-04-27; online 2024-04-27]

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Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer.

Papakyriacou I, Kutkaite G, Rúbies Bedós M, ..., Menden MP, Mao Y

Nat Commun 15 (1) 3581 [2024-04-27; online 2024-04-27]

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Cyanotoxin Occurrence and Diversity in 98 Cyanobacterial Blooms from Swedish Lakes and the Baltic Sea.

Dirks C, Cappelli P, Blomqvist M, ..., Pekar H, Zuberovic Muratovic A

Mar Drugs 22 (5) - [2024-04-27; online 2024-04-27]

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Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa).

Tsardakas Renhuldt N, Bentzer J, Ahrén D, Marmon S, Sirijovski N

Front Plant Sci 15 (-) 1358490 [2024-04-26; online 2024-04-26]

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Deciphering the role of FUS::DDIT3 expression and tumor microenvironment in myxoid liposarcoma development.

Ranji P, Jonasson E, Andersson L, ..., Åman P, Ståhlberg A

J Transl Med 22 (1) 389 [2024-04-26; online 2024-04-26]

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The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids.

Holmberg SM, Feeney RH, Prasoodanan P K V, ..., Skurk T, Schroeder BO

Nat Commun 15 (1) 3502 [2024-04-25; online 2024-04-25]

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N-glycoproteomic analyses of human intestinal enteroids, varying in histo-blood group geno- and phenotypes, reveal a wide repertoire of fucosylated glycoproteins.

Nilsson J, Rimkute I, Sihlbom C, ..., Estes MK, Larson G

Glycobiology 34 (6) - [2024-04-24; online 2024-04-09]

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.

Zhang N, Harbers L, Simonetti M, ..., Bienko M, Crosetto N

Nat Commun 15 (1) 3475 [2024-04-24; online 2024-04-24]

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Exhaustive identification of genome-wide binding events of transcriptional regulators.

Nordin A, Pagella P, Zambanini G, Cantù C

Nucleic Acids Res. 52 (7) e40 [2024-04-24; online 2024-03-19]

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Very short sleep duration reveals a proteomic fingerprint that is selectively associated with incident diabetes mellitus but not with incident coronary heart disease: a cohort study.

Svensson T, Svensson AK, Kitlinski M, ..., Nilsson PM, Melander O

BMC Med 22 (1) 173 [2024-04-23; online 2024-04-23]

Activation of GFRAL+ neurons induces hypothermia and glucoregulatory responses associated with nausea and torpor.

Engström Ruud L, Font-Gironès F, Zajdel J, ..., Bäckhed F, Ruud J

Cell Rep 43 (4) 113960 [2024-04-23; online 2024-03-19]

A chemical inhibitor of IST1-CHMP1B interaction impairs endosomal recycling and induces noncanonical LC3 lipidation.

Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW

Proc. Natl. Acad. Sci. U.S.A. 121 (17) e2317680121 [2024-04-23; online 2024-04-18]

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Combined Metabolic Activators with Different NAD+ Precursors Improve Metabolic Functions in the Animal Models of Neurodegenerative Diseases.

Altay O, Yang H, Yildirim S, ..., Turkez H, Mardinoglu A

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TMAO enhances TNF-α mediated fibrosis and release of inflammatory mediators from renal fibroblasts.

Stefania K, Ashok KK, Geena PV, Katarina P, Isak D

Sci Rep 14 (1) 9070 [2024-04-20; online 2024-04-20]

Patient-Specific Measurable Residual Disease Markers Predict Outcome in Patients With Myelodysplastic Syndrome and Related Diseases After Hematopoietic Stem-Cell Transplantation.

Tobiasson M, Pandzic T, Illman J, ..., Dybedal I, Hellström-Lindberg E

J Clin Oncol 42 (12) 1378-1390 [2024-04-20; online 2024-01-17]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

HIV-2 mediated effects on target and bystander cells induce plasma proteome remodeling.

Johansson E, Nazziwa J, Freyhult E, ..., Jansson M, SWEGUB CORE group

iScience 27 (4) 109344 [2024-04-19; online 2024-02-28]

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Radiolabeled 15-mer peptide internalization is mediated by megalin (LRP2 receptor) in a CRISPR/Cas9-based LRP2 knockout human kidney cell model.

Durinova A, Smutna L, Barta P, ..., Pavek P, Trejtnar F

EJNMMI Radiopharm Chem 9 (1) 32 [2024-04-18; online 2024-04-18]

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Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.

Ten Berk de Boer E, Ameur A, Bunikis I, ..., Eisfeldt J, Lindstrand A

Sci Rep 14 (1) 9000 [2024-04-18; online 2024-04-18]

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Nutrient-deprived growth of streptomycetes reveals a novel growth phenotype with enhanced antimicrobial activity

Söderholm N, Tanner H, Sandblad L

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Integrated Microscopy Technologies Umeå [Collaborative]

Usefulness of Heart Failure Categories Based on Left Ventricular Ejection Fraction.

Christersson M, Gustafsson S, Lampa E, ..., Arefalk G, Sundström J

J Am Heart Assoc 13 (8) e032257 [2024-04-16; online 2024-04-09]

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Effects of bottom trawling and environmental factors on benthic bacteria, meiofauna and macrofauna communities and benthic ecosystem processes.

Bradshaw C, Iburg S, Morys C, ..., Jonsson P, Nascimento FJA

Sci. Total Environ. 921 (-) 171076 [2024-04-15; online 2024-02-19]

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Amperometry and Electron Microscopy show Stress Granules Induce Homotypic Fusion of Catecholamine Vesicles.

Gu H, Gu C, Locker N, Ewing AG

Angew. Chem. Int. Ed. Engl. 63 (16) e202400422 [2024-04-15; online 2024-03-07]

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Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes.

Abdel-Fattah WR, Carlsson M, Hu G, ..., Ronne H, Björklund S

Nucleic Acids Res. - (-) - [2024-04-13; online 2024-04-13]

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Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.

Edelbroek B, Kjellin J, Biryukova I, ..., Friedländer MR, Söderbom F

Nucleic Acids Res. 52 (6) 3121-3136 [2024-04-12; online 2024-02-20]

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Dual molecule targeting HDAC6 leads to intratumoral CD4+ cytotoxic lymphocytes recruitment through MHC-II upregulation on lung cancer cells.

Ducellier S, Demeules M, Letribot B, ..., Nascimento M, Apcher S

J Immunother Cancer 12 (4) - [2024-04-11; online 2024-04-11]

Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.

Kukanja P, Langseth CM, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G

Cell 187 (8) 1990-2009.e19 [2024-04-11; online 2024-03-20]

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A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi.

Roberts KT, Steward RA, Süess P, Lehmann P, Wheat CW

Mol. Ecol. - (-) e17348 [2024-04-10; online 2024-04-10]

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Molecular patterns of resistance to immune checkpoint blockade in melanoma.

Lauss M, Phung B, Borch TH, ..., Donia M, Jönsson G

Nat Commun 15 (1) 3075 [2024-04-09; online 2024-04-09]

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Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD.

Pagano L, Simonetti L, Pennacchietti V, ..., Ivarsson Y, Gianni S

Biochem. Biophys. Res. Commun. 703 (-) 149658 [2024-04-09; online 2024-02-07]

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Deletion of the TMEM30A gene enables leukemic cell evasion of NK cell cytotoxicity.

Kristenson L, Badami C, Ljungberg A, ..., Tang KW, Thorén FB

Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2316447121 [2024-04-09; online 2024-04-01]

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Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.

Huseby DL, Cao S, Zamaratski E, ..., Hughes D, Karlén A

Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2317274121 [2024-04-09; online 2024-04-05]

Drug Discovery and Development (DDD) [Collaborative]

A phenotypic screening approach to target p60AmotL2-expressing invasive cancer cells.

Fonseca P, Cui W, Struyf N, ..., Östling P, Holmgren L

J. Exp. Clin. Cancer Res. 43 (1) 107 [2024-04-09; online 2024-04-09]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Global Proteomics and Proteogenomics [Service]

Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model.

Yaghmaeian Salmani B, Lahti L, Gillberg L, ..., Svenningsson P, Perlmann T

Elife 12 (-) - [2024-04-08; online 2024-04-08]

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Histones are exosome membrane proteins regulated by cell stress

Singh B, Sundbom MF, Muthukrishnan U, ..., Haney M, Gilthorpe JD

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Cryo-EM [Collaborative] Integrated Microscopy Technologies Umeå [Collaborative]

Tissue-specific nonheritable influences drive endometrial immune system variation.

Bister J, Filipovic I, Sun D, ..., Strunz B, Björkström NK

Sci Immunol 9 (94) eadj7168 [2024-04-05; online 2024-04-05]

Functional redundancy revealed by the deletion of the mimivirus GMC-oxidoreductase genes.

Alempic JM, Bisio H, Villalta A, ..., Couté Y, Abergel C

Microlife 5 (-) uqae006 [2024-04-05; online 2024-04-05]

Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.

Feiner N, Yang W, Bunikis I, While GM, Uller T

Sci Adv 10 (14) eadk9315 [2024-04-05; online 2024-04-03]

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Treatment Monitoring of a Patient with Synchronous Metastatic Angiosarcoma and Breast Cancer Using ctDNA.

Vannas C, Escobar M, Österlund T, ..., Fagman H, Ståhlberg A

Int J Mol Sci 25 (7) - [2024-04-04; online 2024-04-04]

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The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.

Lundtoft C, Knight A, Meadows JRS, ..., Lindblad-Toh K, Dahlqvist J

RMD Open 10 (2) - [2024-04-04; online 2024-04-04]

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Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15

Ebenwaldner C, García Saura AG, Ekström S, Bernfur K, Schüler H

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Extracellular vesicles isolated from frozen and fresh human melanoma tissue are similar in purity and protein composition

D’Arrigo D, Lässer C, Urzì O, ..., Lötvall J, Crescitelli R

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Adjusting for covariates and assessing modeling fitness in machine learning using MUVR2.

Yan Y, Schillemans T, Skantze V, Brunius C

Bioinform Adv 4 (1) vbae051 [2024-04-04; online 2024-04-04]

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Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections.

Fredolini C, Dodig-Crnković T, Bendes A, ..., Roxhed N, Schwenk JM

Commun Med (Lond) 4 (1) 55 [2024-04-02; online 2024-04-02]

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Proteome of Personalized Tissue-Engineered Veins.

Larsson S, Holmgren S, Jenndahl L, ..., Synnergren J, Ghosheh N

ACS Omega 9 (13) 14805-14817 [2024-04-02; online 2024-03-19]

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit.

Stenström O, Diehl C, Modig K, Akke M

Proc. Natl. Acad. Sci. U.S.A. 121 (14) e2317747121 [2024-04-02; online 2024-03-25]

Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis.

De Jode A, Faria R, Formenti G, ..., Butlin RK, Leder EH

Genome Biol Evol 16 (4) - [2024-04-02; online 2024-04-08]

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Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

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Morphology and phosphate distribution in bottom ash particles from fixed-bed co-combustion of sewage sludge and two agricultural residues.

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Waste Management 177 (-) 56-65 [2024-04-01; online 2024-01-29]

Increased matrix stiffness enhances pro-tumorigenic traits in a physiologically relevant breast tissue- monocyte 3D model.

Abrahamsson A, Boroojeni FR, Naeimipour S, ..., Aili D, Dabrosin C

Acta Biomater 178 (-) 160-169 [2024-04-01; online 2024-02-20]

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Fast volumetric multifocus structured illumination microscopy of subcellular dynamics in living cells

Senftleben ML, Bajor A, Hirata E, Abrahamsson S, Brismar H

Biomed. Opt. Express 15 (4) 2281 [2024-04-01; online 2024-03-11]

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Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck.

Nilsson J, Eriksson P, Naguib MM, ..., Larson G, Ellström P

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Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis.

Joshi AS, Bapat MV, Singh P, Mijakovic I

Mater Today Bio 25 (-) 100997 [2024-04-00; online 2024-02-11]

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Single-cell RNA sequencing of cells from fresh or frozen tissue reveals a signature of freezing marked by heightened stress and activation.

Stamper CT, Marchalot A, Tibbitt CA, ..., Theorell J, Mjösberg J

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Novel ultrasensitive immunoassay for the selective quantification of tau oligomers and related soluble aggregates.

Islam T, Kvartsberg H, Sehrawat A, ..., Blennow K, Karikari TK

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Nephropathia Epidemica Caused by Puumala Virus in Bank Voles, Scania, Southern Sweden.

Ling J, Lundeberg EE, Wasberg A, ..., Settergren B, Lundkvist Å

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Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations

Saha A, Kurland S, Kutschera VE, ..., Ryman N, Laikre L

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Hellman M, Juhanson J, Wallnäs F, Herbert RB, Hallin S

J Environ Manage 356 (-) 120607 [2024-04-00; online 2024-03-26]

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Meta-analysis of ACE inhibitor-induced angioedema identifies novel risk locus.

Mathey CM, Maj C, Eriksson N, ..., Nöthen MM, Forstner AJ

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Liprin-α proteins are master regulators of human presynapse assembly.

Marcó de la Cruz B, Campos J, Molinaro A, ..., Acuna C, Sterky FH

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Hydrogen evolution mediated by sulfur vacancies and substitutional Mn in few-layered molybdenum disulfide

Rafei M, Piñeiro-García A, Wu X, ..., Wågberg T, Gracia-Espino E

Materials Today Energy 41 (-) 101524 [2024-04-00; online 2024-04-00]

High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler.

Sych T, Schlegel J, Barriga HMG, ..., Stevens MM, Sezgin E

Nat. Biotechnol. 42 (4) 587-590 [2024-04-00; online 2023-06-12]

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High-resolution comparative atomic structures of two Giardiavirus prototypes infecting G. duodenalis parasite.

Wang H, Marucci G, Munke A, ..., Lalle M, Okamoto K

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Habitat is more important than climate for structuring soil fungal communities associated in truffle sites.

Piñuela Y, Alday JG, Oliach D, ..., Peter M, Bonet JA

Fungal Biol 128 (2) 1724-1734 [2024-04-00; online 2024-02-24]

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Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.

Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C

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Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study.

Tesi B, Robinson KL, Abel F, ..., Taylan F, Nordgren A

Lancet Reg Health Eur 39 (-) 100881 [2024-04-00; online 2024-03-19]

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Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes.

Claret JL, Di-Liegro M, Namias A, ..., Milesi P, Labbé P

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Current and emerging sequencing-based tools for precision cancer medicine.

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Cerebrospinal fluid mtDNA concentrations are increased in multiple sclerosis and were normalized after intervention with autologous hematopoietic stem cell transplantation.

Pavlovic I, Zjukovskaja C, Nazir FH, ..., Wiberg A, Burman J

Mult Scler Relat Disord 84 (-) 105482 [2024-04-00; online 2024-02-03]

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Cancer-associated fibroblasts rewire the estrogen receptor response in luminal breast cancer, enabling estrogen independence.

Reid SE, Pantaleo J, Bolivar P, ..., Seashore-Ludlow B, Pietras K

Oncogene 43 (15) 1113-1126 [2024-04-00; online 2024-02-22]

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A step towards more eco-friendly and efficient microalgal harvesting: Inducing flocculation in the non-naturally flocculating strain Chlorella vulgaris (13-1) without chemical additives

Spain O, Funk C

Algal Research 79 (-) 103450 [2024-04-00; online 2024-04-00]

VISION — an open-source software for automated multi-dimensional image analysis of cellular biophysics

Weber F, Iskrak S, Ragaller F, ..., Sezgin E, Andronico LA

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Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.

Eisele AS, Tarbier M, Dormann AA, Pelechano V, Suter DM

Nat Commun 15 (1) 2744 [2024-03-29; online 2024-03-29]

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Designing efficient randstrobes for sequence similarity analyses.

Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K

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Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling.

Mosquera Orgueira A, Krali O, Pérez Míguez C, ..., Schmiegelow K, Nordlund J

Clin Epigenetics 16 (1) 49 [2024-03-28; online 2024-03-28]

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High Oestrogen receptor alpha expression correlates with adverse prognosis and promotes metastasis in colorectal cancer.

Topi G, Satapathy SR, Ghatak S, ..., Lydrup ML, Sjölander A

Cell Commun Signal 22 (1) 198 [2024-03-28; online 2024-03-28]

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Effects of microgravity on neural crest stem cells.

Han Y, Barasa P, Zeger L, ..., Fredriksson R, Kozlova EN

Front. Neurosci. 18 (-) 1379076 [2024-03-27; online 2024-03-27]

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Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming.

Li S, Nilsson E, Seidel L, ..., Dopson M, Hylander S

Front Microbiol 15 (-) 1369102 [2024-03-26; online 2024-03-26]

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Novel Synonymous and Deep Intronic Variants Causing Primary and Secondary Pyruvate Dehydrogenase Complex Deficiency

Bruhn H, Naess K, Ygberg S, ..., Wedell A, Wredenberg A

Hum. Mutat. 2024 (-) 1-16 [2024-03-25; online 2024-03-25]

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Ion mobility-tandem mass spectrometry of mucin-type O-glycans.

Bechtella L, Chunsheng J, Fentker K, ..., Karlsson NG, Pagel K

Nat Commun 15 (1) 2611 [2024-03-23; online 2024-03-23]

Vascular smooth muscle cells in response to cholesterol crystals modulates inflammatory cytokines release and promotes neutrophil extracellular trap formation.

Thazhathveettil J, Kumawat AK, Demirel I, Sirsjö A, Paramel GV

Mol. Med. 30 (1) 42 [2024-03-22; online 2024-03-22]

Abstract 2025: Zeb1 downregulation sensitizes pancreatic cancer-associated fibroblasts to killing by oncolytic reovirus through upregulation of the reovirus receptor junction adhesion molecule A

Dam N, Harryvan TJ, Schmierer B, Hawinkels LJAC, Kemp V

Cancer Res. 84 (6_Supplement) 2025-2025 [2024-03-22; online 2024-03-22]

METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma.

Vaid R, Thombare K, Mendez A, ..., Fischer M, Mondal T

Nucleic Acids Res. 52 (5) 2648-2671 [2024-03-21; online 2024-01-05]

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Modelling age at death reveals Nordic Corded Ware paleodemography

Tornberg A, Vandkilde H

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Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.

ElBeck Z, Hossain MB, Siga H, ..., Végvári Á, Betsholtz C

Nat Commun 15 (1) 2358 [2024-03-20; online 2024-03-20]

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Risk Factors for COVID-19 and Respiratory Tract Infections during the Coronavirus Pandemic.

Mockeliunas L, van Wijk RC, Upton CM, ..., Diacon AH, Simonsson USH

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MicroRNA-155 mediates multiple gene regulations pertinent to the role of human adipose-derived mesenchymal stem cells in skin regeneration.

Shahin H, Belcastro L, Das J, ..., Elmasry M, El-Serafi AT

Front Bioeng Biotechnol 12 (-) 1328504 [2024-03-18; online 2024-03-18]

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Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in Arabidopsis using liquid chromatography-tandem mass spectrometry.

Karady M, Hladík P, Cermanová K, ..., Ljung K, Novák O

Plant Methods 20 (1) 41 [2024-03-16; online 2024-03-16]

Ischemic preconditioning affects phosphosites and accentuates myocardial stunning while reducing infarction size in rats.

Elmahdy A, Shekka Espinosa A, Kakaei Y, ..., Hussain S, Redfors B

Front Cardiovasc Med 11 (-) 1376367 [2024-03-15; online 2024-03-15]

Influence of divalent cations on the extraction of organic acids in coffee determined by GC-MS and NMR.

Bratthäll T, Figueira J, Nording ML

Heliyon 10 (5) e26625 [2024-03-15; online 2024-02-17]

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Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei.

Ye W, Krishna Behra PR, Dyrhage K, ..., Andersson SGE, Jemth P

J. Mol. Biol. 436 (6) 168490 [2024-03-15; online 2024-02-13]

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Comparison of SARS-CoV-2 spike-specific IgA and IgG in nasal secretions, saliva and serum.

Bladh O, Aguilera K, Marking U, ..., Thålin C, Åberg M

Front Immunol 15 (-) 1346749 [2024-03-15; online 2024-03-15]

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Biochemical analysis of the endoribonuclease activity of the human mitochondrial topoisomerase 1

Bader CPJ, Kasho E, Forslund JME, Wessels M, Wanrooij PH

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A distinctive tumor compartment in pancreatic lobules defined by nascent stroma and classical tumor cell phenotype

Söderqvist S, Viljamaa A, Geyer N, ..., Moro CF, Gerling M

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Integrated preservation of water activity as key to intensified chemoenzymatic synthesis of bio-based styrene derivatives.

Petermeier P, Bittner JP, Jonsson T, ..., Byström E, Kara S

Commun Chem 7 (1) 57 [2024-03-14; online 2024-03-14]

Identification and surveillance of rare relapse-initiating stem cells during complete remission after transplantation.

Dimitriou M, Mortera-Blanco T, Tobiasson M, ..., Woll PS, Jacobsen SEW

Blood 143 (11) 953-966 [2024-03-14; online 2023-12-14]

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Characterization of intestinal O-glycome in reactive oxygen species deficiency.

Saldova R, Thomsson KA, Wilkinson H, ..., Karlsson NG, Knaus UG

PLoS ONE 19 (3) e0297292 [2024-03-14; online 2024-03-14]

Cell-Mediated Proteomics, and Serological and Mucosal Humoral Immune Responses after Seasonal Influenza Immunization: Characterization of Serological Responders and Non-Responders.

Carlsson H, Brudin L, Serrander L, Hinkula J, Tjernberg I

Vaccines (Basel) 12 (3) - [2024-03-14; online 2024-03-14]

Transcriptomic and proteomic profiles of fetal versus adult mesenchymal stromal cells and mesenchymal stromal cell-derived extracellular vesicles.

Gençer EB, Lor YK, Abomaray F, ..., Walther-Jallow L, Götherström C

Stem Cell Res Ther 15 (1) 77 [2024-03-13; online 2024-03-13]

Neutralizing IFN-γ autoantibodies are rare and pathogenic in HLA-DRB1*15:02 or 16:02 individuals.

Peel JN, Yang R, Le Voyer T, ..., Ku CL, Casanova JL

J. Clin. Invest. 134 (8) - [2024-03-12; online 2024-03-12]

Complete reference genomes of two ceftriaxone-resistant Neisseria gonorrhoeae strains identified in routine surveillance in Bangkok, Thailand, using Nanopore Q20+ chemistry, VolTRAX V2b, and Illumina sequencing.

Sangprasert P, Golparian D, Paopang P, ..., Kittiyaowanarn R, Unemo M

Microbiol Resour Announc 13 (3) e0123123 [2024-03-12; online 2024-02-01]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.

Suarez C, Rosenqvist T, Dimitrova I, ..., Hermansson M, Persson F

Microbiome 12 (1) 51 [2024-03-12; online 2024-03-12]

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Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure.

Frisk C, Das S, Eriksson MJ, ..., Linde C, Persson B

Sci Rep 14 (1) 5811 [2024-03-09; online 2024-03-09]

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Nuclear RNAi Modulates Influenza A Virus Infectivity By Downregulating Type-I Interferon Response

Huang HC, Nowak I, Lobo V, ..., Angeletti D, Sarshad AA

- - (-) - [2024-03-07; online 2024-03-07]

Identification of microbial pathogens in Neolithic Scandinavian humans.

Bergfeldt N, Kırdök E, Oskolkov N, ..., Storå J, Götherström A

Sci Rep 14 (1) 5630 [2024-03-07; online 2024-03-07]

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Early-life diet and risk of inflammatory bowel disease: a pooled study in two Scandinavian birth cohorts.

Guo A, Ludvigsson J, Brantsæter AL, ..., Størdal K, Mårild K

Gut 73 (4) 590-600 [2024-03-07; online 2024-03-07]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

AutonoMS: Automated Ion Mobility Metabolomic Fingerprinting.

Reder GK, Bjurström EY, Brunnsåker D, ..., McLean JA, King RD

J. Am. Soc. Mass Spectrom. 35 (3) 542-550 [2024-03-06; online 2024-02-04]

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The serological immunogenicity of the third and fourth doses of COVID-19 vaccine in patients with inflammatory rheumatic diseases on different biologic or targeted DMARDs: a Swedish nationwide study (COVID-19-REUMA).

Frodlund M, Nived P, Chatzidionysiou K, ..., Klareskog L, Kapetanovic M

Microbiol Spectr - (-) e0298123 [2024-03-05; online 2024-03-05]

Loss of chromosome Y in regulatory T cells.

Mattisson J, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA

BMC Genomics 25 (1) 243 [2024-03-05; online 2024-03-05]

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Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France.

Simões LG, Peyroteo-Stjerna R, Marchand G, ..., Günther T, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 121 (10) e2310545121 [2024-03-05; online 2024-02-26]

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Biohybrid Energy Storage Circuits Based on Electronically Functionalized Plant Roots.

Parker D, Dar AM, Armada-Moreira A, ..., Mantione D, Stavrinidou E

ACS Appl Mater Interfaces - (-) - [2024-03-05; online 2024-03-05]

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fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles.

Dennhag N, Kahsay A, Nissen I, ..., von Hofsten J, Pedrosa Domellöf F

Nat Commun 15 (1) 1950 [2024-03-02; online 2024-03-02]

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Towards objective measurements of habitual dietary intake patterns: comparing NMR metabolomics and food frequency questionnaire data in a population-based cohort.

Winkvist A, Johansson I, Ellegård L, Lindqvist HM

Nutr J 23 (1) 29 [2024-03-02; online 2024-03-02]

High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex.

Ament-Velásquez SL, Vogan AA, Wallerman O, ..., Giraud T, Johannesson H

Genome Biol Evol 16 (3) - [2024-03-02; online 2024-02-22]

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Multimodal bioimaging across disciplines and scales: challenges, opportunities and breaking down barriers

Bischof J, Fletcher G, Verkade P, ..., Keppler A, Parsons M

npj Imaging 2 (1) - [2024-03-01; online 2024-03-01]

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Development of a canine artificial colonic mucus model for drug diffusion studies.

Barmpatsalou V, Tjakra M, Li L, ..., Pedersen Lomstein B, Bergström CAS

Eur J Pharm Sci 194 (-) 106702 [2024-03-01; online 2024-01-12]

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Aberrant MNX1 expression associated with t(7;12)(q36;p13) pediatric acute myeloid leukemia induces the disease through altering histone methylation.

Waraky A, Östlund A, Nilsson T, ..., Plass C, Palmqvist L

Haematologica 109 (3) 725-739 [2024-03-01; online 2024-03-01]

The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.

Höglund A, Henriksen R, Churcher AM, ..., Jensen P, Wright D

PLoS Genet. 20 (3) e1010719 [2024-03-00; online 2024-03-08]

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The impact of circulating protein levels identified by affinity proteomics on short-term, overall breast cancer risk.

Grassmann F, Mälarstig A, Dahl L, ..., Schwenk JM, Czene K

Br. J. Cancer 130 (4) 620-627 [2024-03-00; online 2023-12-22]

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The astrocyte-produced growth factor HB-EGF limits autoimmune CNS pathology.

Linnerbauer M, Lößlein L, Vandrey O, ..., Quintana FJ, Rothhammer V

Nat. Immunol. 25 (3) 432-447 [2024-03-00; online 2024-02-26]

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Temporal stability of fecal metabolomic profiles in irritable bowel syndrome.

Iribarren C, Savolainen O, Sapnara M, ..., Magnusson MK, Öhman L

Neurogastroenterol. Motil. 36 (3) e14741 [2024-03-00; online 2024-01-19]

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TGFβ-induced long non-coding RNA LINC00313 activates Wnt signaling and promotes cholangiocarcinoma.

Papoutsoglou P, Pineau R, Leroux R, ..., Aubry M, Coulouarn C

EMBO Rep. 25 (3) 1022-1054 [2024-03-00; online 2024-02-08]

Subcutaneous Marzeptacog Alfa (Activated) for On-Demand Treatment of Bleeding Events in Subjects With Hemophilia A or B With Inhibitors.

Faraj A, Nyberg J, Blouse GE, Knudsen T, Simonsson USH

Clin. Pharmacol. Ther. 115 (3) 498-505 [2024-03-00; online 2024-01-16]

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Sorption of pharmaceuticals to foam and aerobic granular sludge with different morphologies

Burzio C, Mohammadi AS, Smith S, ..., Persson F, Wilén BM

Resources, Environment and Sustainability 15 (-) 100149 [2024-03-00; online 2024-03-00]

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Rare coding variants in NOX4 link high ROS levels to psoriatic arthritis mutilans.

Wang S, Nikamo P, Laasonen L, ..., Ståhle M, Tapia-Paez I

EMBO Mol Med 16 (3) 596-615 [2024-03-00; online 2024-02-20]

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Prevalence of SARS-CoV-2 infections among Swedish healthcare workers on duty in December 2023.

Aguilera K, Bladh O, Marking U, ..., Alm JJ, Thålin C

Lancet Reg Health Eur 38 (-) 100872 [2024-03-00; online 2024-02-08]

Metabolites, ions, and the mechanisms behind seasonal cold hardening of Pyrochroa coccinea (Pyrochroidae) larvae.

Jedal JYB, Malmendal A, Ramløv H

J Insect Physiol 153 (-) 104610 [2024-03-00; online 2023-12-24]

Maintenance of Behavioral Variation under Predation Risk: Effects on Personality, Plasticity, and Predictability.

Mitchell DJ, Beckmann C, Biro PA

Am Nat 203 (3) 347-361 [2024-03-00; online 2024-01-23]

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Machine learning predicts system-wide metabolic flux control in cyanobacteria.

Kugler A, Stensjö K

Metab. Eng. 82 (-) 171-182 [2024-03-00; online 2024-02-21]

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Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult.

Di Nunzio G, Hellberg S, Zhang Y, ..., Olofsson PS, Malin SG

Nat Cardiovasc Res 3 (3) 356-371 [2024-03-00; online 2024-03-11]

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Human PRH1, PRH2 susceptibility and resistance and Streptococcus mutans virulence phenotypes specify different microbial profiles in caries.

Sheng N, Mårell L, Sitaram RT, ..., Westerlund A, Strömberg N

EBioMedicine 101 (-) 105001 [2024-03-00; online 2024-02-15]

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Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions.

Johansson J, Lidéus S, Frykholm C, ..., Wilbe M, Bondeson ML

Eur. J. Hum. Genet. 32 (3) 333-341 [2024-03-00; online 2023-06-05]

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Genetic constraints in genes exhibiting splicing plasticity in facultative diapause.

Steward RA, Pruisscher P, Roberts KT, Wheat CW

Heredity (Edinb) 132 (3) 142-155 [2024-03-00; online 2024-01-30]

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.

Zhigulev A, Norberg Z, Cordier J, ..., Gréen H, Sahlén P

Life Sci. Alliance 7 (3) - [2024-03-00; online 2024-01-16]

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Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening.

Gezelius H, Enblad AP, Lundmark A, ..., Andersson C, Nordlund J

NAR Genom Bioinform 6 (1) lqae001 [2024-03-00; online 2024-01-29]

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Associations between inflammatory and angiogenic proteomic biomarkers, and cardiovascular events and mortality in relation to kidney function.

Salzinger B, Lundwall K, Evans M, ..., Spaak J, Jacobson SH

Clin Kidney J 17 (3) sfae050 [2024-03-00; online 2024-03-01]

Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow.

Fuentes-Pardo AP, Stanley R, Bourne C, ..., Andersson L, Ruzzante DE

Evol Appl 17 (3) e13675 [2024-03-00; online 2024-03-14]

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Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs.

Ås J, Bertulyte I, Norgren N, ..., Wadelius M, Hallberg P

PLoS ONE 19 (2) e0299075 [2024-02-29; online 2024-02-29]

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Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.

Rengefors K, Annenkova N, Wallenius J, ..., Kremp A, Ahrén D

Sci Rep 14 (1) 4986 [2024-02-29; online 2024-02-29]

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New insights into complex formation by SARS-CoV-2 nsp10 and nsp14.

Sele C, Krupinska E, Andersson Rasmussen A, ..., Fisher SZ, Knecht W

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Analysis of genetic variant associated with heart failure mortality implicates thymic stromal lymphopoietin as mediator of strain‐induced myocardial fibroblast‐mast cell crosstalk and fibrosis

Pimpalwar N, Celik S, Karbalaei Sadegh M, ..., Gidlöf O, Smith JG

The FASEB Journal 38 (4) - [2024-02-29; online 2024-02-26]

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Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling.

Bivehed E, Hellman B, Wenson L, ..., Söderberg O, Heldin J

Nucleic Acids Res. 52 (4) e22 [2024-02-28; online 2024-01-23]

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Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea.

Kälin C, Piombo E, Bourras S, ..., Elfstrand M, Karlsson M

BMC Plant Biol. 24 (1) 144 [2024-02-28; online 2024-02-28]

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Subcellular protein turnover in human neural progenitor cells revealed by correlative electron microscopy and nanoscale secondary ion mass spectrometry imaging.

Lork AA, Rabasco S, Ernst C, ..., Rizzoli SO, Phan NTN

Chem. Sci. 15 (9) 3311-3322 [2024-02-28; online 2024-01-29]

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Quantifying Fluorescence Lifetime Responsiveness of Environment-Sensitive Probes for Membrane Fluidity Measurements

Ragaller et al

J. Phys. Chem. B - (-) - [2024-02-28; online 2024-02-28] Open Access

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Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer.

Fonseca NM, Maurice-Dror C, Herberts C, ..., Chi KN, Wyatt AW

Nat Commun 15 (1) 1828 [2024-02-28; online 2024-02-28]

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scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.

Chen JP, Diekmann C, Wu H, ..., Bienko M, Crosetto N

Nat Commun 15 (1) 1768 [2024-02-27; online 2024-02-27]

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Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium.

Stańkowska W, Sarkisyan D, Bruhn-Olszewska B, ..., Filipowicz N, Dumanski JP

Cancers (Basel) 16 (5) - [2024-02-27; online 2024-02-27]

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Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD7.

Kinsolving J, Bous J, Kozielewicz P, ..., Dong M, Schulte G

Cell Rep 43 (2) 113727 [2024-02-27; online 2024-02-02]

Primary cilia promote the differentiation of human neurons through the WNT signaling pathway.

Coschiera A, Yoshihara M, Lauter G, ..., Kere J, Swoboda P

BMC Biol. 22 (1) 48 [2024-02-27; online 2024-02-27]

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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).

Jiang Z, Zang W, Ericson PGP, ..., Lei F, Qu Y

BMC Biol. 22 (1) 49 [2024-02-27; online 2024-02-27]

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Equine enteroid-derived monolayers recapitulate key features of parasitic intestinal nematode infection.

Hellman S, Martin F, Tydén E, ..., Svedberg P, Fossum C

Vet Res 55 (1) 25 [2024-02-27; online 2024-02-27]

Epigenome-wide analysis of frailty: Results from two European twin cohorts.

Mak JKL, Skovgaard AC, Nygaard M, ..., Soerensen M, Jylhävä J

Aging Cell - (-) e14135 [2024-02-27; online 2024-02-27]

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Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.

Kvedaraite E, Lourda M, Mouratidou N, ..., Henter JI, Svensson M

Nat Commun 15 (1) 1752 [2024-02-26; online 2024-02-26]

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Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea.

Xu T, Novotny A, Zamora-Terol S, Hambäck PA, Winder M

Microb. Ecol. 87 (1) 48 [2024-02-26; online 2024-02-26]

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Associations of the placental metabolome with immune maturation up to one year of age in the Swedish NICE-cohort.

Hartvigsson O, Barman M, Rabe H, ..., Brunius C, Sandberg A

Metabolomics 20 (2) 28 [2024-02-26; online 2024-02-26]

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UV-Induced Spectral and Morphological Changes in Bacterial Spores for Inactivation Assessment.

Öberg R, Sil TB, Johansson AC, ..., Andersson M, Andersson PO

J. Phys. Chem. B 128 (7) 1638-1646 [2024-02-22; online 2024-02-07]

No link between type I interferon autoantibody positivity and adverse reactions to COVID-19 vaccines.

Yalcinkaya A, Cavalli M, Cederholm A, ..., Wadelius M, Landegren N

NPJ Vaccines 9 (1) 42 [2024-02-22; online 2024-02-22]

The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.

Renström A, Choudhary S, Gandla ML, ..., Jämtgård S, Tuominen H

Physiol Plantarum 176 (1) e14219 [2024-02-21; online 2024-02-21]

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Spatial Neurolipidomics at the Single Amyloid-β Plaque Level in Postmortem Human Alzheimer's Disease Brain.

Michno W, Bowman A, Jha D, ..., Heeren RMA, Hanrieder J

ACS Chem Neurosci 15 (4) 877-888 [2024-02-21; online 2024-02-01]

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Omega-3 and -6 Fatty Acids Alter the Membrane Lipid Composition and Vesicle Size to Regulate Exocytosis and Storage of Catecholamines.

Gu C, Philipsen MH, Ewing AG

ACS Chem Neurosci 15 (4) 816-826 [2024-02-21; online 2024-02-12]

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MIGRENE: The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling.

Bidkhori G, Shoaie S

Metabolites 14 (3) - [2024-02-21; online 2024-02-21]

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Inhibition of Insulin-Regulated Aminopeptidase by Imidazo [1,5-α]pyridines-Synthesis and Evaluation.

Engen K, Lundbäck T, Yadav A, ..., Hallberg M, Larhed M

Int J Mol Sci 25 (5) - [2024-02-21; online 2024-02-21]

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Diversity in genetic risk of recurrent stroke: a genome-wide association study meta-analysis

Aldridge CM, Armstrong ND, Sunmonu NA, ..., Irvin MR, Worrall BB

Front. Stroke 3 (-) - [2024-02-21; online 2024-02-21]

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Corrigendum: Sex differences in the genetics of sarcoidosis across European and African ancestry populations.

Xiong Y, Kullberg S, Garman L, ..., Padyukov L, Rivera NV

Front Med (Lausanne) 11 (-) 1382584 [2024-02-21; online 2024-02-21]

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Clonally heritable gene expression imparts a layer of diversity within cell types.

Mold JE, Weissman MH, Ratz M, ..., Michaëlsson J, Frisén J

Cell Syst 15 (2) 149-165.e10 [2024-02-21; online 2024-02-09]

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Differential gene expression in two consecutive pregnancies between same sex siblings and implications on maternal constraint.

Kallak TK, Serapio S, Visser N, ..., Skalkidou A, Ahlsson F

Sci Rep 14 (1) 4210 [2024-02-20; online 2024-02-20]

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Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.

Hold K, Lord E, Brealey JC, ..., Martin MD, Dussex N

Sci Rep 14 (1) 4143 [2024-02-20; online 2024-02-20]

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MicroRNAs as Plasma Biomarkers of Hepatocellular Carcinoma in Patients with Liver Cirrhosis-A Cross-Sectional Study.

Zenlander R, Salter H, Gilg S, Eggertsen G, Stål P

Int J Mol Sci 25 (4) - [2024-02-19; online 2024-02-19]

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Lymphocytic colitis can be transcriptionally divided into channelopathic and inflammatory lymphocytic colitis.

Bhardwaj A, Münch A, Montague J, ..., Rosenstiel P, Escudero-Hernández C

United European Gastroenterol J - (-) - [2024-02-17; online 2024-02-17]

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Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.

Altincekic N, Jores N, Löhr F, ..., Sreeramulu S, Schwalbe H

ACS Chem. Biol. 19 (2) 563-574 [2024-02-16; online 2024-01-17]

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Long noncoding RNA plasmacytoma variant translocation 1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity.

Li C, Sun C, Mahapatra KD, ..., Sonkoly E, Pivarcsi A

Br J Dermatol 190 (3) 415-426 [2024-02-16; online 2023-11-06]

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Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel.

Zhang SM, Paulin CBJ, Shu H, ..., Helleday T, Rudd SG

iScience 27 (2) 108907 [2024-02-16; online 2024-01-13]

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Sustained looking at faces at 5 months of age is associated with socio-communicative skills in the second year of life.

Viktorsson C, Portugal AM, Taylor MJ, Ronald A, Falck-Ytter T

Infancy 29 (3) 459-478 [2024-02-15; online 2024-02-15]

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Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.

Dube F, Delhomme N, Martin F, ..., Svärd S, Tydén E

PLoS ONE 19 (2) e0298039 [2024-02-15; online 2024-02-15]

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Staphylococcus aureus mutants resistant to the feed-additive monensin show increased virulence and altered purine metabolism.

Warsi OM, Upterworth LM, Breidenstein A, ..., Ingmer H, Andersson DI

MBio 15 (2) e0315523 [2024-02-14; online 2024-01-12]

Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants.

Viktorsson C, Portugal AM, Falck-Ytter T

Sci Rep 14 (1) 3668 [2024-02-14; online 2024-02-14]

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Molecular basis for human aquaporin inhibition.

Huang P, Åbacka H, Wilson CJ, ..., Venskutonytė R, Lindkvist-Petersson K

Proc. Natl. Acad. Sci. U.S.A. 121 (7) e2319682121 [2024-02-13; online 2024-02-06]

Disability and emotional symptoms in women with lipedema: A comparison with overweight/obese women.

Chachaj A, Jeziorek M, Dudka I, ..., Kujawa K, Szuba A

Adv Clin Exp Med - (-) - [2024-02-13; online 2024-02-13]

Exploration of differential responses to FODMAPs and gluten in people with irritable bowel syndrome- a double-blind randomized cross-over challenge study.

Nordin E, Landberg R, Hellström PM, Brunius C

Metabolomics 20 (2) 21 [2024-02-12; online 2024-02-12]

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AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes.

Collins AM, Ohlin M, Corcoran M, ..., Watson CT, Lees WD

Front Immunol 14 (-) 1330153 [2024-02-09; online 2024-02-09]

Exploring the Dispersion and Electrostatic Components in Arene-Arene Interactions between Ligands and G4 DNA to Develop G4-Ligands.

Andreasson M, Donzel M, Abrahamsson A, ..., Wanrooij S, Chorell E

J. Med. Chem. 67 (3) 2202-2219 [2024-02-08; online 2024-01-19]

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The role of extracellular vesicle fusion with target cells in triggering systemic inflammation.

Papareddy P, Tapken I, Kroh K, ..., Holub M, Herwald H

Nat Commun 15 (1) 1150 [2024-02-07; online 2024-02-07]

Spatio-temporal transcriptome and storage compound profiles of developing faba bean (Vicia faba) seed tissues.

Ohm H, Saripella GV, Hofvander P, Grimberg Å

Front Plant Sci 15 (-) 1284997 [2024-02-06; online 2024-02-06]

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Editorial: Decoding the genome of acute lymphoblastic leukemia through genomic and transcriptomic approaches.

Jiménez-Morales S, Rojas-Martinez A, Barbany G

Front Oncol 14 (-) 1368676 [2024-02-06; online 2024-02-06]

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Colony phase variation switch modulates antimicrobial tolerance and biofilm formation in Acinetobacter baumannii.

Mushtaq F, Nadeem A, Yabrag A, ..., Uhlin BE, Ahmad I

Microbiol Spectr 12 (2) e0295623 [2024-02-06; online 2024-01-11]

A macrophage-collagen fragment axis mediates subcutaneous adipose tissue remodeling in mice.

Vujičić M, Broderick I, Salmantabar P, ..., Sihlbom Wallem C, Wernstedt Asterholm I

Proc. Natl. Acad. Sci. U.S.A. 121 (6) e2313185121 [2024-02-06; online 2024-02-01]

Nigral transcriptomic profiles in Engrailed-1 hemizygous mouse models of Parkinson's disease reveal upregulation of oxidative phosphorylation-related genes associated with delayed dopaminergic neurodegeneration.

Belfiori LF, Dueñas Rey A, Ralbovszki DM, ..., Brolin KA, Swanberg M

Front Aging Neurosci 16 (-) 1337365 [2024-02-05; online 2024-02-05]

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N-(Heteroaryl)thiophene sulfonamides as angiotensin AT2 receptor ligands.

Wannberg J, Gising J, Henriksson M, ..., Hallberg M, Larhed M

Eur J Med Chem 265 (-) 116122 [2024-02-05; online 2024-01-03]

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Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children.

Bastard P, Gervais A, Taniguchi M, ..., Cobat A, Casanova JL

J. Exp. Med. 221 (2) - [2024-02-05; online 2024-01-04]

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Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.

Yildirim Y, Kristensson D, Outomuro D, ..., Sniegula S, Johansson F

BMC Ecol Evol 24 (1) 19 [2024-02-03; online 2024-02-03]

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Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies.

Zhao X, Vogirala VK, Liu M, ..., Sandin S, Yan J

Commun Biol 7 (1) 148 [2024-02-03; online 2024-02-03]

Associations between plasma metabolism associated proteins and future development of giant cell arteritis: results from a prospective study.

Wadström K, Jacobsson LTH, Mohammad AJ, ..., Jakobsson ME, Turesson C

Rheumatology (Oxford) - (-) - [2024-02-03; online 2024-02-03]

Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1.

Bacic L, Gaullier G, Mohapatra J, ..., Sabantsev A, Deindl S

Nat Commun 15 (1) 1000 [2024-02-02; online 2024-02-02]

Xist ribonucleoproteins promote female sex-biased autoimmunity.

Dou DR, Zhao Y, Belk JA, ..., Utz PJ, Chang HY

Cell 187 (3) 733-749.e16 [2024-02-01; online 2024-02-03]

Systemic and mucosal adaptive immunity to SARS-CoV-2 during the Omicron wave in patients with chronic lymphocytic leukemia.

Ingelman-Sundberg HM, Blixt L, Wullimann D, ..., Buggert M, Österborg A

Haematologica 109 (2) 646-651 [2024-02-01; online 2024-02-01]

Reagentless impedimetric immunosensor for monitoring of methotrexate in human blood serum using multiwalled carbon nanotube@polypyrrole/polytyramine film electrode.

Adeniyi KO, Osmanaj B, Manavalan G, ..., Berisha A, Tesfalidet S

Talanta 268 (Pt 1) 125316 [2024-02-01; online 2023-10-16]

Obscurin Maintains Myofiber Identity in Extraocular Muscles.

Kahsay A, Dennhag N, Liu JX, ..., von Hofsten J, Pedrosa Domellöf F

Invest Ophthalmol Vis Sci 65 (2) 19 [2024-02-01; online 2024-02-09]

A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.

Höglund J, Dias G, Olsen RA, ..., Talla V, Backström N

Genome Biol Evol 16 (2) - [2024-02-01; online 2024-02-18]

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Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder

Yahia A, Li D, Lejerkrans S, ..., Kalnak N, Tammimies K

Hum Genet 143 (2) 169-183 [2024-02-00; online 2024-02-01]

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Vaginal candida infection is associated with host molecular signatures of neutrophil activation in the adjacent ectocervical mucosa in Kenyan sex workers

Hasselrot T, Boger MF, Kaldhusdal V, ..., Czarnewski P, Broliden K

American J Rep Immunol 91 (2) - [2024-02-00; online 2024-01-31]

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Ultrastructural insights into the microsporidian infection apparatus reveal the kinetics and morphological transitions of polar tube and cargo during host cell invasion.

Sharma H, Jespersen N, Ehrenbolger K, Carlson LA, Barandun J

PLoS Biol. 22 (2) e3002533 [2024-02-00; online 2024-02-29]

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The cryo-EM structure of the BoNT/Wo-NTNH complex reveals two immunoglobulin-like domains.

Košenina S, Škerlová J, Zhang S, Dong M, Stenmark P

FEBS J. 291 (4) 676-689 [2024-02-00; online 2023-09-29]

Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx.

Lucena-Perez M, Paijmans JLA, Nocete F, ..., Barlow A, Godoy JA

Nat Ecol Evol 8 (2) 282-292 [2024-02-00; online 2024-01-15]

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Proteomic profiling of tumour tissue-derived extracellular vesicles in colon cancer.

Cvjetkovic A, Karimi N, Crescitelli R, ..., Lässer C, Lötvall J

J Extracell Biol 3 (2) e127 [2024-02-00; online 2024-02-06]

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Playing with Protic Additives to Improve the Outcome of Rhodium‐Catalyzed Hydroarylation of Fullerene C60 with Arylboronic Acids

Ergun Dönmez M, Eriksson M, Hulu G, Nordström M, Grennberg H

Helvetica Chimica Acta 107 (2) - [2024-02-00; online 2024-01-16]

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Oxylipin profiling by LC-ESI-MS/MS in canine serum and plasma to investigate ovulation-specific changes.

Ramström M, Holst BS, Lindberg R, Nording ML

Prostaglandins Other Lipid Mediat. 170 (-) 106790 [2024-02-00; online 2023-10-31]

Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome.

Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen A

Arthritis & rheumatology (Hoboken, N.J.) 76 (2) 255-267 [2024-02-00; online 2023-12-18]

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MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall.

Ogurtsov A, Alves G, Rubio A, ..., Moore ERB, Yu YK

J Comput Biol 31 (2) 175-178 [2024-02-00; online 2024-02-02]

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Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles.

Geng K, Merino LG, Veiga RG, ..., Brinkman EK, Kutter C

Life Sci. Alliance 7 (2) - [2024-02-00; online 2023-11-20]

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Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster in Sweden.

Marking U, Bladh O, Aguilera K, ..., Sheward DJ, Thålin C

Lancet Infect Dis 24 (2) e80-e81 [2024-02-00; online 2024-01-05]

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago.

Mylopotamitaki D, Weiss M, Fewlass H, ..., Schüler T, Hublin JJ

Nature 626 (7998) 341-346 [2024-02-00; online 2024-01-31]

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Glycoproteomic profile of human tissue-nonspecific alkaline phosphatase expressed in osteoblasts.

Atanasova D, Mirgorodskaya E, Moparthi L, ..., Landberg E, Magnusson P

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Genomic variation in montane bumblebees in Scandinavia: High levels of intraspecific diversity despite population vulnerability.

Liu Y, Olsson A, Larva T, ..., Cederberg B, Webster MT

Mol. Ecol. 33 (4) e17251 [2024-02-00; online 2023-12-19]

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Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.

Longo A, Kurta K, Vanhala T, ..., de Koning DJ, Palaiokostas C

Anim Genet 55 (1) 87-98 [2024-02-00; online 2023-11-23]

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Gastrointestinal parasite community structure in horses after the introduction of selective anthelmintic treatment strategies.

Halvarsson P, Grandi G, Hägglund S, Höglund J

Vet Parasitol 326 (-) 110111 [2024-02-00; online 2023-12-25]

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Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants.

Sletvold N, Joffard N, Söderquist L

Am. J. Bot. 111 (2) e16273 [2024-02-00; online 2024-01-30]

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Evidence from Finland and Sweden on the relationship between early-life diseases and lifetime childlessness in men and women.

Liu A, Akimova ET, Ding X, ..., Mills MC, Ganna A

Nat Hum Behav 8 (2) 276-287 [2024-02-00; online 2023-12-18]

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Correlates of Plasma Citrulline, a Potential Marker of Enterocyte Mass, among Children with Stunting: A Cross-Sectional Study in Uganda.

Pesu H, Mbabazi J, Mutumba R, ..., Friis H, Grenov B

J. Nutr. 154 (2) 765-776 [2024-02-00; online 2023-12-21]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Complex In Vitro Model Characterization for Context of Use in Toxicologic Pathology: Use Cases by Collaborative Teams of Biologists, Bioengineers, and Pathologists.

Stokar-Regenscheit N, Bell L, Berridge B, ..., Sura R, Tomlinson L

Toxicol Pathol 52 (2-3) 123-137 [2024-02-00; online 2024-06-18]

Community-developed checklists for publishing images and image analyses.

Schmied C, Nelson MS, Avilov S, ..., Tischer C, Jambor HK

Nat. Methods 21 (2) 170-181 [2024-02-00; online 2023-09-14]

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CPAP may promote an endothelial inflammatory milieu in sleep apnoea after coronary revascularization

Peker Y, Celik Y, Behboudi A, ..., Gottlieb DJ, Jelic S

EBioMedicine - (-) 105015 [2024-02-00; online 2024-02-00]

Antimicrobial susceptibilities and genomic characteristics of methicillin‐resistant Staphylococcus aureus resistant to mupirocin in Stockholm, Sweden

Vestberg N, Razavi M, Giske CG, Fang H

APMIS 132 (2) 94-99 [2024-02-00; online 2023-11-15]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.

Lindelöf L, Rantapää-Dahlqvist S, Lundtoft C, ..., Svenungsson E, Eriksson O

J. Autoimmun. 143 (-) 103166 [2024-02-00; online 2024-01-13]

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A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors.

Menon I, Sych T, Son Y, ..., Levitz J, Menon AK

J. Biol. Chem. 300 (2) 105649 [2024-02-00; online 2024-01-16]

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The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome†.

Chase MA, Vilcot M, Mugal CF

Proc. Biol. Sci. 291 (2015) 20232382 [2024-01-31; online 2024-01-17]

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Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

Bergh C, Rovšnik U, Howard R, Lindahl E

Elife 12 (-) - [2024-01-30; online 2024-01-30]

Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).

Chondrelli N, Kuehn E, Meurling S, ..., Laurila A, Höglund J

Sci Rep 14 (1) 2495 [2024-01-30; online 2024-01-30]

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A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.

von Beek C, Fahlgren A, Geiser P, ..., Pejler G, Sellin ME

Nat Commun 15 (1) 904 [2024-01-30; online 2024-01-30]

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Single-cell RNA-seq mapping of chicken peripheral blood leukocytes.

Maxwell M, Söderlund R, Härtle S, Wattrang E

BMC Genomics 25 (1) 124 [2024-01-29; online 2024-01-29]

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Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk.

Bodén S, Zheng R, Ribbenstedt A, ..., Van Guelpen B, Brunius C

Sci Rep 14 (1) 2244 [2024-01-26; online 2024-01-26]

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Krzewińska M, Rodríguez-Varela R, Yaka R, ..., Storå J, Götherström A

Heritage 7 (2) 576-584 [2024-01-25; online 2024-01-25]

High-parametric protein maps reveal the spatial organization in early-developing human lung

Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B

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The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma.

Krynina O, de Ståhl TD, Jylhä C, ..., Tham E, Sandvik U

Neurooncol Adv 6 (1) vdae008 [2024-01-24; online 2024-01-24]

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QComics: Recommendations and Guidelines for Robust, Easily Implementable and Reportable Quality Control of Metabolomics Data.

González-Domínguez Á, Estanyol-Torres N, Brunius C, Landberg R, González-Domínguez R

Anal. Chem. 96 (3) 1064-1072 [2024-01-23; online 2024-01-05]

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Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.

Harish A, Lopes Pinto FA, Eriksson S, Johansson AM

BMC Genomics 25 (1) 89 [2024-01-22; online 2024-01-22]

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Three immunizations with Novavax's protein vaccines increase antibody breadth and provide durable protection from SARS-CoV-2.

Lenart K, Arcoverde Cerveira R, Hellgren F, ..., Smith G, Loré K

NPJ Vaccines 9 (1) 17 [2024-01-20; online 2024-01-20]

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Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.

Grujčić V, Saarenpää S, Sundh J, ..., Foster RA, Andersson AF

PLoS ONE 19 (1) e0296672 [2024-01-19; online 2024-01-19]

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Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training.

Emanuelsson EB, Arif M, Reitzner SM, ..., Sundberg CJ, Chapman MA

iScience 27 (1) 108638 [2024-01-19; online 2023-12-05]

Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation.

Clouard C, Nettelblad C

Theor. Appl. Genet. 137 (1) 26 [2024-01-19; online 2024-01-19]

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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.

Kırdök E, Kashuba N, Damlien H, ..., Aravena A, Götherström A

Sci Rep 13 (1) 22125 [2024-01-18; online 2024-01-18]

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Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.

Bergman I, Lindström ES, Sassenhagen I

Microb. Ecol. 87 (1) 33 [2024-01-18; online 2024-01-18]

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Characterization of MdpS: an in-depth analysis of a MUC5B-degrading protease from Streptococcus oralis.

Leo F, Lood R, Thomsson KA, ..., Svensäter G, Wickström C

Front Microbiol 15 (-) 1340109 [2024-01-18; online 2024-01-18]

Evaluation of Genetic or Cellular Impairments in Type I IFN Immunity in a Cohort of Young Adults with Critical COVID-19.

Covill LE, Sendel A, Campbell TM, ..., Bergman P, Bryceson YT

J Clin Immunol 44 (2) 50 [2024-01-17; online 2024-01-17]

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CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs.

Nguyen TH, Nguyen HN, Vu TN

BMC Bioinformatics 25 (1) 31 [2024-01-17; online 2024-01-17]

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OMICs Signatures Linking Persistent Organic Pollutants to Cardiovascular Disease in the Swedish Mammography Cohort.

Schillemans T, Yan Y, Ribbenstedt A, ..., Åkesson A, Brunius C

Environ. Sci. Technol. 58 (2) 1036-1047 [2024-01-16; online 2024-01-04]

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High-throughput analysis of membrane fluidity unveils a hidden dimension in immune cell states

Andronico LA, Jiang Y, Carannante V, ..., Brodin P, Sezgin E

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Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts.

Moura PL, Mortera-Blanco T, Hofman IJ, ..., Jacobsen SEW, Hellström-Lindberg E

Cancer Res. 84 (2) 211-225 [2024-01-16; online 2023-11-03]

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Ultralight Ultrafast Enzymes.

Zhang X, Meng Z, Beusch CM, ..., Gaetani M, Zubarev RA

Angew. Chem. Int. Ed. Engl. 63 (3) e202316488 [2024-01-15; online 2023-12-07]

Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis.

Drexhage LZ, Zhang S, Dupont M, ..., Karaji N, Sattentau QJ

Nat Commun 15 (1) 541 [2024-01-15; online 2024-01-15]

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Profiling of Surface Protein Epitopes on Viral Particles by Multiplex Dual-Reporter Strategy

Sahi M, Andersson S, Mattson C, ..., Chiodi F, Fredolini C

J Vis Exp - (203) - [2024-01-12; online 2024-01-12]

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Furan Distribution as a Severity Indicator upon Organosolv Fractionation of Hardwood Sawdust through a Novel Ternary Solvent System

Thoresen PP, Delgado Vellosillo I, Lange H, ..., Christakopoulos P, Matsakas L

ACS Sustainable Chem. Eng. - (-) - [2024-01-12; online 2024-01-12]

Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis).

Ozerov MY, Noreikiene K, Kahar S, ..., Gross R, Vasemägi A

Comp Biochem Physiol B Biochem Mol Biol 271 (-) 110941 [2024-01-11; online 2024-01-11]

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Identification of circulating autoantibodies to non-modified proteins associated with ACPA status in early rheumatoid arthritis.

Lourido L, Joshua V, Hansson M, ..., Klareskog L, Blanco FJ

Rheumatology (Oxford) - (-) - [2024-01-09; online 2024-01-09]

Autoimmunity and Serology Profiling [Collaborative]

Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents.

Gollnisch R, Ahrén D, Rengefors K

ISME J 18 (1) - [2024-01-08; online 2024-03-15]

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Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris.

Duan T, Sicard A, Glémin S, Lascoux M

Elife 12 (-) - [2024-01-08; online 2024-01-08]

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Climate acts as an environmental filter to plant pathogens.

Caballol M, Redondo MÁ, Catalán N, ..., Stenlid J, Oliva J

ISME J 18 (1) - [2024-01-08; online 2024-02-17]

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Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments.

Broman E, Olsson M, Maciute A, ..., Bonaglia S, Nascimento FJA

ISME J 18 (1) - [2024-01-08; online 2024-02-17]

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A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

Biderre-Petit C, Courtine D, Hennequin C, ..., Divne A, Hochart C

Mol Ecol Resour - (-) e13923 [2024-01-08; online 2024-01-08]

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Antimicrobial Activity of Two Different Types of Silver Nanoparticles against Wide Range of Pathogenic Bacteria.

Holubnycha V, Husak Y, Korniienko V, ..., Ramanavicius A, Pogorielov M

Nanomaterials (Basel) 14 (2) - [2024-01-07; online 2024-01-07]

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.

Bouyssié D, Altıner P, Capella-Gutierrez S, ..., Winkelhardt D, Schwämmle V

J. Proteome Res. 23 (1) 418-429 [2024-01-05; online 2023-12-01]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite.

Cīrulis A, Nordén AK, Churcher AM, ..., Zadesenets KS, Abbott JK

Genome Biol Evol 16 (1) - [2024-01-05; online 2023-12-29]

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Proteomic analysis shows decreased type I fibers and ectopic fat accumulation in skeletal muscle from women with PCOS.

Stener-Victorin E, Eriksson G, Mohan Shrestha M, ..., Lanner J, Benrick A

Elife 12 (-) - [2024-01-05; online 2024-01-05]

Nuclear Hsp104 safeguards the dormant translation machinery during quiescence.

Kohler V, Kohler A, Berglund LL, ..., Andréasson C, Büttner S

Nat Commun 15 (1) 315 [2024-01-05; online 2024-01-05]

Bridging responses to a human telomerase reverse transcriptase-based peptide cancer vaccine candidate in a mechanism-based model.

Ibrahim EIK, Ellingsen EB, Mangsbo SM, Friberg LE

Int Immunopharmacol 126 (-) 111225 [2024-01-05; online 2023-11-20]

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Secretome Analyses Identify FKBP4 as a GBA1-Associated Protein in CSF and iPS Cells from Parkinson's Disease Patients with GBA1 Mutations.

Kojima R, Paslawski W, Lyu G, ..., Zhang X, Svenningsson P

Int J Mol Sci 25 (1) - [2024-01-04; online 2024-01-04]

METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.

Ast T, Itoh Y, Sadre S, ..., Amunts A, Mootha VK

Mol. Cell - (-) - [2024-01-04; online 2024-01-04]

Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease.

Wallenius J, Kafantari E, Jhaveri E, ..., Ehrencrona H, Puschmann A

Am. J. Hum. Genet. 111 (1) 82-95 [2024-01-04; online 2023-11-29]

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Elevated circulating adiponectin levels do not prevent anxiety-like behavior in a PCOS-like mouse model.

Samad M, Ek J, Börchers S, ..., Asterholm IW, Benrick A

Sci Rep 14 (1) 563 [2024-01-04; online 2024-01-04]

Mutation of the cyclooxygenase 2 gene promoter and anastomotic leakage in colorectal cancer patients: retrospective cohort study.

Grahn O, Holmgren K, Hong MG, Sund M, Rutegård M

BJS Open 8 (1) - [2024-01-03; online 2024-01-30]

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Identification of a Notch transcriptomic signature for breast cancer.

Braune EB, Geist F, Tang X, ..., Wienke D, Lendahl U

Breast Cancer Res. 26 (1) 4 [2024-01-03; online 2024-01-03]

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Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.

Hunt G, Vaid R, Pirogov S, ..., Reimegård J, Mannervik M

Genome Biol. 25 (1) 2 [2024-01-02; online 2024-01-02]

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Functional annotation of a divergent genome using sequence and structure-based similarity.

Svedberg D, Winiger RR, Berg A, ..., Vossbrinck CR, Barandun J

BMC Genomics 25 (1) 6 [2024-01-02; online 2024-01-02]

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A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.

Latz MAC, Andersson A, Brugel S, ..., Torstensson A, Andersson AF

Sci Data 11 (1) 18 [2024-01-02; online 2024-01-02]

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Metastasis and recurrence patterns in the molecular subtypes of urothelial bladder cancer.

Sjödahl G, Eriksson P, Holmsten K, ..., Ullén A, Liedberg F

Int. J. Cancer 154 (1) 180-190 [2024-01-01; online 2023-09-06]

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Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF.

Struck EC, Belova T, Hsieh PH, ..., Dusart PJ, Butler LM

J. Immunol. 212 (1) 117-129 [2024-01-01; online 2023-11-29]

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Astrocytic Regulation of Endocannabinoid-Dependent Synaptic Plasticity in the Dorsolateral Striatum.

Adermark L, Stomberg R, Söderpalm B, Ericson M

Int J Mol Sci 25 (1) - [2024-01-01; online 2024-01-01]

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Analysis of stabilization mechanisms in β-lactoglobulin-based amorphous solid dispersions by experimental and computational approaches.

Zhuo X, Foderà V, Larsson P, ..., Löbmann K, Kabedev A

Eur J Pharm Sci 192 (-) 106639 [2024-01-01; online 2023-11-13]

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A biobased binder of carboxymethyl cellulose, citric acid, chitosan and wheat gluten for nonwoven and paper.

Wennman M, Pinon AC, Svagan AJ, Hellberg M, Hedenqvist MS

Carbohydr Polym 323 (-) 121430 [2024-01-01; online 2023-09-23]

pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections.

Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M

Microb Genom 10 (1) - [2024-01-00; online 2024-01-30]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens.

Guo Y, Rubin CJ, Rönneburg T, ..., Hu X, Carlborg Ö

Poult. Sci. 103 (1) 103232 [2024-01-00; online 2023-10-24]

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Viral diversity and host associations in microbial electrolysis cells.

Abadikhah M, Persson F, Farewell A, Wilén BM, Modin O

ISME COMMUN. 4 (1) ycae143 [2024-01-00; online 2024-11-15]

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The genetic legacy of the expansion of Bantu-speaking peoples in Africa.

Fortes-Lima CA, Burgarella C, Hammarén R, ..., Bostoen K, Schlebusch CM

Nature 625 (7995) 540-547 [2024-01-00; online 2023-11-29]

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The functional role of CST1 and CCL26 in asthma development.

Hoyer A, Chakraborty S, Lilienthal I, ..., Katayama S, Söderhäll C

Immun Inflamm Dis 12 (1) e1162 [2024-01-00; online 2024-01-25]

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Substance P, NPY, CCK and their receptors in five brain regions in major depressive disorder with transcriptomic analysis of locus coeruleus neurons.

Barde S, Aguila J, Zhong W, ..., Hedlund E, Hökfelt T

Eur Neuropsychopharmacol 78 (-) 54-63 [2024-01-00; online 2023-11-04]

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Randomized open-label trial of semaglutide and dapagliflozin in patients with type 2 diabetes of different pathophysiology.

Dwibedi C, Ekström O, Brandt J, ..., Abrahamsson B, Rosengren AH

Nat Metab 6 (1) 50-60 [2024-01-00; online 2024-01-04]

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Pulmonary function and atherosclerosis in the general population: causal associations and clinical implications.

Engström G, Lampa E, Dekkers K, ..., Östgren CJ, Sundström J

Eur. J. Epidemiol. 39 (1) 35-49 [2024-01-00; online 2024-01-02]

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Prognostic value of hypoxia-responsive gene expression profile in patients diagnosed with head and neck squamous cell carcinoma.

Matic N, Pettersson L, Sellebjerg F, ..., Roberg K, Wiechec E

Transl Oncol 39 (-) 101841 [2024-01-00; online 2023-11-27]

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Population genomics of the muskox' resilience in the near absence of genetic variation.

Pečnerová P, Lord E, Garcia-Erill G, ..., Moltke I, Siegismund HR

Mol. Ecol. 33 (2) e17205 [2024-01-00; online 2023-11-16]

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Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).

Thureborn O, Wikström N, Razafimandimbison SG, Rydin C

Ecol Evol 14 (1) e10868 [2024-01-00; online 2024-01-25]

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Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles.

Pold G, Bonilla-Rosso G, Saghaï A, ..., Jones CM, Hallin S

ISME COMMUN. 4 (1) ycae020 [2024-01-00; online 2024-02-02]

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Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.

Dopson M, Rezaei Somee M, González-Rosales C, ..., Mehrshad M, Bertilsson S

ISME COMMUN. 4 (1) ycae113 [2024-01-00; online 2024-09-23]

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New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.

Kurland S, Saha A, Keehnen N, ..., Ryman N, Laikre L

Mol. Ecol. 33 (2) e17213 [2024-01-00; online 2023-11-28]

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New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.

Bittner MJ, Bannon CC, Rowland E, ..., Paerl RW, Riemann L

ISME COMMUN. 4 (1) ycad016 [2024-01-00; online 2024-01-10]

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Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors.

FitzGerald EA, Vagrys D, Opassi G, ..., de Esch IJP, Danielson UH

SLAS DISCOVERY: Advancing Life Sciences R&D 29 (1) 40-51 [2024-01-00; online 2023-09-14]

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Molecular profiling of high-level athlete skeletal muscle after acute endurance or resistance exercise – A systems biology approach

Reitzner SM, Emanuelsson EB, Arif M, ..., Chapman MA, Sundberg CJ

Mol Metab 79 (-) 101857 [2024-01-00; online 2024-01-00]

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Molecular blueprints for spinal circuit modules controlling locomotor speed in zebrafish.

Pallucchi I, Bertuzzi M, Madrid D, ..., Higashijima SI, El Manira A

Nat. Neurosci. 27 (1) 78-89 [2024-01-00; online 2023-11-02]

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Heat inactivation of foetal bovine serum performed after EV-depletion influences the proteome of cell-derived extracellular vesicles.

Urzì O, Bergqvist M, Lässer C, ..., Olofsson Bagge R, Crescitelli R

J Extracell Vesicles 13 (1) e12408 [2024-01-00; online 2024-01-24]

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Effects of Wholegrain Compared to Refined Grain Intake on Cardiometabolic Risk Markers, Gut Microbiota, and Gastrointestinal Symptoms in Children: A Randomized Crossover Trial.

Madsen MTB, Landberg R, Nielsen DS, ..., Lauritzen L, Damsgaard CT

Am. J. Clin. Nutr. 119 (1) 18-28 [2024-01-00; online 2023-10-28]

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Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis.

Hung SW, Gaetani M, Li Y, ..., Zubarev RA, Wang CC

J Pharm Anal 14 (1) 100-114 [2024-01-00; online 2023-09-11]

DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems.

Diaz-Suarez A, Noreikiene K, Kahar S, ..., Kisand V, Vasemägi A

Int J Parasitol 54 (1) 33-46 [2024-01-00; online 2023-08-24]

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Compound heterozygous variants in RAB34 in a rare skeletal ciliopathy syndrome.

Batkovskyte D, Komatsu M, Hammarsjö A, ..., Nishimura G, Yamada T

Clin. Genet. 105 (1) 87-91 [2024-01-00; online 2023-08-24]

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Birth Weight, Childhood and Young Adult Overweight, and the Risk of Coronary Heart Disease in Men.

Bramsved R, Bygdell M, Martikainen J, ..., Ohlsson C, Kindblom JM

Arterioscler. Thromb. Vasc. Biol. 44 (1) 314-321 [2024-01-00; online 2023-11-16]

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A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing.

Feng M, Zhang A, Nguyen V, ..., Carlsbecker A, Melnyk CW

NPLANTS 10 (1) 53-65 [2024-01-00; online 2024-01-02]

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Visualizing the Microbial N Uptake During Arctic Extreme Winter Warming Events Using Nanosims

Rasmussen LH, Danielsen BK, Elberling B, ..., Micaroni M, Andresen LC

- - (-) - [2024-00-00; online 2024-00-00]

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Strategies for Multimodal Image Data Transformation to a Common Format for Cloud Integration and Visualization

Camacho R, Berndtsson J, Micaroni M, Zhang K, Fernandez-Rodriguez J

BIO Web Conf. 129 (-) 13019 [2024-00-00; online 2024-10-17]

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Population genomic data reveal low genetic diversity, divergence and local adaptation among threatened Reeves's Pheasant (Syrmaticus reevesii)

Lu Q, Wang P, Chang J, ..., Höglund J, Zhang Z

Avian Research 15 (-) 100156 [2024-00-00; online 2024-00-00]

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One-pot reductive liquefaction of sawdust to renewables over MoOx–Al2O3 variants: insight into structure–activity relationships

Salam MA, Tran QK, Ho PH, ..., Olsson L, Creaser D

Sustainable Energy Fuels 8 (12) 2668-2681 [2024-00-00; online 2024-00-00]

Landscape of Epstein-Barr virus gene expression and perturbations in cancer

K. W. Tang YTGXABIHDVea

Res Sq - (-) - [2024-00-00]

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Ionic liquid strategy for chitosan production from chitin and molecular insights

Dinh VM, Khokarale SG, May PO, ..., Irgum K, Mikkola JP

RSC Sustain. 2 (4) 1154-1164 [2024-00-00; online 2024-00-00]

A surface passivated fluorinated polymer nanocomposite for carbon monoxide resistant plasmonic hydrogen sensing

Östergren I, Darmadi I, Lerch S, ..., Langhammer C, Müller C

J. Mater. Chem. A 12 (13) 7906-7915 [2024-00-00; online 2024-00-00]

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A combination of long- and short-read genomics reveals frequent p-arm breakpoints within chromosome 21 complex genomic rearrangements

Schuy J, Sæther KB, Lisfeld J, ..., Eisfeldt J, Lindstrand A

Genetics in Medicine Open 2 (-) 101863 [2024-00-00; online 2024-00-00]

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Proteomic profiles associated with postsurgical progression in non-functioning pituitary adenomas.

Hallén T, Johannsson G, Thorsell A, ..., Bergquist J, Skoglund T

J. Clin. Endocrinol. Metab. - (-) - [2023-12-29; online 2023-12-29]

Simultaneous detection of membrane contact dynamics and associated Ca2+signals by reversible chemogenetic reporters

Casas PG, Rossini M, Påvénius L, ..., Pizzo P, Filadi R

- - (-) - [2023-12-28; online 2023-12-28] Open Access

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Biodistribution of DNA-origami nanostructures in live zebrafish embryos with single-cell resolution

Kolonelou C, Bräutigam L, Edwards S, ..., Andersson O, Teixeira AI

- - (-) - [2023-12-23; online 2023-12-23]

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Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV.

Ray S, Narayanan A, Vesterbacka J, ..., Sönnerborg A, Nowak P

NPJ Biofilms Microbiomes 9 (1) 104 [2023-12-20; online 2023-12-20]

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Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut.

Wang J, Chen H, Li Y, ..., Qu C, Shan S

Plants (Basel) 13 (1) - [2023-12-20; online 2023-12-20]

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Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish.

Berggren H, Nordahl O, Yıldırım Y, ..., Tibblin P, Forsman A

Proc. Biol. Sci. 290 (2013) 20231608 [2023-12-20; online 2023-12-20]

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Rapid Metabolic Profiling of 1 μL Crude Cerebrospinal Fluid by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Can Differentiate De Novo Parkinson's Disease.

Vallianatou T, Nilsson A, Bjärterot P, ..., Svenningsson P, Andrén PE

Anal. Chem. 95 (50) 18352-18360 [2023-12-19; online 2023-12-07]

Fast volumetric multifocus structured illumination microscopy of subcellular dynamics in living cells

Brismar H, Senftleben M, Bajor A, Hirata E, Abrahamsson S

- - (-) - [2023-12-19; online 2023-12-19]

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Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms.

Pennacchietti F, Alvelid J, Morales RA, ..., Verkhusha VV, Testa I

Nat Commun 14 (1) 8402 [2023-12-19; online 2023-12-19]

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Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.

Hafstað V, Häkkinen J, Larsson M, ..., Vallon-Christersson J, Persson H

BMC Genomics 24 (1) 783 [2023-12-18; online 2023-12-18]

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Giardia intestinalisdeoxyadenosine kinase has a unique tetrameric structure that enables high substrate affinity and makes the parasite sensitive to deoxyadenosine analogues

Ranjbarian F, Rafie K, Shankar K, ..., Carlson LA, Hofer A

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Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans.

Pu L, Wang J, Lu Q, ..., Henriksson J, Chen C

Nat Commun 14 (1) 8410 [2023-12-18; online 2023-12-18]

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Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison.

Kabedev A, Bergström CAS, Larsson P

J Comput Aided Mol Des 38 (1) 5 [2023-12-16; online 2023-12-16]

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Using guaiacol as a capping agent in the hydrothermal depolymerisation of kraft lignin

Ahlbom A, Maschietti M, Nielsen R, Hasani M, Theliander H

- 38 (4) 619-631 [2023-12-15; online 2023-09-26]

Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts.

Akuwudike P, López-Riego M, Marczyk M, ..., Wojcik A, Lundholm L

Front Public Health 11 (-) 1297942 [2023-12-15; online 2023-12-15]

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Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics.

Almazán NM, Rahbar A, Carlsson M, ..., Sörensen B, Söderberg-Nauclér C

iScience 26 (12) 108441 [2023-12-15; online 2023-11-14]

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Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells.

Abadikhah M, Liu M, Persson F, ..., Sun J, Modin O

Biofilm 6 (-) 100161 [2023-12-15; online 2023-10-10]

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Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.

David D, Fino J, Oliveira R, Dória S, Morton CC

Gene 887 (-) 147737 [2023-12-15; online 2023-08-23]

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Csu pili dependent biofilm formation and virulence of Acinetobacter baumannii.

Ahmad I, Nadeem A, Mushtaq F, ..., Wai SN, Uhlin BE

NPJ Biofilms Microbiomes 9 (1) 101 [2023-12-14; online 2023-12-14]

A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.

Arnqvist G, Westerberg I, Galbraith J, ..., Ewels P, Suh A

G3 (Bethesda) - (-) - [2023-12-13; online 2023-12-13]

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Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes.

Saghaï A, Pold G, Jones CM, Hallin S

Nat Commun 14 (1) 8249 [2023-12-12; online 2023-12-12]

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Genes with epigenetic alterations in human pancreatic islets impact mitochondrial function, insulin secretion, and type 2 diabetes

Rönn T, Ofori JK, Perfilyev A, ..., Bacos K, Ling C

Nat Commun 14 (1) 8040 [2023-12-12; online 2023-12-12]

CENP-A and CENP-B collaborate to create an open centromeric chromatin state.

Nagpal H, Ali-Ahmad A, Hirano Y, ..., Sekulić N, Fierz B

Nat Commun 14 (1) 8227 [2023-12-12; online 2023-12-12]

The formation of the Indo-Pacific montane avifauna.

Reeve AH, Kennedy JD, Pujolar JM, ..., Nylander JAA, Jønsson KA

Nat Commun 14 (1) 8215 [2023-12-11; online 2023-12-11]

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Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).

Landi M, Shah T, Falquet L, ..., Bongcam-Rudloff E, Gisel A

Sci Data 10 (1) 887 [2023-12-09; online 2023-12-09]

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The functional and molecular impact of triamcinolone acetonide on primary human bone marrow mesenchymal stem cells.

Kumlin M, Ungerstedt J, Cai H, ..., Felländer-Tsai L, Qian H

Sci Rep 13 (1) 21787 [2023-12-08; online 2023-12-08]

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Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.

Engblom C, Thrane K, Lin Q, ..., Lundeberg J, Frisén J

Science 382 (6675) eadf8486 [2023-12-08; online 2023-12-08]

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Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia.

Krali O, Marincevic-Zuniga Y, Arvidsson G, ..., Syvänen AC, Nordlund J

NPJ Precis Oncol 7 (1) 131 [2023-12-08; online 2023-12-08]

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Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse.

Kurt Z, Cheng J, Barrere-Cain R, ..., Blencowe M, Yang X

Elife 12 (-) - [2023-12-07; online 2023-12-07]

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Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network.

Xu X, Bhalla N, Ståhl P, Jaldén J

BMC Bioinformatics 24 (1) 461 [2023-12-07; online 2023-12-07]

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Gut bacteria at 6 months of age are associated with immune cell status in 1‐year‐old children

Nilsen M, Nygaard UC, Brodin P, ..., Vettukattil R, Rudi K

Scand J Immunol - (-) - [2023-12-07; online 2023-12-07]

Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12

Martinez A, Tai MD, Ochoa L, ..., Valpuesta J, Cuellar J

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Disinfection by-products in drinking water and risk of colorectal cancer: a population-based cohort study.

Helte E, Säve-Söderbergh M, Larsson SC, Martling A, Åkesson A

J. Natl. Cancer Inst. 115 (12) 1597-1604 [2023-12-06; online 2023-08-08]

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Meta-Analyses of Genome-Wide Association Studies for Postpartum Depression.

Guintivano J, Byrne EM, Kiewa J, ..., Meltzer-Brody S, Sullivan P

Am J Psychiatry 180 (12) 884-895 [2023-12-01; online 2023-10-18]

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Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum.

Guo Y, Tian J, Song C, ..., Carlborg Ö, Hu X

Mol. Biol. Evol. 40 (12) - [2023-12-01; online 2023-12-10]

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Genome-Wide Association and Two-Sample Mendelian Randomization Analyses of Plasma Ghrelin and Gastrointestinal Cancer Risk.

Larsson SC, Höijer J, Sun J, ..., Burgess S, Michaëlsson K

Cancer Epidemiol Biomarkers Prev 32 (12) 1771-1776 [2023-12-01; online 2023-10-04]

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Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.

Jensen A, Swift F, de Vries D, ..., Roos C, Guschanski K

Mol. Biol. Evol. 40 (12) - [2023-12-01; online 2023-11-21]

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A beginner's handbook to identify and characterize i-motif DNA.

Sengupta P, Jamroskovic J, Sabouri N

Methods Enzymol 695 (-) 45-70 [2023-12-01; online 2023-12-01]

Three-dimensional reconstruction of interstitial extracellular vesicles in human liver as determined by electron tomography.

Olofsson Bagge R, Berndtsson J, Urzì O, ..., Micaroni M, Crescitelli R

J Extracell Vesicles 12 (12) e12380 [2023-12-00; online 2023-11-27]

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The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15.

Ozden B, Kryshtafovych A, Karaca E

Proteins 91 (12) 1636-1657 [2023-12-00; online 2023-10-20]

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Tertiary structure assessment at CASP15.

Simpkin AJ, Mesdaghi S, Sánchez Rodríguez F, ..., Keegan RM, Rigden DJ

Proteins 91 (12) 1616-1635 [2023-12-00; online 2023-09-25]

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Screening for Circulating Inflammatory Proteins Does Not Reveal Plasma Biomarkers of Constant Tinnitus.

Cederroth CR, Hong MG, Freydin MB, ..., Bulla J, Williams FMK

J Assoc Res Otolaryngol 24 (6) 593-606 [2023-12-00; online 2023-12-11]

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Plasma Protein Profiling of Incident Cardiovascular Diseases: A Multisample Evaluation.

Lind L, Titova O, Zeng R, ..., Assimes T, Michaëlsson K

Circ Genom Precis Med 16 (6) e004233 [2023-12-00; online 2023-11-28]

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Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex.

Johansson US, Irestedt M, Ericson PGP

Mol. Phylogenet. Evol. 189 (-) 107909 [2023-12-00; online 2023-08-22]

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Mitochondrial membrane potential acts as a retrograde signal to regulate cell cycle progression.

Gorospe CM, Carvalho G, Herrera Curbelo A, ..., Niedźwiecka K, Wanrooij PH

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Lipid- and substrate-induced conformational and dynamic changes in a glycosyltransferase involved in E. coli LPS synthesis revealed by 19F and 31P NMR.

Patrick J, Pettersson P, Mäler L

Biochimica et Biophysica Acta (BBA) - Biomembranes 1865 (8) 184209 [2023-12-00; online 2023-08-07]

In-depth immune profiling reveals advanced B- and T-cell differentiation to be associated with Th1-driven immune dysregulation in common variable immunodeficiency.

Hultberg J, Blixt E, Göransson R, ..., Ernerudh J, Nyström S

Clin. Immunol. 257 (-) 109816 [2023-12-00; online 2023-10-31]

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Glycan Complexity and Heterogeneity of Glycoproteins in Somatic Extracts and Secretome of the Infective Stage of the Helminth Fasciola hepatica.

De Marco Verissimo C, Cwiklinski K, Nilsson J, ..., Karlsson NG, Dalton JP

Mol. Cell Proteomics 22 (12) 100684 [2023-12-00; online 2023-11-21]

Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.

Hensen N, Bonometti L, Westerberg I, ..., Hiltunen Thorén M, Johannesson H

Mol. Phylogenet. Evol. 189 (-) 107938 [2023-12-00; online 2023-10-10]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution.

Skalický V, Antoniadi I, Pěnčík A, ..., Ljung K, Novák O

Plant J. 116 (6) 1825-1841 [2023-12-00; online 2023-09-08]

Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development.

Urbancsok J, Donev EN, Sivan P, ..., Street NR, Mellerowicz EJ

New Phytol. 240 (6) 2312-2334 [2023-12-00; online 2023-10-19]

Defective Uterine Spiral Artery Remodeling and Placental Senescence in a Pregnant Rat Model of Polycystic Ovary Syndrome.

Hu M, Zhang Y, Zhang X, ..., Shao LR, Billig H

Am. J. Pathol. 193 (12) 1916-1935 [2023-12-00; online 2023-09-07]

Integrated Microscopy Technologies Gothenburg [Service]

Ataxia Syndrome With Hearing Loss and Nephronophthisis Associated With a Novel Homozygous Variant in XPNPEP3.

Ben-Shabat I, Kvarnung M, Sperker W, ..., Engvall M, Paucar M

Neurol Genet 9 (6) e200100 [2023-12-00; online 2023-11-28]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An epigenome-wide analysis of sex hormone levels and DNA methylation in male blood samples.

Harbs J, Rinaldi S, Keski-Rahkonen P, ..., Van Guelpen B, Harlid S

Epigenetics 18 (1) 2196759 [2023-12-00; online 2023-03-31]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets.

Tatemoto P, Pértille F, Bernardino T, ..., Guerrero-Bosagna C, Zanella AJ

Epigenetics 18 (1) 2196656 [2023-12-00; online 2023-05-16]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Advanced optical imaging reveals preferred spatial orientation of podocyte processes along the axis of glomerular capillaries.

Unnersjö-Jess D, Ramdedovic A, Butt L, ..., Schermer B, Benzing T

Kidney Int. 104 (6) 1164-1169 [2023-12-00; online 2023-09-27]

Integrated Microscopy Technologies Stockholm [Collaborative]

A multi-strategy antimicrobial discovery approach reveals new ways to combatChlamydia

Ölander M, Vázquez DR, Meier K, ..., Schroeder BO, Sixt BS

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Chemical Biology Consortium Sweden (CBCS) [Service]

Using trials of caloric restriction and bariatric surgery to explore the effects of body mass index on the circulating proteome.

Goudswaard LJ, Smith ML, Hughes DA, ..., Timpson NJ, Corbin LJ

Sci Rep 13 (1) 21077 [2023-11-29; online 2023-11-29]

Affinity Proteomics Uppsala [Service] NGI Proteomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Ovarian ERβ cistrome and transcriptome reveal chromatin interaction with LRH-1.

Birgersson M, Indukuri R, Lindquist L, ..., Archer A, Williams C

BMC Biol. 21 (1) 277 [2023-11-29; online 2023-11-29]

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Identification of constrained sequence elements across 239 primate genomes.

Kuderna LFK, Ulirsch JC, Rashid S, ..., Marques Bonet T, Farh KK

Nature - (-) - [2023-11-29; online 2023-11-29]

Bioinformatics Support for Computational Resources [Service]

Pathogenic DDX41 variants, possible response predictors to low-dose melphalan in hypo- and normocellular MDS and AML.

Nyquist OE, Dalgaard J, Spetalen S, ..., Baliakas P, Dybedal I

Br. J. Haematol. - (-) - [2023-11-28; online 2023-11-28]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Calmodulin regulates protease versus co-chaperone activity of a metacaspase.

Eisele-Bürger AM, Eisele F, Malmgren Hill S, ..., Bozhkov PV, Nyström T

Cell Rep 42 (11) 113372 [2023-11-28; online 2023-11-08]

Sociodemographic characteristics and COVID-19 testing rates: spatiotemporal patterns and impact of test accessibility in Sweden

Kennedy B, Varotsis G, Hammar U, ..., Björk J, Fall T

- - (-) - [2023-11-27; online 2023-11-27]

Bioinformatics Support for Computational Resources [Service]

Metabolomic profiles of intact tissues reflect clinically relevant prostate cancer subtypes.

Dudka I, Lundquist K, Wikström P, Bergh A, Gröbner G

J Transl Med 21 (1) 860 [2023-11-27; online 2023-11-27]

Infants' looking preferences for social versus non-social objects reflect genetic variation.

Portugal AM, Viktorsson C, Taylor MJ, ..., Ronald A, Falck-Ytter T

Nat Hum Behav - (-) - [2023-11-27; online 2023-11-27]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DNA elements tether canonical Polycomb Repressive Complex 1 to human genes.

Barrasa JI, Kahn TG, Lundkvist MJ, Schwartz YB

Nucleic Acids Res. 51 (21) 11613-11633 [2023-11-27; online 2023-10-19]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

RecView: an interactive R application for locating recombination positions using pedigree data.

Zhang H, Hansson B

BMC Genomics 24 (1) 712 [2023-11-25; online 2023-11-25]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Selection, characterization and in vivo evaluation of novel CD44v6-targeting antibodies for targeted molecular radiotherapy.

Mortensen ACL, Berglund H, Segerström L, ..., Frejd FY, Nestor M

Sci Rep 13 (1) 20648 [2023-11-24; online 2023-11-24] Open Access

Drug Discovery and Development (DDD) [Collaborative]

Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation.

Mälarstig A, Grassmann F, Dahl L, ..., Czene K, Hedman ÅK

Nat Commun 14 (1) 7680 [2023-11-24; online 2023-11-24]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service]

Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro.

Agback T, Lesovoy D, Han X, ..., Achour A, Agback P

Commun Biol 6 (1) 1193 [2023-11-24; online 2023-11-24]

The heat shock protein LarA activates the Lon protease in response to proteotoxic stress.

Omnus DJ, Fink MJ, Kallazhi A, ..., Landreh M, Jonas K

Nat Commun 14 (1) 7636 [2023-11-22; online 2023-11-22]

Covid-19 vaccine effectiveness against post-covid-19 condition among 589 722 individuals in Sweden: population based cohort study.

Lundberg-Morris L, Leach S, Xu Y, ..., Nyberg F, Bygdell M

BMJ 383 (-) e076990 [2023-11-22; online 2023-11-22]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13.

Jacob P, Lindelöf H, Rustad CF, ..., Girisha KM, Grigelioniene G

npj Genom. Med. 8 (1) 39 [2023-11-22; online 2023-11-22]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth.

Dash L, Swaminathan S, Šimura J, ..., Zabotina OA, Kelley DR

Plant Physiol. 193 (4) 2480-2497 [2023-11-22; online 2023-08-22]

FAIR+E pathogen data for surveillance and research: lessons from COVID-19

Neves A, Cuesta I, Hjerde E, ..., Waheed Z, Blomberg N

Front Public Health 11 (-) - [2023-11-21; online 2023-11-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Elucidation of the Binding Orientation in α2,3- and α2,6-Linked Neu5Ac-Gal Epitopes toward a Hydrophilic Molecularly Imprinted Monolith.

Huynh CM, Mavliutova L, Sparrman T, Sellergren B, Irgum K

ACS Omega 8 (46) 44238-44249 [2023-11-21; online 2023-11-06]

Complex norovirus transmission dynamics at hospital wards revealed by deep sequencing.

Widström J, Andersson ME, Westin J, ..., Lindh M, Rydell GE

J. Clin. Microbiol. 61 (11) e0060823 [2023-11-21; online 2023-10-27]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Structures of theStaphylococcus aureusribosome inhibited by fusidic acid and fusidic acid cyclopentane

González-López A, Larsson DSD, Koripella RK, ..., Sanyal S, Selmer M

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Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.

Karki S, Javanainen M, Rehan S, ..., Happonen L, Paavilainen V

EMBO Rep. - (-) e57910 [2023-11-20; online 2023-11-20]

LC-MS-Based Metabolomics for Dietary Biomarker Discovery in a Cohort of Pregnant and Lactating Women and Their Infants

Stråvik M, Hartvigsson O, Noerman S, ..., Barman M, Sandberg AS

- - (-) - [2023-11-20; online 2023-11-20]

Chalmers Mass Spectrometry Infrastructure [Service]

Dysregulations in hemostasis, metabolism, immune response, and angiogenesis in post-acute COVID-19 syndrome with and without postural orthostatic tachycardia syndrome: a multi-omic profiling study.

Mahdi A, Zhao A, Fredengren E, ..., Pernow J, Ståhlberg M

Sci Rep 13 (1) 20230 [2023-11-19; online 2023-11-19]

Affinity Proteomics Uppsala [Service] NGI Proteomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Shotgun metagenomes from productive lakes in an urban region of Sweden.

Rodríguez-Gijón A, Hampel JJ, Dharamshi J, Bertilsson S, Garcia SL

Sci Data 10 (1) 810 [2023-11-17; online 2023-11-17]

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Serum DHEA and Testosterone Levels Associate Inversely With Coronary Artery Calcification in Elderly Men.

Ohlsson C, Nethander M, Norlén A, ..., Gudnason V, Tivesten Å

J. Clin. Endocrinol. Metab. 108 (12) 3272-3279 [2023-11-17; online 2023-07-01]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Patient-derived xenografts and single-cell sequencing identifies three subtypes of tumor-reactive lymphocytes in uveal melanoma metastases

Karlsson J, Sah VR, Olofsson R, ..., Nilsson LM, Nilsson JA

eLife - (-) - [2023-11-16]

Structure and function of the S. pombe III-IV-cyt c supercomplex.

Moe A, Dimogkioka AR, Rapaport D, Öjemyr LN, Brzezinski P

Proc. Natl. Acad. Sci. U.S.A. 120 (46) e2307697120 [2023-11-14; online 2023-11-08]

Impaired migration and metastatic spread of human melanoma by a novel small molecule targeting the transmembrane domain of death receptor p75NTR

Lopes-Rodrigues V, Nyantakyi SA, Lun X, ..., Senger DL, Ibáñez CF

- - (-) - [2023-11-14; online 2023-11-14]

Chemical Biology Consortium Sweden (CBCS) [Service]

Following the herd: Population genetics of European sheep in time and space

Morell Miranda P

Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology - (-) - [2023-11-14; online 2023-11-14]

Development and validation of a quantitative Proximity Extension Assay instrument with 21 proteins associated with cardiovascular risk (CVD-21).

Siegbahn A, Eriksson N, Assarsson E, ..., Åberg M, Wallentin L

PLoS ONE 18 (11) e0293465 [2023-11-14; online 2023-11-14]

Demonstration of reduced efficacy against cyathostomins without change in species composition after pyrantel embonate treatment in Swedish equine establishments.

Hedberg Alm Y, Halvarsson P, Martin F, ..., Törngren V, Tydén E

International Journal for Parasitology: Drugs and Drug Resistance 23 (-) 78-86 [2023-11-14; online 2023-11-14]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

SNP-based high-resolution typing of Chlamydia psittaci from humans and wild birds in Sweden: circulation of the Mat116 genotype reveals the transmission mode to humans.

Herrmann B, Aaziz R, Kaden R, ..., Sandelin LL, Laroucau K

Microbes Infect 26 (3) 105251 [2023-11-11; online 2023-11-11]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.

Estravis Barcala M, van der Valk T, Chen Z, ..., Nilsson O, Wu HX

Plant J. - (-) - [2023-11-10; online 2023-11-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

A Gradual Transition Toward Anaplasia in Wilms Tumor Through Tolerance to Genetic Damage.

Uno K, Rastegar B, Jansson C, ..., Mengelbier LH, Gisselsson D

Mod. Pathol. 37 (1) 100382 [2023-11-10; online 2023-11-10]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Improving diagnostic precision in primary ovarian insufficiency using comprehensive genetic and autoantibody testing.

Vogt EC, Bratland E, Berland S, ..., Husebye E, Øksnes M

Hum. Reprod. - (-) - [2023-11-09; online 2023-11-09]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia.

Garza R, Sharma Y, Atacho DAM, ..., Jakobsson J, Marklund N

Cell Rep - (-) 113395 [2023-11-08; online 2023-11-08]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Retrieval of long DNA reads from herbarium specimens

Quatela AS, Cangren P, Jafari F, ..., de Boer H, Oxelman B

AoB Plants - (-) - [2023-11-08; online 2023-11-08]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Eurasian back-migration into Northeast Africa was a complex and multifaceted process.

Hammarén R, Goldstein ST, Schlebusch CM

PLoS ONE 18 (11) e0290423 [2023-11-08; online 2023-11-08]

Bioinformatics Support for Computational Resources [Service]

Activity and Stability of Nanoconfined Alpha-Amylase in Mesoporous Silica

Iqbal MN, Jaworski A, Pinon AC, Bengtsson T, Hedin N

ACS Mater. Au 3 (6) 659-668 [2023-11-08; online 2023-08-04]

TGF-β induces matrisome pathological alterations and EMT in patient-derived prostate cancer tumoroids.

Fernandes S, Cruz JO, Morazzo S, ..., Filipensky P, Forte G

Matrix Biol. - (-) - [2023-11-07; online 2023-11-07]

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.

Willink B, Tunström K, Nilén S, ..., Svensson EI, Wheat CW

Nat Ecol Evol - (-) - [2023-11-06; online 2023-11-06]

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Regulation of the general stress response sigma factor σT by Lon-mediated proteolysis.

Akar R, Fink MJ, Omnus DJ, Jonas K

J. Bacteriol. 205 (11) e0022823 [2023-11-06; online 2023-11-06]

On the Conformation of Dimeric Acceptors and Their Polymer Solar Cells with Efficiency over 18 .

Wu J, Ling Z, Franco LR, ..., Anthopoulos TD, Wang E

Angew. Chem. Int. Ed. Engl. 62 (45) e202302888 [2023-11-06; online 2023-07-18]

Candida albicans induces neutrophil extracellular traps and leucotoxic hypercitrullination via candidalysin.

Unger L, Skoluda S, Backman E, ..., Naglik JR, Urban CF

EMBO Rep. 24 (11) e57571 [2023-11-06; online 2023-10-05]

BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.

Höjer P, Frick T, Siga H, ..., Martin M, Ahmadian A

Nucleic Acids Res. - (-) - [2023-11-06; online 2023-11-06]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice.

Aoun M, Coelho A, Krämer A, ..., Burkhardt H, Holmdahl R

J. Exp. Med. 220 (11) - [2023-11-06; online 2023-09-11]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification.

Garza R, Atacho DAM, Adami A, ..., Douse CH, Jakobsson J

Sci Adv 9 (44) eadh9543 [2023-11-03; online 2023-11-01]

Clinical Genomics [Service] Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma tumors.

Chiaro J, Antignani G, Feola S, ..., Lehtiö J, Cerullo V

Nat Commun 14 (1) 7056 [2023-11-03; online 2023-11-03]

Global Proteomics and Proteogenomics [Technology development]

UROSCAN and UROSCANSEQ: a large-scale multicenter effort towards translation of molecular bladder cancer subtypes into clinical practice – from biobank to RNA-sequencing in real time

Liedberg F, Abrahamsson J, Bernardo C, ..., Sjödahl G, Eriksson P

Scandinavian Journal of Urology 57 (1-6) 2-9 [2023-11-02; online 2022-12-20]

Clinical Genomics [Collaborative] Clinical Genomics Lund [Collaborative]

The development of foliar fungal communities of nursery-grown Pinus sylvestris seedlings

Larsson R, Menkis A, Skogström O, ..., Larsson M, Olson Å

Scandinavian Journal of Forest Research - (-) 1-16 [2023-11-02; online 2023-11-02]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel PNKP mutations associated with reduced DNA single-strand break repair and severe microcephaly, seizures, and developmental delay.

Thuresson A, Brazina J, Akram T, ..., Soussi Zander C, Caldecott KW

Mol Genet Genomic Med - (-) e2295 [2023-11-02; online 2023-11-02]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High-resolution comparative atomic structures of two Giardiavirus prototypes infectingG. duodenalisparasite

Wang H, Gianluca M, Munke A, ..., Lalle M, Okamoto K

- - (-) - [2023-11-02; online 2023-11-02]

Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor.

Cowgill J, Fan C, Haloi N, ..., Howard RJ, Lindahl E

Neuron 111 (21) 3450-3464.e5 [2023-11-01; online 2023-09-01]

Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.

Fracasso I, Zaccone C, Oskolkov N, ..., Ventura M, Borruso L

Sci. Total Environ. 908 (-) 168159 [2023-11-01; online 2023-11-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird.

Zhang H, Lundberg M, Tarka M, Hasselquist D, Hansson B

Genome Biol Evol 15 (11) - [2023-11-01; online 2023-10-04]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Demographic reconstruction of the Western sheep expansion from whole-genome sequences.

Morell Miranda P, Soares AER, Günther T

G3 (Bethesda) 13 (11) - [2023-11-01; online 2023-09-07]

Bioinformatics Support for Computational Resources [Service]

The intracellular helical bundle of human glucose transporter GLUT4 is important for complex formation with ASPL.

Huang P, Åbacka H, Varela D, ..., André I, Lindkvist-Petersson K

FEBS Open Bio 13 (11) 2094-2107 [2023-11-00; online 2023-09-28]

Targeting oxidation sites on boreal acid sulfate soil macropore surfaces mitigates acid and metal release to recipient water streams

Högfors-Rönnholm E, Stén P, Christel S, ..., Dopson M, Engblom S

Applied Geochemistry 158 (-) 105779 [2023-11-00; online 2023-11-00]

Bioinformatics Support for Computational Resources [Service]

Structure and electromechanical coupling of a voltage-gated Na+/H+ exchanger.

Yeo H, Mehta V, Gulati A, Drew D

Nature 623 (7985) 193-201 [2023-11-00; online 2023-10-25]

Smoking affects epigenetic ageing of lung bronchoalveolar lavage cells in Multiple Sclerosis.

Klose D, Needhamsen M, Ringh MV, ..., Jagodic M, Kular L

Mult Scler Relat Disord 79 (-) 104991 [2023-11-00; online 2023-09-09]

Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sensitivity of the SARS-CoV-2 BA.2.86 variant to prevailing neutralising antibody responses.

Sheward DJ, Yang Y, Westerberg M, ..., Albert J, Murrell B

Lancet Infect Dis 23 (11) e462-e463 [2023-11-00; online 2023-09-27]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Protein profiling in plasma for biomarkers of seizure.

Akel S, Banote RK, Asztely F, Zelano J

Epilepsy Res 197 (-) 107241 [2023-11-00; online 2023-10-11]

Preanalytic handling of clinical blood samples in assessing immunological proteins - Role of storage duration.

Eren F, Schwieler L, Orhan F, ..., Engberg G, Erhardt S

Brain, Behavior, and Immunity 114 (-) 163-164 [2023-11-00; online 2023-08-16]

Physical activity in childhood and later risk of inflammatory bowel disease: A Scandinavian birth cohort study.

Lerchova T, Östensson M, Sigvardsson I, ..., Mårild K, Ludvigsson J

United European Gastroenterol J 11 (9) 874-883 [2023-11-00; online 2023-10-04]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence.

Lumpi T, Guo X, Lindström ES

Environ. Microbiol. 25 (11) 2289-2302 [2023-11-00; online 2023-06-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.

Broman E, Abdelgadir M, Bonaglia S, ..., Nascimento FJA, Sjöling S

Microb. Ecol. 86 (4) 2357-2372 [2023-11-00; online 2023-05-24]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Intramammary infections and risk factors in freshly calved heifers in Swedish dairy herds.

Persson Waller K, Lundberg Å, Börjesson S, Nyman AK

J Dairy Sci 106 (11) 7893-7907 [2023-11-00; online 2023-05-18]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Inclusion body myositis with early onset: a population-based study.

Lindgren U, Hedberg-Oldfors C, Pullerits R, Lindberg C, Oldfors A

J. Neurol. 270 (11) 5483-5492 [2023-11-00; online 2023-07-27]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.

An Y, Braga MP, Garcia SL, Grudzinska-Sterno M, Hambäck PA

Microb. Ecol. 86 (4) 2477-2487 [2023-11-00; online 2023-06-14]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Graphene Oxide Attenuates Toxicity of Amyloid‐β Aggregates in Yeast by Promoting Disassembly and Boosting Cellular Stress Response

Chen X, Pandit S, Shi L, ..., Petranovic D, Mijakovic I

Adv Funct Materials 33 (45) - [2023-11-00; online 2023-07-07]

Integrated Microscopy Technologies Gothenburg [Service]

Global blood miRNA profiling unravels early signatures of immunogenicity of Ebola vaccine rVSVΔG-ZEBOV-GP

Vianello E, Persson J, Andersson B, ..., Ottenhoff THM, Harandi AM

iScience - (-) 108574 [2023-11-00; online 2023-11-00]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Genotypic characterization of Staphylococcus chromogenes and Staphylococcus simulans from Swedish cases of bovine subclinical mastitis.

Persson Waller K, Myrenås M, Börjesson S, ..., Östlund E, Cha W

J Dairy Sci 106 (11) 7991-8004 [2023-11-00; online 2023-08-23]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Comprehensive analyses of circulating cardiometabolic proteins and objective measures of fat mass.

Titova OE, Brunius C, Warensjö Lemming E, ..., Michaëlsson K, Larsson SC

Int J Obes (Lond) 47 (11) 1043-1049 [2023-11-00; online 2023-08-07]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service]

CGG toolkit: Software components for computational genomics.

Vasileiou D, Karapiperis C, Baltsavia I, ..., Enright AJ, Ouzounis CA

PLoS Comput. Biol. 19 (11) e1011498 [2023-11-00; online 2023-11-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Body Mass Index and the Risk of Rheumatic Disease: Linear and Nonlinear Mendelian Randomization Analyses.

Karlsson T, Hadizadeh F, Rask-Andersen M, Johansson Å, Ek WE

Arthritis & rheumatology (Hoboken, N.J.) 75 (11) 2027-2035 [2023-11-00; online 2023-09-28]

Bioinformatics Support for Computational Resources [Service]

Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency.

Le Voyer T, Parent AV, Liu X, ..., Casanova JL, Puel A

Nature 623 (7988) 803-813 [2023-11-00; online 2023-11-08]

Autoimmunity and Serology Profiling [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An atlas of genetic determinants of forearm fracture.

Nethander M, Movérare-Skrtic S, Kämpe A, ..., Richards JB, Ohlsson C

Nat. Genet. 55 (11) 1820-1830 [2023-11-00; online 2023-11-02]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Synthesis of Metal–Organic Frameworks through Enzymatically Recycled Polyethylene Terephthalate

Cao Z, Fu X, Li H, ..., Zelezniak A, Mijakovic I

ACS Sustainable Chem. Eng. 11 (43) 15506-15512 [2023-10-30; online 2023-09-21]

Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter

Currie MJ, Davies JS, Scalise M, ..., Dobson RCJ, North RA

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Proteomics reveal biomarkers for diagnosis, disease activity and long-term disability outcomes in multiple sclerosis.

Åkesson J, Hojjati S, Hellberg S, ..., Ernerudh J, Gustafsson M

Nat Commun 14 (1) 6903 [2023-10-30; online 2023-10-30]

Affinity Proteomics Uppsala [Service] NGI Proteomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Reduction of body weight by increased loading is associated with activation of norepinephrine neurones in the medial nucleus of the solitary tract.

Zlatkovic J, Dalmau Gasull A, Hägg D, ..., Anesten F, Jansson JO

J Neuroendocrinol - (-) e13352 [2023-10-26; online 2023-10-26]

Integrated Microscopy Technologies Gothenburg [Service]

Mucosal and Serum Antibodies 3 Weeks after Symptomatic BA.2.86 Infection.

Bladh O, Greilert-Norin N, Havervall S, ..., Klingström J, Thålin C

N. Engl. J. Med. 389 (17) 1626-1628 [2023-10-26; online 2023-10-27]

Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations.

Aksoylu IS, Martin P, Robert F, ..., Larsson O, Ramesh V

Mol Autism 14 (1) 39 [2023-10-25; online 2023-10-25]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Release and Spread of Basidiospores of Red-Listed Wood-Decay Fungus Fistulina hepatica in Oak Stands

Marčiulynas A, Menkis A

Diversity 15 (11) 1110 [2023-10-25; online 2023-10-25]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Quantifying fluorescence lifetime responsiveness of environment sensitive probes for membrane fluidity measurements

Ragaller F, Sjule E, Urem YB, ..., Blom H, Sezgin E

- - (-) - [2023-10-25; online 2023-10-25]

Integrated Microscopy Technologies Stockholm [Collaborative]

Complete Mitochondrial DNA Genome Variation in the Swedish Population.

Sturk-Andreaggi K, Bodner M, Ring JD, ..., Marshall C, Allen M

Genes 14 (11) - [2023-10-25; online 2023-10-25]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.

Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N

Genome Biol. 24 (1) 242 [2023-10-23; online 2023-10-23]

Ancient DNA [Technology development] Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Polymorphic parasitic larvae cooperate to build swimming colonies luring hosts.

Krupenko D, Miroliubov A, Kryukov E, ..., Kastriti ME, Adameyko I

Curr. Biol. 33 (20) 4524-4531.e4 [2023-10-23; online 2023-09-22]

Ancient DNA [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

LPMO-supported saccharification of biomass: effects of continuous aeration of reaction mixtures with variable fractions of water-insoluble solids and cellulolytic enzymes.

Tang C, Gandla ML, Jönsson LJ

Biotechnol Biofuels Bioprod 16 (1) 156 [2023-10-21; online 2023-10-21]

Integrated Microscopy Technologies Umeå [Service] Swedish NMR Centre (SNC) [Service]

Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation, and virulence.

Sun WS, Lassinantti L, Järvå M, ..., Ter Beek J, Berntsson RP

Elife 12 (-) - [2023-10-20; online 2023-10-20]

Screening for atypical porcine pestivirus in Swedish boar semen used for artificial insemination and a characterisation of the seminal RNA microbiome including the virome.

Stenberg H, Malmberg M, Hayer J

BMC Vet Res 19 (1) 219 [2023-10-20; online 2023-10-20]

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Synergistic metabolism of salivary MUC5B in oral commensal bacteria during early biofilm formation.

Robertsson C, Svensäter G, Davies JR, ..., Malmodin D, Wickström C

Microbiol Spectr - (-) e0270423 [2023-10-19; online 2023-10-19]

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.

Sendell-Price AT, Tulenko FJ, Pettersson M, ..., Andersson L, Schartl M

Nat Commun 14 (1) 6628 [2023-10-19; online 2023-10-19]

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FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress.

Brunner A, Li Q, Fisicaro S, ..., Orre LM, Sangfelt O

Mol. Cell 83 (20) 3720-3739.e8 [2023-10-19; online 2023-08-16]

Global Proteomics and Proteogenomics [Collaborative]

Autoantibody Profiling and Anti-Kinesin Reactivity in ANCA-Associated Vasculitis.

Mescia F, Bayati S, Brouwer E, ..., Nilsson P, Pin E

Int J Mol Sci 24 (20) - [2023-10-19; online 2023-10-19]

Autoimmunity and Serology Profiling [Collaborative]

Low Circulating Valine Associate With High Risk of Hip Fractures.

Grahnemo L, Eriksson AL, Nethander M, ..., Pettersson-Kymmer U, Ohlsson C

J. Clin. Endocrinol. Metab. 108 (11) e1384-e1393 [2023-10-18; online 2023-05-14]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Untargeted plasma metabolomics and risk of colorectal cancer-an analysis nested within a large-scale prospective cohort.

Vidman L, Zheng R, Bodén S, ..., Brunius C, Van Guelpen B

Cancer Metab 11 (1) 17 [2023-10-17; online 2023-10-17]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose.

Dussex N, Kurland S, Olsen RA, ..., Dalén L, Laikre L

Commun Biol 6 (1) 1035 [2023-10-17; online 2023-10-17]

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Label-Free Quantitative Thermal Proteome Profiling Reveals Target Transcription Factors with Activities Modulated by MC3R Signaling.

Sandbaumhüter FA, Nezhyva M, Andrén PE, Jansson ET

Anal. Chem. 95 (41) 15400-15408 [2023-10-17; online 2023-10-07]

Fungi Inhabiting Stem Wounds of Quercus robur following Bark Stripping by Deer Animals

Marčiulynas A, Sirgedaitė-Šėžienė V, Menkis A

Forests 14 (10) 2077 [2023-10-17; online 2023-10-17]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Modified N-acyl-L-homoserine lactone compounds abrogate Las-dependent quorum-sensing response in human pathogen Pseudomonas aeruginosa.

Ballante F, Turkina MV, Ntzouni M, Magnusson KE, Vikström E

Front Mol Biosci 10 (-) 1264773 [2023-10-16; online 2023-10-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Endothelial VEGFR2-PLCγ signaling regulates vascular permeability and antitumor immunity through eNOS/Src.

Sjöberg E, Melssen M, Richards M, ..., Dimberg A, Claesson-Welsh L

J. Clin. Invest. 133 (20) - [2023-10-16; online 2023-10-16]

Design, structure and plasma binding of ancestral β-CoV scaffold antigens.

Hueting D, Schriever K, Sun R, ..., Andréll J, Syrén PO

Nat Commun 14 (1) 6527 [2023-10-16; online 2023-10-16]

Cryo-EM [Service] Drug Discovery and Development (DDD) [Service]

Associations between the Bacterial Composition of Farm Bulk Milk and the Microbiota in the Resulting Swedish Long-Ripened Cheese.

Sun L, Höjer A, Johansson M, ..., Dicksved J, Lundh Å

Foods 12 (20) - [2023-10-16; online 2023-10-16]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Quantification of membrane fluidity in bacteria using TIR-FCS

Barbotin A, Billaudeau C, Sezgin E, Carballido-López R

- - (-) - [2023-10-15; online 2023-10-15]

Integrated Microscopy Technologies Stockholm [Service]

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.

Mastropasqua F, Oksanen M, Soldini C, ..., Bölte S, Tammimies K

Biol Open 12 (10) - [2023-10-15; online 2023-10-10]

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Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale.

Sounart H, Voronin D, Masarapu Y, ..., Ghedin E, Giacomello S

Nat Commun 14 (1) 6500 [2023-10-14; online 2023-10-14]

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Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.

Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M

Clin. Cancer Res. 29 (20) 4139-4152 [2023-10-13; online 2023-08-04]

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Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication.

Chakraborty C, Nissen I, Vincent CA, ..., Hörnblad A, Remeseiro S

Nat Commun 14 (1) 6446 [2023-10-13; online 2023-10-13]

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Integrated Genomic and Transcriptomic Analysis Improves Disease Classification and Risk Stratification of MDS with Ring Sideroblasts.

Todisco G, Creignou M, Bernard E, ..., Papaemmanuil E, Hellström-Lindberg E

Clin. Cancer Res. 29 (20) 4256-4267 [2023-10-13; online 2023-07-27]

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Genome-wide DNA methylation profiling in Lyme neuroborreliosis reveals altered methylation patterns of HLA genes.

Henningsson AJ, Hellberg S, Lerm M, Sayyab S

J. Infect. Dis. - (-) - [2023-10-12; online 2023-10-12]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists

Lee H, Langseth CM, Salas SM, ..., Grillo M, Nilsson M

- - (-) - [2023-10-11; online 2023-10-11]

Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses.

Ols S, Lenart K, Arcoverde Cerveira R, ..., King NP, Loré K

Immunity 56 (10) 2425-2441.e14 [2023-10-10; online 2023-09-08]

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Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.

Lysenkova Wiklander M, Övernäs E, Lagensjö J, ..., Liljedahl U, Nordlund J

BMC Res Notes 16 (1) 265 [2023-10-10; online 2023-10-10]

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BirthSeq, a new method to isolate and analyze dated cells from any tissue in vertebrates

Rueda-Alaña E, Grillo M, Vazquez E, ..., Nilsson M, García-Moreno F

- - (-) - [2023-10-10; online 2023-10-10]

An end-to-end workflow for multiplexed image processing and analysis.

Windhager J, Zanotelli VRT, Schulz D, ..., Bodenmiller B, Eling N

Nat Protoc - (-) - [2023-10-10; online 2023-10-10]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Transfer of cetirizine/levocetirizine into human breast milk and estimation of drug exposure to infants through breastfeeding - a human lactation study from the ConcePTION project.

Nordeng H, Wegler C, Lindqvist A, ..., Baranczewski P, Spigset O

Basic Clin Pharmacol Toxicol - (-) - [2023-10-09; online 2023-10-09]

Drug Discovery and Development (DDD) [Collaborative]

Exploring the differences in serum metabolite profiles after intake of red meat in women with rheumatoid arthritis and a matched control group.

Lindqvist HM, Gjertsson I, Hulander E, Bärebring L, Winkvist A

Eur J Nutr - (-) - [2023-10-09; online 2023-10-09]

Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).

Hill J, Enbody ED, Bi H, ..., Widemo F, Andersson L

Mol. Biol. Evol. 40 (12) msad224 [2023-10-06; online 2023-10-06]

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Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.

Rancilhac L, Enbody ED, Harris R, ..., Andersson L, Alström P

Syst. Biol. - (-) - [2023-10-06; online 2023-10-06]

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Mitochondrial heteroplasmic shifts reveal a positive selection of breast cancer.

Li Y, Sundquist K, Vats S, ..., Sundquist J, Memon AA

J Transl Med 21 (1) 696 [2023-10-05; online 2023-10-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Proteomic profiling identifies novel inflammation-related plasma proteins associated with ischemic stroke outcome.

Angerfors A, Brännmark C, Lagging C, ..., Jern C, Stanne TM

J Neuroinflammation 20 (1) 224 [2023-10-04; online 2023-10-04]

Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.

Merino I, Guasca AO, Krmela A, ..., Schulzova V, Sitbon F

Front Plant Sci 14 (-) 1210850 [2023-10-04; online 2023-10-04]

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Copy number variations and their effect on the plasma proteome.

Schmitz D, Li Z, Lo Faro V, ..., Rafati N, Johansson Å

Genetics - (-) - [2023-10-04; online 2023-10-04]

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Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures.

Figiel S, Yin W, Doultsinos D, ..., Cussenot O, Lamb AD

Mol. Cancer 22 (1) 162 [2023-10-03; online 2023-10-03]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Photo-physical characterization of high triplet yield brominated fluoresceins by transient state (TRAST) spectroscopy.

Demirbay B, Baryshnikov G, Haraldsson M, ..., Ågren H, Widengren J

Methods Appl. Fluoresc. 11 (4) - [2023-10-03; online 2023-10-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Clinical and genetic analyses of a Swedish patient series diagnosed with ataxia.

Gorcenco S, Kafantari E, Wallenius J, ..., Karrman K, Puschmann A

J. Neurol. - (-) - [2023-10-03; online 2023-10-03]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

The long non-coding RNA LINC00707 interacts with Smad proteins to regulate TGFβ signaling and cancer cell invasion.

Gélabert C, Papoutsoglou P, Golán I, ..., Caja L, Moustakas A

Cell Commun Signal 21 (1) 271 [2023-10-02; online 2023-10-02]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo.

Giannakopoulou E, Lehander M, Virding Culleton S, ..., Woll PS, Olweus J

Nat Cancer - (-) - [2023-10-02; online 2023-10-02]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Elevated Adipocyte Membrane Phospholipid Saturation Does Not Compromise Insulin Signaling.

Palmgren H, Petkevicius K, Bartesaghi S, ..., Peng XR, Pilon M

Diabetes 72 (10) 1350-1363 [2023-10-01; online 2022-12-30]

Integrated Microscopy Technologies Gothenburg [Service]

The dynamics of touch-responsive gene expression in cereals.

Darwish E, Ghosh R, Bentzer J, ..., Sirijovski N, Van Aken O

Plant J. 116 (1) 282-302 [2023-10-00; online 2023-06-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The disease-causing mutation p.F907I reveals a novel pathogenic mechanism for POLγ-related diseases.

Erdinc D, Macao B, Valenzuela S, ..., Wredenberg A, Falkenberg M

Biochim Biophys Acta Mol Basis Dis 1869 (7) 166786 [2023-10-00; online 2023-06-10]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Dahlberg J, Pelve E, Dicksved J

Microbiologyopen 12 (5) e1383 [2023-10-00; online 2023-10-25]

Blom K, Fjällström P, Molnár C, ..., Forsell MNE, Johansson AF

Lancet Infect Dis 23 (10) e393-e394 [2023-10-00; online 2023-09-13]

Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation.

Mengal K, Kor G, Siino V, ..., Levander F, Niksirat H

Dev. Comp. Immunol. 147 (-) 104760 [2023-10-00; online 2023-06-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Precision medicine in rare diseases: What is next?

Tesi B, Boileau C, Boycott KM, ..., Nordgren A, Lindstrand A

J. Intern. Med. 294 (4) 397-412 [2023-10-00; online 2023-06-01]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Precision cancer medicine: Concepts, current practice, and future developments.

Edsjö A, Holmquist L, Geoerger B, ..., Siu LL, Stenzinger A

J. Intern. Med. 294 (4) 455-481 [2023-10-00; online 2023-08-28]

Global Proteomics and Proteogenomics [Technology development]

Origin matters: Using a local reference genome improves measures in population genomics.

Thorburn DJ, Sagonas K, Binzer-Panchal M, ..., Lenz TL, Eizaguirre C

Mol Ecol Resour 23 (7) 1706-1723 [2023-10-00; online 2023-07-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Lowering of Circulating Sclerostin May Increase Risk of Atherosclerosis and Its Risk Factors: Evidence From a Genome-Wide Association Meta-Analysis Followed by Mendelian Randomization.

Zheng J, Wheeler E, Pietzner M, ..., Davey Smith G, Tobias JH

Arthritis & rheumatology (Hoboken, N.J.) 75 (10) 1781-1792 [2023-10-00; online 2023-08-03]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia.

Fehr A, Arvidsson G, Nordlund J, ..., Stenman G, Andersson MK

Genes Chromosomes Cancer 62 (10) 597-606 [2023-10-00; online 2023-05-23]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Durability of antireflective SiO2 coatings with closed pore structure

Zäll E, Karlsson S, Järn M, ..., Lundberg P, Wågberg T

Solar Energy Materials and Solar Cells 261 (-) 112521 [2023-10-00; online 2023-10-00]

Decontamination of biofilm-contaminated implant surfaces: An in vitro evaluation.

Ichioka Y, Virto L, Nuevo P, ..., Sanz M, Berglundh T

Clin Oral Implants Res 34 (10) 1058-1072 [2023-10-00; online 2023-07-20]

Integrated Microscopy Technologies Gothenburg [Service]

Circulating soluble IL-6 receptor associates with plaque inflammation but not with atherosclerosis severity and cardiovascular risk.

Edsfeldt A, Gonçalves I, Vigren I, ..., Khan F, Nilsson J

Vascul Pharmacol 152 (-) 107214 [2023-10-00; online 2023-08-25]

B cell polygenic risk scores associate with anti-dsDNA antibodies and nephritis in systemic lupus erythematosus.

Hedenstedt A, Reid S, Sayadi A, ..., Sandling JK, Leonard D

Lupus Sci Med 10 (2) - [2023-10-00; online 2023-10-17]

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Alterations in the Serum Proteome Following Electroconvulsive Therapy for a Major Depressive Episode: A Longitudinal Multicenter Study.

Göteson A, Clements CC, Juréus A, ..., Pålsson E, Landén M

Biol Psychiatry Glob Open Sci 3 (4) 884-892 [2023-10-00; online 2022-12-12]

APP-BACE1 Interaction and Intracellular Localization Regulate Aβ Production in iPSC-Derived Cortical Neurons.

Roselli S, Satir TM, Camacho R, ..., Zetterberg H, Agholme L

Cell Mol Neurobiol 43 (7) 3653-3668 [2023-10-00; online 2023-06-24]

Integrated Microscopy Technologies Gothenburg [Service]

A glycomic workflow for LC-MS/MS analysis of urine glycosaminoglycan biomarkers in mucopolysaccharidoses.

Nilsson J, Persson A, Vorontsov E, ..., Larson G, Blomqvist M

Glycoconj J 40 (5) 523-540 [2023-10-00; online 2023-07-18]

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).

Steffen K, Proux-Wéra E, Soler L, ..., Sundh J, Cárdenas P

G3 (Bethesda) 13 (10) - [2023-09-30; online 2023-08-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Inflammatory Gene Profile and Particle Presence in Peri-Implant Mucosa: a Pilot Study on 9 Patients.

Olander J, Barkarmo S, Hammarström Johansson P, Wennerberg A, Stenport VF

J Oral Maxillofac Res 14 (3) e2 [2023-09-30; online 2023-09-30]

Integrated Microscopy Technologies Gothenburg [Service]

Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs.

Petruk G, Puthia M, Samsudin F, ..., Lindstedt S, Schmidtchen A

Nat Commun 14 (1) 6097 [2023-09-29; online 2023-09-29]

Clinical Genomics [Service] Clinical Genomics Lund [Service] Structural Proteomics [Collaborative]

Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.

Enbody ED, Sendell-Price AT, Sprehn CG, ..., Grant PR, Andersson L

Science 381 (6665) eadf6218 [2023-09-29; online 2023-09-29]

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Oral fungal profiling and risk of nasopharyngeal carcinoma: a population-based case-control study.

Chen Y, Li W, Chang ET, ..., Zhang Z, Ye W

EBioMedicine 96 (-) 104813 [2023-09-28; online 2023-09-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype.

Earley TS, Feiner N, Alvarez MF, Coolon JD, Sultan SE

Proc. Biol. Sci. 290 (2007) 20230824 [2023-09-27; online 2023-09-27]

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Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.

Riihimäki M, Fegraeus K, Nordlund J, ..., Hellman L, Raine A

Sci Rep 13 (1) 16261 [2023-09-27; online 2023-09-27]

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Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022-2023.

Haars J, Palanisamy N, Wallin F, ..., Kaden R, Lennerstrand J

Microorganisms 11 (10) - [2023-09-27; online 2023-09-27]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Exploiting solid-state dynamic nuclear polarization NMR spectroscopy to establish the spatial distribution of polymorphic phases in a solid material.

Cousin SF, Hughes CE, Ziarelli F, ..., Pinon AC, Thureau P

Chem. Sci. 14 (37) 10121-10128 [2023-09-27; online 2023-06-23]

CO2 Mineralization by MgO Nanocubes in Nanometric Water Films.

Luong NT, Veyret N, Boily JF

ACS Appl Mater Interfaces 15 (38) 45055-45063 [2023-09-27; online 2023-09-14]

Unraveling mucolipidosis type III gamma through whole genome sequencing in late-onset retinitis pigmentosa: a case report.

De Geer K, Mascianica K, Naess K, ..., Lindstrand A, Björck E

BMC Ophthalmol 23 (1) 394 [2023-09-26; online 2023-09-26]

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The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes.

Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U

Front Genet 14 (-) 1244493 [2023-09-26; online 2023-09-26]

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Single-cell multiomics of human fetal hematopoiesis define a developmental-specific population and a fetal signature.

Sommarin MNE, Olofzon R, Palo S, ..., Karlsson G, Böiers C

Blood Adv 7 (18) 5325-5340 [2023-09-26; online 2023-06-28]

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Combined GLUT1 and OXPHOS inhibition eliminates acute myeloid leukemia cells by restraining their metabolic plasticity.

Rodriguez-Zabala M, Ramakrishnan R, Reinbach K, ..., Woods NB, Järås M

Blood Adv 7 (18) 5382-5395 [2023-09-26; online 2023-07-28]

Clinical Genomics [Service] Clinical Genomics Lund [Service] Swedish Metabolomics Centre (SMC) [Service]

Molecular anatomy of adult mouse leptomeninges.

Pietilä R, Del Gaudio F, He L, ..., Andrae J, Betsholtz C

Neuron - (-) - [2023-09-25; online 2023-09-25]

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Fast and sensitive validation of fusion transcripts in whole-genome sequencing data.

Hafstað V, Häkkinen J, Persson H

BMC Bioinformatics 24 (1) 359 [2023-09-23; online 2023-09-23]

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A subset of type-II collagen-binding antibodies prevents experimental arthritis by inhibiting FCGR3 signaling in neutrophils.

Xu Z, Xu B, Lundström SL, ..., Zubarev RA, Holmdahl R

Nat Commun 14 (1) 5949 [2023-09-23; online 2023-09-23]

Drug Discovery and Development (DDD) [Collaborative]

The microbial biodiversity at the archeological site of Tel Megiddo (Israel).

Zhang Y, Ruff SE, Oskolkov N, ..., Mason CE, Elhaik E

Front Microbiol 14 (-) 1253371 [2023-09-22; online 2023-09-22]

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Multivalent design of the monoclonal SynO2 antibody improves binding strength to soluble α-Synuclein aggregates.

Petersen I, Ali MI, Petrovic A, ..., Bondza S, Hultqvist G

MAbs 15 (1) 2256668 [2023-09-22; online 2023-09-22]

Drug Discovery and Development (DDD) [Collaborative]

Comprehensive proteomics and meta-analysis of COVID-19 host response.

Babačić H, Christ W, Araújo JE, ..., Klingström J, Pernemalm M

Nat Commun 14 (1) 5921 [2023-09-22; online 2023-09-22]

Global Proteomics and Proteogenomics [Collaborative]

Selected β-glucans act as immune-training agents by improving anti-mycobacterial activity in human macrophages - a pilot study.

Braian C, Karlsson L, Das J, Lerm M

J Innate Immun 15 (1) 751-764 [2023-09-21; online 2023-09-21]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]

Non-classical HLA-E restricted CMV 15-mer peptides are recognized by adaptive NK cells and induce memory responses.

Martín Almazán N, Sala BM, Sandalova T, ..., Achour A, Sarhan D

Front Immunol 14 (-) 1230718 [2023-09-21; online 2023-09-21]

Imaging of fibrogenesis in the liver by [18F]TZ-Z09591, an Affibody molecule targeting platelet derived growth factor receptor β.

Wegrzyniak O, Zhang B, Rokka J, ..., Eriksson J, Eriksson O

EJNMMI Radiopharm Chem 8 (1) 23 [2023-09-21; online 2023-09-21]

Drug Discovery and Development (DDD) [Collaborative]

Strict self-isolation did not protect Swedish cancer patients on active treatment from the risk of becoming seropositive for SARS-CoV-2.

Ginman B, Pahnke S, Freyhult E, ..., Enblad G, Glimelius I

Acta Oncol - (-) 1-9 [2023-09-20; online 2023-09-20]

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Identification of Novel Glycans in the Mucus Layer of Shark and Skate Skin.

Bachar-Wikstrom E, Thomsson KA, Sihlbom C, ..., Lindén SK, Wikstrom JD

Int J Mol Sci 24 (18) - [2023-09-20; online 2023-09-20]

Single-cell sequencing of tumor-associated macrophages in a Drosophila model.

Khalili D, Mohammed M, Kunc M, ..., Ankarklev J, Theopold U

Front Immunol 14 (-) 1243797 [2023-09-19; online 2023-09-19]

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Prosaposin maintains lipid homeostasis in dopamine neurons and counteracts experimental parkinsonism in rodents.

He Y, Kaya I, Shariatgorji R, ..., Andren PE, Svenningsson P

Nat Commun 14 (1) 5804 [2023-09-19; online 2023-09-19]

Self-Assembly of RGD-Functionalized Recombinant Spider Silk Protein into Microspheres in Physiological Buffer and in the Presence of Hyaluronic Acid.

Ornithopoulou E, Åstrand C, Gustafsson L, Crouzier T, Hedhammar M

ACS Appl Bio Mater 6 (9) 3696-3705 [2023-09-18; online 2023-08-14]

Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick.

Rahlff J, Wietz M, Giebel HA, ..., Antson A, Holmfeldt K

ISME COMMUN. 3 (1) 97 [2023-09-18; online 2023-09-18]

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Novel pathological variants of NHP2 affect N-terminal domain flexibility, protein stability, H/ACA Ribonucleoprotein (RNP) complex formation and telomerase activity.

Maliński B, Vertemara J, Faustini E, ..., Cammenga J, Lottersberger F

Hum. Mol. Genet. 32 (19) 2901-2912 [2023-09-16; online 2023-07-13]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Plasma type I collagen α1 chain in relation to coronary artery disease: findings from a prospective population-based cohort and an acute myocardial infarction prospective cohort in Sweden.

Hammaréus F, Nilsson L, Ong KL, ..., Holm Nielsen S, Jonasson L

BMJ Open 13 (9) e073561 [2023-09-15; online 2023-09-15]

Ki67 and prostate specific antigen are prognostic in metastatic hormone naïve prostate cancer.

Spyratou V, Freyhult E, Bergh A, ..., Welén K, Josefsson A

Acta Oncol - (-) 1-9 [2023-09-15; online 2023-09-15]

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In vivo gene expression profile of Haemophilus influenzae during human pneumonia.

Polland L, Rydén H, Su Y, Paulsson M

Microbiol Spectr 11 (5) e0163923 [2023-09-14; online 2023-09-14]

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Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster.

Corthals K, Andersson V, Churcher A, Reimegård J, Enjin A

Sci Rep 13 (1) 15202 [2023-09-14; online 2023-09-14]

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Dissecting the genetic basis of drought responses in common bean using natural variation.

Labastida D, Ingvarsson PK, Rendón-Anaya M

Front Plant Sci 14 (-) 1143873 [2023-09-14; online 2023-09-14]

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Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.

Mihalič F, Benz C, Kassa E, ..., Jemth P, Ivarsson Y

Nat Commun 14 (1) 5636 [2023-09-13; online 2023-09-13]

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Cerebrospinal Fluid Metabolomics Identified Ongoing Analgesic Medication in Neuropathic Pain Patients.

Bäckryd E, Thordeman K, Gerdle B, Ghafouri B

Biomedicines 11 (9) - [2023-09-13; online 2023-09-13]

Sustained and intermittent hypoxia differentially modulate primary monocyte immunothrombotic responses to IL-1β stimulation.

Wahlund CJE, Çaglayan S, Czarnewski P, Hansen JB, Snir O

Front Immunol 14 (-) 1240597 [2023-09-11; online 2023-09-11]

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Impact of estrogen on IgG glycosylation and serum protein glycosylation in a murine model of healthy postmenopause.

Gupta P, Sághy T, Nordqvist J, ..., Henning P, Engdahl C

Front Endocrinol (Lausanne) 14 (-) 1243942 [2023-09-11; online 2023-09-11]

Ectomycorrhizal fungi integrate nitrogen mobilisation and mineral weathering in boreal forest soil.

Mahmood S, Fahad Z, Bolou-Bi EB, ..., Ekblad A, Finlay RD

New Phytol. - (-) - [2023-09-11; online 2023-09-11]

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A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration.

Sørensen MES, Zlatogursky VV, Onuţ-Brännström I, ..., Foster RA, Burki F

Curr. Biol. 33 (17) 3571-3584.e6 [2023-09-11; online 2023-08-02]

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Pyrroloquinoline quinone drives ATP synthesis in vitro and in vivo and provides retinal ganglion cell neuroprotection.

Canovai A, Tribble JR, Jöe M, ..., Dal Monte M, Williams PA

Acta Neuropathol Commun 11 (1) 146 [2023-09-08; online 2023-09-08]

Estrogen receptor activation remodelsTEAD1gene expression to alleviate nonalcoholic fatty liver disease

Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C

- - (-) - [2023-09-08; online 2023-09-08]

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PLK1 as a cooperating partner for BCL2-mediated antiapoptotic program in leukemia.

Shah K, Nasimian A, Ahmed M, ..., Lock RB, Kazi JU

Blood Cancer J 13 (1) 139 [2023-09-07; online 2023-09-07]

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Epigenetic modifications appear in the human placenta following anxiety and depression during pregnancy.

Martinez CA, Marteinsdottir I, Josefsson A, ..., Theodorsson E, Rodriguez-Martinez H

Placenta 140 (-) 72-79 [2023-09-07; online 2023-08-01]

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Transforming growth factor-β2 is associated with atherosclerotic plaque stability and lower risk for cardiovascular events.

Edsfeldt A, Singh P, Matthes F, ..., Sun J, Gonçalves I

Cardiovasc. Res. 119 (11) 2061-2073 [2023-09-05; online 2023-05-18]

Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development.

Witman N, Zhou C, Häneke T, ..., Chien KR, Sahara M

Nat Commun 14 (1) 5435 [2023-09-05; online 2023-09-05]

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Spatial multimodal analysis of transcriptomes and metabolomes in tissues.

Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J

Nat. Biotechnol. - (-) - [2023-09-04; online 2023-09-04]

In Situ Sequencing (ISS) [Collaborative] Spatial Mass Spectrometry [Collaborative]

Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus).

Kurta K, Jeuthe H, Naboulsi R, de Koning DJ, Palaiokostas C

BMC Genomics 24 (1) 519 [2023-09-04; online 2023-09-04]

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Large-scale proximity extension assay reveals CSF midkine and DOPA decarboxylase as supportive diagnostic biomarkers for Parkinson's disease.

Paslawski W, Khosousi S, Hertz E, ..., Boxer A, Svenningsson P

Transl Neurodegener 12 (1) 42 [2023-09-04; online 2023-09-04]

The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis.

Schoeler M, Ellero-Simatos S, Birkner T, ..., Burcelin R, Caesar R

Nat Commun 14 (1) 5329 [2023-09-01; online 2023-09-01]

Chalmers Mass Spectrometry Infrastructure [Service]

The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees.

Everitt T, Wallberg A, Christmas MJ, ..., Neumann P, Webster MT

Genome Biol Evol 15 (9) - [2023-09-01; online 2023-08-26]

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Stratified genetic analysis reveals sex differences in MPO-ANCA-associated vasculitis.

Ekman D, Sennblad B, Knight A, ..., Lindblad-Toh K, Dahlqvist J

Rheumatology (Oxford) 62 (9) 3213-3218 [2023-09-01; online 2023-04-03]

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Pseudomonas ability to utilize different carbon substrates and adaptation influenced by protozoan grazing.

Ramasamy KP, Brugel S, Eriksson KIA, Andersson A

Environ. Res. 232 (-) 116419 [2023-09-01; online 2023-06-14]

Inhibiting metabotropic glutamate receptor 5 after stroke restores brain function and connectivity.

Hakon J, Quattromani MJ, Sjölund C, ..., Bauer AQ, Wieloch T

Brain - (-) - [2023-09-01; online 2023-09-01]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

IBS randomized study: FODMAPs alter bile acids, phenolic- and tryptophan metabolites, while gluten modifies lipids.

Nordin E, Hellström PM, Vuong E, ..., Brunius C, Landberg R

Am. J. Physiol. Regul. Integr. Comp. Physiol. 325 (3) R248-R259 [2023-09-01; online 2023-07-03]

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Verticillium longisporum phospholipase VlsPLA2 is a virulence factor that targets host nuclei and modulates plant immunity.

Rafiei V, Vélëz H, Piombo E, Dubey M, Tzelepis G

Mol. Plant Pathol. 24 (9) 1078-1092 [2023-09-00; online 2023-05-12]

Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Tuning of lattice thermal conductivity of amorphous Fe0.85Zr0.15 by nanostructured voids, pressure and temperature

Gürbüz E, Sanyal B

Journal of Non-Crystalline Solids 616 (-) 122430 [2023-09-00; online 2023-09-00]

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Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.

Shaw D, Abad R, Amin-Chowdhury Z, ..., Zhou F, Brueggemann AB

Lancet Digit Health 5 (9) e582-e593 [2023-09-00; online 2023-07-27]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Transcriptome network analysis links perinatal Staphylococcus epidermidis infection to microglia reprogramming in the immature hippocampus.

Gravina G, Ardalan M, Chumak T, ..., Ek CJ, Mallard C

Glia 71 (9) 2234-2249 [2023-09-00; online 2023-05-29]

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The role of NLRP3 in regulating gingival epithelial cell responses evoked by Aggregatibacter actinomycetemcomitans.

Jayaprakash Demirel K, Wu R, Neves Guimaraes A, Demirel I

Cytokine 169 (-) 156316 [2023-09-00; online 2023-08-02]

Structure and dynamics of the mitochondrial DNA-compaction factor Abf2 from S. cerevisiae.

Lidman J, Sallova Y, Matečko-Burmann I, Burmann BM

J. Struct. Biol. 215 (3) 108008 [2023-09-00; online 2023-08-03]

Quantification of chondroitin sulfate, hyaluronic acid and N-glycans in synovial fluid - A technical performance study.

Andersson E, Tykesson E, Lohmander LS, ..., Swärd P, Struglics A

Osteoarthr Cartil Open 5 (3) 100380 [2023-09-00; online 2023-06-10]

Mosaic Loss of Chromosome Y Is Associated With Functional Outcome After Ischemic Stroke.

Dorvall M, Pedersen A, Dumanski JP, ..., Stanne TM, Jern C

Stroke 54 (9) 2434-2437 [2023-09-00; online 2023-07-19]

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Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus.

Puthanveed V, Singh K, Poimenopoulou E, ..., Siddique AB, Kvarnheden A

Phytopathology 113 (9) 1788-1798 [2023-09-00; online 2023-11-01]

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Methane Producing and Oxidizing Microorganisms Display a High Resilience to Drought in a Swedish Hemi‐Boreal Mire

White JD, Ahrén D, Ström L, ..., Keane B, Parmentier FJW

JGR Biogeosciences 128 (9) - [2023-09-00; online 2023-09-08]

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Increased plasma levels of soluble programmed death ligand 1 (sPD-L1) and fibroblast growth factor 23 (FGF-23) in patients with Graves' ophthalmopathy in comparison to hyperthyroid patients without Graves' ophthalmopathy.

Khamisi S, Anders Karlsson F, Ljunggren Ö, Thulin M, Larsson A

Cytokine 169 (-) 156269 [2023-09-00; online 2023-06-10]

Fine-tuning of p-coumaric acid synthesis to increase (2S)-naringenin production in yeast.

Mao J, Mohedano MT, Fu J, ..., Siewers V, Chen Y

Metab. Eng. 79 (-) 192-202 [2023-09-00; online 2023-08-22]

Chalmers Mass Spectrometry Infrastructure [Service]

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer.

Burnett HA, Bieker VC, Le Moullec M, ..., Hansen BB, Martin MD

Evol Appl 16 (9) 1531-1548 [2023-09-00; online 2023-08-22]

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Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows.

Catalán A, Merondun J, Knief U, Wolf JBW

PLoS Genet. 19 (9) e1010901 [2023-09-00; online 2023-09-25]

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Breast Milk Oligosaccharides Contain Immunomodulatory Glucuronic Acid and LacdiNAc.

Jin C, Lundstrøm J, Korhonen E, Luis AS, Bojar D

Mol. Cell Proteomics 22 (9) 100635 [2023-09-00; online 2023-08-18]

Antimicrobial susceptibilities and genomic epidemiology of Neisseria gonorrhoeae in Stockholm, Sweden

Vestberg N, Bhattarai KH, Fang H

Eur J Clin Microbiol Infect Dis 42 (9) 1073-1079 [2023-09-00; online 2023-07-13]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants.

Tran HC, Schmitt V, Lama S, ..., Delannoy E, Van Aken O

Science 381 (6661) eadg0995 [2023-09-00; online 2023-09-01]

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A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone.

Berdan EL, Roger F, Wellenreuther M, ..., Butlin RK, André C

Environ. Microbiol. 25 (9) 1659-1673 [2023-09-00; online 2023-04-09]

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Trunk neural crest gene MOXD1 affects embryonic development

Fredlund E, Andersson S, Ferreira M, Mohlin S

- - (-) - [2023-08-31; online 2023-08-31]

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The Chlamydia effector CpoS modulates the inclusion microenvironment and restricts the interferon response by acting on Rab35.

Meier K, Jachmann LH, Türköz G, ..., Kroemer G, Sixt BS

MBio 14 (4) e0319022 [2023-08-31; online 2023-08-02]

Chemical Biology Consortium Sweden (CBCS) [Service]

De novoassembled single-cell transcriptomes from aquatic phytoflagellates reveal a metabolically distinct cell population

Florenza J, Jeevannavar A, Divne AM, Tamminen M, Bertilsson S

- - (-) - [2023-08-31; online 2023-08-31]

Microbial Single Cell Genomics [Technology development]

Public and patient involvement: a survey on knowledge, experience and opinions among researchers within a precision oncology European project.

Mosconi P, Colombo C, Paletta P, ..., Brunelli C, CEE_DART Consortium

BMC Cancer 23 (1) 814 [2023-08-30; online 2023-08-30]

Global Proteomics and Proteogenomics [Technology development]

Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles.

Seeger C, Dyrhage K, Näslund K, Andersson SGE

Microlife 4 (-) uqad037 [2023-08-29; online 2023-08-29]

The yeast guanine nucleotide exchange factor Sec7 is a bottleneck in spatial protein quality control and detoxifies neurological disease proteins.

Babazadeh R, Schneider KL, Fischbach A, ..., Liu B, Nystrom T

Sci Rep 13 (1) 14068 [2023-08-28; online 2023-08-28]

Integrated Microscopy Technologies Gothenburg [Service]

Kraft cooking of birch wood chips: differences between the dissolved organic material in pore and bulk liquor

Kron L, Marion de Godoy C, Hasani M, Theliander H

- 77 (8) 598-609 [2023-08-28; online 2023-07-07]

Deciphering the Role of p60AmotL2 in Epithelial Extrusion and Cell Detachment.

Cui W, Subramani A, Fonseca P, ..., Lundqvist A, Holmgren L

Cells 12 (17) - [2023-08-28; online 2023-08-28]

Chemogenetic inhibition of IST1-CHMP1B interaction impairs endosomal recycling and promotes unconventional LC3 lipidation at stalled endosomes

Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW

- - (-) - [2023-08-28; online 2023-08-28]

O304 ameliorates hyperglycemia in mice by dually promoting muscle glucose effectiveness and preserving β-cell function.

Norlin S, Axelsson J, Ericsson M, Edlund H

Commun Biol 6 (1) 877 [2023-08-25; online 2023-08-25]

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Long-read whole-genome analysis of human single cells.

Hård J, Mold JE, Eisfeldt J, ..., Michaëlsson J, Ameur A

Nat Commun 14 (1) 5164 [2023-08-24; online 2023-08-24]

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Highly multiplexed targeted sequencing strategy for infectious disease surveillance.

Hernández-Neuta I, Magoulopoulou A, Pineiro F, ..., Gulberg M, Nilsson M

BMC Biotechnol. 23 (1) 31 [2023-08-23; online 2023-08-23]

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Atomic-level structure determination of amorphous molecular solids by NMR.

Cordova M, Moutzouri P, Nilsson Lill SO, ..., Schantz S, Emsley L

Nat Commun 14 (1) 5138 [2023-08-23; online 2023-08-23]

Mass Transport in “Water-in-Polymer Salt” Electrolytes

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Chem. Mater. 35 (16) 6382-6395 [2023-08-22; online 2023-07-31]

Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour.

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Cell Oncol (Dordr) - (-) - [2023-08-22; online 2023-08-22]

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Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes.

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FEMS Microbiol. Ecol. 99 (9) - [2023-08-22; online 2023-08-17]

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Insights into cellular behavior and micromolecular communication in urothelial micrografts.

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Sci Rep 13 (1) 13589 [2023-08-21; online 2023-08-21]

The acute effect of different NAD+ precursors included in the combined metabolic activators.

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Free Radic. Biol. Med. 205 (-) 77-89 [2023-08-20; online 2023-06-02]

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Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation.

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Microb. Cell Fact. 22 (1) 160 [2023-08-19; online 2023-08-19]

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Multiplexed Guide RNA Expression Leads to Increased Mutation Frequency in Targeted Window Using a CRISPR-Guided Error-Prone DNA Polymerase in Saccharomyces cerevisiae.

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ACS Synth Biol 12 (8) 2271-2277 [2023-08-18; online 2023-07-24]

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Decoding pancreatic endocrine cell differentiation and β cell regeneration in zebrafish.

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Sci Adv 9 (33) eadf5142 [2023-08-18; online 2023-08-18]

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Bacterial bioindicators enable biological status classification along the continental Danube river.

Fontaine L, Pin L, Savio D, ..., Farnleitner AH, Eiler A

Commun Biol 6 (1) 862 [2023-08-18; online 2023-08-18]

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An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver.

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Nat Commun 14 (1) 5024 [2023-08-18; online 2023-08-18]

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Sustained Transmission of Neisseria gonorrhoeae Strains with High-Level Azithromycin Resistance (MIC ≥ 256 μg/mL) in Argentina, 2018 to 2022.

Gianecini RA, Poklepovich T, Golparian D, ..., Campos J, Galarza P

Microbiol Spectr 11 (4) e0097023 [2023-08-17; online 2023-06-20]

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Amyloids of α-Synuclein Promote Chemical Transformations of Neuronal Cell Metabolites.

Horvath I, Mohamed KA, Kumar R, Wittung-Stafshede P

Int J Mol Sci 24 (16) - [2023-08-16; online 2023-08-16]

Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration.

Munguba H, Nikouei K, Hochgerner H, ..., Linnarsson S, Hjerling-Leffler J

Neuron - (-) - [2023-08-15; online 2023-08-15]

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Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.

Meadows JRS, Kidd JM, Wang G, ..., Zhang Y, Ostrander EA

Genome Biol. 24 (1) 187 [2023-08-15; online 2023-08-15]

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Integrating a Polygenic Risk Score into a clinical setting would impact risk predictions in familial breast cancer.

Baliakas P, Munters AR, Kämpe A, ..., Ladenvall C, Eriksson D

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Inbreeding or outbreeding depression? How to manage an endangered and locally adapted population of red grouseLagopus scotica

Walsh G, McMahon BJ, Thörn F, ..., Irestedt M, Höglund J

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Silvério-Alves R, Kurochkin I, Rydström A, ..., Martin-Gonzalez J, Pereira CF

Nat Commun 14 (1) 4645 [2023-08-14; online 2023-08-14]

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Rezayee F, Eisfeldt J, Skaftason A, ..., Rosenquist R, Barbany G

Front Oncol 13 (-) 1217712 [2023-08-14; online 2023-08-14]

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Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase.

Andriianov A, Trigüis S, Drobiazko A, ..., Severinov K, Isaev A

Cell Rep 42 (8) 112972 [2023-08-13; online 2023-08-13]

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Jacob T, Annusver K, Czarnewski P, ..., Björklund ÅK, Kasper M

Dev. Cell - (-) - [2023-08-13; online 2023-08-13]

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Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.

Doimo M, Chaudhari N, Abrahamsson S, ..., Chorell E, Wanrooij S

Nucleic Acids Res. 51 (14) 7392-7408 [2023-08-11; online 2023-06-23]

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Complementarity-determining region clustering may cause CAR-T cell dysfunction.

Sarén T, Saronio G, Marti Torrell P, ..., Yu D, Essand M

Nat Commun 14 (1) 4732 [2023-08-10; online 2023-08-10]

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Cinnamic acid and p-coumaric acid are metabolized to 4-hydroxybenzoic acid by Yarrowia lipolytica.

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AMB Express 13 (1) 84 [2023-08-10; online 2023-08-10]

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Limited genetic changes observed during in situ and ex situ conservation in Nordic populations of red clover (Trifolium pratense).

Hagenblad J, Aloisi K, Marum P, ..., Asdal Å, Palmé A

Front Plant Sci 14 (-) 1233838 [2023-08-09; online 2023-08-09]

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Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.

Mattila TM, Svensson EM, Juras A, ..., Malmström H, Jakobsson M

Commun Biol 6 (1) 793 [2023-08-09; online 2023-08-09]

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Water Film-Driven Brucite Nanosheet Growth and Stacking.

Luong NT, Boily JF

Langmuir 39 (31) 11090-11098 [2023-08-08; online 2023-07-24]

Graded expression of the chemokine receptor CX3CR1 marks differentiation states of human and murine T cells and enables cross-species interpretation.

Zwijnenburg AJ, Pokharel J, Varnaitė R, ..., Eidsmo L, Gerlach C

Immunity 56 (8) 1955-1974.e10 [2023-08-08; online 2023-07-24]

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DNA Methylation Signatures of Multiple Sclerosis Occur Independently of Known Genetic Risk and Are Primarily Attributed to B Cells and Monocytes.

Xavier A, Maltby VE, Ewing E, ..., Lea RA, Lechner-Scott J

Int J Mol Sci 24 (16) - [2023-08-08; online 2023-08-08]

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A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing.

Johansson J, Lidéus S, Höijer I, ..., Bondeson ML, Wilbe M

Sci Rep 13 (1) 12856 [2023-08-08; online 2023-08-08]

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Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds.

Tan HZ, Jansen JJFJ, Allport GA, ..., Gwee CY, Rheindt FE

Elife 12 (-) - [2023-08-07; online 2023-08-07]

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Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe.

Mishcherikova V, Lynikienė J, Marčiulynas A, ..., Marčiulynienė D, Menkis A

JoF 9 (8) - [2023-08-06; online 2023-08-06]

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Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.

Almamoun R, Pierozan P, Manoharan L, Karlsson O

Ecotoxicol Environ Saf 262 (-) 115321 [2023-08-05; online 2023-08-05]

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The structure of immature tick-borne encephalitis virus

Anastasina M, Füzik T, Domanska A, ..., Plevka P, Butcher SJ

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Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles.

Kaufmann P, Wiberg RAW, Papachristos K, ..., Tellgren-Roth C, Immonen E

Mol. Biol. Evol. 40 (8) - [2023-08-03; online 2023-07-22]

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Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells.

Boussardon C, Carrie C, Keech O

J. Exp. Bot. 74 (14) 4110-4124 [2023-08-03; online 2023-04-08]

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The development of blood protein profiles in extremely preterm infants follows a stereotypic evolution pattern.

Zhong W, Danielsson H, Brusselaers N, ..., Uhlén M, Hellström A

Commun Med (Lond) 3 (1) 107 [2023-08-02; online 2023-08-02]

Relation between HLA and copy number variation of steroid 21-hydroxylase in a Swedish cohort of patients with autoimmune Addison's disease.

Lundtoft C, Eriksson D, Bianchi M, ..., Rönnblom L, Kämpe O

Eur. J. Endocrinol. 189 (2) 235-241 [2023-08-02; online 2023-08-09]

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Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA.

Nilsson JR, Benitez-Martin C, Sansom HG, ..., Magennis SW, Wilhelmsson LM

Phys Chem Chem Phys 25 (30) 20218-20224 [2023-08-02; online 2023-08-02]

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Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20.

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J. Antimicrob. Chemother. 78 (8) 1982-1991 [2023-08-02; online 2023-06-23]

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Genetic insights into resting heart rate and its role in cardiovascular disease.

van de Vegte YJ, Eppinga RN, van der Ende MY, ..., Verweij N, van der Harst P

Nat Commun 14 (1) 4646 [2023-08-02; online 2023-08-02]

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Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT

Borry M, Forsythe A, Andrades Valtueña A, ..., Warinner C, Fellows Yates JA

F1000Res 12 (-) 926 [2023-08-02; online 2023-08-02]

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Alternating L4 loop architecture of the bacterial polysaccharide co-polymerase WzzE.

Wiseman B, Widmalm G, Högbom M

Commun Biol 6 (1) 802 [2023-08-02; online 2023-08-02]

Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia.

Eriksson A, Engvall M, Mathot L, ..., Ladenvall C, Baliakas P

Clin. Cancer Res. 29 (15) 2826-2834 [2023-08-01; online 2023-04-07]

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Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.

Chyleński M, Makarowicz P, Juras A, ..., Jakobsson M, Malmström H

Nat Commun 14 (1) 4395 [2023-08-01; online 2023-08-01]

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Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators.

Yang H, Li X, Jin H, ..., Borén J, Mardinoglu A

Free Radic. Biol. Med. 204 (-) 347-358 [2023-08-01; online 2023-05-26]

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Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by E. coli Adenylate Kinase.

Tischlik S, Oelker M, Rogne P, ..., Drescher M, Wolf-Watz M

Biochemistry 62 (15) 2238-2243 [2023-08-01; online 2023-07-07]

Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.

Näsvall K, Boman J, Talla V, Backström N

Genome Biol Evol 15 (8) - [2023-08-01; online 2023-08-11]

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Two different isoforms of osteopontin modulate myelination and axonal integrity.

Nilsson G, Mottahedin A, Zelco A, ..., Leavenworth JW, Wang X

FASEB Bioadv 5 (8) 336-353 [2023-08-00; online 2023-06-17]

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Synergy and oxygen adaptation for development of next-generation probiotics.

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Surface decontamination of explanted peri-implantitis-affected implants.

Ichioka Y, Derks J, Larsson L, Berglundh T

J Clin Periodontol 50 (8) 1113-1122 [2023-08-00; online 2023-06-04]

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Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL

Nat. Biotechnol. 41 (8) 1085-1088 [2023-08-00; online 2023-01-05]

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STE20-type kinases MST3 and MST4 promote the progression of hepatocellular carcinoma: Evidence from human cell culture and expression profiling of liver biopsies.

Caputo M, Xia Y, Anand SK, ..., Peter A, Mahlapuu M

FASEB J. 37 (8) e23105 [2023-08-00; online 2023-07-25]

SARS-CoV-2 Antibodies in Commercial Immunoglobulin Products Show Markedly Reduced Cross-reactivities Against Omicron Variants.

Lindahl H, Chen P, Åberg M, ..., Smith CIE, Bergman P

J Clin Immunol 43 (6) 1075-1082 [2023-08-00; online 2023-04-14]

Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia.

Hedberg-Oldfors C, Mitra S, Molinaro A, ..., Sterky FH, Darin N

Eur. J. Hum. Genet. 31 (8) 887-894 [2023-08-00; online 2023-03-20]

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Real-world assessment of immunogenicity in immunocompromised individuals following SARS-CoV-2 mRNA vaccination: a one-year follow-up of the prospective clinical trial COVAXID.

Chen P, Bergman P, Blennow O, ..., Aleman S, Ljunggren H

EBioMedicine 94 (-) 104700 [2023-08-00; online 2023-07-13]

Novel catalyst configuration to boost the yield of longer hydrocarbons from methanol-mediated CO2 hydrogenation

Sharma P, Ho PH, Di W, Creaser D, Olsson L

Journal of CO2 Utilization 74 (-) 102549 [2023-08-00; online 2023-08-00]

Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements.

Näsvall K, Boman J, Höök L, ..., Wiklund C, Backström N

PLoS Genet. 19 (8) e1010717 [2023-08-00; online 2023-08-07]

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N-terminal proteoforms may engage in different protein complexes.

Bogaert A, Fijalkowska D, Staes A, ..., Calderwood MA, Gevaert K

Life Sci. Alliance 6 (8) - [2023-08-00; online 2023-06-14]

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Mucosal IgA protects against BQ.1 and BQ.1.1 infection.

Marking U, Bladh O, Havervall S, ..., Klingström J, Thålin C

Lancet Infect Dis 23 (8) e272-e273 [2023-08-00; online 2023-07-12]

Methylation of lysine 36 on histone H3 is required to control transposon activities in somatic cells.

Lindehell H, Schwartz YB, Larsson J

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Mapping the Human Chondroitin Sulfate Glycoproteome Reveals an Unexpected Correlation Between Glycan Sulfation and Attachment Site Characteristics.

Noborn F, Nilsson J, Sihlbom C, ..., Kjellén L, Larson G

Mol. Cell Proteomics 22 (8) 100617 [2023-08-00; online 2023-07-14]

Low-grade intestinal inflammation two decades after pelvic radiotherapy.

Devarakonda S, Thorsell A, Hedenström P, ..., Steineck G, Bull C

EBioMedicine 94 (-) 104691 [2023-08-00; online 2023-07-20]

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Local and Systemic Immunity During Five Vaccinations Against SARS-CoV-2 in Zanubrutinib-Treated Patients With Chronic Lymphocytic Leukemia.

Andersson M, Wu J, Wullimann D, ..., Ingelman-Sundberg HM, Osterborg A

J Hematol 12 (4) 170-175 [2023-08-00; online 2023-08-08]

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.

Vromman M, Anckaert J, Bortoluzzi S, ..., Vandesompele J, Volders PJ

Nat. Methods 20 (8) 1159-1169 [2023-08-00; online 2023-07-13]

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Historical RNA expression profiles from the extinct Tasmanian tiger.

Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR

Genome Res. 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]

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Exposures to perfluoroalkyl substances and asthma phenotypes in childhood: an investigation of the COPSAC2010 cohort.

Sevelsted A, Pedersen CT, Gürdeniz G, ..., Chawes B, Bisgaard H

EBioMedicine 94 (-) 104699 [2023-08-00; online 2023-07-08]

Examining neurodevelopmental problems in 15q11.2 (BP1-BP2) copy number variation carriers at ages 9/12 and 18 in a Swedish twin sample.

Jonsson L, Martin J, Lichtenstein P, ..., Westberg L, Tammimies K

Mol Genet Genomic Med 11 (8) e2191 [2023-08-00; online 2023-05-08]

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Evaluation of genetic demultiplexing of single-cell sequencing data from model species.

Cardiello JF, Joven Araus A, Giatrellis S, ..., Simon A, Leigh ND

Life Sci. Alliance 6 (8) e202301979 [2023-08-00; online 2023-05-17]

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Engineering of layered iron vanadate nanostructure for electrocatalysis: Simultaneous detection of methotrexate and folinic acid in blood serum

Adeniyi KO, Osmanaj B, Manavalan G, ..., Boily JF, Tesfalidet S

Electrochimica Acta 458 (-) 142538 [2023-08-00; online 2023-08-00]

Direct additive genetics and maternal effect contribute to the risk of Tourette disorder.

Mahjani B, Klei L, Buxbaum Grice AS, ..., Buxbaum JD, Grice DE

J Neurol Neurosurg Psychiatry 94 (8) 638-642 [2023-08-00; online 2023-04-26]

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Differential DNA Methylation of MicroRNA-Encoding Genes in Psoriatic Epidermis Highlights the Wnt Pathway.

Verma D, Kasic NK, Jeppsson F, ..., Das J, Enerbäck C

J. Invest. Dermatol. 143 (8) 1594-1597.e14 [2023-08-00; online 2023-02-27]

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Clones on the run: The genomics of a recently expanded partially clonal species.

Pereyra RT, Rafajlović M, De Wit P, ..., Töpel M, Johannesson K

Mol. Ecol. 32 (15) 4209-4223 [2023-08-00; online 2023-05-18]

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Characterisation of a low methane emission rice cultivar suitable for cultivation in high latitude light and temperature conditions.

Hu J, Bettembourg M, Moreno S, ..., Sundström J, Jin Y

Environ Sci Pollut Res 30 (40) 92950-92962 [2023-08-00; online 2023-07-27]

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A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing

Plaza DF, Zerebinski J, Broumou I, ..., Sundling C, Färnert A

Cell Reports Methods - (-) 100574 [2023-08-00; online 2023-08-00]

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Observation of defect density dependent elastic modulus of graphene

Li H, Gürbüz E, Haldar S, ..., Sanyal B, Leifer K

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Cell Membranes Sustain Phospholipid Imbalance Via Cholesterol Asymmetry

Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I

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Transposable element insertions in 1000 Swedish individuals.

Bilgrav Saether K, Nilsson D, Thonberg H, ..., Eisfeldt J, Lindstrand A

PLoS ONE 18 (7) e0289346 [2023-07-28; online 2023-07-28]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Register-based and genetic studies of Prader-Willi syndrome show a high frequency of gonadal tumors and a possible mechanism for tumorigenesis through imprinting relaxation.

Maya-González C, Wessman S, Lagerstedt-Robinson K, ..., Skarin Nordenvall A, Nordgren A

Front Med (Lausanne) 10 (-) 1172565 [2023-07-28; online 2023-07-28]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics.

Hildebrandt F, Mohammed M, Dziedziech A, ..., Henriksson J, Ankarklev J

Front Immunol 14 (-) 1224591 [2023-07-27; online 2023-07-27]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PVT1 interacts with polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma.

Nylund P, Garrido-Zabala B, Párraga AA, ..., Kalushkova A, Wiklund HJ

Haematologica - (-) - [2023-07-27; online 2023-07-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

Hank EC, D'Arcy-Evans N, Wallner O, ..., de Vega M, Michel M

- - (-) - [2023-07-27; online 2023-07-27]

Chemical Biology Consortium Sweden (CBCS) [Service]

Spatial lipidomics reveals brain region-specific changes of sulfatides in an experimental MPTP Parkinson's disease primate model.

Kaya I, Nilsson A, Luptáková D, ..., Bezard E, Andrén PE

NPJ Parkinsons Dis 9 (1) 118 [2023-07-26; online 2023-07-26]

Cutaneous squamous cell carcinoma-derived extracellular vesicles exert an oncogenic role by activating cancer-associated fibroblasts.

Li C, Sun C, Lohcharoenkal W, ..., Sonkoly E, Pivarcsi A

Cell Death Discov 9 (1) 260 [2023-07-26; online 2023-07-26]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Ciclopirox Ethanolamine Preserves the Immature State of Human HSCs by Mediating Intracellular Iron Content.

Safaee Talkhoncheh M, Baudet A, Ek F, ..., Will B, Larsson J

Blood Adv - (-) - [2023-07-24; online 2023-07-24]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

An Okinawan-Based Nordic Diet Leads to Profound Effects on Gut Microbiota and Plasma Metabolites Linked to Glucose and Lipid Metabolism.

Manoharan L, Roth B, Bang C, Stenlund H, Ohlsson B

Nutrients 15 (14) - [2023-07-24; online 2023-07-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]

Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper.

Fridolfsson E, Bunse C, Lindehoff E, ..., Legrand C, Hylander S

Sci Rep 13 (1) 11865 [2023-07-22; online 2023-07-22]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Vegetation, topography, and soil depth drive microbial community structure in two Swedish grasslands.

Guasconi D, Juhanson J, Clemmensen KE, ..., Roth N, Fransson P

FEMS Microbiol. Ecol. 99 (8) - [2023-07-21; online 2023-07-21]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Transplantation of gut microbiota from old mice into young healthy mice reduces lean mass but not bone mass.

Lawenius L, Cowardin C, Grahnemo L, ..., Sjögren K, Ohlsson C

Gut Microbes 15 (1) 2236755 [2023-07-21; online 2023-07-21]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB).

Okeke DC, Lidman J, Matečko-Burmann I, Burmann BM

Nucleic Acids Res. 51 (13) 7036-7052 [2023-07-21; online 2023-06-01]

Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27.

Jensen M, Chandrasekaran V, García-Bonete MJ, ..., Bokarewa I M, Katona G

iScience 26 (7) 106976 [2023-07-21; online 2023-05-29]

Proteomics identifies lipocalin-2 in neonatal inflammation associated with cerebrovascular alteration in mice and preterm infants.

Gravina G, Ardalan M, Chumak T, ..., Hellström A, Mallard C

iScience 26 (7) 107217 [2023-07-21; online 2023-06-27]

Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.

Ginja C, Guimarães S, da Fonseca RR, ..., Pires AE, Valenzuela-Lamas S

iScience 26 (7) 107196 [2023-07-21; online 2023-06-24]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A machine learning based approach to identify carotid subclinical atherosclerosis endotypes.

Chen QS, Bergman O, Ziegler L, ..., Gigante B, IMPROVE study group

Cardiovasc. Res. - (-) - [2023-07-21; online 2023-07-21]

FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples.

Iwaszkiewicz-Eggebrecht E, Łukasik P, Buczek M, ..., Ronquist F, Miraldo A

PLoS ONE 18 (7) e0286272 [2023-07-19; online 2023-07-19]

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Endophytic Beauveria bassiana induces biosynthesis of flavonoids in oilseed rape following both seed inoculation and natural colonization.

Muola A, Birge T, Helander M, ..., Saikkonen K, Fuchs B

Pest Manag Sci - (-) - [2023-07-19; online 2023-07-19]

Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature.

Lihavainen J, Šimura J, Bag P, ..., Ljung K, Jansson S

Nat Commun 14 (1) 4288 [2023-07-18; online 2023-07-18]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]

ReprogrammingYarrowia lipolyticametabolism for efficient synthesis of itaconic acid from flask to semi-pilot scale

Fu J, Zaghen S, Lu H, ..., Di Bartolomeo F, Kerkhoven EJ

- - (-) - [2023-07-18; online 2023-07-18]

Chalmers Mass Spectrometry Infrastructure [Service]

Phospholipid Removal for Enhanced Chemical Exposomics in Human Plasma

Sdougkou K, Xie H, Papazian S, ..., Bergdahl IA, Martin JW

Environ. Sci. Technol. 57 (28) 10173-10184 [2023-07-18; online 2023-07-03]

Next generation pan-cancer blood proteome profiling using proximity extension assay.

Álvez MB, Edfors F, von Feilitzen K, ..., Fagerberg L, Uhlén M

Nat Commun 14 (1) 4308 [2023-07-18; online 2023-07-18]

Affinity Proteomics Uppsala [Collaborative] Bioinformatics Support for Computational Resources [Service] NGI Proteomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants.

Hanifah NASB, Ghadamgahi F, Ghosh S, ..., Vetukuri RR, Kalyandurg PB

Front Plant Sci 14 (-) 1141692 [2023-07-18; online 2023-07-18]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Serum proteome profiles in patients treated with targeted temperature management after out-of-hospital cardiac arrest.

Lileikyte G, Bakochi A, Ali A, ..., Malmström J, Nielsen N

Intensive Care Med Exp 11 (1) 43 [2023-07-17; online 2023-07-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Impact of xylan on field productivity and wood saccharification properties in aspen.

Derba-Maceluch M, Sivan P, Donev EN, ..., Jönsson LJ, Mellerowicz EJ

Front Plant Sci 14 (-) 1218302 [2023-07-17; online 2023-07-17]

Biosensor-Assisted Laboratory Evolution of Malonyl-CoA production inSaccharomyces cerevisiae

Ferreira R, Hedin KA, Nielsen J, David F

- - (-) - [2023-07-17; online 2023-07-17]

Chalmers Mass Spectrometry Infrastructure [Service]

Restoring tumor immunogenicity with dendritic cell reprogramming.

Zimmermannova O, Ferreira AG, Ascic E, ..., Svane IM, Pereira CF

Sci Immunol 8 (85) eadd4817 [2023-07-14; online 2023-07-07]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution.

Rastegar B, Andersson N, Petersson A, ..., Holmquist Mengelbier L, Gisselsson D

Clin. Cancer Res. 29 (14) 2668-2677 [2023-07-14; online 2023-05-04]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Absence of gut microbiota reduces neonatal survival and exacerbates liver disease in Cyp2c70-deficient mice with a human-like bile acid composition.

Sjöland W, Wahlström A, Makki K, ..., Bäckhed F, Marschall HU

Clin Sci (Lond) 137 (13) 995-1011 [2023-07-14; online 2023-06-29]

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Irradiation and lithium treatment alter the global DNA methylation pattern and gene expression underlying a shift from gliogenesis towards neurogenesis in human neural progenitors.

Neofytou C, Backlund A, Blomgren K, Hermanson O

Transl Psychiatry 13 (1) 258 [2023-07-13; online 2023-07-13]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Quantitative Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) Imaging of Individual Vesicles to Investigate the Relation between Fraction of Chemical Release and Vesicle Size.

Nguyen TDK, Rabasco S, Lork AA, Toit AD, Ewing AG

Angew. Chem. Int. Ed. Engl. 62 (28) e202304098 [2023-07-10; online 2023-06-05]

Integrated Microscopy Technologies Gothenburg [Technology development]

Giant spin-splitting and tunable spin-momentum locked transport in room temperature collinear antiferromagnetic semimetallic CrO monolayer

Chen X, Wang D, Li L, Sanyal B

- 123 (2) - [2023-07-10; online 2023-07-11]

Bioinformatics Support for Computational Resources [Service]

Autologous hematopoietic stem cell transplantation significantly alters circulating ceramides in peripheral blood of relapsing-remitting multiple sclerosis patients.

Vaivade A, Wiberg A, Khoonsari PE, ..., Burman J, Kultima K

Lipids Health Dis 22 (1) 97 [2023-07-07; online 2023-07-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression.

Deiana M, Andrés Castán JM, Josse P, ..., Cabanetos C, Sabouri N

Nucleic Acids Res. 51 (12) 6264-6285 [2023-07-07; online 2023-05-16]

High-level in vitro resistance to gentamicin acquired in a stepwise manner in Neisseria gonorrhoeae.

Golparian D, Jacobsson S, Holley CL, Shafer WM, Unemo M

J. Antimicrob. Chemother. 78 (7) 1769-1778 [2023-07-05; online 2023-05-30]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Effects of FODMAPs and Gluten on Gut Microbiota and Their Association with the Metabolome in Irritable Bowel Syndrome: A Double-Blind, Randomized, Cross-Over Intervention Study.

Nordin E, Hellström PM, Dicksved J, ..., Landberg R, Brunius C

Nutrients 15 (13) - [2023-07-05; online 2023-07-05]

Bioinformatics Support for Computational Resources [Service] Chalmers Mass Spectrometry Infrastructure [Collaborative]

Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data.

Potdar S, Ianevski F, Ianevski A, ..., Aittokallio T, Saarela J

Nucleic Acids Res. 51 (W1) W57-W61 [2023-07-05; online 2023-05-14]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta).

Squires TE, Rödin-Mörch P, Formenti G, ..., Höglund J, Magnússon KP

G3 (Bethesda) 13 (7) - [2023-07-05; online 2023-05-04]

Bioinformatics Support for Computational Resources [Service]

Vascular endothelial growth factor-D plasma levels and VEGFD genetic variants are independently associated with outcomes in patients with cardiovascular disease.

Davidsson P, Eketjäll S, Eriksson N, ..., White H, Wallentin L

Cardiovasc. Res. 119 (7) 1596-1605 [2023-07-04; online 2023-03-05]

Affinity Proteomics Uppsala [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function.

Laudette M, Lindbom M, Arif M, ..., Levin MC, Borén J

Cardiovasc. Res. 119 (7) 1537-1552 [2023-07-04; online 2023-03-08]

Integrated Microscopy Technologies Gothenburg [Service]

Bone mineral density loci specific to the skull portray potential pleiotropic effects on craniosynostosis.

Medina-Gomez C, Mullin BH, Chesi A, ..., Kague E, Rivadeneira F

Commun Biol 6 (1) 691 [2023-07-04; online 2023-07-04]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Physical Activity, Sedentary Behavior, and Type 2 Diabetes: Mendelian Randomization Analysis.

Yuan S, Li X, Liu Q, ..., Burgess S, Larsson SC

J Endocr Soc 7 (8) bvad090 [2023-07-03; online 2023-06-26]

Loss of ctnnd2b affects neuronal differentiation and behavior in zebrafish.

Vaz R, Edwards S, Dueñas-Rey A, Hofmeister W, Lindstrand A

Front. Neurosci. 17 (-) 1205653 [2023-07-03; online 2023-07-03]

Integrated Microscopy Technologies Stockholm [Service]

Incidence and Characteristics in Children with Post-COVID-19 Condition in Sweden.

Bygdell M, Kindblom JM, Martikainen J, Li H, Nyberg F

JAMA Netw Open 6 (7) e2324246 [2023-07-03; online 2023-07-03]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Domain landscapes of somatic NF1 mutations in pheochromocytoma and paraganglioma.

Tabebi M, Frikha F, Volpe M, Gimm O, Söderkvist P

Gene 872 (-) 147432 [2023-07-01; online 2023-04-14]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]

Arabinoxylan supplemented bread: From extraction of fibers to effect of baking, digestion, and fermentation.

Zhang D, Rudjito RC, Pietiäinen S, ..., Vilaplana F, Jiménez-Quero A

Food Chem 413 (-) 135660 [2023-07-01; online 2023-02-10]

Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.

Adolfsson E, Kling D, Gunnarsson C, ..., Gréen H, Gréen A

Int J Legal Med 137 (4) 1215-1234 [2023-07-00; online 2022-11-08]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Urodrill - a novel MRI-guided endoscopic biopsy technique to sample and molecularly classify muscle-invasive bladder cancer without fractionating the specimen during transurethral resection.

Eriksson P, Berg J, Bernardo C, ..., Zackrisson S, Liedberg F

Eur Urol Open Sci 53 (-) 78-82 [2023-07-00; online 2023-06-02]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

The organization of double-stranded RNA in the chikungunya virus replication organelle.

Laurent T, Carlson L

PLoS Negl Trop Dis 17 (7) e0011404 [2023-07-00; online 2023-07-05]

The influence of the capping ligands on the optoelectronic performance, morphology, and ion liberation of CsPbBr3 perovskite quantum dots

Liu Y, Tang S, Gao Z, ..., Edman L, Wang J

Nano Res. 16 (7) 10626-10633 [2023-07-00; online 2023-04-19]

Role of the supports during phosphorus poisoning of diesel oxidation catalysts

Ho PH, Shao J, Yao D, ..., Creaser D, Olsson L

Chemical Engineering Journal 468 (-) 143548 [2023-07-00; online 2023-07-00]

Proteomic and transcriptomic screening demonstrates increased mast cell-derived CCL23 in systemic mastocytosis.

Söderlund S, Boey D, van Midden W, ..., Dahlin JS, Ungerstedt J

J. Allergy Clin. Immunol. 152 (1) 205-213 [2023-07-00; online 2023-02-21]

NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Plasma levels of per- and polyfluoroalkyl substances (PFAS) are associated with altered levels of proteins previously linked to inflammation, metabolism and cardiovascular disease.

Dunder L, Salihovic S, Lind PM, Elmståhl S, Lind L

Environ Int 177 (-) 107979 [2023-07-00; online 2023-05-24]

N-Arylation of primary and tertiary sulfonimidamides (SIAs) with benzyne precursors under transition metal-free conditions

Ambala S, Govender KB, Rajbongshi KK, ..., Naicker T, Arvidsson PI

Tetrahedron Letters 124 (-) 154583 [2023-07-00; online 2023-07-00]

Drug Discovery and Development (DDD) [Technology development]

Multiplex protein analysis and ensemble machine learning methods of fine needle aspirates from prostate cancer patients reveal potential diagnostic signatures associated with tumour grade.

Röbeck P, Franzén B, Cantera-Ahlman R, ..., Häggman M, Ladjevardi S

Cytopathology 34 (4) 286-294 [2023-07-00; online 2023-03-20]

Mucosal immune responses following a fourth SARS-CoV-2 vaccine dose.

Bladh O, Marking U, Havervall S, ..., Klingström J, Thålin C

Lancet Microbe 4 (7) e488 [2023-07-00; online 2023-04-20]

Metabolic profiles reflect weight loss maintenance and the composition of diet after very-low-energy diet.

Näätänen M, Kårlund A, Mikkonen S, ..., Hanhineva K, Kolehmainen M

Clin Nutr 42 (7) 1126-1141 [2023-07-00; online 2023-05-17]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Individualised human phenotype ontology gene panels improve clinical whole exome and genome sequencing analytical efficacy in a cohort of developmental and epileptic encephalopathies.

Henry OJ, Stödberg T, Båtelson S, ..., Stranneheim H, Wedell A

Mol Genet Genomic Med 11 (7) e2167 [2023-07-00; online 2023-03-26]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Immunological protein profiling of first-episode psychosis patients identifies CSF and blood biomarkers correlating with disease severity.

Eren F, Schwieler L, Orhan F, ..., Engberg G, Erhardt S

Brain, Behavior, and Immunity 111 (-) 376-385 [2023-07-00; online 2023-05-04]

Human resident liver myeloid cells protect against metabolic stress in obesity.

Barreby E, Strunz B, Nock S, ..., Chen P, Aouadi M

Nat Metab 5 (7) 1188-1203 [2023-07-00; online 2023-07-06]

High temperature interactions between K-rich biomass ash and MgO-based refractories

Wagri NK, Carlborg M, Eriksson M, ..., Broström M, Andersson BM

Journal of the European Ceramic Society 43 (8) 3770-3777 [2023-07-00; online 2023-07-00]

Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.

Kluting K, Strid Y, Six D, Rosling A

Microb. Ecol. 86 (1) 224-239 [2023-07-00; online 2022-07-13]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Forensic prediction of sex, age, height, body mass index, hip-to-waist ratio, smoking status and lipid lowering drugs using epigenetic markers and plasma proteins.

Llobet MO, Johansson Å, Gyllensten U, Allen M, Enroth S

Forensic Sci Int Genet 65 (-) 102871 [2023-07-00; online 2023-04-07]

Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Expanding the phenotype of Seckel syndrome associated with biallelic loss-of-function variants in CEP63.

Pekkola Pacheco N, Pettersson M, Lindstrand A, Grigelioniene G

Am. J. Med. Genet. A 191 (7) 1929-1934 [2023-07-00; online 2023-04-05]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Esr1+ hypothalamic-habenula neurons shape aversive states.

Calvigioni D, Fuzik J, Le Merre P, ..., Carlén M, Meletis K

Nat. Neurosci. 26 (7) 1245-1255 [2023-07-00; online 2023-06-22]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui).

Boman J, Zhu Y, Höök L, ..., Talavera G, Backström N

Mol. Ecol. 32 (13) 3513-3523 [2023-07-00; online 2023-04-23]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Core genome multilocus sequence typing (cgMLST) confirms systemic spread of avian pathogenic Escherichia coli (APEC) in broilers with cellulitis.

Jonare L, Östlund E, Söderlund R, ..., Aspán A, Jansson DS

Vet. Microbiol. 282 (-) 109755 [2023-07-00; online 2023-04-24]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Complex life cycles drive community assembly through immigration and adaptive diversification.

Saltini M, Vasconcelos P, Rueffler C

Ecol. Lett. 26 (7) 1084-1094 [2023-07-00; online 2023-05-01]

Bioinformatics Support for Computational Resources [Service]

Actionable cancer vulnerability due to translational arrest, p53 aggregation and ribosome biogenesis stress evoked by the disulfiram metabolite CuET.

Kanellis DC, Zisi A, Skrott Z, ..., Lindström MS, Bartek J

Cell Death Differ. 30 (7) 1666-1678 [2023-07-00; online 2023-05-04]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A phase I prospective, non-randomized trial of autologous dendritic cell-based cryoimmunotherapy in patients with metastatic castration-resistant prostate cancer.

Thomsen LCV, Honoré A, Reisæter LAR, ..., Kalland KH, Beisland C

Cancer Immunol. Immunother. 72 (7) 2357-2373 [2023-07-00; online 2023-03-20]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

A model of photosynthetic CO2 assimilation in C3 leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway.

Wieloch T, Augusti A, Schleucher J

New Phytol. 239 (2) 518-532 [2023-07-00; online 2023-05-23]

Transport Properties of Protic Ionic Liquids Based on Triazolium and Imidazolium: Development of an Air-Free Conductivity Setup.

Morais EM, Idström A, Evenäs L, Martinelli A

Molecules 28 (13) - [2023-06-30; online 2023-06-30]

Single cell-resolutionin situsequencing elucidates spatial dynamics of multiple sclerosis lesion and disease evolution

Langseth CM, Kukanja P, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G

- - (-) - [2023-06-30; online 2023-06-30]

Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Service]

Elevated levels of MMP12 sourced from macrophages are associated with poor prognosis in urothelial bladder cancer.

Kerzeli IK, Kostakis A, Türker P, ..., Lord M, Mangsbo SM

BMC Cancer 23 (1) 605 [2023-06-30; online 2023-06-30]

Combined effects of isolation temperature and pH on functionality and beany flavor of pea protein isolates for meat analogue applications.

Sajib M, Forghani B, Kumar Vate N, Abdollahi M

Food Chem 412 (-) 135585 [2023-06-30; online 2023-01-27]

Chalmers Mass Spectrometry Infrastructure [Service]

Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics.

Arora A, Becker M, Marques C, ..., Lanekoff I, Tammimies K

Sci Rep 13 (1) 10519 [2023-06-29; online 2023-06-29]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community.

Massing JC, Fahimipour AK, Bunse C, Pinhassi J, Gross T

mSystems 8 (3) e0002823 [2023-06-29; online 2023-05-31]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genetic markers associated with bone composition in Rhode Island Red laying hens.

Sallam M, Wilson PW, Andersson B, ..., De Koning DJ, Johnsson M

Genet. Sel. Evol. 55 (1) 44 [2023-06-29; online 2023-06-29]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Restricting Promiscuity of Plant Flavonoid 3'-Hydroxylase and 4'-O-Methyltransferase Improves the Biosynthesis of (2S)-Hesperetin in E. coli.

Liu J, Xiao Z, Zhang S, ..., Chen Y, Shan Y

J. Agric. Food Chem. 71 (25) 9826-9835 [2023-06-28; online 2023-06-13]

Chalmers Mass Spectrometry Infrastructure [Service]

BTK and PLCG2 remain unmutated in one-third of patients with CLL relapsing on ibrutinib.

Bonfiglio S, Sutton LA, Ljungström V, ..., Rosenquist R, Ghia P

Blood Adv 7 (12) 2794-2806 [2023-06-27; online 2023-01-26]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

A Highly Substituted Ring-Fused 2-Pyridone Compound Targeting PrfA and the Efflux Regulator BrtA in Listeria monocytogenes.

Tükenmez H, Singh P, Sarkar S, ..., Almqvist F, Johansson J

MBio 14 (3) e0044923 [2023-06-27; online 2023-04-25]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Identification of potential biomarkers in active Lyme borreliosis.

Tjernberg I, Lager M, Furset Jensen G, ..., Brudin L, Henningsson AJ

PLoS ONE 18 (6) e0287586 [2023-06-26; online 2023-06-26]

Fluorometric Quantification of Total Cell-Free DNA as a Prognostic Biomarker in Non-Small-Cell Lung Cancer Patients Treated with Immune Checkpoint Blockade.

Oliver J, Onieva JL, Garrido-Barros M, ..., Rueda-Domínguez A, Barragán I

Cancers (Basel) 15 (13) - [2023-06-26; online 2023-06-26]

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Ancient Sheep Genomes reveal four Millennia of North European Short-Tailed Sheep in the Baltic Sea region

Larsson MN, Miranda PM, Pan L, ..., Storå J, Günther T

bioRxiv - (-) - [2023-06-26; online 2023-06-26]

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MgO nanocube hydroxylation by nanometric water films.

Luong NT, Holmboe M, Boily JF

Nanoscale 15 (24) 10286-10294 [2023-06-23; online 2023-06-23]

Case report: Extending the spectrum of clinical and molecular findings in FOXC1 haploinsufficiency syndrome.

Garza Flores A, Nordgren I, Pettersson M, ..., Nishimura G, Grigelioniene G

Front Genet 14 (-) 1174046 [2023-06-23; online 2023-06-23]

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Unmodified rabies mRNA vaccine elicits high cross-neutralizing antibody titers and diverse B cell memory responses.

Hellgren F, Cagigi A, Arcoverde Cerveira R, ..., Petsch B, Loré K

Nat Commun 14 (1) 3713 [2023-06-22; online 2023-06-22]

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Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield.

Lopez-Fernandez M, Westmeijer G, Turner S, ..., Bertilsson S, Dopson M

NPJ Biofilms Microbiomes 9 (1) 41 [2023-06-22; online 2023-06-22]

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Dietary biomarkers and food records indicate compliance to study diets in the ADIRA (Anti-inflammatory Diet In Rheumatoid Arthritis) trial.

Wadell AT, Bärebring L, Hulander E, ..., Lindqvist H, Winkvist A

Front Nutr 10 (-) 1209787 [2023-06-22; online 2023-06-22]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.

Lauterbur ME, Cavassim MIA, Gladstein AL, ..., Schrider DR, Gronau I

Elife 12 (-) - [2023-06-21; online 2023-06-21]

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Microbial Profiling of Amniotic Fluid, Umbilical Blood and Placenta of the Foaling Mare.

Hemberg E, Niazi A, Guo Y, ..., Morrell JM, Kútvölgyi G

Animals (Basel) 13 (12) - [2023-06-18; online 2023-06-18]

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Rapid Construction of a Chloromethyl-Substituted Duocarmycin-like Prodrug.

Bengtsson C, Gravenfors Y

Molecules 28 (12) - [2023-06-16; online 2023-06-16]

Drug Discovery and Development (DDD) [Collaborative]

Disease phenotype prediction in multiple sclerosis.

Herman S, Arvidsson McShane S, Zjukovskaja C, ..., Spjuth O, Kultima K

iScience 26 (6) 106906 [2023-06-16; online 2023-05-19]

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Investigation of cellulose dissolution in morpholinium-based solvents: impact of solvent structural features on cellulose dissolution.

Naserifar S, Koschella A, Heinze T, Bernin D, Hasani M

RSC Adv. 13 (27) 18639-18650 [2023-06-15; online 2023-06-20]

Gene expression of S100a8/a9 predicts Staphylococcus aureus-induced septic arthritis in mice.

Deshmukh M, Subhash S, Hu Z, ..., Jin T, Kopparapu PK

Front Microbiol 14 (-) 1146694 [2023-06-15; online 2023-06-15]

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Deciphering the contribution of microbial biomass to the properties of dissolved and particulate organic matter in anaerobic digestates.

Fernández-Domínguez D, Yekta SS, Hedenström M, Patureau D, Jimenez J

Sci. Total Environ. 877 (-) 162882 [2023-06-15; online 2023-03-17]

Human skin-resident CD8+ T cells require RUNX2 and RUNX3 for induction of cytotoxicity and expression of the integrin CD49a.

Zitti B, Hoffer E, Zheng W, ..., Eidsmo L, Bryceson YT

Immunity 56 (6) 1285-1302.e7 [2023-06-13; online 2023-06-02]

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A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function

Schlesinger D, Dirks C, Luzon CN, ..., Eirich J, Elsässer SJ

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A Base‐Free, Low Temperature Click and Release Reaction for the In Situ Generation of Diazomethane

Schembri LS, Olaniran E, Söderström M, Skillinghaug B, Odell LR

Adv. Synth. Catal. 365 (11) 1839-1845 [2023-06-13; online 2023-05-23]

Spatial Mass Spectrometry [Service]

Tailoring vascular phenotype through AAV therapy promotes anti-tumor immunity in glioma.

Ramachandran M, Vaccaro A, van de Walle T, ..., Essand M, Dimberg A

Cancer Cell 41 (6) 1134-1151.e10 [2023-06-12; online 2023-05-11]

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Scalablein-vitroimmunostimulation of human blood for in-depth profiling of acute immune response effects

Reitzner SM, Brodin P, Mikeš J

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Production and Characterization of Poly(3-hydroxybutyrate) from Halomonas boliviensis LC1 Cultivated in Hydrolysates of Quinoa Stalks

Miranda DA, Marín K, Sundman O, ..., Carrasco C, Martín C

Fermentation 9 (6) 556 [2023-06-10; online 2023-06-10]

Integrated Microscopy Technologies Umeå [Service] Swedish NMR Centre (SNC) [Collaborative]

Mutations in the CYP27B1 gene cause vitamin D dependent rickets in pugs.

Rohdin C, Wang C, Brander G, ..., Ljungvall I, Lindblad-Toh K

J. Vet. Intern. Med. 37 (4) 1507-1513 [2023-06-09; online 2023-06-09]

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Adipokines and risk of rheumatoid arthritis: A two-sample multivariable Mendelian randomisation study.

Vasileiadis GK, Sayols S, Zhao SS, Fatima T, Maglio C

PLoS ONE 18 (6) e0286981 [2023-06-09; online 2023-06-09]

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The clinical picture of ERCC6L2 disease: from bone marrow failure to acute leukemia.

Hakkarainen M, Kaaja I, Douglas SPM, ..., Kilpivaara O, Wartiovaara-Kautto U

Blood 141 (23) 2853-2866 [2023-06-08; online 2023-03-24]

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Molecular Pixelation: Single cell spatial proteomics by sequencing

Karlsson F, Kallas T, Thiagarajan D, ..., Barrio AM, Fredriksson S

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Epidemiology, validation, and clinical characteristics of inflammatory bowel disease: the ABIS birth cohort study.

Östensson M, Björkqvist O, Guo A, ..., Mårild K, Ludvigsson J

BMC Gastroenterol 23 (1) 199 [2023-06-08; online 2023-06-08]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Engineering Yeast to Improve Heterologous Abscisic Acid Production

Otto M, Gossing M, David F, Siewers V

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Chalmers Mass Spectrometry Infrastructure [Service]

Absence of changes in the milk microbiota during Escherichia coli endotoxin induced experimental bovine mastitis.

Dahlberg J, Johnzon CF, Sun L, ..., Östensson K, Dicksved J

Vet Res 54 (1) 46 [2023-06-08; online 2023-06-08]

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One, Two Three - Phosphaalkene Decoration Tailoring Solubility and Electronic Properties of Truxene-Based Electron Acceptors.

Shameem MA, Wells JAL, Gupta AK, Orthaber A

Chemistry 29 (32) e202300563 [2023-06-07; online 2023-04-25]

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Mating modifies the expression of crucial oxidative-reductive transcripts in the pig oviductal sperm reservoir: is the female ensuring sperm survival?

Álvarez-Rodríguez M, Roca J, Martínez EA, Rodríguez-Martínez H

Front Endocrinol (Lausanne) 14 (-) 1042176 [2023-06-07; online 2023-06-07]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Challenges in supplying empirical proof for predictions derived from Species Distribution Models (SDMs): the case of an invasive cyanobacterium.

Meriggi C, Mehrshad M, Johnson RK, Laugen AT, Drakare S

ISME COMMUN. 3 (1) 56 [2023-06-06; online 2023-06-06]

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Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes.

Younis S, Jouneau A, Larsson M, ..., Brochard V, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 120 (23) e2216799120 [2023-06-06; online 2023-05-30]

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RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.

Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM

BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]

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Dysregulated peripheral proteome reveals NASH-specific signatures identifying patient subgroups with distinct liver biology.

Stiglund N, Hagström H, Stål P, Cornillet M, Björkström NK

Front Immunol 14 (-) 1186097 [2023-06-05; online 2023-06-05]

Investigation of enzalutamide, docetaxel, and cabazitaxel resistance in the castration resistant prostate cancer cell line C4 using genome-wide CRISPR/Cas9 screening.

Haldrup J, Weiss S, Schmidt L, Sørensen KD

Sci Rep 13 (1) 9043 [2023-06-03; online 2023-06-03]

Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring.

Bag P, Shutova T, Shevela D, ..., Messinger J, Jansson S

Nat Commun 14 (1) 3210 [2023-06-03; online 2023-06-03]

Small molecule-mediated disruption of ribosome biogenesis synergizes with FGFR inhibitors to suppress glioma cell growth

Zisi A, Kanellis DC, Moussaud S, ..., Bartek J, Lindström MS

Neuro-oncology 25 (6) 1058-1072 [2023-06-02; online 2022-12-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Creation of distinctive Bax-lipid complexes at mitochondrial membrane surfaces drives pore formation to initiate apoptosis.

Clifton LA, Wacklin-Knecht HP, Ådén J, ..., Sparrman T, Gröbner G

Sci Adv 9 (22) eadg7940 [2023-06-02; online 2023-06-02]

Role of myeloid cells in system-level immunometabolic dysregulation during prolonged successful HIV-1 treatment.

Svensson Akusjärvi S, Krishnan S, Ambikan AT, ..., Sönnerborg A, Neogi U

AIDS 37 (7) 1023-1033 [2023-06-01; online 2023-03-21]

Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican.

Gómez-Martínez D, Bengtson J, Nilsson AK, ..., Kristiansson E, Corcoll N

Sci. Total Environ. 875 (-) 162604 [2023-06-01; online 2023-03-05]

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Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

Gomez-Garrido J, Cruz F, Alioto TS, ..., Otalora Acevedo KE, Baldo L

DNA Res. 30 (3) - [2023-06-01; online 2023-05-04]

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An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).

Peona V, Palacios-Gimenez OM, Lutgen D, ..., Suh A, Burri R

G3 (Bethesda) 13 (6) - [2023-06-01; online 2023-04-25]

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Transcriptome and metabolome profiling identify factors potentially involved in pro-vitamin A accumulation in cassava landraces.

Olayide P, Alexandersson E, Tzfadia O, ..., Gisel A, Stavolone L

Plant Physiol Biochem 199 (-) 107713 [2023-06-00; online 2023-04-24]

The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus).

Fuentes-Pardo AP, Farrell ED, Pettersson ME, Sprehn CG, Andersson L

Evol Appl 16 (6) 1201-1219 [2023-06-00; online 2023-06-06]

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The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.

Yazdi HP, Olito C, Kawakami T, ..., Hansson B, Cornwallis CK

PLoS Genet. 19 (6) e1010801 [2023-06-00; online 2023-06-30]

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The BioLymph study - implementing precision medicine approaches in lymphoma diagnostics, treatment and follow-up: feasibility and first results.

Smedby KE, Wästerlid T, Tham E, ..., Sonnevi K, Rosenquist R

Acta Oncol 62 (6) 560-564 [2023-06-00; online 2023-07-06]

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Retention of essential fatty acids in fish differs by species, habitat use and nutritional quality of prey.

Bandara T, Brugel S, Andersson A, Lau DCP

Ecol Evol 13 (6) e10158 [2023-06-00; online 2023-06-01]

Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration.

Brodmerkel MN, De Santis E, Caleman C, Marklund EG

Protein J 42 (3) 205-218 [2023-06-00; online 2023-04-08]

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Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma.

Panizza E, Regalado BD, Wang F, ..., Cerione RA, Antonyak MA

Life Sci. Alliance 6 (6) - [2023-06-00; online 2023-04-10]

Persistent immunosuppressive effects of dibutyl phthalate exposure in adult male mice

Pierozan P, Källsten L, Theodoropoulou E, Almamoun R, Karlsson O

Science of The Total Environment 878 (-) 162741 [2023-06-00; online 2023-06-00]

Pathogenic antibody response to glucose-6-phosphate isomerase targets a modified epitope uniquely exposed on joint cartilage.

Li T, Ge C, Krämer A, ..., Gjertsson I, Holmdahl R

Ann. Rheum. Dis. 82 (6) 799-808 [2023-06-00; online 2023-03-01]

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Northwest African Neolithic initiated by migrants from Iberia and Levant.

Simões LG, Günther T, Martínez-Sánchez RM, ..., Valdiosera C, Jakobsson M

Nature 618 (7965) 550-556 [2023-06-00; online 2023-06-07]

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Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag.

Bartosovic M, Castelo-Branco G

Nat. Biotechnol. 41 (6) 794-805 [2023-06-00; online 2022-12-19]

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High temperature interactions between coal ash and MgO-based refractories in lime kiln conditions

Wagri NK, Carlborg M, Eriksson M, ..., Broström M, Andersson BM

Fuel 342 (-) 127711 [2023-06-00; online 2023-06-00]

Genome-wide association study and functional characterization identifies candidate genes for insulin-stimulated glucose uptake.

Williamson A, Norris DM, Yin X, ..., Fazakerley DJ, Langenberg C

Nat. Genet. 55 (6) 973-983 [2023-06-00; online 2023-06-08]

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Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer.

Wadensten E, Wessman S, Abel F, ..., Gisselsson D, Genomic Medicine Sweden Childhood Cancer Working Group

JCO Precision Oncology 7 (-) e2300039 [2023-06-00; online 2023-06-29]

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Correlative Chemical Imaging Identifies Amyloid Peptide Signatures of Neuritic Plaques and Dystrophy in Human Sporadic Alzheimer's Disease.

Koutarapu S, Ge J, Jha D, ..., Michno W, Hanrieder J

Brain Connect 13 (5) 297-306 [2023-06-00; online 2022-10-07]

Integrated Microscopy Technologies Gothenburg [Service]

Contrasting plant-soil-microbial feedbacks stabilize vegetation types and uncouple topsoil C and N stocks across a subarctic-alpine landscape.

Castaño C, Hallin S, Egelkraut D, ..., Olofsson J, Clemmensen KE

New Phytol. 238 (6) 2621-2633 [2023-06-00; online 2022-12-29]

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Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities.

Seidel L, Broman E, Nilsson E, ..., Forsman A, Dopson M

ISME J 17 (6) 855-869 [2023-06-00; online 2023-03-28]

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CO2 hydrogenation to light olefins using In2O3 and SSZ-13 catalyst − Understanding the role of zeolite acidity in olefin production

Di W, Ho PH, Achour A, ..., Olsson L, Creaser D

Journal of CO2 Utilization 72 (-) 102512 [2023-06-00; online 2023-06-00]

Atlas of mRNA translation and decay for bacteria.

Huch S, Nersisyan L, Ropat M, ..., Engstrand L, Pelechano V

Nat Microbiol 8 (6) 1123-1136 [2023-06-00; online 2023-05-22]

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AdipoR2 recruits protein interactors to promote fatty acid elongation and membrane fluidity.

Ruiz M, Devkota R, Kaper D, ..., Borén J, Pilon M

J. Biol. Chem. 299 (6) 104799 [2023-06-00; online 2023-05-08]

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Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data.

Klar PB, Krysiak Y, Xu H, ..., Zou X, Palatinus L

Nat Chem 15 (6) 848-855 [2023-06-00; online 2023-04-20]

AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets.

Lees WD, Christley S, Peres A, ..., Busse CE, AIRR Community

Immunoinformatics (Amst) 10 (-) - [2023-06-00; online 2023-02-19]

A highly selective cell-based fluorescent biosensor for genistein detection

Chao LFI, Liu D, Siewers V

Engineering Microbiology 3 (2) 100078 [2023-06-00; online 2023-06-00]

Chalmers Mass Spectrometry Infrastructure [Service]

Triazole fungicides induce adipogenesis and repress osteoblastogenesis in zebrafish.

Thrikawala S, Mesmar F, Bhattacharya B, ..., Williams C, Bondesson M

Toxicol. Sci. 193 (2) 119-130 [2023-05-31; online 2023-03-24]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Reply to Pandey: IgG3 allotypes, modulation of antigen binding by constant domain changes, and therapeutic applications of Fc engineering.

Izadi A, Bahnan W, Ohlin M, Nordenfelt P

Proc. Natl. Acad. Sci. U.S.A. 120 (22) e2306562120 [2023-05-30; online 2023-05-22]

Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle.

Knöppel A, Broström O, Gras K, Elf J, Fange D

Proc. Natl. Acad. Sci. U.S.A. 120 (22) e2213795120 [2023-05-30; online 2023-05-23]

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Discovery of non-reference processed pseudogenes in the Swedish population.

Ten Berk de Boer E, Bilgrav Saether K, Eisfeldt J

Front Genet 14 (-) 1176626 [2023-05-30; online 2023-05-30]

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Unraveling effects of electron correlation in two-dimensional FenGeTe2 (n = 3, 4, 5) by dynamical mean field theory

Ghosh S, Ershadrad S, Borisov V, Sanyal B

npj Comput Mater 9 (1) - [2023-05-29; online 2023-05-29]

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Reduced cone photoreceptor function and subtle systemic manifestations in two siblings with loss of SCLT1.

Grudzinska Pechhacker MK, Molnar A, Pekkola Pacheco N, ..., Nordgren A, Lindstrand A

Ophthalmic Genet - (-) 1-8 [2023-05-29; online 2023-05-29]

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Directionality of developing skeletal muscles is set by mechanical forces.

Sunadome K, Erickson AG, Kah D, ..., Fried K, Adameyko I

Nat Commun 14 (1) 3060 [2023-05-27; online 2023-05-27]

Integrated Microscopy Technologies Stockholm [Service]

Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.

Jurdzinski KT, Mehrshad M, Delgado LF, ..., Bertilsson S, Andersson AF

Sci Adv 9 (21) eadg2059 [2023-05-26; online 2023-05-26]

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Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein.

Watts ME, Oksanen M, Lejerkrans S, ..., Gorospe M, Tammimies K

BMC Biol. 21 (1) 127 [2023-05-26; online 2023-05-26]

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Balancing selection on the complement system of a wild rodent.

Nandakumar M, Lundberg M, Carlsson F, Råberg L

BMC Ecol Evol 23 (1) 21 [2023-05-25; online 2023-05-25]

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The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.

Díaz de Ståhl T, Shamikh A, Mayrhofer M, ..., Sandgren J, Nistér M

J Transl Med 21 (1) 342 [2023-05-23; online 2023-05-23]

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Variation in fatty acid content among benthic invertebrates in a seasonally driven system

Hedberg P, Lau DCP, Albert S, Winder M

Limnol Oceanogr Letters - (-) - [2023-05-22; online 2023-05-22]

Sequence enrichment profiles enable target-agnostic antibody generation for a broad range of antigens.

Mattsson J, Ljungars A, Carlsson A, ..., Ohlin M, Frendéus B

Cell Reports Methods 3 (5) 100475 [2023-05-22; online 2023-05-09]

RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins.

Stenum TS, Kumar AD, Sandbaumhüter FA, ..., Jansson ET, Holmqvist E

Nucleic Acids Res. 51 (9) 4572-4587 [2023-05-22; online 2023-03-30]

Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR.

Obana N, Takada H, Crowe-McAuliffe C, ..., Wilson DN, Hauryliuk V

Nucleic Acids Res. 51 (9) 4536-4554 [2023-05-22; online 2023-03-24]

Cisplatin toxicity is counteracted by the activation of the p38/ATF-7 signaling pathway in post-mitotic C. elegans.

Raj D, Kraish B, Martikainen J, ..., Kao G, Naredi P

Nat Commun 14 (1) 2886 [2023-05-20; online 2023-05-20]

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Phase identification and discovery of hidden crystal forms in a polycrystalline pharmaceutical sample using high-throughput 3D electron diffraction

Lightowler M, Li S, Ou X, ..., Lu M, Xu H

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Cryo-EM [Technology development]

Detoxified synthetic bacterial membrane vesicles as a vaccine platform against bacteria and SARS-CoV-2.

Park KS, Svennerholm K, Crescitelli R, ..., Farewell A, Lötvall J

J Nanobiotechnology 21 (1) 156 [2023-05-19; online 2023-05-19]

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Cross-reactive EBNA1 immunity targets alpha-crystallin B and is associated with multiple sclerosis.

Thomas OG, Bronge M, Tengvall K, ..., Olsson T, Kockum I

Sci Adv 9 (20) eadg3032 [2023-05-19; online 2023-05-17]

Sense and Screen-ability: Development of tuneable, biosensor-based screening platforms for abscisic acid

Otto M, Dabirian Y, David F, Siewers V

- - (-) - [2023-05-18; online 2023-05-18]

Chalmers Mass Spectrometry Infrastructure [Service]

Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.

Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å

Front Microbiol 14 (-) 1159811 [2023-05-18; online 2023-05-18]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.

Ahlstrom CA, Woksepp H, Sandegren L, Ramey AM, Bonnedahl J

Appl. Environ. Microbiol. - (-) e0031923 [2023-05-17; online 2023-05-17]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.

Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P

J. Am. Chem. Soc. 145 (19) 10700-10711 [2023-05-17; online 2023-05-04]

The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis.

Kokkinou E, Soini T, Pandey RV, ..., Rolandsdotter H, Mjösberg J

Cell Reports Medicine 4 (5) 101038 [2023-05-16; online 2023-05-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

DNA methylation variations and epigenetic aging in telomere biology disorders.

Carlund O, Norberg A, Osterman P, ..., Degerman S, Hultdin M

Sci Rep 13 (1) 7955 [2023-05-16; online 2023-05-16]

Clinical Genomics [Service] Clinical Genomics Umeå [Service]

Soluble CD14 and osteoprotegerin associate with ankle-brachial index as a measure of arterial stiffness in patients with mild to moderate chronic kidney disease in a five-year prospective study.

Sendic S, Mansouri L, Hong M, ..., Lundahl J, Jacobson SH

Cardiorenal Med - (-) 1 [2023-05-15; online 2023-05-15]

Metagenomic sequencing of human cardiac tissue reveals Microbial RNA which correlates with Toll-like receptor-associated inflammation in patients with heart disease.

Sandstedt J, Vukusic K, Dellgren G, ..., Mattsson Hultén L, Rotter Sopasakis V

Sci Rep 13 (1) 7884 [2023-05-15; online 2023-05-15]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Development of a machine learning framework for radiation biomarker discovery and absorbed dose prediction.

Andersson B, Langen B, Liu P, Dávila López M

Front Oncol 13 (-) 1156009 [2023-05-15; online 2023-05-15]

Clinical Genomics [Technology development] Clinical Genomics Gothenburg [Technology development]

Complement C3a treatment accelerates recovery after stroke via modulation of astrocyte reactivity and cortical connectivity.

Stokowska A, Aswendt M, Zucha D, ..., Pekny M, Pekna M

J. Clin. Invest. 133 (10) - [2023-05-15; online 2023-05-15]

Integrated Microscopy Technologies Gothenburg [Service]

Biomarkers of seafood intake during pregnancy - Pollutants versus fatty acids and micronutrients.

Stråvik M, Gustin K, Barman M, ..., Kippler M, Vahter M

Environ. Res. 225 (-) 115576 [2023-05-15; online 2023-03-05]

Chalmers Mass Spectrometry Infrastructure [Service]

Can molecular dynamics be used to simulate biomolecular recognition?

Lüking M, van der Spoel D, Elf J, Tribello GA

J Chem Phys 158 (18) - [2023-05-14; online 2023-05-09]

Bioinformatics Support for Computational Resources [Service]

The impact of immunomodulating treatment on the immunogenicity of COVID-19 vaccines in patients with immune-mediated inflammatory rheumatic diseases compared to healthy controls. A Swedish nationwide study (COVID19-REUMA).

Frodlund M, Nived P, Chatzidionysiou A, ..., Klareskog L, Kapetanovic MC

Vaccine 41 (20) 3247-3257 [2023-05-11; online 2023-04-04]

Structural, vibrational, elastic, electronic, and piezoelectric properties of binary <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">γ<mml:mtext>−</mml:mtext><mml:mrow>GeX</mml:mrow></mml:math> and ternary <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">γ<mml:mtext>−</mml:mtext><mml:mrow><mml:msub>Ge2</mml:msub>X<mml:msup>X′</mml:msup></mml:mrow></mml:math> monolayers ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">X</mml:math> , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup>X′</mml:msup>=<mml:mi mathvariant="normal">S</mml:math> , Se, and Te)

Varjovi MJ, Ershadrad S, Sanyal B

Phys. Rev. B 107 (19) - [2023-05-11; online 2023-05-11]

Bioinformatics Support for Computational Resources [Service]

Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins.

Elliott K, Singh VK, Boström M, Larsson E

Nat Commun 14 (1) 2701 [2023-05-11; online 2023-05-11]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Warmer temperatures favor slower-growing bacteria in natural marine communities.

Abreu CI, Dal Bello M, Bunse C, Pinhassi J, Gore J

Sci Adv 9 (19) eade8352 [2023-05-10; online 2023-05-10]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Glycan Stability and Flexibility: Thermodynamic and Kinetic Characterization of Nonconventional Hydrogen Bonding in Lewis Antigens.

Kwon J, Ruda A, Azurmendi HF, ..., Widmalm G, Freedberg DI

J. Am. Chem. Soc. 145 (18) 10022-10034 [2023-05-10; online 2023-04-26]

Effects of rye inclusion in dog food on fecal microbiota and short-chain fatty acids.

Palmqvist H, Ringmark S, Höglund K, ..., Lundh T, Dicksved J

BMC Vet Res 19 (1) 70 [2023-05-10; online 2023-05-10]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Multiparametric and High-Throughput Platform for Host–Virus Binding Screens

Schlegel J, Porebski B, Andronico L, ..., Fernandez-Capetillo O, Sezgin E

Nano Lett. 23 (9) 3701-3707 [2023-05-10; online 2023-03-09]

Integrated Microscopy Technologies Stockholm [Service]

The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots

Lazarian G, Leroy B, Theves F, ..., Baran-Marszak F, Soussi T

Hum. Mutat. 2023 (-) 1-17 [2023-05-09; online 2023-05-09]

NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Stress-sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis.

Örkenby L, Skog S, Ekman H, ..., Nätt D, Öst A

Mol. Syst. Biol. 19 (5) e11148 [2023-05-09; online 2023-03-20]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

CRISPR-Cas9 knockout screen identifies novel treatment targets in childhood high-grade glioma.

Wenger A, Karlsson I, Kling T, Carén H

Clin Epigenetics 15 (1) 80 [2023-05-09; online 2023-05-09]

CRISPR Functional Genomics [Service] Integrated Microscopy Technologies Gothenburg [Service]

A topical rectal douche product containing Q-Griffithsin does not disrupt the epithelial border or alter CD4+ cell distribution in the human rectal mucosa.

Franzén Boger M, Benhach N, Hasselrot T, ..., Broliden K, Tjernlund A

Sci Rep 13 (1) 7547 [2023-05-09; online 2023-05-09]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

The spatial landscape of gene expression isoforms in tissue sections.

Lebrigand K, Bergenstråhle J, Thrane K, ..., Waldmann R, Lundeberg J

Nucleic Acids Res. 51 (8) e47 [2023-05-08; online 2023-03-18]

NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Reduced binding of apoE4 to complement factor H promotes amyloid-β oligomerization and neuroinflammation.

Chernyaeva L, Ratti G, Teirilä L, ..., Nissilä E, Haapasalo K

EMBO Rep. - (-) e56467 [2023-05-08; online 2023-05-08]

Genomics of adaptive evolution in the woolly mammoth.

Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, ..., van der Valk T, Dalén L

Curr. Biol. 33 (9) 1753-1764.e4 [2023-05-08; online 2023-04-07]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Longitudinal Study of Individual Radiation Responses in Pediatric Patients Treated with Proton and Photon Radiotherapy, and Interventional Cardiology: Rationale and Research Protocol of the HARMONIC Project.

Andreassi MG, Haddy N, Harms-Ringdahl M, ..., Fuentes M, Haghdoost S

Int J Mol Sci 24 (9) - [2023-05-08; online 2023-05-08]

Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study.

Vikström L, Fjällström P, Gwon YD, ..., Johansson AF, Forsell MNE

Lancet Reg Health Eur 30 (-) 100646 [2023-05-06; online 2023-05-06]

A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.

Pettersson ME, Fuentes-Pardo AP, Rochus CM, ..., Väinölä R, Andersson L

Genome Biol Evol 15 (5) - [2023-05-05; online 2023-04-30]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Shiga toxin-producing Escherichia coli (STEC) and atypical enteropathogenic E. coli (aEPEC) in Swedish retail wheat flour.

Söderlund R, Flink C, Aspán A, Eriksson E

Access Microbiol 5 (5) - [2023-05-03; online 2023-05-03]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

On-Tissue Chemical Derivatization for Comprehensive Mapping of Brain Carboxyl and Aldehyde Metabolites by MALDI-MS Imaging.

Kaya I, Schembri LS, Nilsson A, ..., Odell LR, Andrén PE

J. Am. Soc. Mass Spectrom. 34 (5) 836-846 [2023-05-03; online 2023-04-13]

Imaging Radial Distribution Functions of Complex Particles by Relayed Dynamic Nuclear Polarization.

Berruyer P, Cibaka-Ndaya C, Pinon A, ..., Drisko GL, Emsley L

J. Am. Chem. Soc. 145 (17) 9700-9707 [2023-05-03; online 2023-04-19]

descSPIM: Affordable and Easy-to-Build Light-Sheet Microscopy for Tissue Clearing Technique Users

Otomo K, Omura T, Nozawa Y, Saito Y, Susaki EA

- - (-) - [2023-05-02; online 2023-05-02]

Integrated Microscopy Technologies Stockholm [Technology development]

SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.

Gollnisch R, Wallenius J, Gribble KE, Ahrén D, Rengefors K

Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Resolution enhancement of NMR by decoupling with the low-rank Hankel model.

Qiu T, Jahangiri A, Han X, ..., Qu X, Orekhov V

Chem. Commun. (Camb.) 59 (36) 5475-5478 [2023-05-02; online 2023-05-02]

Nontarget Analysis of Polluted Surface Waters in Bangladesh Using Open Science Workflows

Bonnefille B, Karlsson O, Rian MB, ..., Islam MS, Martin JW

Environ. Sci. Technol. 57 (17) 6808-6824 [2023-05-02; online 2023-04-21]

Micro Germline-Restricted Chromosome in Blue Tits: Evidence for Meiotic Functions.

Mueller JC, Schlebusch SA, Pei Y, ..., Suh A, Kempenaers B

Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Structural elucidation of 3-nitrophenylhydrazine derivatives of tricarboxylic acid cycle acids and optimization of their fragmentation to boost sensitivity in liquid chromatography-mass spectrometry.

Hodek O, Henderson J, Argemi-Muntadas L, Khan A, Moritz T

Journal of Chromatography B 1222 (-) 123719 [2023-05-01; online 2023-04-11]

Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.

Mosquera KD, Nilsson LKJ, de Oliveira MR, ..., de Souza AQL, Terenius O

Parasit Vectors 16 (1) 156 [2023-05-01; online 2023-05-01]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Bile acids accumulate norovirus-like particles and enhance binding to and entry into human enteric epithelial cells

Palm E, Danskog K, Nord S, ..., Lenman A, Arnberg N

- - (-) - [2023-05-01; online 2023-05-01]

Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.

Grüttner J, van Rijn JM, Geiser P, ..., Sellin ME, Svärd SG

PLoS Pathog. 19 (5) e1011372 [2023-05-00; online 2023-05-04]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data.

Pielawski N, Andersson A, Avenel C, ..., Solorzano L, Wählby C

Heliyon 9 (5) e15306 [2023-05-00; online 2023-04-17]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.

Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E

Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Plasma protein and venous thromboembolism: prospective cohort and mendelian randomisation analyses.

Yuan S, Titova OE, Zhang K, ..., Damrauer SM, Larsson SC

Br. J. Haematol. 201 (4) 783-792 [2023-05-00; online 2023-02-02]

Overweight in childhood and young adulthood increases the risk for adult thromboembolic events.

Lilja L, Bygdell M, Martikainen J, ..., Kindblom JM, Ohlsson C

J. Intern. Med. 293 (5) 615-623 [2023-05-00; online 2023-03-01]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Melanocortin-4 receptors on neurons in the parabrachial nucleus mediate inflammation-induced suppression of food-seeking behavior.

Shionoya K, Nilsson A, Engström Ruud L, Engblom D, Blomqvist A

Brain, Behavior, and Immunity 110 (-) 80-84 [2023-05-00; online 2023-02-20]

Integrated Microscopy Technologies Gothenburg [Service]

Insulin thermostability in a real-world setting.

Pendsey S, James S, Garrett TJ, ..., Forsander G, Ogle GD

Lancet Diabetes Endocrinol 11 (5) 310-312 [2023-05-00; online 2023-03-29]

Inhibition of VEGF-B signaling prevents non-alcoholic fatty liver disease development by targeting lipolysis in the white adipose tissue.

Falkevall A, Mehlem A, Folestad E, ..., Nash A, Eriksson U

J Hepatol 78 (5) 901-913 [2023-05-00; online 2023-01-27]

Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates.

Mierke F, Brink DP, Norbeck J, Siewers V, Andlid T

Fungal Genet. Biol. 166 (-) 103783 [2023-05-00; online 2023-03-03]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Flexible Organic Electronic Ion Pump for Flow-Free Phytohormone Delivery into Vasculature of Intact Plants.

Bernacka-Wojcik I, Talide L, Abdel Aziz I, ..., Niittylä T, Stavrinidou E

Adv Sci (Weinh) 10 (14) e2206409 [2023-05-00; online 2023-03-19]

Extracellular Vesicle-Associated TWEAK Contributes to Vascular Inflammation and Remodeling During Acute Cellular Rejection.

Celik S, Sadrian J, Grossi M, ..., Smith JG, Gidlöf O

JACC Basic Transl Sci 8 (5) 439-456 [2023-05-00; online 2023-01-11]

Divergent and dominant anti-inflammatory effects of patient-derived anticitrullinated protein antibodies (ACPA) in arthritis development.

Raposo B, Afonso M, Israelsson L, ..., Klareskog L, Malmström V

Ann. Rheum. Dis. 82 (5) 724-726 [2023-05-00; online 2023-01-05]

Different spatial structure of plant-associated fungal communities above- and belowground.

Faticov M, Abdelfattah A, Hambäck P, Roslin T, Tack AJM

Ecol Evol 13 (5) e10065 [2023-05-00; online 2023-05-21]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Circulating proteins and peripheral artery disease risk: observational and Mendelian randomization analyses.

Yuan S, Titova OE, Zhang K, ..., VA Million Veteran Program , Larsson SC

Eur Heart J Open 3 (3) oead056 [2023-05-00; online 2023-05-30]

Characterisation of ash particles from co-combustion of bark and sludges from pulp and paper industry

Skoglund N, Thyrel M, Perrin J, Strandberg A

Fuel 340 (-) 127597 [2023-05-00; online 2023-05-00]

B4GALNT3 regulates glycosylation of sclerostin and bone mass.

Movérare-Skrtic S, Voelkl J, Nilsson KH, ..., Henning P, Ohlsson C

EBioMedicine 91 (-) 104546 [2023-05-00; online 2023-04-04]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Al-Gazali Skeletal Dysplasia Constitutes the Lethal End of ADAMTSL2-Related Disorders.

Batkovskyte D, McKenzie F, Taylan F, ..., Nishimura G, Grigelioniene G

J. Bone Miner. Res. 38 (5) 692-706 [2023-05-00; online 2023-03-27]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An extracellular matrix stiffness-induced breast cancer cell transcriptome resembles the transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC).

Göransson S, Chen S, Olofsson H, Larsson O, Strömblad S

Biochem. Biophys. Res. Commun. 654 (-) 73-79 [2023-04-30; online 2023-03-02]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.

Moon KL, Huson HJ, Morrill K, ..., Karlsson EK, Shapiro B

Science 380 (6643) eabn5887 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Three-dimensional genome rewiring in loci with human accelerated regions.

Keough KC, Whalen S, Inoue F, ..., Pollen A, Pollard KS

Science 380 (6643) eabm1696 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The functional and evolutionary impacts of human-specific deletions in conserved elements.

Xue JR, Mackay-Smith A, Mouri K, ..., Sabeti PC, Reilly SK

Science 380 (6643) eabn2253 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The contribution of historical processes to contemporary extinction risk in placental mammals.

Wilder AP, Supple MA, Subramanian A, ..., Ryder OA, Shapiro B

Science 380 (6643) eabn5856 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.

Kaplow IM, Lawler AJ, Schäffer DE, ..., Meyer WK, Pfenning AR

Science 380 (6643) eabm7993 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

No fitness impact of the knockout of the two main components of mimivirus genomic fiber and fibril layer

Alempic JM, Bisio H, Villalta A, ..., Couté Y, Abergel C

- - (-) - [2023-04-28; online 2023-04-28]

Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.

Andrews G, Fan K, Pratt HE, ..., Moore JE, Weng Z

Science 380 (6643) eabn7930 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Leveraging base-pair mammalian constraint to understand genetic variation and human disease.

Sullivan PF, Meadows JRS, Gazal S, ..., Karlsson EK, Lindblad-Toh K

Science 380 (6643) eabn2937 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Investigating New Applications of a Photoswitchable Fluorescent Norbornadiene as a Multifunctional Probe for Delineation of Amyloid Plaque Polymorphism.

Dreos A, Ge J, Najera F, ..., Zetterberg H, Hanrieder J

ACS Sens. 8 (4) 1500-1509 [2023-04-28; online 2023-03-22]

Integrated Microscopy Technologies Gothenburg [Service]

Integrating gene annotation with orthology inference at scale.

Kirilenko BM, Munegowda C, Osipova E, ..., Zoonomia Consortium‡ , Hiller M

Science 380 (6643) eabn3107 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Insights into mammalian TE diversity through the curation of 248 genome assemblies.

Osmanski AB, Paulat NS, Korstian J, ..., Lindblad-Toh K, Ray DA

Science 380 (6643) eabn1430 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolutionary constraint and innovation across hundreds of placental mammals.

Christmas MJ, Kaplow IM, Genereux DP, ..., Lindblad-Toh K, Karlsson EK

Science 380 (6643) eabn3943 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A genomic timescale for placental mammal evolution.

Foley NM, Mason VC, Harris AJ, ..., Springer MS, Murphy WJ

Science 380 (6643) eabl8189 [2023-04-28; online 2023-04-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prominent epigenetic and transcriptomic changes in CD4+ and CD8+ T cells during and after pregnancy in women with multiple sclerosis and controls.

Zenere A, Hellberg S, Papapavlou Lingehed G, ..., Gustafsson M, Ernerudh J

J Neuroinflammation 20 (1) 98 [2023-04-27; online 2023-04-27]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Temporal multimodal single-cell profiling of native hematopoiesis illuminates altered differentiation trajectories with age.

Konturek-Ciesla A, Dhapola P, Zhang Q, ..., Karlsson G, Bryder D

Cell Rep 42 (4) 112304 [2023-04-25; online 2023-03-23]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.

Rosenbaum A, Dahlin AM, Andersson U, ..., Wibom C, Melin B

Sci Rep 13 (1) 6777 [2023-04-25; online 2023-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]

Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.

Majumdar S, Emmerich A, Krakovka S, ..., Svärd SG, Sanyal S

Nucleic Acids Res. 51 (7) 3436-3451 [2023-04-24; online 2023-03-14]

Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]

Transcriptomics unravels molecular changes associated with cilia and COVID-19 in chronic rhinosinusitis with nasal polyps.

Torinsson Naluai Å, Östensson M, Fowler PC, ..., Harandi AM, Bende M

Sci Rep 13 (1) 6592 [2023-04-21; online 2023-04-21]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Optimizing yeast for high-level production of kaempferol and quercetin.

Tartik M, Liu J, Mohedano MT, Mao J, Chen Y

Microb. Cell Fact. 22 (1) 74 [2023-04-20; online 2023-04-20]

Chalmers Mass Spectrometry Infrastructure [Service]

Identification of three bacterial species associated with increased appendicular lean mass: the HUNT study.

Grahnemo L, Nethander M, Coward E, ..., Hveem K, Ohlsson C

Nat Commun 14 (1) 2250 [2023-04-20; online 2023-04-20]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.

Koskela von Sydow A, Lindqvist CM, Asghar N, ..., Mölling P, Stenmark B

Sci Rep 13 (1) 6461 [2023-04-20; online 2023-04-20]

Clinical Genomics [Technology development] Clinical Genomics Örebro [Technology development]

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Pucci M, Moschetti M, Urzì O, ..., Alessandro R, Fontana S

Cancer Cell Int 23 (1) 77 [2023-04-18; online 2023-04-18]

Integrated Microscopy Technologies Gothenburg [Service]

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J Am Heart Assoc 12 (8) e029248 [2023-04-18; online 2023-04-07]

Affinity Proteomics Uppsala [Service] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells.

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BMC Genomics 24 (1) 205 [2023-04-17; online 2023-04-17]

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Front Immunol 14 (-) - [2023-04-17; online 2023-04-17]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Achieving symptom relief in patients with myalgic encephalomyelitis by targeting the neuro-immune interface and optimizing disease tolerance.

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Oxf Open Immunol 4 (1) iqad003 [2023-04-17; online 2023-04-17]

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Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19.

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Nat Commun 14 (1) 2164 [2023-04-15; online 2023-04-15]

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Data Processing Methods: Fourier and Beyond

Orekhov V, Kasprzak P, Kazimierczuk K

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Age Rather Than Supplementation with Oat β-Glucan Influences Development of the Intestinal Microbiota and SCFA Concentrations in Suckling Piglets.

Arapovic L, Huang Y, Manell E, ..., Lindberg JE, Dicksved J

Animals (Basel) 13 (8) - [2023-04-14; online 2023-04-14]

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A glycan epitope correlates with tau in serum and predicts progression to Alzheimer's disease in combination with APOE4 allele status.

Zhou RZ, Vetrano DL, Grande G, ..., Tjernberg L, Schedin-Weiss S

Alzheimers Dement - (-) - [2023-04-12; online 2023-04-12]

The complement receptor C3AR constitutes a novel therapeutic target in NPM1-mutated AML.

von Palffy S, Thorsson H, Peña-Martínez P, ..., Lilljebjörn H, Fioretos T

Blood Adv 7 (7) 1204-1218 [2023-04-11; online 2022-11-17]

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Izadi A, Hailu A, Godzwon M, ..., Bahnan W, Nordenfelt P

Proc. Natl. Acad. Sci. U.S.A. 120 (15) e2217590120 [2023-04-11; online 2023-04-03]

SHP-1 localization to the activating immune synapse promotes NK cell tolerance in MHC class I deficiency.

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Sci Signal 16 (780) eabq0752 [2023-04-11; online 2023-04-11]

Integrated Microscopy Technologies Stockholm [Service]

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Chotiwan N, Rosendal E, Willekens SMA, ..., Marcellino D, Överby AK

Nat Commun 14 (1) - [2023-04-10; online 2023-04-10]

The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis

Planells J, Jordán-Pla A, Jain S, ..., Pelechano V, Visa N

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Chachaj A, Dudka I, Jeziorek M, ..., Adaszyńska A, Szuba A

Front Physiol 14 (-) 1099555 [2023-04-10; online 2023-04-10]

Longitudinal associations between use of antihypertensive, antidiabetic, and lipid-lowering medications and biological aging.

Tang B, Li X, Wang Y, ..., Pedersen NL, Hägg S

Geroscience - (-) - [2023-04-10; online 2023-04-10]

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Seasonal and Site-Specific Patterns of Airborne Fungal Diversity Revealed Using Passive Spore Traps and High-Throughput DNA Sequencing

Marčiulynas A, Lynikienė J, Marčiulynienė D, Gedminas A, Menkis A

Diversity 15 (4) 539 [2023-04-09; online 2023-04-09]

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The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins.

Gallego P, Garcia-Bonete MJ, Trillo-Muyo S, ..., Johansson MEV, Hansson GC

Nat Commun 14 (1) 1969 [2023-04-08; online 2023-04-08]

The First Swedish Outbreak with VIM-2-Producing Pseudomonas aeruginosa, Occurring between 2006 and 2007, Was Probably Due to Contaminated Hospital Sinks.

Fraenkel CJ, Starlander G, Tano E, Sütterlin S, Melhus Å

Microorganisms 11 (4) - [2023-04-08; online 2023-04-08]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

High-throughput metabolomics for the design and validation of a diauxic shift model.

Brunnsåker D, Reder GK, Soni NK, ..., Tiukova IA, King RD

npj Syst Biol Appl 9 (1) 11 [2023-04-07; online 2023-04-07]

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Serum metabolomic profiling identifies potential biomarkers in arthritis in older adults: an exploratory study.

Cedeno M, Murillo-Saich J, Coras R, ..., Martinez-Morillo M, Guma M

Metabolomics 19 (4) 37 [2023-04-06; online 2023-04-06]

Cross-Sectional Gene-Smoking Interaction Analysis in Relation to Subclinical Atherosclerosis-Results From the IMPROVE Study.

Maitusong B, Laguzzi F, Strawbridge RJ, ..., Leander K, IMPROVE Study group†

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Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Matuozzo D, Talouarn E, Marchal A, ..., Abel L, Cobat A

Genome Med 15 (1) - [2023-04-05; online 2023-04-05]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.

Magoulopoulou A, Salas SM, Tiklová K, ..., Hilscher MM, Nilsson M

Annu Rev Genomics Hum Genet - (-) - [2023-04-05; online 2023-04-05]

A wide scan of plasma proteins demonstrates thioredoxin reductase 1 as a potential new diagnostic biomarker for hepatocellular carcinoma.

Zenlander R, Fredolini C, Schwenk JM, ..., Eggertsen G, Stål P

Scand. J. Gastroenterol. - (-) 1-11 [2023-04-05; online 2023-04-05]

The genetic basis of wing spots in Pieris canidia butterflies.

Wee JLQ, Murugesan SN, Wheat CW, Monteiro A

BMC Genomics 24 (1) 169 [2023-04-04; online 2023-04-04]

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Abstract 3778: Genome-Scale CRISPRa and CRISPRi screening for lncRNA drivers of prostate cancer progression

Weiss S, Lord A, Schmierer B, ..., Borre M, Sørensen KD

Cancer Res. 83 (7_Supplement) 3778-3778 [2023-04-04; online 2023-04-04]

methylR: a graphical interface for comprehensive DNA methylation array data analysis.

Volpe M, Das J

Bioinformatics 39 (4) - [2023-04-03; online 2023-04-12]

Clinical Genomics [Technology development] Clinical Genomics Linköping [Technology development]

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Jambagi S, Hodén KP, Öhlund L, Dixelius C

J Appl Microbiol 134 (4) - [2023-04-03; online 2023-04-04]

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Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation.

Petkova M, Kraft M, Stritt S, ..., Betsholtz C, Mäkinen T

J. Exp. Med. 220 (4) - [2023-04-03; online 2023-01-23]

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Dynamin2 functions as an accessory protein to reduce the rate of caveola internalization.

Larsson E, Morén B, McMahon KA, Parton RG, Lundmark R

J. Cell Biol. 222 (4) - [2023-04-03; online 2023-02-02]

Integrated Microscopy Technologies Stockholm [Service]

Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.

Shuoker B, Pichler MJ, Jin C, ..., Karlsson NG, Abou Hachem M

Nat Commun 14 (1) 1833 [2023-04-01; online 2023-04-01]

Metabolomics of early myocardial ischemia.

Hasselbalch RB, Kristensen JH, Strandkjær N, ..., Malmendal A, Iversen KK

Metabolomics 19 (4) 33 [2023-04-01; online 2023-04-01]

Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls.

Derba-Maceluch M, Mitra M, Hedenström M, ..., Master ER, Mellerowicz EJ

New Phytol. 238 (1) 297-312 [2023-04-00; online 2023-01-31]

Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.

Pappas F, Kurta K, Vanhala T, ..., Beirão J, Palaiokostas C

Evol Appl 16 (4) 797-813 [2023-04-00; online 2023-02-27]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The human bone marrow plasma cell compartment in rheumatoid arthritis - Clonal relationships and anti-citrulline autoantibody producing cells.

Hensvold A, Horuluoglu B, Sahlström P, ..., Malmström V, Grönwall C

J. Autoimmun. 136 (-) 103022 [2023-04-00; online 2023-03-29]

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Microbial gene activity in straw residue amendments reveals carbon sequestration mechanisms in agricultural soils

Kozjek K, Manoharan L, Urich T, Ahrén D, Hedlund K

Soil Biology and Biochemistry 179 (-) 108994 [2023-04-00; online 2023-04-00]

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Lung macrophages utilize unique cathepsin K-dependent phagosomal machinery to degrade intracellular collagen.

Fabrik I, Bilkei-Gorzo O, Öberg M, ..., Göransson M, Härtlova A

Life Sci. Alliance 6 (4) - [2023-04-00; online 2023-01-25]

Interleukin-6 trans-signaling induced laminin switch contributes to reduced trans-endothelial migration of granulocytic cells.

Zegeye MM, Matic L, Lengquist M, ..., Ljungberg LU, Kumawat AK

Atherosclerosis 371 (-) 41-53 [2023-04-00; online 2023-03-22]

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.

Morez A, Britton K, Noble G, ..., Donald C, Girdland-Flink L

PLoS Genet. 19 (4) e1010360 [2023-04-00; online 2023-04-27]

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Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Ahlberg E, Martí M, Govindaraj D, ..., Jenmalm MC, Tingö L

Pediatr Allergy Immunol 34 (4) e13952 [2023-04-00; online 2023-04-27]

Genetically and environmentally predicted obesity in relation to cardiovascular disease: a nationwide cohort study.

Ojalehto E, Zhan Y, Jylhävä J, ..., Dahl Aslan AK, Karlsson IK

EClinicalMedicine 58 (-) 101943 [2023-04-00; online 2023-04-06]

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From high masked to high realized genetic load in inbred Scandinavian wolves.

Smeds L, Ellegren H

Mol. Ecol. 32 (7) 1567-1580 [2023-04-00; online 2022-12-13]

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Formate overflow drives toxic folate trapping in MTHFD1 inhibited cancer cells.

Green AC, Marttila P, Kiweler N, ..., Henriksson M, Meiser J

Nat Metab 5 (4) 642-659 [2023-04-00; online 2023-04-03]

Drug Discovery and Development (DDD) [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]

Epigenetic changes in the CYP2D6 gene are related to severity of suicide attempt: A cross-sectional study of suicide attempters.

Boström AED, Jamshidi E, Manu DM, ..., Åsberg M, Jokinen J

J Psychiatr Res 160 (-) 217-224 [2023-04-00; online 2023-02-24]

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Effect of alkalinity on the diffusion of solvent-fractionated lignin through cellulose membranes

Ghaffari R, Almqvist H, Idström A, ..., Lawoko M, Larsson A

Cellulose 30 (6) 3685-3698 [2023-04-00; online 2023-02-28]

Cardiac Plin5 interacts with SERCA2 and promotes calcium handling and cardiomyocyte contractility.

Cinato M, Mardani I, Miljanovic A, ..., Borén J, Levin MC

Life Sci. Alliance 6 (4) - [2023-04-00; online 2023-01-30]

A Room-Temperature Spin-Valve with van der Waals Ferromagnet Fe5 GeTe2 /Graphene Heterostructure.

Zhao B, Ngaloy R, Ghosh S, ..., Sanyal B, Dash SP

Adv Mater 35 (16) e2209113 [2023-04-00; online 2023-03-08]

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Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers.

Edfeldt G, Kaldhusdal V, Czarnewski P, ..., Kwon DS, Broliden K

Microbiome 11 (1) 67 [2023-03-31; online 2023-03-31]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

C-type lectin receptor agonists elicit functional IL21-expressing Tfh cells and induce primary B cell responses in neonates.

Vono M, Mastelic-Gavillet B, Mohr E, ..., Lambert P, Siegrist C

Front Immunol 14 (-) 1155200 [2023-03-31; online 2023-03-31]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

SLC38A10 Deficiency in Mice Affects Plasma Levels of Threonine and Histidine in Males but Not in Females: A Preliminary Characterization Study of SLC38A10-/- Mice.

Lindberg FA, Nordenankar K, Forsberg EC, Fredriksson R

Genes 14 (4) - [2023-03-30; online 2023-03-30]

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Lingonberry (Vaccinium vitis-idaea) press-cake as a new processing aid during isolation of protein from herring (Clupea harengus) co-products.

Zhang J, Abdollahi M, Ström A, Undeland I

Food Chem X 17 (-) 100592 [2023-03-30; online 2023-02-04]

Chalmers Mass Spectrometry Infrastructure [Service]

Analysis of human lung mast cells by single cell RNA sequencing.

Rönnberg E, Ravindran A, Mazzurana L, ..., Mjösberg J, Nilsson G

Front Immunol 14 (-) 1151754 [2023-03-30; online 2023-03-30]

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Novel Insights into the Molecular Mechanisms Underlying Robustness and Stability in Probiotic Bifidobacteria.

Schöpping M, Goel A, Jensen K, ..., Franzén CJ, Zeidan AA

Appl. Environ. Microbiol. 89 (3) e0008223 [2023-03-29; online 2023-02-21]

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Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments.

Seidel L, Sachpazidou V, Ketzer M, ..., Forsman A, Dopson M

Front Microbiol 14 (-) 1099445 [2023-03-29; online 2023-03-29]

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On the hydrothermal depolymerisation of kraft lignin using glycerol as a capping agent

Ahlbom A, Maschietti M, Nielsen R, Hasani M, Theliander H

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Trimethylamine N-Oxide (TMAO) Mediates Increased Inflammation and Colonization of Bladder Epithelial Cells during a Uropathogenic E. coli Infection In Vitro.

Wu R, Kumawat AK, Demirel I

Pathogens 12 (4) - [2023-03-27; online 2023-03-27]

Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce.

Chen ZQ, Klingberg A, Hallingbäck HR, Wu HX

BMC Genomics 24 (1) 147 [2023-03-27; online 2023-03-27]

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Linking prokaryotic genome size variation to metabolic potential and environment.

Rodríguez-Gijón A, Buck M, Andersson AF, ..., Nascimento FJA, Garcia SL

ISME COMMUN. 3 (1) 25 [2023-03-27; online 2023-03-27]

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Insights into Photosensitized Reactions for Upgrading Lignin

Riddell A, Hynynen J, Baena-Moreno F, ..., Parkås J, Bernin D

ACS Sustainable Chem. Eng. 11 (12) 4850-4859 [2023-03-27; online 2023-03-15]

Deep learning-based segmentation and quantification of podocyte foot process morphology suggests differential patterns of foot process effacement across kidney pathologies.

Unnersjö-Jess D, Butt L, Höhne M, ..., Bozek K, Benzing T

Kidney Int. - (-) - [2023-03-27; online 2023-03-27]

Integrated Microscopy Technologies Stockholm [Collaborative]

Correlative Chemical Imaging and Spatial Chemometrics Delineate Alzheimer Plaque Heterogeneity at High Spatial Resolution.

Wehrli PM, Ge J, Michno W, ..., Blennow K, Hanrieder J

JACS Au 3 (3) 762-774 [2023-03-27; online 2023-03-07]

Integrated Microscopy Technologies Gothenburg [Service]

A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration.

Subramanian E, Elewa A, Brito G, ..., Andersson O, Simon A

Dev. Cell 58 (6) 450-460.e6 [2023-03-27; online 2023-03-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Simultaneous Ultra-Sensitive Detection of Structural and Single Nucleotide Variants Using Multiplex Droplet Digital PCR in Liquid Biopsies from Children with Medulloblastoma.

Arthur C, Jylhä C, de Ståhl TD, ..., Sandvik U, Tham E

Cancers (Basel) 15 (7) - [2023-03-25; online 2023-03-25]

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Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia.

Woodward EL, Yang M, Moura-Castro LH, ..., Foijer F, Paulsson K

Nat Commun 14 (1) 1658 [2023-03-25; online 2023-03-25]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents.

Piombo E, Kelbessa BG, Sundararajan P, ..., Vetukuri RR, Dubey M

Front Microbiol 14 (-) 1076522 [2023-03-24; online 2023-03-24]

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Prediction model for drug response of acute myeloid leukemia patients.

Trac QT, Pawitan Y, Mou T, ..., Kallioniemi O, Vu TN

NPJ Precis Oncol 7 (1) 32 [2023-03-24; online 2023-03-24]

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Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants.

Mäkelä AR, Uğurlu H, Hannula L, ..., Rissanen I, Saksela K

Nat Commun 14 (1) 1637 [2023-03-24; online 2023-03-24]

New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus.

Durcik M, Cotman AE, Toplak Ž, ..., Tomašič T, Peterlin Mašič L

J. Med. Chem. 66 (6) 3968-3994 [2023-03-23; online 2023-03-06]

Neutralizing Carbapenem Resistance by Co-Administering Meropenem with Novel β-Lactam-Metallo-β-Lactamase Inhibitors.

Reddy N, Girdhari L, Shungube M, ..., Govender T, Naicker T

Antibiotics (Basel) 12 (4) - [2023-03-23; online 2023-03-23] Open Access

Drug Discovery and Development (DDD) [Collaborative]

Micro-scale spatial preference and temporal cyclicity linked to foraging in harbour porpoises

Stedt J, Wahlberg M, Carlström J, ..., Oskolkov N, Carlsson P

Mar. Ecol. Prog. Ser. 708 (-) 143-161 [2023-03-23; online 2023-03-23]

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Exposure to nonanoic acid alters small intestinal neuroendocrine tumor phenotype.

Almobarak B, Amlani V, Inge L, ..., Arvidsson Y, Elias E

BMC Cancer 23 (1) 267 [2023-03-23; online 2023-03-23]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Evidence for a single, ancient origin of a genus-wide alternative life history strategy.

Tunström K, Woronik A, Hanly JJ, ..., Martin A, Wheat CW

Sci Adv 9 (12) eabq3713 [2023-03-22; online 2023-03-22]

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Correlates of protection and viral load trajectories in omicron breakthrough infections in triple vaccinated healthcare workers.

Marking U, Havervall S, Norin NG, ..., Klingström J, Thålin C

Nat Commun 14 (1) 1577 [2023-03-22; online 2023-03-22]

Affinity Proteomics Uppsala [Collaborative] Autoimmunity and Serology Profiling [Collaborative]

Serum immuno-oncology markers carry independent prognostic information in patients with newly diagnosed metastatic breast cancer, from a prospective observational study.

Gunnarsdottir FB, Bendahl PO, Johansson A, ..., Bergenfelz C, Larsson AM

Breast Cancer Res. 25 (1) 29 [2023-03-21; online 2023-03-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Motor nerves direct the development of the sympathetic nervous system

Erickson A, Motta A, Kastriti ME, ..., Bonanomi D, Adameyko I

- - (-) - [2023-03-18; online 2023-03-18]

Integrated Microscopy Technologies Stockholm [Collaborative]

Complete Reference Genome Sequence of the Clinical Neisseria gonorrhoeae Strain H035, with Resistance to the Novel Antimicrobial Zoliflodacin, Identified in Japan in 2000.

Golparian D, Jacobsson S, Ohnishi M, Unemo M

Microbiol Resour Announc 12 (3) e0113022 [2023-03-16; online 2023-02-28]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Rapid and accurate determination of protein content in North Atlantic seaweed by NIR and FTIR spectroscopies.

Niemi C, Mortensen AM, Rautenberger R, ..., Gorzsás A, Gentili FG

Food Chem 404 (Pt B) 134700 [2023-03-15; online 2022-10-19]

Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis.

Geroldinger-Simić M, Bayati S, Pohjanen E, ..., Nilsson P, Pin E

Int J Mol Sci 24 (6) - [2023-03-15; online 2023-03-15]

Autoimmunity and Serology Profiling [Collaborative]

An integrated single cell and spatial transcriptomic map of human white adipose tissue.

Massier L, Jalkanen J, Elmastas M, ..., Rydén M, Mejhert N

Nat Commun 14 (1) 1438 [2023-03-15; online 2023-03-15]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A proinsulin-dependent interaction between ENPL-1 and ASNA-1 in neurons is required to maintain insulin secretion in C. elegans.

Podraza-Farhanieh A, Raj D, Kao G, Naredi P

Development 150 (6) - [2023-03-15; online 2023-03-20]

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Tetramodal Chemical Imaging Delineates the Lipid-Amyloid Peptide Interplay at Single Plaques in Transgenic Alzheimer's Disease Models.

Ge J, Koutarapu S, Jha D, ..., Blennow K, Hanrieder J

Anal. Chem. 95 (10) 4692-4702 [2023-03-14; online 2023-03-01]

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A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena.

Conde E Silva N, Leguilloux M, Bellec A, ..., Berges H, Deveaux Y

J. Exp. Bot. 74 (5) 1448-1459 [2023-03-13; online 2022-12-14]

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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization.

Amselem E, Broadwater B, Hävermark T, Johansson M, Elf J

Nat Commun 14 (1) 1336 [2023-03-11; online 2023-03-11]

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Proteome integral solubility alteration high-throughput proteomics assay identifies Collectin-12 as a non-apoptotic microglial caspase-3 substrate.

Grabert K, Engskog-Vlachos P, Škandík M, ..., Joseph B, Cheray M

Cell Death Dis 14 (3) 192 [2023-03-11; online 2023-03-11]

In Vitro and In Vivo Development of a β-Lactam-Metallo-β-Lactamase Inhibitor: Targeting Carbapenem-Resistant Enterobacterales.

Peters BK, Reddy N, Shungube M, ..., Naicker T, Govender T

ACS Infect Dis 9 (3) 486-496 [2023-03-10; online 2023-02-14] Open Access

Drug Discovery and Development (DDD) [Collaborative]

Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes.

Martín-Hernández GC, Chmielarz M, Müller B, ..., Hölzer M, Passoth V

Biotechnol Biofuels Bioprod 16 (1) 42 [2023-03-10; online 2023-03-10]

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One Health surveillance-A cross-sectoral detection, characterization, and notification of foodborne pathogens.

Tast Lahti E, Karamehmedovic N, Riedel H, ..., Zajac M, Jernberg C

Front Public Health 11 (-) 1129083 [2023-03-08; online 2023-03-08]

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Comprehensive transcriptome analysis of different potato cultivars provides insight into early blight disease caused by Alternaria solani.

Sajeevan RS, Abdelmeguid I, Saripella GV, Lenman M, Alexandersson E

BMC Plant Biol. 23 (1) 130 [2023-03-08; online 2023-03-08]

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Melatonin Prescription in Children and Adolescents in Relation to Body Weight and Age.

Kimland EE, Dahlén E, Martikainen J, Célind J, Kindblom JM

Pharmaceuticals (Basel) 16 (3) - [2023-03-06; online 2023-03-06]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing.

Li H, Bräunig S, Dhapolar P, ..., Lang S, Scheding S

Elife 12 (-) - [2023-03-06; online 2023-03-06]

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Venetoclax-Resistant T-ALL Cells Display Distinct Cancer Stem Cell Signatures and Enrichment of Cytokine Signaling.

Shah K, Al Ashiri L, Nasimian A, Ahmed M, Kazi JU

Int J Mol Sci 24 (5) - [2023-03-05; online 2023-03-05]

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miRNome and Proteome Profiling of Human Keratinocytes and Adipose Derived Stem Cells Proposed miRNA-Mediated Regulations of Epidermal Growth Factor and Interleukin 1-Alpha.

Shahin H, Abdallah S, Das J, ..., Elmasry M, El-Serafi AT

Int J Mol Sci 24 (5) - [2023-03-04; online 2023-03-04]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]

A highly efficient transcriptome-based biosynthesis of non-ethanol chemicals in Crabtree negative Saccharomyces cerevisiae.

Yao Z, Guo Y, Wang H, ..., Nielsen J, Dai Z

Biotechnol Biofuels Bioprod 16 (1) 37 [2023-03-04; online 2023-03-04]

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Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming.

Pateras IS, Williams C, Gianniou DD, ..., Gilthorpe JD, Frisan T

J Transl Med 21 (1) 169 [2023-03-03; online 2023-03-03]

Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.

Rifkin RF, Vikram S, Alcorta J, ..., Schlebusch CM, Lombard M

Commun Biol 6 (1) 240 [2023-03-03; online 2023-03-03]

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ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.

Mainwaring OJ, Weishaupt H, Zhao M, ..., Hutter S, Swartling FJ

Nat Commun 14 (1) 1221 [2023-03-03; online 2023-03-03]

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A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).

Onuț-Brännström I, Stairs CW, Campos KIA, ..., Bass D, Burki F

Genome Biol Evol 15 (3) - [2023-03-03; online 2023-02-16]

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Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

Mathieson I, Day FR, Barban N, ..., Mills MC, Perry JRB

Nat Hum Behav - (-) - [2023-03-02; online 2023-03-02]

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Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.

Pushparaj P, Nicoletto A, Dopico XC, ..., Corcoran M, Karlsson Hedestam GB

Front Virol 3 (-) 1128253 [2023-03-01; online 2023-04-13]

Clonal relationships of memory B cell subsets in autoimmune mice.

Aranburu A, Engström E, Gerasimcik N, ..., Grimsholm O, Mårtensson IL

Front Immunol 14 (-) 1129234 [2023-03-01; online 2023-03-01]

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Subtyping of cardiac amyloidosis by mass spectrometry-based proteomics of endomyocardial biopsies.

Noborn F, Thomsen C, Vorontsov E, ..., Oldfors A, Larson G

Amyloid 30 (1) 96-108 [2023-03-00; online 2022-10-09]

Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.

Mühleip A, Flygaard RK, Baradaran R, ..., Sharma V, Amunts A

Nature 615 (7954) 934-938 [2023-03-00; online 2023-03-22]

Striking membrane defects in AdipoR-deficient cells.

Ruiz M, Panagaki D, Höög JL, Pilon M

J. Lipid Res. 64 (3) 100335 [2023-03-00; online 2023-01-20]

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Serum metabolites associated with wholegrain consumption using nontargeted metabolic profiling: a discovery and reproducibility study.

Noerman S, Virtanen JK, Lehtonen M, Brunius C, Hanhineva K

Eur J Nutr 62 (2) 713-726 [2023-03-00; online 2022-10-06]

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Rapid adaptations of Legionella pneumophila to the human host.

Leenheer D, Moreno AB, Paranjape K, ..., Ginevra C, Guy L

Microb Genom 9 (3) - [2023-03-00; online 2023-03-23]

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Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children.

Stratmann S, Vesterlund M, Umer HM, ..., Lehtiö J, Holmfeldt L

Leukemia 37 (3) 550-559 [2023-03-00; online 2022-12-26]

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Population structure and hybridisation in a population of Hawaiian feral chickens.

Martin Cerezo ML, López S, van Dorp L, ..., Henriksen R, Wright D

Heredity (Edinb) 130 (3) 154-162 [2023-03-00; online 2023-02-01]

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Occupational inhalable agents constitute major risk factors for rheumatoid arthritis, particularly in the context of genetic predisposition and smoking.

Tang B, Liu Q, Ilar A, ..., Alfredsson L, Jiang X

Ann. Rheum. Dis. 82 (3) 316-323 [2023-03-00; online 2022-12-06]

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Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group.

Baião GC, Schneider DI, Miller WJ, Klasson L

Mol. Phylogenet. Evol. 180 (-) 107683 [2023-03-00; online 2022-12-24]

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Multidrug-resistant Neisseria gonorrhoeae isolate SE690: mosaic penA-60.001 gene causing ceftriaxone resistance internationally has spread to the more antimicrobial-susceptible genomic lineage, Sweden, September 2022.

Golparian D, Vestberg N, Södersten W, ..., Bhattarai KH, Unemo M

Euro Surveill. 28 (10) - [2023-03-00; online 2023-03-10]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.

Shrine N, Izquierdo AG, Chen J, ..., Hall IP, Tobin MD

Nat. Genet. 55 (3) 410-422 [2023-03-00; online 2023-03-13]

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Membrane permeability based on mesh analysis

Stenqvist B, Ericson MB, Gregoire S, ..., Engblom J, Sparr E

Journal of Colloid and Interface Science 633 (-) 526-535 [2023-03-00; online 2023-03-00]

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Isobaric labeling-based quantitative proteomics of FACS-purified immune cells and epithelial cells from the intestine of Crohn's disease patients reveals proteome changes of potential importance in disease pathogenesis.

Alfredsson J, Fabrik I, Gorreja F, ..., Lindskog EB, Wick MJ

Proteomics 23 (5) e2200366 [2023-03-00; online 2022-12-25]

Increasing Complexity of the N-Glycome During Caenorhabditis Development.

Wilson IBH, Yan S, Jin C, ..., Schnabel R, Paschinger K

Mol. Cell Proteomics 22 (3) 100505 [2023-03-00; online 2023-01-28]

Fate of phosphorus in pulverized fuel co-combustion of sewage sludge and agricultural residues

Häggström G, Karl Hannl T, Holmgren P, ..., Skoglund N, Öhman M

Fuel 335 (-) 127059 [2023-03-00; online 2023-03-00]

Fast three-dimensional image generation for healthy brain aging using diffeomorphic registration.

Fu J, Tzortzakakis A, Barroso J, ..., Moreno R, Alzheimer's Disease Neuroimaging Initiative

Hum Brain Mapp 44 (4) 1289-1308 [2023-03-00; online 2022-12-05]

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Ectomycorrhizal fungi with hydrophobic mycelia and rhizomorphs dominate in young pine trees surviving experimental drought stress

Castaño C, Suarez-Vidal E, Zas R, ..., Oliva J, Sampedro L

Soil Biology and Biochemistry 178 (-) 108932 [2023-03-00; online 2023-03-00]

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Comprehensive characterization of complex glycosphingolipids in human pancreatic cancer tissues.

Hořejší K, Jin C, Vaňková Z, ..., Teneberg S, Holčapek M

J. Biol. Chem. 299 (3) 102923 [2023-03-00; online 2023-01-19]

Cardiovascular disease-linked plasma proteins are mainly associated with lung volume.

Rydell A, Nerpin E, Zhou X, ..., Ärnlöv J, Malinovschi A

ERJ Open Res 9 (2) - [2023-03-00; online 2023-03-27]

NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions.

Luo H, Urbonaviciute V, Saei AA, ..., Zubarev RA, Holmdahl R

JCI Insight - (-) - [2023-02-28; online 2023-02-28]

Muc2-dependent microbial colonization of the jejunal mucus layer is diet sensitive and confers local resistance to enteric pathogen infection.

Birchenough GMH, Schroeder BO, Sharba S, ..., Bäckhed F, Hansson GC

Cell Rep 42 (2) 112084 [2023-02-28; online 2023-02-06]

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Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins.

Kahle M, Appelgren S, Elofsson A, Carroni M, Ädelroth P

BMC Biol. 21 (1) 47 [2023-02-28; online 2023-02-28]

Chitosan-Modified Polyethyleneimine Nanoparticles for Enhancing the Carboxylation Reaction and Plants' CO2 Uptake.

Routier C, Vallan L, Daguerre Y, ..., Pavlopoulou E, Stavrinidou E

ACS Nano 17 (4) 3430-3441 [2023-02-28; online 2023-02-16]

Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.

Davies JS, Currie MJ, North RA, ..., Mace PD, Dobson RCJ

Nat Commun 14 (1) 1120 [2023-02-27; online 2023-02-27]

Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.

Mohammed M, Dziedziech A, Sekar V, ..., Vega-Rodriguez J, Ankarklev J

Microbiol Spectr 11 (2) e0367122 [2023-02-27; online 2023-02-27]

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Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia.

Palma Medina LM, Babačić H, Dzidic M, ..., Strålin K, Norrby-Teglund A

Respir. Res. 24 (1) 62 [2023-02-24; online 2023-02-24]

Reproducing extracellular matrix adverse remodelling of non-ST myocardial infarction in a large animal model.

Contessotto P, Spelat R, Ferro F, ..., Pandit A, Da Costa M

Nat Commun 14 (1) 995 [2023-02-22; online 2023-02-22]

Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.

Jun S, Toosi H, Mold J, ..., Roth A, Lagergren J

Nat Commun 14 (1) 982 [2023-02-22; online 2023-02-22]

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Metagenomic and single-cell RNA-Seq survey of the Helicobacter pylori-infected stomach in asymptomatic individuals.

Sorini C, Tripathi KP, Wu S, ..., Du J, Villablanca EJ

JCI Insight 8 (4) - [2023-02-22; online 2023-02-22]

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Accelerated epigenetic aging in women with emotionally unstable personality disorder and a history of suicide attempts.

Boström ADE, Andersson P, Jamshidi E, ..., Åsberg M, Jokinen J

Transl Psychiatry 13 (1) 66 [2023-02-22; online 2023-02-22]

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Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.

Sjödin KS, Sjödin A, Ruszczyński M, ..., Szajewska H, West CE

BMC Biol. 21 (1) 38 [2023-02-20; online 2023-02-20]

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Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest.

Xu W, Sato H, Bente H, Santos-González J, Köhler C

Plant Cell 35 (2) 874-888 [2023-02-20; online 2022-11-26]

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Multi-organ single-cell analysis reveals an on/off switch system with potential for personalized treatment of immunological diseases.

Lilja S, Li X, Smelik M, ..., Wang H, Benson M

Cell Reports Medicine - (-) 100956 [2023-02-17; online 2023-02-17]

Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.

Li B, Zeis P, Zhang Y, ..., Steinmetz LM, Pelechano V

Nat Commun 14 (1) 910 [2023-02-17; online 2023-02-17]

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Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria.

Parajuli NP, Emmerich A, Mandava CS, Pavlov MY, Sanyal S

Nat Commun 14 (1) 918 [2023-02-17; online 2023-02-17]

Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica.

Zaghen S, Konzock O, Fu J, Kerkhoven EJ

J Ind Microbiol Biotechnol 50 (1) - [2023-02-17; online 2023-09-24] Open Access

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Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor.

Moe A, Ädelroth P, Brzezinski P, Näsvik Öjemyr L

Commun Chem 6 (1) 32 [2023-02-16; online 2023-02-16]

Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris.

Christensen S, Stenström O, Akke M, Bülow L

Int J Mol Sci 24 (4) - [2023-02-16; online 2023-02-16]

Boron-Mediated Regioselective Aromatic C-H Functionalization via an Aryl BF2 Complex.

Shinde GH, Sundén H

Chemistry 29 (10) e202203505 [2023-02-16; online 2022-12-23]

Prognostic importance of biomarkers associated with haemostatic, vascular and endothelial disturbances in acute coronary syndrome patients in relation to kidney function.

Mörtberg J, Salzinger B, Lundwall K, ..., Lindahl B, Spaak J

Int. J. Cardiol. 373 (-) 64-71 [2023-02-15; online 2022-12-05]

Associations of DNA Methylation With Behavioral Problems, Gray Matter Volumes, and Negative Life Events Across Adolescence: Evidence From the Longitudinal IMAGEN Study.

Sun Y, Jia T, Barker ED, ..., Schumann G, Desrivières S

Biol. Psychiatry 93 (4) 342-351 [2023-02-15; online 2022-06-22]

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A Novel and Functionally Diverse Class of Acetylcholine-Gated Ion Channels.

Hardege I, Morud J, Courtney A, Schafer WR

J. Neurosci. 43 (7) 1111-1124 [2023-02-15; online 2023-01-05]

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Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows

Salas SM, Czarnewski P, Kuemmerle LB, ..., Ishaque N, Nilsson M

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Array-Based Multiplex and High-Throughput Serology Assays.

Olofsson J, Hellström C, Andersson E, ..., Nilsson P, Pin E

Methods Mol. Biol. 2628 (-) 535-553 [2023-02-14; online 2023-02-14]

Autoimmunity and Serology Profiling [Technology development]

Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students.

Olof S, Lorraine E, Berhane A I, ..., Paula M, Susanne J

Epidemiol. Infect. 151 (-) e25 [2023-02-13; online 2023-02-13]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer.

Wallander K, Haider Z, Jeggari A, ..., Lindblad M, Tham E

Cancers (Basel) 15 (4) - [2023-02-11; online 2023-02-11]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

DNA methylation changes and increased mRNA expression of coagulation proteins, factor V and thrombomodulin in Fuchs endothelial corneal dystrophy.

Westin IM, Landfors M, Giannopoulos A, ..., Degerman S, Golovleva I

Cell. Mol. Life Sci. 80 (3) 62 [2023-02-11; online 2023-02-11]

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Genomic architecture of migration timing in a long-distance migratory songbird.

de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC

Sci Rep 13 (1) 2437 [2023-02-10; online 2023-02-10]

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Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent.

Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M

Anim Microbiome 5 (1) 9 [2023-02-10; online 2023-02-10]

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Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics.

Salvà-Serra F, Jaén-Luchoro D, Marathe NP, ..., Moore ERB, Karlsson R

Front Microbiol 13 (-) 1089140 [2023-02-09; online 2023-02-09]

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Combinatory analysis of immune cell subsets and tumor-specific genetic variants predict clinical response to PD-1 blockade in patients with non-small cell lung cancer.

Dutta N, Rohlin A, Eklund EA, ..., Hallqvist A, Raghavan S

Front Oncol 12 (-) 1073457 [2023-02-09; online 2023-02-09]

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Primary Structure of Glycans by NMR Spectroscopy.

Fontana C, Widmalm G

Chem. Rev. 123 (3) 1040-1102 [2023-02-08; online 2023-01-09]

A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function.

Bahnan W, Happonen L, Khakzad H, ..., Malmström J, Nordenfelt P

EMBO Mol Med 15 (2) e16208 [2023-02-08; online 2022-12-12]

Microneedle Patch for Painless Intradermal Collection of Interstitial Fluid Enabling Multi-analyte Measurement of Small Molecules, SARS-CoV-2 Antibodies, and Protein Profiling.

Ribet F, Bendes A, Fredolini C, ..., Stemme G, Roxhed N

Adv Healthc Mater - (-) e2202564 [2023-02-07; online 2023-02-07]

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data.

Gustafsson J, Anton M, Roshanzamir F, ..., Robinson JL, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 120 (6) e2217868120 [2023-02-07; online 2023-01-31]

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A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.

Sarhan MS, Wurst C, Tzankov A, ..., Zink A, Maixner F

BMC Biol. 21 (1) 9 [2023-02-07; online 2023-02-07]

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The anti-leprosy drug clofazimine reduces polyQ toxicity through activation of PPAR

Li X, Hernandez I, Häggblad M, ..., Hühn D, Fernandez-Capetillo O

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Plasma Concentrations of Gut Hormones Acyl Ghrelin and Peptide YY and Subsequent Risk of Colorectal Cancer and Molecular Tumor Subtypes.

Bodén S, Harbs J, Sundkvist A, ..., Harlid S, Van Guelpen B

Cancer Prev Res (Phila) 16 (2) 75-87 [2023-02-06; online 2022-11-12]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

Cohort profile: The Clinical and Multi-omic (CAMO) cohort, part of the Norwegian Women and Cancer (NOWAC) study.

Delgado AB, Tylden ES, Lukic M, ..., Lund E, Olsen KS

PLoS ONE 18 (2) e0281218 [2023-02-06; online 2023-02-06]

Larval transcriptomes reflect the evolutionary history of plant-insect associations.

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Evolution 77 (2) 519-533 [2023-02-04; online 2023-01-11]

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Cryo-EM structure supports a role of AQP7 as a junction protein.

Huang P, Venskutonytė R, Prasad RB, ..., Artner I, Lindkvist-Petersson K

Nat Commun 14 (1) 600 [2023-02-03; online 2023-02-03]

Proteomic Analysis of Mucosal and Systemic Responses to SARS-CoV-2 Antigen.

Martinson N, Gordhan B, Petkov S, ..., Kana B, Herrera C

Vaccines (Basel) 11 (2) - [2023-02-02; online 2023-02-02]

Proteogenomics decodes the evolution of human ipsilateral breast cancer.

De Marchi T, Pyl PT, Sjöström M, ..., Malmstöm J, Niméus E

Commun Biol 6 (1) 139 [2023-02-02; online 2023-02-02]

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Survival Outcomes, Digital TILs, and On-treatment PET/CT During Neoadjuvant Therapy for HER2-positive Breast Cancer: Results from the Randomized PREDIX HER2 Trial.

Matikas A, Johansson H, Grybäck P, ..., Hatschek T, Foukakis T

Clin. Cancer Res. 29 (3) 532-540 [2023-02-01; online 2022-12-01]

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Evolution Letters 7 (1) 24-36 [2023-02-01; online 2023-01-31]

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Genes Chromosomes Cancer 62 (2) 93-100 [2023-02-00; online 2022-09-30]

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Chemometrics and Intelligent Laboratory Systems 233 (-) 104733 [2023-02-00; online 2023-02-00]

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Toxicology 485 (-) 153425 [2023-02-00; online 2023-01-05]

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Signal Processing 203 (-) 108809 [2023-02-00; online 2023-02-00]

High-content analysis shows synergistic effects of low perfluorooctanoic acid (PFOS) and perfluorooctane sulfonic acid (PFOA) mixture concentrations on human breast epithelial cell carcinogenesis.

Pierozan P, Kosnik M, Karlsson O

Environ Int 172 (-) 107746 [2023-02-00; online 2023-01-12]

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Evaluation of kraft and hydrolysis lignin hydroconversion over unsupported NiMoS catalyst

Achour A, Bernin D, Creaser D, Olsson L

Chemical Engineering Journal 453 (-) 139829 [2023-02-00; online 2023-02-00]

Distinct T cell subsets in adipose tissue are associated with obesity.

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Eur. J. Immunol. 53 (2) e2249990 [2023-02-00; online 2022-12-13]

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Diseased thyroid tissue classification in OCT images using deep learning: Towards surgical decision support.

Tampu IE, Eklund A, Johansson K, Gimm O, Haj-Hosseini N

J. Biophotonics 16 (2) e202200227 [2023-02-00; online 2022-11-11]

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Chemical composition and species identification of microalgal biomass grown at pilot-scale with municipal wastewater and CO2 from flue gases.

Lage S, Gentili FG

Chemosphere 313 (-) 137344 [2023-02-00; online 2022-11-26]

Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions

Maheshwari A, Jones CM, Tiemann M, Hallin S

Soil Biology and Biochemistry 177 (-) 108909 [2023-02-00; online 2023-02-00]

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An annotated high-content fluorescence microscopy dataset with Hoechst 33342-stained nuclei and manually labelled outlines.

Arvidsson M, Rashed SK, Aits S

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An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis.

Le Moan A, Panova M, De Jode A, ..., Butlin R, Johannesson K

Evol Appl 16 (2) 279-292 [2023-02-00; online 2022-06-26]

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Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]

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7-month duration of SARS-CoV-2 mucosal immunoglobulin-A responses and protection.

Marking U, Bladh O, Havervall S, ..., Klingström J, Thålin C

Lancet Infect Dis 23 (2) 150-152 [2023-02-00; online 2023-01-11]

6α-hydroxylated bile acids mediate TGR5 signalling to improve glucose metabolism upon dietary fiber supplementation in mice.

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Gut 72 (2) 314-324 [2023-02-00; online 2022-06-13]

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BMC Genomics 24 (1) 53 [2023-01-28; online 2023-01-28]

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Brain Commun 5 (1) fcad017 [2023-01-27; online 2023-01-27]

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Nat Commun 14 (1) 452 [2023-01-27; online 2023-01-27]

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Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.

Cotman AE, Durcik M, Benedetto Tiz D, ..., Sterk GJ, Kikelj D

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BMC Med 21 (1) 27 [2023-01-24; online 2023-01-24]

Ginsenoside Rg3 Reduces the Toxicity of Graphene Oxide Used for pH-Responsive Delivery of Doxorubicin to Liver and Breast Cancer Cells.

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Integrated Microscopy Technologies Gothenburg [Service]

Direct structure determination of vemurafenib polymorphism from compact spherulites using 3D electron diffraction.

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Commun Chem 6 (1) 18 [2023-01-23; online 2023-01-23]

Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment.

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npj Syst Biol Appl 9 (1) 2 [2023-01-21; online 2023-01-21]

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Biocontrol Effect of Clonostachys rosea on Fusarium graminearum Infection and Mycotoxin Detoxification in Oat (Avena sativa).

Khairullina A, Micic N, Jørgensen HJL, ..., Collinge DB, Jensen B

Plants (Basel) 12 (3) - [2023-01-21; online 2023-01-21]

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).

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Chromosome Res. 31 (1) 2 [2023-01-20; online 2023-01-20]

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High cardiomyocyte diversity in human early prenatal heart development.

Sylvén C, Wärdell E, Månsson-Broberg A, ..., Björklund Å, Giacomello S

iScience 26 (1) 105857 [2023-01-20; online 2022-12-21]

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Cerebellar granule neurons induce Cyclin D1 before the onset of motor symptoms in Huntington's disease mice.

Bauer S, Chen CY, Jonson M, ..., Magadi SS, Jackson WS

Acta Neuropathol Commun 11 (1) 17 [2023-01-20; online 2023-01-20]

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Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis.

Shemirani MI, Tilevik D, Tilevik A, ..., Enroth H, Pernestig AK

BMC Infect. Dis. 23 (1) 39 [2023-01-20; online 2023-01-20]

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Single-cell analysis of myeloid cells in HPV+ tonsillar cancer.

Jimenez DG, Altunbulakli C, Swoboda S, ..., Greiff L, Lindstedt M

Front Immunol 13 (-) 1087843 [2023-01-19; online 2023-01-19]

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MOXD1 is a gate-keeper of organ homeostasis and functions as a tumor-suppressor in neuroblastoma

Fredlund E, Andersson S, Hilgert E, ..., van Nes J, Mohlin S

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Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex.

Ottenburghs J, Honka J, Heikkinen ME, ..., Müskens GJDM, Ellegren H

BMC Ecol Evol 23 (1) 2 [2023-01-19; online 2023-01-19]

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Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1viaa comprehensive screening funnel

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Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A chemical screen underscores the essential role of STAT1-dependent IFNγ signaling to regulate HLA-I expression in cancer cells.

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MicroPubl Biol 2023 (-) - [2023-01-18; online 2023-01-18]

Chemical Biology Consortium Sweden (CBCS) [Service]

Zero-Degree Celsius Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry.

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Anal. Chem. 95 (2) 1149-1158 [2023-01-17; online 2022-12-22]

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.

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Fluorogenic properties of 4-dimethylaminocinnamaldehyde (DMACA) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues.

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Front Plant Sci 13 (-) 1060804 [2023-01-16; online 2023-01-16]

Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.

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J Hazard Mater 442 (-) 130057 [2023-01-15; online 2022-09-23]

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Methylmercury formation in biofilms of Geobacter sulfurreducens.

Yunda E, Gutensohn M, Ramstedt M, Björn E

Front Microbiol 14 (-) 1079000 [2023-01-13; online 2023-01-13]

PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.

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Sci Rep 13 (1) 632 [2023-01-12; online 2023-01-12]

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A hypomorphic variant in the translocase of the outer mitochondrial membrane complex subunit TOMM7 causes short stature and developmental delay.

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HGG Adv 4 (1) 100148 [2023-01-12; online 2022-10-04]

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Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.

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Stem Cell Reports 18 (1) 337-353 [2023-01-10; online 2022-11-17]

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Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV.

Ghorbani M, Al-Manei K, Naud S, ..., Aleman S, Sällberg Chen M

Front Immunol 13 (-) 1079995 [2023-01-10; online 2023-01-10]

Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones.

Scharf L, Axelsson H, Emmanouilidi A, ..., Bemark M, Angeletti D

JCI Insight 8 (1) - [2023-01-10; online 2023-01-10]

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Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.

Pushparaj P, Nicoletto A, Sheward DJ, ..., Corcoran M, Karlsson Hedestam GB

Immunity 56 (1) 193-206.e7 [2023-01-10; online 2022-12-12]

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Front Pediatr 10 (-) 1082986 [2023-01-10; online 2023-01-10]

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Antibiotic perseverance increases the risk of resistance development.

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Proc. Natl. Acad. Sci. U.S.A. 120 (2) e2216216120 [2023-01-10; online 2023-01-03]

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Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.

Koptekin D, Yüncü E, Rodríguez-Varela R, ..., Götherström A, Somel M

Curr. Biol. 33 (1) 41-57.e15 [2023-01-09; online 2022-12-08]

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Identification of novel autoantigens as potential biomarkers in juvenile idiopathic arthritis associated uveitis.

Arve-Butler S, Mossberg A, Kahn F, ..., Månsson B, Kahn R

Front Pediatr 10 (-) 1091308 [2023-01-09; online 2023-01-09]

High-fat diet and estrogen modulate the gut microbiota in a sex-dependent manner in mice.

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The effect of side chain variations on quinazoline-pyrimidine G-quadruplex DNA ligands.

Bhuma N, Chand K, Andréasson M, ..., Öhlund D, Chorell E

Eur J Med Chem 248 (-) 115103 [2023-01-08; online 2023-01-08]

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Nat Commun 14 (1) 115 [2023-01-07; online 2023-01-07]

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Deep Learning on Ultrasound Images Visualizes the Femoral Nerve with Good Precision.

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GotEnzymes: an extensive database of enzyme parameter predictions.

Li F, Chen Y, Anton M, Nielsen J

Nucleic Acids Res. 51 (D1) D583-D586 [2023-01-06; online 2022-09-29]

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The genetic history of Scandinavia from the Roman Iron Age to the present.

Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, ..., Helgason A, Götherström A

Cell 186 (1) 32-46.e19 [2023-01-05; online 2023-01-08]

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Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas.

Weishaupt H, Čančer M, Rosén G, ..., Ameur A, Swartling FJ

Neuro-oncology 25 (1) 97-107 [2023-01-05; online 2022-06-24]

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ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.

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BMC Bioinformatics 24 (1) 6 [2023-01-05; online 2023-01-05]

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Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression.

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Clin Epigenetics 15 (1) 1 [2023-01-04; online 2023-01-04]

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Identification of Novel Small Molecule Ligands for JAK2 Pseudokinase Domain.

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Pharmaceuticals (Basel) 16 (1) - [2023-01-04; online 2023-01-04]

Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.

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A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.

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Optimization of N-Piperidinyl-Benzimidazolone Derivatives as Potent and Selective Inhibitors of 8-Oxo-Guanine DNA Glycosylase 1.

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ChemMedChem 18 (1) e202200310 [2023-01-03; online 2022-10-13]

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Extracellular Galectin 4 Drives Immune Evasion and Promotes T-cell Apoptosis in Pancreatic Cancer.

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Cancer Immunol Res 11 (1) 72-92 [2023-01-03; online 2022-12-09]

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Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction.

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Proc. Natl. Acad. Sci. U.S.A. 120 (1) e2209856120 [2023-01-03; online 2022-12-27]

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Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.

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The injury-induced transcription factor SOX9 alters the expression of LBR, HMGA2, and HIPK3 in the human kidney.

Kha M, Krawczyk K, Choong OK, ..., Swärd K, Johansson ME

Am. J. Physiol. Renal Physiol. 324 (1) F75-F90 [2023-01-01; online 2022-12-01]

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Nuclear and mitochondrial DNA alterations in pheochromocytomas and paragangliomas, and their potential treatment.

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Widespread CNS pathology in amyotrophic lateral sclerosis homozygous for the D90A SOD1 mutation

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Acta Neuropathol 145 (1) 13-28 [2023-01-00; online 2022-11-16]

Three Adult Cases of STAT1 Gain-of-Function with Chronic Mucocutaneous Candidiasis Treated with JAK Inhibitors.

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Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.

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Mol. Psychiatry 28 (1) 475-482 [2023-01-00; online 2022-11-16]

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Palmoplantar keratoderma and digital clubbing in 2 sisters with hypertrophic osteoarthropathy.

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JAAD Case Rep 31 (-) 133-136 [2023-01-00; online 2022-12-01]

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NMR spectrum reconstruction as a pattern recognition problem.

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J Magn Reson 346 (-) 107342 [2023-01-00; online 2022-11-24]

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.

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PLoS Comput. Biol. 19 (1) e1010457 [2023-01-00; online 2023-01-20]

Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.

Peng G, Sinkko HM, Alenius H, ..., Bräutigam L, Fadeel B

Nat Nanotechnol 18 (1) 42-48 [2023-01-00; online 2022-12-12]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genotype-first approach to identify associations between CDH1 germline variants and cancer phenotypes: a multicentre study by the European Reference Network on Genetic Tumour Risk Syndromes.

Garcia-Pelaez J, Barbosa-Matos R, Lobo S, ..., Hoogerbrugge N, Oliveira C

Lancet Oncol 24 (1) 91-106 [2023-01-00; online 2022-11-24]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Gene gain facilitated endosymbiotic evolution of Chlamydiae.

Dharamshi JE, Köstlbacher S, Schön ME, ..., Ettema TJG, Horn M

Nat Microbiol 8 (1) 40-54 [2023-01-00; online 2023-01-05]

Bioinformatics Support for Computational Resources [Service]

Enantioselective CE-MS analysis of ketamine metabolites in urine.

Sandbaumhüter FA, Aerts JT, Theurillat R, ..., Thormann W, Jansson ET

Electrophoresis 44 (1-2) 125-134 [2023-01-00; online 2022-12-09]

Cerebral small vessel disease: Recent advances and future directions.

Markus HS, de Leeuw FE

Int J Stroke 18 (1) 4-14 [2023-01-00; online 2022-12-29]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs.

Lingaas F, Tengvall K, Jansen JH, ..., Lindblad-Toh K, Wang C

PLoS Genet. 19 (1) e1010599 [2023-01-00; online 2023-01-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Automatic Time-Resolved Cardiovascular Segmentation of 4D Flow MRI Using Deep Learning.

Bustamante M, Viola F, Engvall J, Carlhäll CJ, Ebbers T

J Magn Reson Imaging 57 (1) 191-203 [2023-01-00; online 2022-05-04]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Aerosol-based deposition of broadband antireflective silica coating with closed mesoporous structure

Zäll E, Järn M, Karlsson S, ..., Sundin M, Wågberg T

Solar Energy Materials and Solar Cells 250 (-) 112078 [2023-01-00; online 2023-01-00]

A comprehensive characterization of patients diagnosed with post-COVID-19 condition in Sweden 16 months after the introduction of the International Classification of Diseases Tenth Revision diagnosis code (U09.9): a population-based cohort study.

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Int J Infect Dis 126 (-) 104-113 [2023-01-00; online 2022-11-21]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3

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Biol. Imaging 3 (-) - [2023-00-00; online 2023-02-20]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Systematics of the avian family Alaudidae using multilocus and genomic data

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Avian Research 14 (-) 100095 [2023-00-00; online 2023-00-00]

Bioinformatics Support for Computational Resources [Service]

Sequential extraction of hemicelluloses by subcritical water improves saccharification of hybrid aspen wood grown in greenhouse and field conditions

Sivan P, Heinonen E, Latha Gandla M, ..., Mellerowicz EJ, Vilaplana F

Green Chem. 25 (14) 5634-5646 [2023-00-00; online 2023-00-00]

On the understanding of bio-oil formation from the hydrothermal liquefaction of organosolv lignin isolated from softwood and hardwood sawdust

Paulsen Thoresen P, Fahrni J, Lange H, ..., Christakopoulos P, Matsakas L

Sustainable Energy Fuels 7 (22) 5361-5373 [2023-00-00; online 2023-00-00]

Metabolomics-based analysis in Daphnia magna after exposure to low environmental concentrations of polystyrene nanoparticles

Kelpsiene E, Cedervall T, Malmendal A

Environ. Sci.: Nano 10 (7) 1858-1866 [2023-00-00; online 2023-00-00]

Fluorescent carbon dots from birch leaves for sustainable electroluminescent devices

Tang S, Liu Y, Opoku H, ..., Edman L, Wang J

Green Chem. 25 (23) 9884-9895 [2023-00-00; online 2023-00-00]

Exploring the impact of select anchor groups for norbornadiene/quadricyclane single-molecule switches

Ghasemi S, Ornago L, Liasi Z, ..., Lara-Avila S, Moth-Poulsen K

J. Mater. Chem. C 11 (44) 15412-15418 [2023-00-00; online 2023-00-00]

Drug repurposing screens identify compounds that inhibit α-synuclein oligomers' membrane disruption and block antibody interactions

Somavarapu AK, Kleijwegt G, Nagaraj M, ..., Nielsen J, Otzen DE

Chem. Sci. 14 (11) 3030-3047 [2023-00-00; online 2023-00-00]

Chemical Biology Consortium Sweden (CBCS) [Service]

Building a precision medicine infrastructure at a national level: The Swedish experience

Edsjö A, Lindstrand A, Gisselsson D, ..., Fioretos T, Rosenquist R

Camb. prisms Precis. med. 1 (-) - [2023-00-00; online 2023-02-27]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Branched polyesters from radical ring-opening polymerization of cyclic ketene acetals: synthesis, chemical hydrolysis and biodegradation

Mousa M, Jonsson M, Wilson O, ..., Larsson Kron A, Malmström E

Polym. Chem. 14 (47) 5154-5165 [2023-00-00; online 2023-00-00]

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Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host–Pathogen Protein–Protein Complexes

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A novel biorefinery concept based on marginally used halophyte biomass

Monção M, Thoresen PP, Wretborn T, ..., Christakopoulos P, Matsakas L

Sustainable Energy Fuels 7 (16) 3902-3918 [2023-00-00; online 2023-00-00]

A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant (Azure Tit Cyanistes cyanus (Pallas, 1770))

Irestedt M, Thörn F, Ericson PGP, ..., Johansson F, Nylander JAA

Avian Research 14 (-) 100130 [2023-00-00; online 2023-00-00]

Bioinformatics Support for Computational Resources [Service]

Metataxonomic and metaproteomic profiling of the oral microbiome in oral lichen planus - a pilot study.

Bankvall M, Carda-Diéguez M, Mira A, ..., Karlsson R, Robledo-Sierra J

Journal of Oral Microbiology 15 (1) 2161726 [2022-12-28; online 2022-12-28]

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Kanoni S, Graham SE, Wang Y, ..., Assimes TL, Peloso GM

Genome Biol. 23 (1) 268 [2022-12-27; online 2022-12-27]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Developmental cues license megakaryocyte priming in murine hematopoietic stem cells.

Kristiansen TA, Zhang Q, Vergani S, ..., Ungerbäck J, Yuan J

Blood Adv 6 (24) 6228-6241 [2022-12-27; online 2022-05-19]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Leukocyte DNA methylation in Alzheimer´s disease associated genes: replication of findings from neuronal cells.

Karlsson IK, Ploner A, Wang Y, ..., Pedersen NL, Hägg S

Epigenetics - (-) 1-5 [2022-12-26; online 2022-12-26]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Microfluidic Device for Patient-Centric Multiplexed Assays with Readout in Centralized Laboratories.

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Anal. Chem. - (-) - [2022-12-22; online 2022-12-22]

Affinity Proteomics Stockholm [Technology development]

Matched Analyses of Brain Metastases versus Primary Non-Small Cell Lung Cancer Reveal a Unique microRNA Signature.

Tsakonas G, Koulouris A, Kazmierczak D, ..., Hydbring P, Ekman S

Int J Mol Sci 24 (1) - [2022-12-22; online 2022-12-22]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

A protein signature associated with active tuberculosis identified by plasma profiling and network-based analysis.

Mousavian Z, Folkesson E, Fröberg G, ..., Källenius G, Sundling C

iScience 25 (12) 105652 [2022-12-22; online 2022-11-22]

Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.

Cholleti H, de Jong J, Blomström AL, Berg M

Pathogens 12 (1) - [2022-12-21; online 2022-12-21]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exhaled phospholipid transfer protein and hepatocyte growth factor receptor in lung adenocarcinoma.

Andreasson J, Bodén E, Fakhro M, ..., Hallgren O, Lindstedt S

Respir. Res. 23 (1) 369 [2022-12-21; online 2022-12-21]

An investigation of metabolome in blood in patients with chronic peripheral, posttraumatic/postsurgical neuropathic pain.

Ghafouri B, Thordeman K, Hadjikani R, ..., Gerdle B, Bäckryd E

Sci Rep 12 (1) 21714 [2022-12-15; online 2022-12-15]

Loss of Y in leukocytes as a risk factor for critical COVID-19 in men

Bruhn-Olszewska B, Davies H, Sarkisyan D, ..., Frithiof R, Dumanski JP

Genome Med 14 (1) 139 [2022-12-14; online 2022-12-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Upper gut heat shock proteins HSP70 and GRP78 promote insulin resistance, hyperglycemia, and non-alcoholic steatohepatitis.

Angelini G, Castagneto-Gissey L, Salinari S, ..., Tremaroli V, Mingrone G

Nat Commun 13 (1) 7715 [2022-12-13; online 2022-12-13]

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Metabolic reprogramming and membrane glycan remodeling as potential drivers of zebrafish heart regeneration.

Spelat R, Ferro F, Contessotto P, ..., Kilcoyne M, Pandit A

Commun Biol 5 (1) 1365 [2022-12-13; online 2022-12-13]

Structural mechanism of signal transduction in a phytochrome histidine kinase.

Wahlgren WY, Claesson E, Tuure I, ..., Takala H, Westenhoff S

Nat Commun 13 (1) 7673 [2022-12-12; online 2022-12-12]

Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells.

Najafi M, Guo Y, Andersson G, Humblot P, Bongcam-Rudloff E

Genes 13 (12) - [2022-12-12; online 2022-12-12]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma Concentrations of Short-Chain Fatty Acids in Active and Recovered Anorexia Nervosa.

Xu J, Landberg R, Lavebratt C, ..., Landén M, Nilsson IAK

Nutrients 14 (24) - [2022-12-09; online 2022-12-09]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ.

Al-Amin RA, Johansson L, Abdurakhmanov E, ..., Lundbäck T, Landegren U

Nucleic Acids Res. 50 (22) e129 [2022-12-09; online 2022-10-04]

Autoimmunity and Serology Profiling [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Endoreplication mediates cell size control via mechanochemical signaling from cell wall.

Ma Y, Jonsson K, Aryal B, ..., Hamant O, Bhalerao RP

Sci Adv 8 (49) eabq2047 [2022-12-09; online 2022-12-09]

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study.

Lüking M, Elf J, Levy Y

J. Phys. Chem. B 126 (48) 9971-9984 [2022-12-08; online 2022-11-23]

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Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.

Tengvall K, Sundström E, Wang C, ..., Andersson G, Lindblad-Toh K

Commun Biol 5 (1) 1348 [2022-12-08; online 2022-12-08]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]

A third dose of the unmodified COVID-19 mRNA vaccine CVnCoV enhances quality and quantity of immune responses.

Lenart K, Hellgren F, Ols S, ..., Petsch B, Loré K

Mol Ther Methods Clin Dev 27 (-) 309-323 [2022-12-08; online 2022-10-06]

Affinity Proteomics Stockholm [Service] Affinity Proteomics Uppsala [Service]

Fecal Luminal Factors from Patients with Gastrointestinal Diseases Alter Gene Expression Profiles in Caco-2 Cells and Colonoids.

Holst LM, Iribarren C, Sapnara M, ..., Magnusson MK, Öhman L

Int J Mol Sci 23 (24) - [2022-12-07; online 2022-12-07]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Adopting transfer learning for neuroimaging: a comparative analysis with a custom 3D convolution neural network model.

Soliman A, Chang JR, Etminani K, ..., Alzheimer’s Disease Neuroimaging Initiative , Ochoa-Figueroa M

BMC Med Inform Decis Mak 22 (Suppl 6) 318 [2022-12-07; online 2022-12-07]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

V. cholerae MakA is a cholesterol-binding pore-forming toxin that induces non-canonical autophagy.

Jia X, Knyazeva A, Zhang Y, ..., Corkery DP, Wu YW

J. Cell Biol. 221 (12) - [2022-12-05; online 2022-10-04]

Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis.

von Berlin L, Westholm JO, Ratz M, Frisén J

Hippocampus - (-) - [2022-12-05; online 2022-12-05]

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Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).

Hempel E, Bibi F, Faith JT, ..., Hofreiter M, Westbury MV

Mol. Biol. Evol. 39 (12) - [2022-12-05; online 2022-11-03]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

An extension to the NK fitness landscape model to study pleiotropy, epistasis, and ruggedness independently

Mehra P, Hintze A

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Autoantigenic properties of the aminoacyl tRNA synthetase family in idiopathic inflammatory myopathies.

Preger C, Notarnicola A, Hellström C, ..., Gräslund S, Jakobsson P

J. Autoimmun. 134 (-) 102951 [2022-12-02; online 2022-12-02]

Autoimmunity and Serology Profiling [Service] Drug Discovery and Development (DDD) [Collaborative]

The structure of cellulose nanofibril networks at low concentrations and their stabilizing action on colloidal particles.

Nordenström M, Benselfelt T, Hollertz R, ..., Söderberg D, Wågberg L

Carbohydr Polym 297 (-) 120046 [2022-12-01; online 2022-09-01]

Integrated Microscopy Technologies Stockholm [Collaborative]

The genetic diagnosis of rare endocrine disorders of sex development and maturation: a survey among Endo-ERN centres.

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Endocr Connect 11 (12) - [2022-12-01; online 2022-11-14]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems.

Johnsson M, Wall H, Lopes Pinto FA, ..., Kindmark A, de Koning DJ

G3 (Bethesda) - (-) - [2022-12-01; online 2022-12-01]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils

Högfors-Rönnholm E, Lundin D, Brambilla D, ..., Österholm P, Dopson M

Commun Earth Environ 3 (1) - [2022-12-01; online 2022-12-01]

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Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.

Pinhassi J, Farnelid H, García SM, ..., Labrenz M, Riemann L

Front Microbiol 13 (-) 869093 [2022-12-01; online 2022-12-01]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Extracellular vesicle DNA from human melanoma tissues contains cancer-specific mutations.

Crescitelli R, Filges S, Karimi N, ..., Lässer C, Olofsson Bagge R

Front Cell Dev Biol 10 (-) 1028854 [2022-12-01; online 2022-12-01]

Integrated Microscopy Technologies Gothenburg [Service]

The role of inputs of marine wrack and carrion in sandy-beach ecosystems: a global review.

Hyndes GA, Berdan EL, Duarte C, ..., Olds A, Schlacher TA

Biol Rev Camb Philos Soc 97 (6) 2127-2161 [2022-12-00; online 2022-08-11]

Bioinformatics Support for Computational Resources [Service]

The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.

Liu I, Jiang L, Samuelsson ER, ..., Nilsson M, Filbin MG

Nat. Genet. 54 (12) 1881-1894 [2022-12-00; online 2022-12-05]

The emerging landscape of spatial profiling technologies.

Moffitt JR, Lundberg E, Heyn H

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Species composition of shoreline wolf spider communities vary with salinity, but their diets vary with wrack inflow.

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Ecol Evol 12 (12) e9701 [2022-12-00; online 2022-12-28]

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Spatial and temporal heterogeneity in the lineage progression of fine oligodendrocyte subtypes

Hilscher MM, Langseth CM, Kukanja P, ..., Nilsson M, Castelo-Branco G

BMC Biol. 20 (1) 122 [2022-12-00; online 2022-05-25]

Seroprevalence of SARS-CoV-2 antibodies among public transport workers in Sweden.

Sjörs Dahlman A, Anund A

Journal of Transport & Health 27 (-) 101508 [2022-12-00; online 2022-09-28]

Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden.

Tilevik D, Pernestig AK, Fagerlind M, ..., Johansson M, Enroth H

Microb Pathog 173 (Pt A) 105836 [2022-12-00; online 2022-10-17]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Screening patients with autoimmune endocrine disorders for cytokine autoantibodies reveals monogenic immune deficiencies.

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J. Autoimmun. 133 (-) 102917 [2022-12-00; online 2022-09-30]

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Resistance of subarctic soil fungal and invertebrate communities to disruption of below‐ground carbon supply

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J Ecol 110 (12) 2883-2897 [2022-12-00; online 2022-10-17]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Quantitative image analysis of protein foam microstructure and its correlation with rheological properties: Egg white foam

Bonilla JC, Sørensen JL, Warming AS, Clausen MP

Food Hydrocolloids 133 (-) 108010 [2022-12-00; online 2022-12-00]

Integrated Microscopy Technologies Gothenburg [Collaborative]

Lower plasma concentrations of short-chain fatty acids (SCFAs) in patients with ADHD.

Yang LL, Stiernborg M, Skott E, ..., Giacobini M, Lavebratt C

J Psychiatr Res 156 (-) 36-43 [2022-12-00; online 2022-09-28]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Long-term ley and manure managements have consistent effects on microbial functional profiles and organic C groups across soils from a latitudinal gradient

Shi A, Nunan N, Figueira J, Herrmann AM, Wetterlind J

Agron. Sustain. Dev. 42 (6) - [2022-12-00; online 2022-11-03]

Isolation and characterization of a main porin from the outer membrane of Salinibacter ruber.

Farci D, Cocco E, Tanas M, ..., Schröder WP, Piano D

J Bioenerg Biomembr 54 (5-6) 273-281 [2022-12-00; online 2022-10-13]

Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases.

Nicoś M, Harbers L, Patrucco E, ..., Ambrogio C, Crosetto N

JTO Clin Res Rep 3 (12) 100435 [2022-12-00; online 2022-11-11]

Genome-wide association and Mendelian randomization study of fibroblast growth factor 21 reveals causal associations with hyperlipidemia and possibly NASH.

Larsson SC, Michaëlsson K, Mola-Caminal M, Höijer J, Mantzoros CS

Metabolism 137 (-) 155329 [2022-12-00; online 2022-10-05]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Fusion transcript analysis reveals slower response kinetics than multiparameter flow cytometry in childhood acute myeloid leukaemia.

Karlsson L, Nyvold CG, Soboli A, ..., Abrahamsson J, Fogelstrand L

Int J Lab Hematol 44 (6) 1094-1101 [2022-12-00; online 2022-08-02]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Effects of conventionally treated and ozonated wastewater on the damselfly larva oxylipidome in response to on-site exposure.

Späth J, Brodin T, Falås P, ..., Fick J, Nording M

Chemosphere 309 (Pt 1) 136604 [2022-12-00; online 2022-09-27]

Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway.

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New Phytol. 236 (5) 1951-1963 [2022-12-00; online 2022-09-16]

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Comparison of ROS1-rearrangement detection methods in a cohort of surgically resected non-small cell lung carcinomas.

Thurfjell V, Micke P, Yu H, ..., Goldmann T, Mattsson JSM

Transl Lung Cancer Res 11 (12) 2477-2494 [2022-12-00; online 2023-01-14]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Characterization of a Clostridioides difficile outbreak caused by PCR ribotype 046, associated with increased mortality.

Magnusson C, Mernelius S, Bengnér M, ..., Forshell S, Matussek A

Emerg Microbes Infect 11 (1) 850-859 [2022-12-00; online 2022-03-05]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An overlooked subset of Cx3cr1wt/wt microglia in the Cx3cr1CreER-Eyfp/wt mouse has a repopulation advantage over Cx3cr1CreER-Eyfp/wt microglia following microglial depletion

Zhou K, Han J, Lund H, ..., Harris RA, Blomgren K

J Neuroinflammation 19 (1) 20 [2022-12-00; online 2022-01-21]

Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Aeromonas salmonicida binds α2-6 linked sialic acid, which is absent among the glycosphingolipid repertoires from skin, gill, stomach, pyloric caecum, and intestine.

Benktander J, Sundh H, Sharba S, Teneberg S, Lindén SK

Virulence 13 (1) 1741-1751 [2022-12-00; online 2022-10-08]

Dynamic patterns of blood lipids and DNA methylation in response to statin therapy.

Qin X, Wang Y, Pedersen NL, Tang B, Hägg S

Clin Epigenetics 14 (1) 153 [2022-11-28; online 2022-11-28]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Deep mutational scan of a drug efflux pump reveals its structure-function landscape.

Meier G, Thavarasah S, Ehrenbolger K, ..., Barandun J, Seeger MA

Nat. Chem. Biol. - (-) - [2022-11-28; online 2022-11-28]

Anti-citrullinated protein antibody specificities and pulmonary fibrosis in relation to genetic loci in early rheumatoid arthritis.

Brink M, Ljung L, Hansson M, ..., Klareskog L, Rantapää-Dahlqvist S

Rheumatology (Oxford) 61 (12) 4985-4990 [2022-11-28; online 2022-05-10]

Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma protein biomarker profiling reveals major differences between acute leukaemia, lymphoma patients and controls.

Abu Sabaa A, Shen Q, Lennmyr EB, ..., Enblad G, Eriksson A

N Biotechnol 71 (-) 21-29 [2022-11-25; online 2022-06-29]

Affinity Proteomics Uppsala [Service] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Mucosal IgA against SARS-CoV-2 Omicron Infection. Reply.

Åberg M, Smed-Sörensen A, Thålin C

N. Engl. J. Med. 387 (21) e55 [2022-11-24; online 2022-11-24]

The mechanical regulation of RNA binding protein hnRNPC in the failing heart.

Martino F, Varadarajan NM, Perestrelo AR, ..., Pagliari S, Forte G

Sci Transl Med 14 (672) eabo5715 [2022-11-23; online 2022-11-23]

Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery.

Mosquim Junior S, Siino V, Rydén L, Vallon-Christersson J, Levander F

Cancers (Basel) 14 (23) - [2022-11-23; online 2022-11-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis.

Ruiz M, Devkota R, Panagaki D, ..., Borén J, Pilon M

Nat Commun 13 (1) 7162 [2022-11-22; online 2022-11-22]

Short and long-term associations between serum proteins linked to cardiovascular disease and particle exposure among constructions workers.

Gliga AR, Grahn K, Gustavsson P, ..., Selander J, Broberg K

Scand J Work Environ Health - (-) - [2022-11-21; online 2022-11-21]

Macrophages support healing of ischemic injury by transdifferentiating towards mural cells and adopting functions important for vascular support

Parv K, Hidalgo CH, Xu F, ..., Christoffersson G, Phillipson M

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Bioinformatics Support for Computational Resources [Service]

Detection of SARS-CoV-2 antibodies in serum and dried blood spot samples of vaccinated individuals using a sensitive homogeneous proximity extension assay.

Zhao H, Wang M, Muthelo P, ..., Mei YF, Landegren U

N Biotechnol 72 (-) 139-148 [2022-11-21; online 2022-11-21]

Affinity Proteomics Uppsala [Technology development]

Plasma proteins from several components of the immune system differentiate chronic widespread pain patients from healthy controls - an exploratory case-control study combining targeted and non-targeted protein identification.

Gerdle B, Wåhlén K, Gordh T, ..., Carlsson A, Ghafouri B

Medicine 101 (46) e31013 [2022-11-18; online 2022-11-20]

Organochemical Characterization of Peat Reveals Decomposition of Specific Hemicellulose Structures as the Main Cause of Organic Matter Loss in the Acrotelm.

Serk H, Nilsson MB, Figueira J, ..., Alewell C, Schleucher J

Environ. Sci. Technol. - (-) - [2022-11-18; online 2022-11-18]

Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo.

Tonge JJ, Notley SV, Dunning MJ, ..., Panoutsos G, Gad AKB

Sci Rep 12 (1) 19835 [2022-11-18; online 2022-11-18]

Integrated Microscopy Technologies Stockholm [Service]

Self-reported symptom severity, general health, and impairment in post-acute phases of COVID-19: retrospective cohort study of Swedish public employees.

Larsson SB, von Feilitzen GS, Andersson ME, ..., Nilsson S, Sigström R

Sci Rep 12 (1) 19818 [2022-11-17; online 2022-11-17]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis.

Needhamsen M, Khoonsari PE, Zheleznyakova GY, ..., Ekman D, Jagodic M

Front Genet 13 (-) 1042483 [2022-11-17; online 2022-11-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.

Osbeck CMG, Lundin D, Karlsson C, ..., Moran MA, Pinhassi J

PLoS ONE 17 (11) e0243406 [2022-11-17; online 2022-11-17]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades.

Hiltunen M, Ament-Velásquez SL, Ryberg M, Johannesson H

Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2208575119 [2022-11-16; online 2022-11-07]

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Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores.

Jespersen N, Ehrenbolger K, Winiger RR, ..., Vossbrinck CR, Barandun J

Nat Commun 13 (1) 6962 [2022-11-15; online 2022-11-15]

Meta-analysis of genome-wide association studies of hoarding symptoms in 27,537 individuals.

Strom NI, Smit DJA, Silzer T, ..., Mataix-Cols D, Cath D

Transl Psychiatry 12 (1) 479 [2022-11-15; online 2022-11-15]

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ID1 and CEBPA coordinate epidermal progenitor cell differentiation.

Kantzer CG, Yang W, Grommisch D, ..., Shirokova V, Genander M

Development 149 (22) - [2022-11-15; online 2022-11-16]

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Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus).

Cockerill CA, Hasselgren M, Dussex N, ..., Sokolova N, Norén K

Genes 13 (11) - [2022-11-15; online 2022-11-15]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dominantly inherited myosin IIa myopathy caused by aberrant splicing of MYH2.

Hedberg-Oldfors C, Elíasdóttir Ó, Geijer M, Lindberg C, Oldfors A

BMC Neurol 22 (1) 428 [2022-11-15; online 2022-11-15]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Abstract A007: Pancreatic cancer comprises co-existing transcriptional states regulated by distinct master regulator programs

Laise P, Turunen M, Maurer HC, ..., Olive KPP, Califano A

Cancer Res. 82 (22_Supplement) A007-A007 [2022-11-15; online 2022-11-15]

A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint.

Leyhr J, Waldmann L, Filipek-Górniok B, ..., Allalou A, Haitina T

Elife 11 (-) - [2022-11-15; online 2022-11-15]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Proteomic Analysis of Pleural Effusions from COVID-19 Deceased Patients: Enhanced Inflammatory Markers.

Razaghi A, Szakos A, Alouda M, ..., Björnstedt M, Szekely L

Diagnostics 12 (11) 2789 [2022-11-14; online 2022-11-14]

Early changes in gene expression profiles in AML patients during induction chemotherapy.

Jakobsen I, Sundkvist M, Björn N, Gréen H, Lotfi K

BMC Genomics 23 (1) 752 [2022-11-14; online 2022-11-14]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A multivesicular body-like organelle mediates stimulus-regulated trafficking of olfactory ciliary transduction proteins.

Maurya DK, Berghard A, Bohm S

Nat Commun 13 (1) 6889 [2022-11-12; online 2022-11-12]

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.

Liu L, Khan A, Sanchez-Rodriguez E, ..., Gharavi AG, Kiryluk K

Nat Commun 13 (1) 6859 [2022-11-11; online 2022-11-11]

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Dietary restriction and medical therapy drive PPARα-regulated improvements in early diabetic kidney disease in male rats.

Martin WP, Nair M, Chuah YHD, ..., le Roux CW, Docherty NG

Clin Sci (Lond) 136 (21) 1485-1511 [2022-11-11; online 2022-10-20]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative] Swedish NMR Centre (SNC) [Collaborative]

Genomic trajectories of a near-extinction event in the Chatham Island black robin.

von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N

BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Fungal Communities in Leaves and Roots of Healthy-Looking and Diseased Ulmusglabra.

Marčiulynas A, Marčiulynienė D, Lynikienė J, Bakys R, Menkis A

Microorganisms 10 (11) - [2022-11-10; online 2022-11-10]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A new cut&run low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/b-catenin tissue-specific genomic targets.

Zambanini G, Nordin A, Jonasson M, Pagella P, Cantù C

Development - (-) - [2022-11-10; online 2022-11-10]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Mapping the Landscape of Care Providers' Quality Assurance Approaches for AI in Diagnostic Imaging.

Lundström C, Lindvall M

J Digit Imaging - (-) - [2022-11-09; online 2022-11-09]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Systems Biology in ELIXIR: modelling in the spotlight.

Martins Dos Santos V, Anton M, Szomolay B, ..., Evelo CT, Hancock JM

F1000Res 11 (-) 1265 [2022-11-07; online 2022-11-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Stabilizing Mechanisms of β-Lactoglobulin in Amorphous Solid Dispersions of Indomethacin.

Kabedev A, Zhuo X, Leng D, ..., Bergström CAS, Löbmann K

Mol. Pharm. 19 (11) 3922-3933 [2022-11-07; online 2022-09-22]

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Read-Based Phasing and Analysis of Phased Variants with WhatsHap.

Martin M, Ebert P, Marschall T

Methods Mol. Biol. 2590 (-) 127-138 [2022-11-07; online 2022-11-07]

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Case report: Two sisters with a germline CHEK2 variant and distinct endocrine neoplasias.

Vallera RD, Ding Y, Hatanpaa KJ, ..., Dahia PLM, Ghayee HK

Front Endocrinol (Lausanne) 13 (-) 1024108 [2022-11-07; online 2022-11-07]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

FRET-FISH probes chromatin compaction at individual genomic loci in single cells.

Mota A, Berezicki S, Wernersson E, ..., Crosetto N, Bienko M

Nat Commun 13 (1) 6680 [2022-11-05; online 2022-11-05]

Spatial Proteomics [Collaborative]

Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.

Verma A, Åberg-Zingmark E, Sparrman T, ..., Sauer-Eriksson E, Wolf-Watz M

Sci Adv 8 (44) eabm4089 [2022-11-04; online 2022-11-04]

Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.

Dyrhage K, Garcia-Montaner A, Tamarit D, ..., Webster MT, Andersson SGE

Genome Biol Evol 14 (11) - [2022-11-04; online 2022-10-21]

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A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition.

Altınışık NE, Kazancı DD, Aydoğan A, ..., Erim Özdoğan A, Somel M

Sci Adv 8 (44) eabo3609 [2022-11-04; online 2022-11-04]

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The ESSENCE-Questionnaire in Medical Records Screening for Neurodevelopmental Symptoms/Problems: Utility and Clinical Validity.

Landgren V, Raanan Soltis Z, Svensson E, ..., Landgren M, Knez R

Neuropsychiatr Dis Treat 18 (-) 2559-2574 [2022-11-03; online 2022-11-03]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.

Ament-Velásquez SL, Gilchrist C, Rêgo A, ..., Rafati N, Stelkens R

Mol. Biol. Evol. 39 (11) - [2022-11-03; online 2022-11-06]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Population dynamics and demographic history of Eurasian collared lemmings.

Lord E, Marangoni A, Baca M, ..., Fedorov VB, Dalén L

BMC Ecol Evol 22 (1) 126 [2022-11-03; online 2022-11-03]

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Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831).

Michell CT, Pohjoismäki JLO, Spong G, Thulin CG

Sci Data 9 (1) 667 [2022-11-03; online 2022-11-03]

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Domain-specific insight into the recognition of BH3-death motifs by the pro-survival Bcl-2 protein.

Mushtaq AU, Ådén J, Ali K, Gröbner G

Biophysical Journal - (-) - [2022-11-02; online 2022-11-02]

DAR 16-II Primes Endothelial Cells for Angiogenesis Improving Bone Ingrowth in 3D-Printed BCP Scaffolds and Regeneration of Critically Sized Bone Defects.

Alfayez E, Veschini L, Dettin M, ..., Coward T, Di Silvio L

Biomolecules 12 (11) 1619 [2022-11-02; online 2022-11-02]

Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides.

Gharibi H, Chernobrovkin AL, Saei AA, ..., Makarov AA, Zubarev RA

Anal. Chem. 94 (43) 15048-15056 [2022-11-01; online 2022-10-17]

Novel TPR::ROS1 Fusion Gene Activates MAPK, PI3K and JAK/STAT Signaling in an Infant-type Pediatric Glioma.

Deland L, Keane S, Bontell TO, ..., Sabel M, Abel F

Cancer Genomics Proteomics 19 (6) 711-726 [2022-11-01; online 2022-11-01]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Ydj1 interaction at nucleotide-binding-domain of yeast Ssa1 impacts Hsp90 collaboration and client maturation.

Gaur D, Kumar N, Ghosh A, ..., Nystrom T, Sharma D

PLoS Genet. 18 (11) e1010442 [2022-11-00; online 2022-11-09]

Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.

Sahraei SE, Sánchez-García M, Montoliu-Nerin M, ..., Rosendahl S, Rosling A

Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]

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Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates.

Schneider KL, Ahmadpour D, Keuenhof KS, ..., Nyström T, Widlund PO

J. Biol. Chem. 298 (11) 102476 [2022-11-00; online 2022-09-09]

Integrated Microscopy Technologies Gothenburg [Service]

Translatome profiling in fatal familial insomnia implicates TOR signaling in somatostatin neurons.

Bauer S, Dittrich L, Kaczmarczyk L, ..., Benfeitas R, Jackson WS

Life Sci. Alliance 5 (11) - [2022-11-00; online 2022-10-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.

Lundtoft C, Sjöwall C, Rantapää-Dahlqvist S, ..., Leonard D, Rönnblom L

Arthritis & rheumatology (Hoboken, N.J.) 74 (11) 1842-1850 [2022-11-00; online 2022-10-07]

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Stroke genetics informs drug discovery and risk prediction across ancestries.

Mishra A, Malik R, Hachiya T, ..., Dichgans M, Debette S

Nature 611 (7934) 115-123 [2022-11-00; online 2022-09-30]

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Spatial genomics maps the structure, nature and evolution of cancer clones.

Lomakin A, Svedlund J, Strell C, ..., Nilsson M, Yates LR

Nature 611 (7936) 594-602 [2022-11-00; online 2022-11-09]

Organic Base-Mediated Carboxylation of (Hetero)aromatic Compounds Using Supercritical Carbon Dioxide (scCO2)

Govender T, Chetty LC, Kruger HG, Arvidsson PI, Naicker T

Synthesis 54 (21) 4827-4833 [2022-11-00; online 2022-08-16]

Drug Discovery and Development (DDD) [Collaborative]

Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies.

Sheward DJ, Kim C, Fischbach J, ..., Peacock TP, Murrell B

Lancet Infect Dis 22 (11) 1538-1540 [2022-11-00; online 2022-10-14]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks.

Murach KA, Liu Z, Jude B, ..., Vechetti IJ, von Walden F

J. Biol. Chem. 298 (11) 102515 [2022-11-00; online 2022-09-21]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Metabolite Pattern Derived from Lactiplantibacillus plantarum-Fermented Rye Foods and In Vitro Gut Fermentation Synergistically Inhibits Bacterial Growth.

Koistinen VM, Hedberg M, Shi L, ..., Hanhineva K, Landberg R

Mol Nutr Food Res 66 (21) e2101096 [2022-11-00; online 2022-08-19]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.

Yavuz S, Pucholt P, Sandling JK, ..., Lindblad-Toh K, Rönnblom L

Lupus Sci Med 9 (1) - [2022-11-00; online 2022-11-05]

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Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly.

Shipilina D, Näsvall K, Höök L, ..., Talavera G, Backström N

Genomics 114 (6) 110481 [2022-11-00; online 2022-09-14]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability.

Lindstrand A, Ek M, Kvarnung M, ..., Pettersson M, Nordgren A

Genet Med 24 (11) 2296-2307 [2022-11-00; online 2022-09-06]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Genetic and immunologic evaluation of children with inborn errors of immunity and severe or critical COVID-19.

Abolhassani H, Delavari S, Landegren N, ..., Hammarström L, Pan-Hammarström Q

J. Allergy Clin. Immunol. 150 (5) 1059-1073 [2022-11-00; online 2022-09-13]

Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.

Butler-Laporte G, Povysil G, Kosmicki JA, ..., Ferreira MAR, Richards JB

PLoS Genet. 18 (11) e1010367 [2022-11-00; online 2022-11-03]

NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Enzymatically dissociated muscle fibers display rapid dedifferentiation and impaired mitochondrial calcium control

Gineste C, Youhanna S, Vorrink SU, ..., Lauschke VM, Westerblad H

iScience - (-) 105654 [2022-11-00; online 2022-11-00]

Integrated Microscopy Technologies Umeå [Collaborative]

Circum‐Arctic distribution of chemical anti‐herbivore compounds suggests biome‐wide trade‐off in defence strategies in Arctic shrubs

Lindén E, te Beest M, Abreu IN, ..., Zimmermann H, Olofsson J

Ecography 2022 (11) - [2022-11-00; online 2022-08-30]

Chloride binding in Portland composite cements containing metakaolin and silica fume

Babaahmadi A, Machner A, Kunther W, ..., Hemstad P, De Weerdt K

Cement and Concrete Research 161 (-) 106924 [2022-11-00; online 2022-11-00]

Chemical traits of cerebral amyloid angiopathy in familial British-, Danish-, and non-Alzheimer's dementias.

Michno W, Koutarapu S, Camacho R, ..., Lashley T, Hanrieder J

J. Neurochem. 163 (3) 233-246 [2022-11-00; online 2022-09-25]

Integrated Microscopy Technologies Gothenburg [Collaborative]

Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.

Banijamali M, Höjer P, Nagy A, ..., Viktorsson K, Ahmadian A

J Extracell Vesicles 11 (11) e12277 [2022-11-00; online 2022-11-05]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Altered expression of the IGF2‑H19 locus and mitochondrial respiratory complexes in adrenocortical carcinoma.

Scicluna P, Caramuta S, Kjellin H, ..., Lui WO, Larsson C

Int. J. Oncol. 61 (5) - [2022-11-00; online 2022-09-28]

Global Proteomics and Proteogenomics [Collaborative]

A Complex Connection Between the Diversity of Human Gastric Mucin O-Glycans, Helicobacter pylori Binding, Helicobacter Infection and Fucosylation.

Chahal G, Padra M, Erhardsson M, ..., Karlsson NG, Lindén SK

Mol. Cell Proteomics 21 (11) 100421 [2022-11-00; online 2022-09-29]

Structural Consequences of Deproteinating the 50S Ribosome.

Larsson DSD, Kanchugal P S, Selmer M

Biomolecules 12 (11) - [2022-10-31; online 2022-10-31]

GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.

Golparian D, Jacobsson S, Sánchez-Busó L, ..., Ohnishi M, Unemo M

J. Antimicrob. Chemother. - (-) - [2022-10-29; online 2022-10-29]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.

Mañas A, Aaltonen K, Andersson N, ..., Gisselsson D, Bexell D

Sci Adv 8 (43) eabq4617 [2022-10-28; online 2022-10-28]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Structural Insights into Common and Host-Specific Receptor-Binding Mechanisms in Algal Picorna-like Viruses.

Wang H, Munke A, Li S, Tomaru Y, Okamoto K

Viruses 14 (11) - [2022-10-27; online 2022-10-27]

Changes in Chemical Properties and Fungal Communities of Mineral Soil after Clear-Cutting and Reforestation of Scots Pine (Pinus sylvestris L.) Sites

Povilaitienė A, Gedminas A, Varnagirytė-Kabašinskienė I, ..., Mishcherikova V, Menkis A

Forests 13 (11) 1780 [2022-10-27; online 2022-10-27]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Next-Generation Sequencing Analysis of CpG Methylation of a Tumor Suppressor Gene SHP-1 Promoter in Stable Cell Lines and HCV-Positive Patients.

Devi P, Engdahl K, Punga T, Bergqvist A

Viruses 14 (11) - [2022-10-26; online 2022-10-26]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Going Viral: An Investigation into the Chameleonic Behavior or Antiviral Compounds.

Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J

Chemistry - (-) - [2022-10-26; online 2022-10-26]

ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.

Schuster J, Klar J, Khalfallah A, ..., Birnir B, Dahl N

Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]

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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.

Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T

Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]

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Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.

Lovrić A, Rassolie A, Alam S, ..., Gustafsson T, Rullman E

Commun Biol 5 (1) 1121 [2022-10-22; online 2022-10-22]

Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris.

Marčiulynienė D, Marčiulynas A, Mischerikova V, ..., Franic I, Menkis A

JoF 8 (10) - [2022-10-21; online 2022-10-21]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Do ectomycorrhizal exploration types reflect mycelial foraging strategies?

Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD

New Phytol. - (-) - [2022-10-21; online 2022-10-21]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rapid antibiotic susceptibility testing and species identification for mixed samples.

Kandavalli V, Karempudi P, Larsson J, Elf J

Nat Commun 13 (1) 6215 [2022-10-20; online 2022-10-20]

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Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

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Nat Commun 13 (1) 6226 [2022-10-20; online 2022-10-20]

Global Proteomics and Proteogenomics [Technology development]

Architecture of the chikungunya virus replication organelle.

Laurent T, Kumar P, Liese S, ..., Carlson A, Carlson LA

Elife 11 (-) - [2022-10-19; online 2022-10-19]

SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing.

Mannsverk S, Bergholm J, Palanisamy N, ..., Lindh J, Lennerstrand J

Virol J 19 (1) 164 [2022-10-18; online 2022-10-18]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Global microRNA and protein expression in human term placenta.

Östling H, Lodefalk M, Backman H, Kruse R

Front Med (Lausanne) 9 (-) 952827 [2022-10-18; online 2022-10-18]

Assessment of the genetic and clinical determinants of hip fracture risk: Genome-wide association and Mendelian randomization study.

Nethander M, Coward E, Reimann E, ..., Hveem K, Ohlsson C

Cell Reports Medicine 3 (10) 100776 [2022-10-18; online 2022-10-20]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

Tobiasson V, Berzina I, Amunts A

Nat Commun 13 (1) 6132 [2022-10-17; online 2022-10-17]

Targeting Myd88 using peptide-loaded mesenchymal stem cell membrane-derived synthetic vesicles to treat systemic inflammation.

Park KS, Bergqvist M, Lässer C, Lötvall J

J Nanobiotechnology 20 (1) 451 [2022-10-15; online 2022-10-15]

Glucocorticoids and glucolipotoxicity alter the DNA methylome and function of human EndoC-βH1 cells.

Dos Santos C, Karagiannopoulos A, Rafacho A, ..., Ling C, Bacos K

Life Sciences 307 (-) 120854 [2022-10-15; online 2022-07-30]

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Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.

Behra PRK, Pettersson BMF, Ramesh M, ..., Dasgupta S, Kirsebom LA

BMC Genomics 23 (1) 704 [2022-10-15; online 2022-10-15]

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Cellulose interactions with CO2 in NaOH(aq): The (un)expected coagulation creates potential in cellulose technology.

Kozlowski AM, Hasani M

Carbohydr Polym 294 (-) 119771 [2022-10-15; online 2022-06-26]

TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis

Petkevicius K, Palmgren H, Glover MS, ..., Maresca M, Peng XR

Nat Commun 13 (1) 6020 [2022-10-14; online 2022-10-14]

Soil Microbiome Influences on Seedling Establishment and Growth of Prosopis chilensis and Prosopis tamarugo from Northern Chile.

Castro D, Concha C, Jamett F, Ibáñez C, Hurry V

Plants (Basel) 11 (20) - [2022-10-14; online 2022-10-14]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth.

Antoniadi I, Mateo-Bonmatí E, Pernisová M, ..., Ljung K, Novák O

Front Plant Sci 13 (-) 932008 [2022-10-14; online 2022-10-14]

The Expression of the Immunoproteasome Subunit PSMB9 Is Related to Distinct Molecular Subtypes of Uterine Leiomyosarcoma.

Maia Falcão R, Kokaraki G, De Wispelaere W, ..., Carlson JW, Petta TB

Cancers (Basel) 14 (20) - [2022-10-13; online 2022-10-13]

Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report.

Oldoni E, Saunders G, Bietrix F, ..., Andreu AL, van Gool AJ

Front Mol Biosci 9 (-) 974799 [2022-10-13; online 2022-10-13]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.

Hill J, Lillie M, Pettersson ME, ..., Andersson L, Jern P

Nat Commun 13 (1) 6033 [2022-10-13; online 2022-10-13]

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Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.

Kahsay A, Rodriguez-Marquez E, López-Pérez A, Hörnblad A, von Hofsten J

Sci Rep 12 (1) 17149 [2022-10-13; online 2022-10-13]

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Manganese-driven CoQ deficiency.

Diessl J, Berndtsson J, Broeskamp F, ..., Ott M, Büttner S

Nat Commun 13 (1) 6061 [2022-10-13; online 2022-10-13]

Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia, and solid tumor metastasis.

Grigoryan A, Zacharaki D, Balhuizen A, ..., Bexell D, Bourgine PE

Sci Transl Med 14 (666) eabm6391 [2022-10-12; online 2022-10-12]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.

Gui M, Croft JT, Zabeo D, ..., Höög JL, Brown A

Proc. Natl. Acad. Sci. U.S.A. 119 (41) e2207605119 [2022-10-11; online 2022-10-03]

Dormant SOX9-positive cells facilitate MYC-driven recurrence of medulloblastoma.

Borgenvik A, Holmberg KO, Bolin S, ..., Weishaupt H, Swartling FJ

Cancer Res. - (-) - [2022-10-11; online 2022-10-11]

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Membrane-assisted assembly and selective secretory autophagy of enteroviruses.

Dahmane S, Kerviel A, Morado DR, ..., Altan-Bonnet N, Carlson LA

Nat Commun 13 (1) 5986 [2022-10-10; online 2022-10-10]

DNA promoter hypermethylation of melanocyte lineage genes determines melanoma phenotype.

Sanna A, Phung B, Mitra S, ..., Pietras K, Jönsson G

JCI Insight 7 (19) - [2022-10-10; online 2022-10-10]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Liver Graft Proteomics Reveals Potential Incipient Mechanisms behind Early Renal Dysfunction after Liver Transplantation.

Norén Å, Oltean M, Friman S, ..., Herlenius G, Thorsell A

Int J Mol Sci 23 (19) - [2022-10-08; online 2022-10-08]

Differences in Metabolite Composition of Aloe barbadensis Mill. Extracts Lead to Differential Effects on Human Blood T Cell Activity In Vitro.

Ahluwalia B, Magnusson MK, Larsson F, ..., Ross AB, Öhman L

Molecules 27 (19) - [2022-10-06; online 2022-10-06]

Chalmers Mass Spectrometry Infrastructure [Service]

Calcium and magnesium in drinking water and risk of myocardial infarction and stroke-a population-based cohort study.

Helte E, Säve-Söderbergh M, Larsson SC, Åkesson A

Am. J. Clin. Nutr. 116 (4) 1091-1100 [2022-10-06; online 2022-07-12]

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Anti-Spike Mucosal IgA Protection against SARS-CoV-2 Omicron Infection.

Havervall S, Marking U, Svensson J, ..., Smed-Sörensen A, Thålin C

N. Engl. J. Med. 387 (14) 1333-1336 [2022-10-06; online 2022-09-14]

Affinity Proteomics Uppsala [Collaborative] Autoimmunity and Serology Profiling [Collaborative]

House crickets (Othroptera: Gryllidae: Acheta domesticus) reared in small-scale laboratory conditions harbour limited viral flora

Cholleti H, Vaga M, Jansson A, Blomström AL, Berg M

Journal of Insects as Food and Feed 8 (10) 1149-1155 [2022-10-04; online 2022-10-04]

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Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.

Liu T, Li X, Yekta SS, ..., Schnürer A, Enrich-Prast A

Sci Rep 12 (1) 16570 [2022-10-04; online 2022-10-04]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Biomarkers of demyelination and axonal damage are decreased after autologous hematopoietic stem cell transplantation for multiple sclerosis.

Zjukovskaja C, Larsson A, Cherif H, Kultima K, Burman J

Mult Scler Relat Disord 68 (-) 104210 [2022-10-03; online 2022-10-03]

The oncogenic transcription factor FOXQ1 is a differential regulator of Wnt target genes.

Pizzolato G, Moparthi L, Söderholm S, Cantù C, Koch S

J. Cell. Sci. 135 (19) - [2022-10-01; online 2022-10-10]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

The effects of pH on the production of volatile fatty acids and microbial dynamics in long-term reactor operation.

Atasoy M, Cetecioglu Z

J Environ Manage 319 (-) 115700 [2022-10-01; online 2022-07-20]

Bioinformatics Support for Computational Resources [Service]

Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount.

Gaetani M, Zubarev RA

Methods Mol. Biol. 2554 (-) 91-106 [2022-10-01; online 2022-10-01]

Mycobiota Associated with Symptomatic and Asymptomatic Fraxinus excelsior in Post-Dieback Forest Stands

Bakys R, Pliūra A, Bajerkevičienė G, ..., Lynikienė J, Menkis A

Forests 13 (10) 1609 [2022-10-01; online 2022-10-01]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Modest Conformity Between Self-Reporting of Bristol Stool Form and Fecal Consistency Measured by Stool Water Content in Irritable Bowel Syndrome and a FODMAP and Gluten Trial.

Nordin E, Hellström PM, Brunius C, Landberg R

Am J Gastroenterol 117 (10) 1668-1674 [2022-10-01; online 2022-08-12]

Bioinformatics Support for Computational Resources [Service] Chalmers Mass Spectrometry Infrastructure [Collaborative]

iP & OEIP – Cytokinin Micro Application Modulates Root Development with High Spatial Resolution

Pařízková B, Antoniadi I, Poxson DJ, ..., Novák O, Ljung K

Adv Materials Technologies 7 (10) 2101664 [2022-10-00; online 2022-04-28]

The dark side of foetal bovine serum in extracellular vesicle studies.

Urzì O, Bagge RO, Crescitelli R

J Extracell Vesicles 11 (10) e12271 [2022-10-00; online 2022-10-11]

Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.

Geng K, Merino LG, Wedemann L, ..., White RJ, Kutter C

Genome Res. 32 (10) 1876-1891 [2022-10-00; online 2022-09-30]

Bioinformatics Support for Computational Resources [Service]

Salinity induces discontinuous protoxylem via a DELLA-dependent mechanism promoting salt tolerance in Arabidopsis seedlings.

Augstein F, Carlsbecker A

New Phytol. 236 (1) 195-209 [2022-10-00; online 2022-07-12]

Bioinformatics Support for Computational Resources [Service]

Reproductive homing and fine‐scaled genetic structuring of anadromous Baltic Sea perch ( Perca fluviatilis )

Hall M, Koch‐Schmidt P, Larsson P, ..., Yıldırım Y, Sunde J

Fisheries Management Eco 29 (5) 586-596 [2022-10-00; online 2022-03-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system.

Pontiller B, Martínez-García S, Joglar V, ..., Teira E, Pinhassi J

ISME J 16 (10) 2360-2372 [2022-10-00; online 2022-07-08]

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Prostate cancer disease recurrence after radical prostatectomy is associated with HLA type and local cytomegalovirus immunity.

Classon J, Zamboni M, Engblom C, ..., Mold J, Frisén J

Mol Oncol 16 (19) 3452-3464 [2022-10-00; online 2022-08-31]

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PubMed

Pediatric Hip Disease Increases the Risk for Opioid Use in Adulthood: Long-term Burden of Pain and Depression.

Wadström MG, Hailer YD

Pain Physician 25 (7) E1153-E1160 [2022-10-00; online 2022-10-27]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Patterns of community composition and diversity in latent fungi of living Quercus serrata trunks across a range of oak wilt prevalence and climate variables in Japan

Fukasawa Y, Matsukura K, Stephan JG, ..., Yamashita S, Ushio M

Fungal Ecology 59 (-) 101095 [2022-10-00; online 2022-10-00]

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Parvimonas micra is associated with tumour immune profiles in molecular subtypes of colorectal cancer.

Löwenmark T, Li X, Löfgren-Burström A, ..., Edin S, Palmqvist R

Cancer Immunol. Immunother. 71 (10) 2565-2575 [2022-10-00; online 2022-03-17]

Affinity Proteomics Uppsala [Service] Clinical Genomics [Service] Clinical Genomics Umeå [Service]

Osteoclasts directly influence castration-resistant prostate cancer cells.

Huang J, Freyhult E, Buckland R, ..., Damber JE, Welén K

Clin Exp Metastasis 39 (5) 801-814 [2022-10-00; online 2022-08-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

New regulators of the tetracycline‐inducible gene expression system identified by chemical and genetic screens

Colicchia V, Häggblad M, Sirozh O, ..., Hühn D, Fernandez‐Capetillo O

FEBS Open Bio 12 (10) 1896-1908 [2022-10-00; online 2022-09-11]

CRISPR Functional Genomics [Service] Chemical Biology Consortium Sweden (CBCS) [Service]

Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with Populus tremula × Populus tremuloides.

Chowdhury J, Kemppainen M, Delhomme N, ..., Pardo AG, Lundberg-Felten J

New Phytol. 236 (2) 639-655 [2022-10-00; online 2022-07-27]

Bioinformatics Support for Computational Resources [Service]

Implementing precision medicine in a regionally organized healthcare system in Sweden.

Fioretos T, Wirta V, Cavelier L, ..., Edsjö A, Rosenquist R

Nat. Med. 28 (10) 1980-1982 [2022-10-00; online 2022-09-20]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Linköping [Service] Clinical Genomics Stockholm [Collaborative] Clinical Genomics Umeå [Service] Clinical Genomics Uppsala [Collaborative]

Global patterns and rates of habitat transitions across the eukaryotic tree of life.

Jamy M, Biwer C, Vaulot D, ..., Massana R, Burki F

Nat Ecol Evol 6 (10) 1458-1470 [2022-10-00; online 2022-08-04]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genome-wide association study of liver enzyme elevation in an extended cohort of rheumatoid arthritis patients starting low-dose methotrexate.

Cavalli M, Eriksson N, Sundbaum JK, ..., Hallberg P, Wadelius M

Pharmacogenomics 23 (15) 813-820 [2022-10-00; online 2022-09-07]

Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Generation of Human iPSC-Derived Astrocytes with a mature star-shaped phenotype for CNS modeling.

Voulgaris D, Nikolakopoulou P, Herland A

Stem Cell Rev Rep 18 (7) 2494-2512 [2022-10-00; online 2022-04-30]

Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids.

Iribarren C, Nordlander S, Sundin J, ..., Simrén M, Öhman L

Neurogastroenterol. Motil. 34 (10) e14390 [2022-10-00; online 2022-04-29]

Chalmers Mass Spectrometry Infrastructure [Service] Integrated Microscopy Technologies Gothenburg [Service]

Familial platelet disorder due to germline exonic deletions in RUNX1: a diagnostic challenge with distinct alterations of the transcript isoform equilibrium.

Engvall M, Karlsson Y, Kuchinskaya E, ..., Cammenga J, Baliakas P

Leuk. Lymphoma 63 (10) 2311-2320 [2022-10-00; online 2022-05-09]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Endophytes dominate fungal communities in six-year-old veteranisation wounds in living oak trunks

Menkis A, Redr D, Bengtsson V, ..., Nordén B, Dahlberg A

Fungal Ecology 59 (-) 101020 [2022-10-00; online 2022-10-00]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic.

Rasmussen PU, Abrego N, Roslin T, ..., Hugerth LW, Tack AJM

New Phytol. 236 (2) 671-683 [2022-10-00; online 2022-07-15]

Bioinformatics Support for Computational Resources [Service]

Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia.

Pilheden M, Ahlgren L, Hyrenius-Wittsten A, ..., Gawad C, Hagström-Andersson AK

Hemasphere 6 (10) e785 [2022-10-00; online 2022-09-30]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Cytokine responses to LPS in reprogrammed monocytes are associated with the transcription factor PU.1.

Tuerxun K, Midtbö K, Särndahl E, ..., Eklund D, X-HiDE Consortium

J Leukoc Biol 112 (4) 679-692 [2022-10-00; online 2022-03-13]

Bacteraemia and infective endocarditis with Streptococcus bovis-Streptococcus equinus-complex: a retrospective cohort study.

Öberg J, Nilson B, Gilje P, Rasmussen M, Inghammar M

Infect Dis (Lond) 54 (10) 760-765 [2022-10-00; online 2022-06-22]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL3 domain in solution.

Han X, Levkovets M, Lesovoy D, ..., Agback P, Orekhov VY

Biomol NMR Assign 16 (2) 363-371 [2022-10-00; online 2022-09-12]

A saturated map of common genetic variants associated with human height.

Yengo L, Vedantam S, Marouli E, ..., Visscher PM, Hirschhorn JN

Nature 610 (7933) 704-712 [2022-10-00; online 2022-10-12]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?

Arnqvist G, Sayadi A

Ecol Evol 12 (10) e9440 [2022-10-00; online 2022-10-27]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air-liquid interface.

Rahman M, Irmler M, Introna M, ..., Upadhyay S, Ganguly K

Sci Rep 12 (1) 16396 [2022-09-30; online 2022-09-30]

Early Mid-pregnancy Blood-Based Proteins as Possible Biomarkers of Increased Infant Birth Size in Sex-Stratified Analyses.

Lindberger E, Ahlsson F, Junus K, ..., Wikström AK, Sundström Poromaa I

Reprod Sci - (-) 1-11 [2022-09-30; online 2022-09-30]

Discovery of druggable cancer-specific pathways with application in acute myeloid leukemia.

Trac QT, Zhou T, Pawitan Y, Vu TN

Gigascience 11 (-) - [2022-09-29; online 2022-09-30]

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Proteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic mouse.

Diaz Lozano IM, Sork H, Stone VM, ..., Gabrielsson S, Flodström-Tullberg M

Front Endocrinol (Lausanne) 13 (-) 971313 [2022-09-28; online 2022-09-28]

Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells.

Tsirigoti C, Ali MM, Maturi V, Heldin CH, Moustakas A

Cell Death Dis 13 (9) 832 [2022-09-28; online 2022-09-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Parasitic strongyle nemabiome communities in wild ruminants in Sweden.

Halvarsson P, Baltrušis P, Kjellander P, Höglund J

Parasit Vectors 15 (1) 341 [2022-09-27; online 2022-09-27]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize.

Blankenagel S, Eggels S, Frey M, ..., Schön CC, Avramova V

Plant Cell 34 (10) 3860-3872 [2022-09-27; online 2022-07-07]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Identification of Single and Combined Serum Metabolites Associated with Food Intake.

Karlsson T, Winkvist A, Rådjursöga M, ..., Pedersen A, Lindqvist HM

Metabolites 12 (10) - [2022-09-27; online 2022-09-27]

A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds.

Sigeman H, Zhang H, Ali Abed S, Hansson B

J. Evol. Biol. - (-) - [2022-09-26; online 2022-09-26]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Untargeted Metabolomics Based on Liquid Chromatography-Mass Spectrometry for the Analysis of Plasma and Erythrocyte Samples in Childhood Obesity.

González-Domínguez Á, Armeni M, Savolainen O, ..., Landberg R, González-Domínguez R

Methods Mol. Biol. 2571 (-) 115-122 [2022-09-25; online 2022-09-25]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

A chromosome-scale reference genome for Spironucleus salmonicida.

Xu F, Jiménez-González A, Kurt Z, ..., Andersson JO, Svärd SG

Sci Data 9 (1) 585 [2022-09-24; online 2022-09-24]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Meiotic drive is associated with sexual incompatibility in Neurospora.

Vogan AA, Svedberg J, Grudzinska-Sterno M, Johannesson H

Evolution - (-) - [2022-09-23; online 2022-09-23]

Bioinformatics Support for Computational Resources [Service]

Hybrid immunity in immunocompromised patients with CLL after SARS-CoV-2 infection followed by booster mRNA vaccination.

Lisa B, Gao Y, Wullimann D, ..., Hansson L, Osterborg A

Blood - (-) - [2022-09-23; online 2022-09-23]

Autoimmunity and Serology Profiling [Collaborative]

Inflation of test accuracy due to data leakage in deep learning-based classification of OCT images.

Tampu IE, Eklund A, Haj-Hosseini N

Sci Data 9 (1) 580 [2022-09-22; online 2022-09-22]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Truncated lubricin glycans in osteoarthritis stimulate the synoviocyte secretion of VEGFA, IL-8, and MIP-1α: Interplay between O-linked glycosylation and inflammatory cytokines.

Huang S, Thomsson KA, Jin C, ..., Krawetz R, Karlsson NG

Front Mol Biosci 9 (-) 942406 [2022-09-21; online 2022-09-21]

Silicone Foam for Passive Sampling and Nontarget Analysis of Air

Papazian S, Fornaroli C, Bonnefille B, ..., Xie H, Martin JW

Environ Sci Technol Lett - (-) - [2022-09-21; online 2022-09-21]

To Modify or Not to Modify: Allele-Specific Effects of 3'UTR-KCNQ1 Single Nucleotide Polymorphisms on Clinical Phenotype in a Long QT 1 Founder Population Segregating a Dominant-Negative Mutation.

Winbo A, Diamant UB, Persson J, Jensen SM, Rydberg A

J Am Heart Assoc 11 (18) e025981 [2022-09-20; online 2022-09-14]

Clinical Genomics [Service] Clinical Genomics Umeå [Service]

Synergistic Effects of Sanglifehrin-Based Cyclophilin Inhibitor NV651 with Cisplatin in Hepatocellular Carcinoma.

Simón Serrano S, Tavecchio M, Mallik J, ..., Hansson MJ, Massoumi R

Cancers (Basel) 14 (19) 4553 [2022-09-20; online 2022-09-20]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters.

Capo E, Feng C, Bravo AG, ..., Hawkes J, Björn E

Environ. Sci. Technol. 56 (18) 13119-13130 [2022-09-20; online 2022-09-07]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Clearance of small intestinal crypts involves goblet cell mucus secretion by intracellular granule rupture and enterocyte ion transport.

Dolan B, Ermund A, Martinez-Abad B, Johansson MEV, Hansson GC

Sci Signal 15 (752) eabl5848 [2022-09-20; online 2022-09-20]

Integrated Microscopy Technologies Gothenburg [Service]

The genomic basis of hybrid male sterility in Ficedula flycatchers

Segami JC, Mugal CF, Cunha C, ..., Semon M, Qvarnström A

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Microbial Single Cell Genomics [Service]

Multifocal Neuroblastoma and Central Hypoventilation in An Infant with Germline ALK F1174I Mutation.

Djos A, Treis D, Fransson S, ..., Kogner P, Martinsson T

Diagnostics 12 (9) - [2022-09-19; online 2022-09-19]

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Complete Reference Genome Sequence of the Extensively Drug-Resistant Strain Neisseria gonorrhoeae AT159, with Ceftriaxone Resistance and High-Level Azithromycin Resistance, Using Nanopore Q20+ Chemistry and Illumina Sequencing.

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An induced pluripotent stem cell t(7;12)(q36;p13) acute myeloid leukemia model shows high expression of MNX1 and a block in differentiation of the erythroid and megakaryocytic lineages.

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A small molecule screen for paqr-2 suppressors identifies Tyloxapol as a membrane fluidizer for C. elegans and mammalian cells.

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J Child Psychol Psychiatry 63 (9) 1068-1077 [2022-09-00; online 2021-12-23]

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Proteins associated with future suicide attempts in bipolar disorder: A large-scale biomarker discovery study.

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Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.

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Clin Transl Med 12 (9) e1023 [2022-09-00; online 2022-09-15]

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Journal of Analytical and Applied Pyrolysis 166 (-) 105623 [2022-09-00; online 2022-09-00]

Immunomodulation by intravenous omega-3 fatty acid treatment in older subjects hospitalized for COVID-19: A single-blind randomized controlled trial.

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Clin Transl Med 12 (9) e895 [2022-09-00; online 2022-09-20]

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Nat Ecol Evol 6 (9) 1330-1342 [2022-09-00; online 2022-07-18]

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Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.

Wang Z, Emmerich A, Pillon NJ, ..., Loos RJF, Hoed Md

Nat. Genet. 54 (9) 1332-1344 [2022-09-00; online 2022-09-07]

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Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection.

Ambikan AT, Svensson-Akusjärvi S, Krishnan S, ..., Benfeitas R, Neogi U

Life Sci. Alliance 5 (9) - [2022-09-00; online 2022-05-10]

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Enhanced cytotoxicity of a novel family of ATPase inhibitors in colorectal cancer cells with high NAT2 activity

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Biochemical Pharmacology 203 (-) 115184 [2022-09-00; online 2022-09-00]

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Effects of denosumab treatment on the expression of receptor activator of nuclear kappa-B ligand (RANKL) and TNF-receptor TNFRSF9 after total hip arthroplasty-results from a randomized placebo-controlled clinical trial.

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Osteoporos Int 33 (9) 1-8 [2022-09-00; online 2022-05-24]

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Open Biol 12 (9) 220175 [2022-09-00; online 2022-09-14]

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Automated detection of vascular remodeling in tumor-draining lymph nodes by the deep-learning tool HEV-finder.

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Archaic chaperone-usher pili self-secrete into superelastic zigzag springs.

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Nature 609 (7926) 335-340 [2022-09-00; online 2022-07-19]

Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses.

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MBio 13 (4) e0015622 [2022-08-30; online 2022-07-20]

Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae.

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Gåtfulla Gårdby: kyrkor, skelett och DNA berättar om en öländsk socken

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Uncovering the genomic basis of an extraordinary plant invasion.

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Sci Adv 8 (34) eabo5115 [2022-08-26; online 2022-08-24]

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PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.

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Sci Adv 8 (34) eabo1543 [2022-08-26; online 2022-08-26]

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Methylation associated with long- or short-term survival in glioblastoma patients from the Nordic phase 3 trial.

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Front Genet 13 (-) 934519 [2022-08-25; online 2022-08-25]

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Genomic and gene expression associations to morphology of a sexual ornament in the chicken.

Bakovic V, Höglund A, Martin Cerezo ML, Henriksen R, Wright D

G3 (Bethesda) 12 (9) jkac174 [2022-08-25; online 2022-07-09]

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Electroactive Covalent Organic Framework Enabling Photostimulus-Responsive Devices.

Yang Y, Sandra AP, Idström A, ..., Evenäs L, Börjesson K

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Treatment of Metastatic Melanoma at First Diagnosis: Review of the Literature.

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Mapping the GALNT1 substrate landscape with versatile proteomics tools

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Epigenetic clock indicates accelerated aging in glial cells of progressive multiple sclerosis patients.

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Front Aging Neurosci 14 (-) 926468 [2022-08-24; online 2022-08-24]

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A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.

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Commun Biol 5 (1) 857 [2022-08-23; online 2022-08-23]

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Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.

Zufia JA, Legrand C, Farnelid H

Sci Rep 12 (1) 14330 [2022-08-22; online 2022-08-22]

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JCI Insight 7 (16) - [2022-08-22; online 2022-08-22]

Multi-Omic Investigations of a 17-19 Translocation Links MINK1 Disruption to Autism, Epilepsy and Osteoporosis.

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Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.

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iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]

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Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.

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iScience 25 (8) 104850 [2022-08-19; online 2022-08-02]

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Cerebrospinal fluid proteomic study of two bipolar disorder cohorts.

Isgren A, Göteson A, Holmén-Larsson J, ..., Jakobsson J, Landén M

Mol. Psychiatry - (-) - [2022-08-19; online 2022-08-19]

Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.

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ISME J 16 (12) 2635-2643 [2022-08-18; online 2022-08-18]

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Nat Commun 13 (1) 4837 [2022-08-17; online 2022-08-17]

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Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.

Ambikan AT, Yang H, Krishnan S, ..., Benfeitas R, Neogi U

Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]

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Isolated Grauer's gorilla populations differ in diet and gut microbiome.

Michel A, Minocher R, Niehoff PP, ..., Caillaud D, Guschanski K

Mol. Ecol. - (-) - [2022-08-17; online 2022-08-17]

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Learning Representations with Contrastive Self-Supervised Learning for Histopathology Applications

Stacke K, Unger J, Lundström C, Eilertsen G

Machine Learning for Biomedical Imaging 1 (August 2022 issue) - [2022-08-16; online 2022-08-16]

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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.

Broman E, Izabel-Shen D, Rodríguez-Gijón A, ..., Garcia SL, Nascimento FJA

Microbiome 10 (1) 126 [2022-08-15; online 2022-08-15]

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Feasibility and reliability of measures of bioactive lipids in human plasma and nasal mucosa.

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Journal of Chromatography B 1206 (-) 123357 [2022-08-15; online 2022-07-03]

Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation.

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Nat Commun 13 (1) 4755 [2022-08-13; online 2022-08-13]

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Nucleic Acids Res. 50 (14) 8349-8362 [2022-08-12; online 2022-07-25]

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Parasit Vectors 15 (1) 290 [2022-08-11; online 2022-08-11]

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Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.

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Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]

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Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.

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Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]

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Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.

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Detailed Characterization of the Cell Wall Structure and Composition of Nordic Green Microalgae.

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J. Agric. Food Chem. 70 (31) 9711-9721 [2022-08-10; online 2022-07-27]

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Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.

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Gigascience 11 (-) - [2022-08-10; online 2022-08-11]

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Ageing desexualizes the Drosophila brain transcriptome.

Malacrinò A, Brengdahl MI, Kimber CM, ..., Mirabello C, Friberg U

Proc. Biol. Sci. 289 (1980) 20221115 [2022-08-10; online 2022-08-10]

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Single-cell transcriptomics reveals the identity and regulators of human mast cell progenitors.

Wu C, Boey D, Bril O, ..., Nilsson G, Dahlin JS

Blood Adv 6 (15) 4439-4449 [2022-08-09; online 2022-05-03]

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Infection-induced membrane ruffling initiates danger and immune signaling via the mechanosensor PIEZO1.

Tadala L, Langenbach D, Dannborg M, ..., Cisneros DA, Puhar A

Cell Rep 40 (6) 111173 [2022-08-09; online 2022-08-11]

Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data.

Dhapola P, Rodhe J, Olofzon R, ..., Soneji S, Karlsson G

Nat Commun 13 (1) 4616 [2022-08-08; online 2022-08-08]

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Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing.

Tellgren-Roth C, Couturier M

Methods Mol. Biol. 2516 (-) 39-50 [2022-08-04; online 2022-08-04]

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Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy, and periventricular calcifications.

Rosenhahn E, O'Brien TJ, Zaki MS, ..., Maroofian R, Platzer K

Am. J. Hum. Genet. 109 (8) 1421-1435 [2022-08-04; online 2022-07-12]

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van Dijk LJA, Regazzoni EDE, Albrectsen BR, ..., Pawlowski K, Tack AJM

Front Plant Sci 13 (-) 897186 [2022-08-03; online 2022-08-03]

Polymer Dots as Photoactive Membrane Vesicles for [FeFe]-Hydrogenase Self-Assembly and Solar-Driven Hydrogen Evolution.

Pavliuk MV, Lorenzi M, Morado DR, ..., Berggren G, Tian H

J. Am. Chem. Soc. 144 (30) 13600-13611 [2022-08-03; online 2022-07-21]

Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.

Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K

Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]

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A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes.

Tunstrom K, Wheat CW, Parmesan C, Singer MC, Mikheyev AS

Genome Biol Evol 14 (8) - [2022-08-03; online 2022-07-26]

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Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms

Nilsson RH, Andersson AF, Bissett A, ..., Svenningsen CS, Schigel D

MBMG 6 (-) - [2022-08-02; online 2022-08-02]

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Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia.

Zhang Q, Matuozzo D, Le Pen J, ..., Cobat A, Casanova JL

J. Exp. Med. 219 (8) - [2022-08-01; online 2022-06-16]

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Metabolic control of arginine and ornithine levels paces the progression of leaf senescence.

Liebsch D, Juvany M, Li Z, ..., Guo H, Keech O

Plant Physiol. 189 (4) 1943-1960 [2022-08-01; online 2022-05-24]

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A relationship between phages and organic carbon in wastewater treatment plant effluents.

Modin O, Fuad N, Abadikhah M, ..., Persson F, Wilén BM

Water Res X 16 (-) 100146 [2022-08-01; online 2022-06-16]

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The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.

Westerdahl H, Mellinger S, Sigeman H, ..., Wolf JBW, Strandh M

Mol Ecol Resour 22 (6) 2379-2395 [2022-08-00; online 2022-04-11]

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The discovAIR project: a roadmap towards the Human Lung Cell Atlas.

Luecken MD, Zaragosi LE, Madissoon E, ..., Meyer KB, Nawijn MC

Eur. Respir. J. 60 (2) - [2022-08-00; online 2022-08-18]

TCF4 trinucleotide repeat expansion in Swedish cases with Fuchs' endothelial corneal dystrophy.

Viberg A, Westin IM, Golovleva I, Byström B

Acta Ophthalmol 100 (5) 541-548 [2022-08-00; online 2021-10-13]

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Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota.

Luis AS, Baslé A, Byrne DP, ..., Martens EC, Cartmell A

Nat. Chem. Biol. 18 (8) 841-849 [2022-08-00; online 2022-06-16]

SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.

Arslan T, Pan Y, Mermelekas G, ..., Orre LM, Lehtiö J

Nat Protoc 17 (8) 1832-1867 [2022-08-00; online 2022-06-22]

Global Proteomics and Proteogenomics [Technology development]

Spatially resolved clonal copy number alterations in benign and malignant tissue.

Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J

Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]

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Solvent-free synthesis of protic ionic liquids. Synthesis, characterization and computational studies of triazolium based ionic liquids

Morais EM, Abdurrokhman I, Martinelli A

Journal of Molecular Liquids 360 (-) 119358 [2022-08-00; online 2022-08-00]

Site-specific glycosylation of proteoglycans: A revisited frontier in proteoglycan research.

Noborn F, Nilsson J, Larson G

Matrix Biol. 111 (-) 289-306 [2022-08-00; online 2022-07-15]

Simple and rapid quantification of cetirizine, venlafaxine, and O-desmethylvenlafaxine in human breast milk, and metformin in human milk and plasma with UHPLC-MS/MS

Wegler C, Saleh A, Lindqvist A, ..., Smeraglia J, Baranczewski P

Journal of Chromatography B 1205 (-) 123340 [2022-08-00; online 2022-08-00]

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SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images.

Gupta A, Sabirsh A, Wahlby C, Sintorn IM

IEEE J Biomed Health Inform 26 (8) 4079-4089 [2022-08-00; online 2022-08-11]

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Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.

Latz MAC, Grujcic V, Brugel S, ..., Andersson A, Andersson AF

Mol Ecol Resour 22 (6) 2304-2318 [2022-08-00; online 2022-05-06]

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Seawater browning alters community composition and reduces nutritional quality of plankton in a subarctic marine ecosystem

Bandara T, Brugel S, Andersson A, Lau DCP

Can. J. Fish. Aquat. Sci. 79 (8) 1291-1301 [2022-08-00; online 2022-08-00]

Reactive melt crosslinking of cellulose nanocrystals/poly(ε-caprolactone) for heat-shrinkable network

Avella A, Idström A, Mincheva R, ..., Raquez JM, Lo Re G

Composites Part A: Applied Science and Manufacturing - (-) 107166 [2022-08-00; online 2022-08-00]

Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution.

Jamroskovic J, Deiana M, Sabouri N

Biochimie 199 (-) 81-91 [2022-08-00; online 2022-04-20]

Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals.

Berdan EL, Blanckaert A, Butlin RK, ..., Slotte T, Wielstra B

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 377 (1856) 20210199 [2022-08-00; online 2022-06-13]

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Mosaic Deletions of Known Genes Explain Skeletal Dysplasias With High and Low Bone Mass.

Muurinen M, Taylan F, Tournis S, ..., Mäkitie O, Costantini A

JBMR Plus 6 (8) e10660 [2022-08-00; online 2022-07-05]

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Human adaptation to arsenic in Bolivians living in the Andes.

De Loma J, Vicente M, Tirado N, ..., Schlebusch CM, Broberg K

Chemosphere 301 (-) 134764 [2022-08-00; online 2022-04-28]

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Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce.

Redondo MA, Oliva J, Elfstrand M, ..., Karlsson B, Berlin A

Environ. Microbiol. 24 (8) 3640-3654 [2022-08-00; online 2022-03-22]

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Five Percent Variant Allele Frequency Is a Reliable Reporting Threshold for TP53 Variants Detected by Next Generation Sequencing in Chronic Lymphocytic Leukemia in the Clinical Setting.

Pandzic T, Ladenvall C, Engvall M, ..., Ljungström V, Baliakas P

Hemasphere 6 (8) e761 [2022-08-00; online 2022-08-02]

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Esterified Lignin from Construction and Demolition Waste (CDW) as a Versatile Additive for Polylactic-Acid (PLA) Composites-The Effect of Artificial Weathering on its Performance.

Anugwom I, Lahtela V, Hedenström M, ..., Kärki T, Kallioinen-Mänttäri M

Glob Chall 6 (8) 2100137 [2022-08-00; online 2022-06-11]

Ericaceous dwarf shrubs contribute a significant but drought‐sensitive fraction of soil respiration in a boreal pine forest

Mielke LA, Ekblad A, Finlay RD, ..., Lindahl BD, Clemmensen KE

J Ecol 110 (8) 1928-1941 [2022-08-00; online 2022-06-15]

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Deep Visual Proteomics defines single-cell identity and heterogeneity.

Mund A, Coscia F, Kriston A, ..., Horvath P, Mann M

Nat. Biotechnol. 40 (8) 1231-1240 [2022-08-00; online 2022-05-19]

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.

Marco Salas S, Yuan X, Sylven C, ..., Wählby C, Partel G

PLoS Comput. Biol. 18 (8) e1010366 [2022-08-00; online 2022-08-12]

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Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.

Lundtoft C, Pucholt P, Martin M, ..., Svenungsson E, Rönnblom L

Arthritis & rheumatology (Hoboken, N.J.) 74 (8) 1440-1450 [2022-08-00; online 2022-06-27]

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Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.

Lundgren E, Romero-Severson E, Albert J, Leitner T

PLoS Comput. Biol. 18 (8) e1009741 [2022-08-00; online 2022-08-26]

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A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.

Gramlich S, Liu X, Favre A, Buerkle CA, Karrenberg S

New Phytol. 235 (4) 1641-1652 [2022-08-00; online 2022-06-23]

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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

Ramdas S, Judd J, Graham SE, ..., Zhu X, Brown CD

The American Journal of Human Genetics 109 (8) 1366-1387 [2022-08-00; online 2022-08-00]

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Validated Growth Rate-Dependent Regulation of Lipid Metabolism in Yarrowia lipolytica.

Poorinmohammad N, Fu J, Wabeke B, Kerkhoven EJ

Int J Mol Sci 23 (15) - [2022-07-31; online 2022-07-31]

Plasma protein profiling reveals dynamic immunomodulatory changes in multiple sclerosis patients during pregnancy.

Papapavlou Lingehed G, Hellberg S, Huang J, ..., Olsson T, Ernerudh J

Front Immunol 13 (-) 930947 [2022-07-29; online 2022-07-29]

Genomic surveillance and antimicrobial resistance in Neisseria gonorrhoeae isolates in Bangkok, Thailand in 2018.

Golparian D, Kittiyaowamarn R, Paopang P, ..., Wi T, Unemo M

J. Antimicrob. Chemother. 77 (8) 2171-2182 [2022-07-28; online 2022-05-12]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.

Cholleti H, de Jong J, Blomström AL, Berg M

Viruses 14 (8) - [2022-07-28; online 2022-07-28]

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Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria.

Li P, Hendricks AL, Wang Y, ..., Wang K, Gourdon P

Nat Commun 13 (1) 4339 [2022-07-27; online 2022-07-27]

Cryo-EM

Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies.

Swaegers J, Sánchez-Guillén RA, Chauhan P, Wellenreuther M, Hansson B

Proc. Biol. Sci. 289 (1979) 20220968 [2022-07-27; online 2022-07-20]

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Mobilization of systemic CCL4 following HIV pre-exposure prophylaxis in young men in Africa.

Petkov S, Herrera C, Else L, ..., Fox J, Chiodi F

Front Immunol 13 (-) 965214 [2022-07-27; online 2022-07-27]

Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.

Rodríguez J, Andersson A, Björn E, ..., Skrobonja A, Rowe O

Front Microbiol 13 (-) 809166 [2022-07-27; online 2022-07-27]

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Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells.

Khatri B, Tessneer KL, Rasmussen A, ..., Nordmark G, Lessard CJ

Nat Commun 13 (1) 4287 [2022-07-27; online 2022-07-27]

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Assessment of phylogenetic approaches to study the timing of recombination cessation on sex chromosomes.

Zhang H, Sigeman H, Hansson B

J. Evol. Biol. - (-) - [2022-07-27; online 2022-07-27]

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Targeted Chromosome Conformation Capture (HiCap).

Zhigulev A, Sahlén P

Methods Mol. Biol. 2532 (-) 75-94 [2022-07-23; online 2022-07-23]

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Proliferation and Immune Response Gene Signatures Associated with Clinical Outcome to Immunotherapy and Targeted Therapy in Metastatic Cutaneous Malignant Melanoma.

Costa Svedman F, Das I, Tuominen R, ..., Höiom V, Egyhazi Brage S

Cancers (Basel) 14 (15) - [2022-07-22; online 2022-07-22]

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A Drosophila melanogaster model for TMEM43-related arrhythmogenic right ventricular cardiomyopathy type 5.

Klinke N, Meyer H, Ratnavadivel S, ..., Milting H, Paululat A

Cell. Mol. Life Sci. 79 (8) 444 [2022-07-22; online 2022-07-22]

Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.

Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L

Elife 11 (-) - [2022-07-21; online 2022-07-21]

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Using multimarker screening to identify biomarkers associated with cardiovascular death in patients with atrial fibrillation.

Pol T, Hijazi Z, Lindbäck J, ..., Siegbahn A, Wallentin L

Cardiovasc. Res. 118 (9) 2112-2123 [2022-07-20; online 2021-08-07]

Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup.

Martinez-Monleon A, Kryh Öberg H, Gaarder J, ..., Fransson S, Martinsson T

Sci Rep 12 (1) 12420 [2022-07-20; online 2022-07-20]

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The Influence of Plant Stress Hormones and Biotic Elicitors on Cyclotide Production in Viola uliginosa Cell Suspension Cultures.

Slazak B, Jędrzejska A, Badyra B, ..., Andrén PE, Göransson U

Plants (Basel) 11 (14) - [2022-07-19; online 2022-07-19]

Sensitive Protein Detection Using Site-Specifically Oligonucleotide-Conjugated Nanobodies.

Al-Amin RA, Muthelo PM, Abdurakhmanov E, ..., Danielson UH, Landegren U

Anal. Chem. 94 (28) 10054-10061 [2022-07-19; online 2022-07-05]

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Plaque characteristics and biomarkers predicting regression and progression of carotid atherosclerosis.

Khan F, Gonçalves I, Shore AC, ..., Kozakova M, Nilsson J

Cell Reports Medicine 3 (7) 100676 [2022-07-19; online 2022-07-21]

Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening.

Schaal W, Ameur A, Olsson-Strömberg U, ..., Cavelier L, Spjuth O

Cancer Inform 21 (-) 11769351221110872 [2022-07-15; online 2022-07-15]

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Lipoxins reduce obesity-induced adipose tissue inflammation in 3D-cultured human adipocytes and explant cultures.

Soták M, Rajan MR, Clark M, ..., Lange S, Börgeson E

iScience 25 (7) 104602 [2022-07-15; online 2022-06-11]

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Effect and function of β-N-methylamino-L-alanine in the diatom Phaeodactylum tricornutum.

Kim SY, Rasmussen U, Rydberg S

Sci. Total Environ. 830 (-) 154778 [2022-07-15; online 2022-03-24]

Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.

Kuhl H, Du K, Schartl M, ..., Stöck M, Lamatsch DK

Nat Commun 13 (1) 4092 [2022-07-14; online 2022-07-14]

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A Hitchhiker's guide through the bio-image analysis software universe.

Haase R, Fazeli E, Legland D, ..., Klemm A, Tischer C

FEBS Lett. - (-) - [2022-07-14; online 2022-07-14]

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Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.

Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR

Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]

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Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.

Hardt U, Carlberg K, Af Klint E, ..., Ståhl PL, Malmström V

Sci Rep 12 (1) 11876 [2022-07-13; online 2022-07-13]

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High Variability of Fungal Communities Associated with the Functional Tissues and Rhizosphere Soil of Picea abies in the Southern Baltics

Marčiulynas A, Marčiulynienė D, Mishcherikova V, ..., Gedminas A, Menkis A

Forests 13 (7) 1103 [2022-07-13; online 2022-07-13]

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Ultra-sensitive monitoring of leukemia patients using superRCA mutation detection assays.

Chen L, Eriksson A, Weström S, ..., Cavelier L, Landegren U

Nat Commun 13 (1) 4033 [2022-07-12; online 2022-07-12]

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Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea.

Piombo E, Vetukuri RR, Sundararajan P, ..., Karlsson M, Dubey M

Appl. Environ. Microbiol. 88 (13) e0064322 [2022-07-12; online 2022-06-13]

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An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.

Ballarino R, Bouwman BAM, Agostini F, ..., Bienko M, Crosetto N

Sci Data 9 (1) 400 [2022-07-12; online 2022-07-12]

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FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees.

André D, Marcon A, Lee KC, ..., Schmid M, Nilsson O

Curr. Biol. 32 (13) 2988-2996.e4 [2022-07-11; online 2022-06-03]

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Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes

Hoffman T, Sjödin A, Öhrman C, ..., Lundkvist Å, Olsen B

Microorganisms 10 (7) 1393 [2022-07-11; online 2022-07-11]

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Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules.

Rubin CJ, Enbody ED, Dobreva MP, ..., Grant PR, Andersson L

Sci Adv 8 (27) eabm5982 [2022-07-08; online 2022-07-08]

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Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation.

Stenberg S, Li J, Gjuvsland AB, ..., Omholt SW, Warringer J

Elife 11 (-) - [2022-07-08; online 2022-07-08]

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B-cell repopulation dynamics and drug pharmacokinetics impact SARS-CoV-2 vaccine efficacy in anti-CD20-treated multiple sclerosis patients.

Asplund Högelin K, Ruffin N, Pin E, ..., Piehl F, Al Nimer F

Eur. J. Neurol. - (-) - [2022-07-08; online 2022-07-08]

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The onset of PI3K-related vascular malformations occurs during angiogenesis and is prevented by the AKT inhibitor miransertib.

Kobialka P, Sabata H, Vilalta O, ..., Castillo SD, Graupera M

EMBO Mol Med 14 (7) e15619 [2022-07-07; online 2022-06-13]

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Quantifying the ion coordination strength in polymer electrolytes.

Andersson R, Hernández G, Mindemark J

Phys Chem Chem Phys 24 (26) 16343-16352 [2022-07-06; online 2022-07-06]

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms.

Varg JE, Outomuro D, Kunce W, ..., Svanbäck R, Johansson F

Environ Microbiome 17 (1) 36 [2022-07-06; online 2022-07-06]

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Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.

Petitpré C, Faure L, Uhl P, ..., Hadjab S, Lallemend F

Nat Commun 13 (1) 3878 [2022-07-05; online 2022-07-05]

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Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.

Martínez-García S, Bunse C, Pontiller B, ..., Legrand C, Pinhassi J

Front Microbiol 13 (-) 834675 [2022-07-05; online 2022-07-05]

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Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study.

Arthur C, Rezayee F, Mogensen N, ..., Tham E, Barbany G

Front Oncol 12 (-) 899325 [2022-07-05; online 2022-07-05]

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In vivo Characterization of Endogenous Protein Interactomes in Drosophila Larval Brain, Using a CRISPR/Cas9-based Strategy and BioID-based Proximity Labeling.

Uçkun E, Wolfstetter G, Fuchs J, Palmer RH

BIO-PROTOCOL 12 (13) - [2022-07-05; online 2022-07-05]

Respiratory viral infections in otherwise healthy humans with inherited IRF7 deficiency.

Campbell TM, Liu Z, Zhang Q, ..., Meyts I, Bryceson YT

J. Exp. Med. 219 (7) - [2022-07-04; online 2022-06-07]

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High-throughput muscle fiber typing from RNA sequencing data.

Oskolkov N, Santel M, Parikh HM, ..., Pääbo S, Hansson O

Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]

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Galectin-4 levels in hospitalized versus non-hospitalized subjects with obesity: the Malmö Preventive Project.

Korduner J, Holm H, Jujic A, ..., Olsen MH, Magnusson M

Cardiovasc Diabetol 21 (1) 125 [2022-07-02; online 2022-07-02]

Role of endogenous incretins in the regulation of postprandial lipoprotein metabolism

Taskinen MR, Matikainen N, Björnson E, ..., Packard CJ, Borén J

Eur. J. Endocrinol. 187 (1) 75-84 [2022-07-01; online 2022-05-19]

Regulatory networks and 5' partner usage of miRNA host gene fusions in breast cancer.

Hafstað V, Søkilde R, Häkkinen J, ..., Rovira C, Persson H

Int. J. Cancer 151 (1) 95-106 [2022-07-01; online 2022-02-26]

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Practical application of a Bayesian network approach to poultry epigenetics and stress.

Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, ..., Jensen P, Smith VA

BMC Bioinformatics 23 (1) 261 [2022-07-01; online 2022-07-01]

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Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden.

Ellerstrand SJ, Choudhury S, Svensson K, ..., Hansson B, Runemark A

Ecol Evol 12 (7) e9078 [2022-07-00; online 2022-07-06]

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Suppressors of amyloid-β toxicity improve recombinant protein production in yeast by reducing oxidative stress and tuning cellular metabolism.

Chen X, Li X, Ji B, ..., Siewers V, Engqvist MKM

Metab. Eng. 72 (-) 311-324 [2022-07-00; online 2022-05-01]

Mercury–Selenium Accumulation Patterns in Muscle Tissue of Two Freshwater Fish Species, Eurasian Perch (Perca fluviatilis) and Vendace (Coregonus albula)

Regnell O, Tesson SVM, Oskolkov N, Nerentorp M

Water Air Soil Pollut 233 (7) - [2022-07-00; online 2022-06-20]

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Longitudinal assessment of inflammatory markers in the peripartum period by depressive symptom trajectory groups.

Bränn E, Skalkidou A, Schwarz J, ..., Sundström Poromaa I, Fransson E

Brain Behav Immun Health 22 (-) 100468 [2022-07-00; online 2022-05-02]

Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit.

Casanova-Sáez R, Mateo-Bonmatí E, Šimura J, ..., Staswick P, Ljung K

New Phytol. 235 (1) 263-275 [2022-07-00; online 2022-04-16]

Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant.

Zacharaki V, Ponnu J, Crepin N, ..., Rolland F, Schmid M

New Phytol. 235 (1) 220-233 [2022-07-00; online 2022-04-08]

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Immune responses after omicron infection in triple-vaccinated health-care workers with and without previous SARS-CoV-2 infection.

Blom K, Marking U, Havervall S, ..., Klingström J, Thålin C

Lancet Infect Dis 22 (7) 943-945 [2022-07-00; online 2022-06-09]

Affinity Proteomics Uppsala [Collaborative] Autoimmunity and Serology Profiling [Collaborative]

Identification of a novel compound that simultaneously impairs the ubiquitin-proteasome system and autophagy.

Giovannucci TA, Salomons FA, Stoy H, ..., Vallin M, Dantuma NP

Autophagy 18 (7) 1486-1502 [2022-07-00; online 2021-11-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Grey wolf genomic history reveals a dual ancestry of dogs.

Bergström A, Stanton DWG, Taron UH, ..., Dalén L, Skoglund P

Nature 607 (7918) 313-320 [2022-07-00; online 2022-06-29]

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Genomic profile - a possible diagnostic and prognostic marker in upper tract urothelial carcinoma.

Grahn A, Eisfeldt J, Malm C, ..., Tham E, Brehmer M

BJU Int. 130 (1) 92-101 [2022-07-00; online 2021-08-29]

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Genomic dynamics of brown trout populations released to a novel environment.

Kurland S, Rafati N, Ryman N, Laikre L

Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]

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Cross-sectional associations between the gut microbe Ruminococcus gnavus and features of the metabolic syndrome.

Grahnemo L, Nethander M, Coward E, ..., Hveem K, Ohlsson C

Lancet Diabetes Endocrinol 10 (7) 481-483 [2022-07-00; online 2022-06-01]

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Clonal haematopoiesis as a risk factor for therapy-related myeloid neoplasms in patients with chronic lymphocytic leukaemia treated with chemo-(immuno)therapy.

Voso MT, Pandzic T, Falconi G, ..., Fabiani E, Baliakas P

Br. J. Haematol. 198 (1) 103-113 [2022-07-00; online 2022-03-11]

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Characterization of Decellularized Implants for Extracellular Matrix Integrity and Immune Response Elicitation.

Banerjee D, Nayakawde NB, Antony D, ..., Ul Haq U, Olausson M

Tissue Eng Part A 28 (13-14) 621-639 [2022-07-00; online 2022-06-21]

Glycoproteomics and MS Proteomics [Collaborative] Integrated Microscopy Technologies Gothenburg [Collaborative]

An Adaptable Antibody‐Based Platform for Flexible Synthetic Peptide Delivery Built on Agonistic CD40 Antibodies

Eltahir M, Laurén I, Lord M, ..., Persson H, Mangsbo SM

Advanced Therapeutics 5 (7) 2200008 [2022-07-00; online 2022-06-14]

Drug Discovery and Development (DDD) [Collaborative]

Allorecognition genes drive reproductive isolation in Podospora anserina.

Ament-Velásquez SL, Vogan AA, Granger-Farbos A, ..., Clavé C, Johannesson H

Nat Ecol Evol 6 (7) 910-923 [2022-07-00; online 2022-05-12]

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Age-dependent aneuploidy in mammalian oocytes instigated at the second meiotic division.

Kouznetsova A, Liu JG, Valentiniene S, Brismar H, Höög C

Aging Cell 21 (7) e13649 [2022-07-00; online 2022-06-03]

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A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears.

Wang MS, Murray GGR, Mann D, ..., Green RE, Shapiro B

Nat Ecol Evol 6 (7) 936-944 [2022-07-00; online 2022-06-16]

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A high content screening assay for discovery of antimycobacterial compounds based on primary human macrophages infected with virulent Mycobacterium tuberculosis.

Kalsum S, Otrocka M, Andersson B, ..., Lundbäck T, Lerm M

Tuberculosis 135 (-) 102222 [2022-07-00; online 2022-06-16]

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Evidence for further non-coding RNA genes in the fungal rDNA region.

Rosenblad MA, Larsson E, Walker A, ..., Wurzbacher C, Nilsson RH

MycoKeys 90 (-) 203-213 [2022-06-30; online 2022-06-30]

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Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.

Domenzain I, Sánchez B, Anton M, ..., Sonnenschein N, Nielsen J

Nat Commun 13 (1) 3766 [2022-06-30; online 2022-06-30]

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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy.

Novotny A, Jan KMG, Dierking J, Winder M

Sci Rep 12 (1) 10952 [2022-06-29; online 2022-06-29]

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High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing.

Kostecka A, Nowikiewicz T, Olszewski P, ..., Dumanski JP, Piotrowski A

NPJ Breast Cancer 8 (1) 76 [2022-06-29; online 2022-06-29]

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Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections.

Rosendal E, Mihai IS, Becker M, ..., Överby AK, Lenman A

MBio 13 (3) e0089222 [2022-06-28; online 2022-05-09]

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Pelvic U-Net: multi-label semantic segmentation of pelvic organs at risk for radiation therapy anal cancer patients using a deeply supervised shuffle attention convolutional neural network.

Lempart M, Nilsson MP, Scherman J, ..., Munck Af Rosenschöld P, Olsson LE

Radiat Oncol 17 (1) 114 [2022-06-28; online 2022-06-28]

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Molecular International Prognostic Scoring System for Myelodysplastic Syndromes

Bernard E, Tuechler H, Greenberg PL, ..., Hellström-Lindberg E, Papaemmanuil E

NEJM Evidence 1 (7) - [2022-06-28; online 2022-06-28]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.

Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V

Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]

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Immunological differences between heart- and kidney-transplanted children: a cross-sectional study.

Ekman-Joelsson BM, Brandström P, Allén M, ..., Mellgren K, Ekwall O

Cardiol Young - (-) 1-6 [2022-06-24; online 2022-06-24]

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Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization.

Zhu X, Xie X, Das H, ..., Hällberg BM, Falkenberg M

Cell 185 (13) 2309-2323.e24 [2022-06-23; online 2022-06-02]

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Ultrafast and selective labeling of endogenous proteins using affinity-based benzotriazole chemistry.

Xin X, Zhang Y, Gaetani M, ..., Corkery DP, Wu Y

Chem. Sci. 13 (24) 7240-7246 [2022-06-22; online 2022-05-30] Open Access

Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches.

Lagos AC, Sundqvist M, Dyrkell F, ..., Söderquist B, Mölling P

Sci Rep 12 (1) 10541 [2022-06-22; online 2022-06-22]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners.

Arnold H, Panara V, Hußmann M, ..., Schulte-Merker S, Koltowska K

Cell Rep 39 (12) 110982 [2022-06-21; online 2022-06-23]

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The immune cell atlas of human neuroblastoma.

Verhoeven BM, Mei S, Olsen TK, ..., Johnsen JI, Baryawno N

Cell Reports Medicine 3 (6) 100657 [2022-06-21; online 2022-06-09]

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Screening for Biomarkers Associated with Left Ventricular Function During Follow-up After Acute Coronary Syndrome.

Christersson C, Baron T, Flachskampf F, ..., Lindahl B, Siegbahn A

J. of Cardiovasc. Trans. Res. - (-) - [2022-06-21; online 2022-06-21]

Membrane insertion mechanism of the caveola coat protein Cavin1.

Liu KC, Pace H, Larsson E, ..., Hubert M, Lundmark R

Proc. Natl. Acad. Sci. U.S.A. 119 (25) e2202295119 [2022-06-21; online 2022-06-13]

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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.

Blixt MKE, Hellsand M, Konjusha D, ..., Ring H, Hallböök F

Oncogenesis 11 (1) 34 [2022-06-21; online 2022-06-21]

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Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies.

Gorski M, Rasheed H, Teumer A, ..., Kronenberg F, Heid IM

Kidney Int. - (-) - [2022-06-16; online 2022-06-16]

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Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite.

Kotila T, Wioland H, Selvaraj M, ..., Romet-Lemonne G, Lappalainen P

Nat Commun 13 (1) 3442 [2022-06-15; online 2022-06-15]

Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation.

Petrus-Reurer S, Lederer AR, Baqué-Vidal L, ..., La Manno G, Lanner F

Stem Cell Reports 17 (6) 1458-1475 [2022-06-14; online 2022-06-16]

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CRISPR-Cas9 treatment partially restores amyloid-β 42/40 in human fibroblasts with the Alzheimer's disease PSEN 1 M146L mutation.

Konstantinidis E, Molisak A, Perrin F, ..., Berezovska O, Ingelsson M

Mol Ther Nucleic Acids 28 (-) 450-461 [2022-06-14; online 2022-03-28]

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GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.

Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D

BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]

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Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.

Winkler TW, Rasheed H, Teumer A, ..., Pattaro C, Heid IM

Commun Biol 5 (1) 580 [2022-06-13; online 2022-06-13]

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Combining metabolic phenotype determination with metabolomics and transcriptional analyses to reveal pathways regulated by hydroxycarboxylic acid receptor 2.

Rabe P, Gehmlich M, Peters A, ..., Nordström A, Stäubert C

Discov Oncol 13 (1) 47 [2022-06-13; online 2022-06-13]

Case Report: Inversion of LMX1B - A Novel Cause of Nail-Patella Syndrome in a Swedish Family and a Longtime Follow-Up.

Lindelöf H, Horemuzova E, Voss U, ..., Grigelioniene G, Hammarsjö A

Front Endocrinol (Lausanne) 13 (-) 862908 [2022-06-13; online 2022-06-13]

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Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.

Hatano T, Palani S, Papatziamou D, ..., Robinson NP, Balasubramanian M

Nat Commun 13 (1) 3398 [2022-06-13; online 2022-06-13]

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Long-Term Warming of Baltic Sea Coastal Waters Affects Bacterial Communities in Bottom Water and Sediments Differently.

Seidel L, Broman E, Ståhle M, ..., Hylander S, Dopson M

Front Microbiol 13 (-) 873281 [2022-06-10; online 2022-06-10]

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Unusual Magnetic Features in Two-Dimensional Fe5GeTe2 Induced by Structural Reconstructions.

Ershadrad S, Ghosh S, Wang D, Kvashnin Y, Sanyal B

J Phys Chem Lett 13 (22) 4877-4883 [2022-06-09; online 2022-05-26]

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FOXO1 and FOXO3 Cooperatively Regulate Innate Lymphoid Cell Development.

Luu TT, Søndergaard JN, Peña-Pérez L, ..., Månsson R, Kadri N

Front Immunol 13 (-) 854312 [2022-06-09; online 2022-06-09]

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Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.

Suarez C, Sedlacek CJ, Gustavsson DJI, ..., Hermansson M, Persson F

NPJ Biofilms Microbiomes 8 (1) 47 [2022-06-08; online 2022-06-08]

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Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.

Srigyan M, Bolívar H, Ureña I, ..., Günther T, Valdiosera C

Commun Biol 5 (1) 554 [2022-06-07; online 2022-06-07]

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Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis.

van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G

Dev. Cell 57 (11) 1421-1436.e5 [2022-06-06; online 2022-05-05]

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A novel non-invasive method allowing for discovery of pathologically relevant proteins from small airways.

Östling J, Van Geest M, Olsson HK, ..., Mirgorodskaya E, Olin AC

Clin Proteomics 19 (1) 20 [2022-06-06; online 2022-06-06]

LymphoTrack Is Equally Sensitive as PCR GeneScan and Sanger Sequencing for Detection of Clonal Rearrangements in ALL Patients.

Paulsen K, Marincevic M, Cavelier L, Hollander P, Amini RM

Diagnostics 12 (6) - [2022-06-04; online 2022-06-04]

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Applicability of polygenic risk scores in endometriosis clinical presentation.

Svensson A, Garcia-Etxebarria K, Åkesson A, ..., D'Amato M, Ohlsson B

BMC Womens Health 22 (1) 208 [2022-06-03; online 2022-06-03]

The Karolinska KI/K COVID-19 Immune Atlas: An open resource for immunological research and educational purposes.

Ljunggren HG, Ask EH, Cornillet M, ..., Strålin K, Björkström NK

Scand. J. Immunol. - (-) e13195 [2022-06-02; online 2022-06-02]

Secondary resistance to idelalisib is characterized by upregulation of IGF1R rather than by MAPK/ERK pathway mutations.

Tausch E, Ljungström V, Agathangelidis A, ..., Rosenquist R, Stilgenbauer S

Blood 139 (22) 3340-3344 [2022-06-02; online 2022-04-05]

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C1QTNF3 is Upregulated During Subcutaneous Adipose Tissue Remodeling and Stimulates Macrophage Chemotaxis and M1-Like Polarization.

Micallef P, Vujičić M, Wu Y, ..., Cardell SL, Wernstedt Asterholm I

Front Immunol 13 (-) 914956 [2022-06-02; online 2022-06-02]

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Accelerated epigenetic aging in suicide attempters uninfluenced by high intent-to-die and choice of lethal methods.

Jokinen J, Andersson P, Chatzittofis A, ..., Åsberg M, Boström ADE

Transl Psychiatry 12 (1) 224 [2022-06-02; online 2022-06-02]

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Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data.

Bengtsson VEG, Pacoste L, de la Rosa-Trevin JM, ..., Zou X, Xu H

J Appl Crystallogr 55 (Pt 3) 638-646 [2022-06-01; online 2022-04-22]

Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.

Alekseenko Z, Dias JM, Adler AF, ..., Parmar M, Ericson J

Nat Commun 13 (1) 3046 [2022-06-01; online 2022-06-01]

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Mutation in the TACI gene and autoimmune neutropenia: A case report.

Bergman P, Broliden PA, Ratcliffe P, ..., Höglund P, Palmblad J

Am. J. Hematol. 97 (6) E207-E210 [2022-06-01; online 2022-03-26]

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Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach.

Alves G, Ogurtsov A, Karlsson R, ..., Moore ERB, Yu YK

J. Am. Soc. Mass Spectrom. 33 (6) 917-931 [2022-06-01; online 2022-05-02]

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The mosaic oat genome gives insights into a uniquely healthy cereal crop.

Kamal N, Tsardakas Renhuldt N, Bentzer J, ..., Spannagl M, Sirijovski N

Nature 606 (7912) 113-119 [2022-06-00; online 2022-05-18]

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The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.

Ma L, Bryce NS, Turner AW, ..., Björkegren JLM, Kovacic JC

PLoS Genet. 18 (6) e1010261 [2022-06-00; online 2022-06-17]

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TGFβ selects for pro-stemness over pro-invasive phenotypes during cancer cell epithelial-mesenchymal transition.

Tsubakihara Y, Ohata Y, Okita Y, ..., Heldin CH, Moustakas A

Mol Oncol 16 (12) 2330-2354 [2022-06-00; online 2022-04-10]

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Site-specific N-glycan profiles of α5 β1 integrin from rat liver.

Mirgorodskaya E, Dransart E, Shafaq-Zadah M, ..., Leffler H, Johannes L

Biol Cell 114 (6) 160-176 [2022-06-00; online 2022-03-31]

Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia.

Gunnarsson R, Yang M, Biloglav A, ..., Paulsson K, Johansson B

Leukemia 36 (6) 1681-1684 [2022-06-00; online 2022-04-01]

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Eur. Urol. 81 (6) e143-e144 [2022-06-00; online 2022-02-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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Cancer Res Commun 2 (6) 434-446 [2022-06-00; online 2022-06-14]

Global Proteomics and Proteogenomics [Collaborative]

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Hum. Mutat. 43 (6) 708-716 [2022-06-00; online 2022-03-07]

Clinical Genomics [Technology development] Clinical Genomics Stockholm [Technology development]

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Pregnancy Hypertens 28 (-) 74-80 [2022-06-00; online 2022-02-26]

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J Matern Fetal Neonatal Med 35 (11) 2054-2062 [2022-06-00; online 2020-06-16]

Chalmers Mass Spectrometry Infrastructure [Service]

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Nature 606 (7914) 603-608 [2022-06-00; online 2022-06-08]

Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]

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Am. J. Med. Genet. A 188 (6) 1676-1687 [2022-06-00; online 2022-02-15]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Uppsala [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Improving lithium dose prediction using population pharmacokinetics and pharmacogenomics: a cohort genome-wide association study in Sweden

Millischer V, Matheson GJ, Bergen SE, ..., Lavebratt C, Schalling M

The Lancet Psychiatry 9 (6) 447-457 [2022-06-00; online 2022-06-00]

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Impaired oxygen-sensitive regulation of mitochondrial biogenesis within the von Hippel-Lindau syndrome.

Li S, Li W, Yuan J, ..., Cao Y, Schlisio S

Nat Metab 4 (6) 739-758 [2022-06-00; online 2022-06-27]

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Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.

Dahlin M, Singleton SS, David JA, ..., Mazumder R, Prast-Nielsen S

EBioMedicine 80 (-) 104061 [2022-06-00; online 2022-05-19]

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Genetic determinants of mannose-binding lectin activity predispose to thromboembolic complications in critical COVID-19.

Hultström M, Frithiof R, Grip J, ..., Zeberg H, Eriksson O

Nat. Immunol. 23 (6) 861-864 [2022-06-00; online 2022-05-27]

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Extensively drug-resistant (XDR) Neisseria gonorrhoeae causing possible gonorrhoea treatment failure with ceftriaxone plus azithromycin in Austria, April 2022.

Pleininger S, Indra A, Golparian D, ..., Heidler S, Unemo M

Euro Surveill. 27 (24) - [2022-06-00; online 2022-06-18]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells

Saghaleyni R, Malm M, Moruzzi N, ..., Robinson JL, Rockberg J

Cell Rep 39 (11) 110936 [2022-06-00; online 2022-06-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Do cold weather temperatures affect the efficacy of skin decontamination?

Thors L, Wästerby P, Wigenstam E, ..., Öberg L, Bucht A

J Appl Toxicol 42 (6) 961-969 [2022-06-00; online 2021-12-01]

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Bandara T, Brugel S, Andersson A, Lau DCP

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Chen X, Li X, Ji B, ..., Siewers V, Engqvist MKM

Data Brief 42 (-) 108322 [2022-06-00; online 2022-05-27]

Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase.

Diamanti R, Srinivas V, Johansson AI, ..., Lebrette H, Högbom M

FEBS Lett. 596 (12) 1600-1610 [2022-06-00; online 2022-03-04]

Chronic Obstructive Pulmonary Disease Is Associated with Epigenome-Wide Differential Methylation in BAL Lung Cells.

Eriksson Ström J, Kebede Merid S, Pourazar J, ..., Behndig AF, Melén E

Am J Respir Cell Mol Biol 66 (6) 638-647 [2022-06-00; online 2022-03-15]

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Childhood overweight and risk of obesity-related adult cancer in men.

Célind J, Bygdell M, Martikainen J, Ohlsson C, Kindblom JM

Cancer Commun (Lond) 42 (6) 576-579 [2022-06-00; online 2022-04-08]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Carbon nanodots: A metal-free, easy-to-synthesize, and benign emitter for light-emitting electrochemical cells

Liu Y, Tang S, Wu X, ..., Edman L, Wang J

Nano Res. 15 (6) 5610-5618 [2022-06-00; online 2022-03-15]

Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.

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R. Soc. open sci. 9 (6) 220104 [2022-06-00; online 2022-06-15]

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Accumulation dynamics of ARGONAUTE proteins during meiosis in Arabidopsis.

Oliver C, Martinez G

Plant Reprod 35 (2) 153-160 [2022-06-00; online 2021-11-23]

Bioinformatics Support for Computational Resources [Service]

A new transgenic reporter line reveals expression of protocadherin 9 at a cellular level within the zebrafish central nervous system.

Habicher J, Manuel R, Pedroni A, ..., Ampatzis K, Boije H

Gene Expr Patterns 44 (-) 119246 [2022-06-00; online 2022-04-12]

Genome Engineering Zebrafish [Collaborative]

A breathing mask attenuates acute airway responses to exercise in sub-zero environment in healthy subjects.

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Eur J Appl Physiol 122 (6) 1473-1484 [2022-06-00; online 2022-04-07]

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Sci Rep 12 (1) 9080 [2022-05-31; online 2022-05-31]

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An empirical evaluation of genotype imputation of ancient DNA.

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Large-scale whole-genome sequencing of migratory Bogong moths Agrotis infusa reveals genetic variants associated with migratory direction in a panmictic population

Wallace JR, Maleszka R, Warrant EJ

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Sorafenib and nitazoxanide disrupt mitochondrial function and inhibit regrowth capacity in three-dimensional models of hepatocellular and colorectal carcinoma.

Ek F, Blom K, Selvin T, ..., Jarvius M, Fryknäs M

Sci Rep 12 (1) 8943 [2022-05-27; online 2022-05-27]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Nitrogen represses haustoria formation through abscisic acid in the parasitic plant Phtheirospermum japonicum.

Kokla A, Leso M, Zhang X, ..., Yoshida S, Melnyk CW

Nat Commun 13 (1) 2976 [2022-05-27; online 2022-05-27]

Bioinformatics Support for Computational Resources [Service] Swedish Metabolomics Centre (SMC) [Service]

The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase.

Kerr AG, Wang Z, Wang N, ..., Arner P, Gao H

Nat Commun 13 (1) 2958 [2022-05-26; online 2022-05-26]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.

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Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]

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Pregnancy outcomes with differences in grain consumption: a randomized controlled trial.

Yamada P, Paetow A, Chan M, ..., Landberg R, Young BK

J Perinat Med 50 (4) 411-418 [2022-05-25; online 2022-01-03]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater.

Hellman M, Valhondo C, Martínez-Landa L, ..., Juhanson J, Hallin S

Front Microbiol 13 (-) 877990 [2022-05-24; online 2022-05-24]

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Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health.

Manu DM, Mwinyi J, Schiöth HB

Int J Mol Sci 23 (10) - [2022-05-23; online 2022-05-23]

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Quantitative Analysis of the Transcriptome of Two Commonly Used Human Monocytic Cell Lines-THP-1 and Mono Mac 6-Reveals Their Arrest during Early Monocyte/Neutrophil Differentiation.

Akula S, Lara S, Olsson AK, Hellman L

Int J Mol Sci 23 (10) - [2022-05-22; online 2022-05-22]

NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Ultrastructure and nuclear architecture of telomeric chromatin revealed by correlative light and electron microscopy.

Hübner B, von Otter E, Ahsan B, ..., Ludwig A, Sandin S

Nucleic Acids Res. 50 (9) 5047-5063 [2022-05-20; online 2022-05-01]

Integrated Microscopy Technologies Umeå [Technology development]

Touch signaling and thigmomorphogenesis are regulated by complementary CAMTA3- and JA-dependent pathways.

Darwish E, Ghosh R, Ontiveros-Cisneros A, ..., Khan K, Van Aken O

Sci Adv 8 (20) eabm2091 [2022-05-20; online 2022-05-20]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.

Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T

iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]

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Critical role of Lama4 for hematopoiesis regeneration and acute myeloid leukemia progression.

Cai H, Kondo M, Sandhow L, ..., Ekblom M, Qian H

Blood 139 (20) 3040-3057 [2022-05-19; online 2021-12-28]

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Spatial Resolution of Mycobacterium tuberculosis Bacteria and Their Surrounding Immune Environments Based on Selected Key Transcripts in Mouse Lungs.

Magoulopoulou A, Qian X, Pediatama Setiabudiawan T, ..., Nilsson M, Carow B

Front Immunol 13 (-) 876321 [2022-05-18; online 2022-05-18]

Generalisation effects of predictive uncertainty estimation in deep learning for digital pathology.

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Sci Rep 12 (1) 8329 [2022-05-18; online 2022-05-18]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

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Long M, Sanchez-Martinez A, Longo M, ..., Whitworth AJ, McWilliams TG

EMBO J. 41 (10) e109390 [2022-05-16; online 2022-04-12]

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Nat Commun 13 (1) 2700 [2022-05-16; online 2022-05-16]

Early Bactericidal Activity of Meropenem plus Clavulanate (with or without Rifampin) for Tuberculosis: The COMRADE Randomized, Phase 2A Clinical Trial.

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Am. J. Respir. Crit. Care Med. 205 (10) 1228-1235 [2022-05-15; online 2022-03-09]

Bioinformatics Support for Computational Resources [Service]

Optimized sample preparation and data analysis for TMT proteomic analysis of cerebrospinal fluid applied to the identification of Alzheimer's disease biomarkers.

Weiner S, Sauer M, Visser PJ, ..., Zetterberg H, Gobom J

Clin Proteomics 19 (1) 13 [2022-05-14; online 2022-05-14]

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Sci Rep 12 (1) 7976 [2022-05-13; online 2022-05-13]

Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts.

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Nat Commun 13 (1) 2634 [2022-05-12; online 2022-05-12]

Bioinformatics Support for Computational Resources [Service]

Genome-wide association meta-analysis identifies 48 risk variants and highlights the role of the stria vascularis in hearing loss.

Trpchevska N, Freidin MB, Broer L, ..., Williams FMK, Nagtegaal AP

Am. J. Hum. Genet. 109 (6) 1077-1091 [2022-05-12; online 2022-05-12]

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Orsucci M, Yang X, Vanikiotis T, ..., Lascoux M, Glémin S

Ann. Bot. 129 (6) 697-708 [2022-05-12; online 2022-03-25]

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The impact of digital media on children's intelligence while controlling for genetic differences in cognition and socioeconomic background.

Sauce B, Liebherr M, Judd N, Klingberg T

Sci Rep 12 (1) 7720 [2022-05-11; online 2022-05-11]

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Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden.

Olsson LM, Boulund F, Nilsson S, ..., Tremaroli V, Bäckhed F

Cell Host Microbe 30 (5) 726-739.e3 [2022-05-11; online 2022-03-28]

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The SARS-CoV-2 receptor ACE2 is expressed in mouse pericytes but not endothelial cells: Implications for COVID-19 vascular research.

Muhl L, He L, Sun Y, ..., Lendahl U, Betsholtz C

Stem Cell Reports 17 (5) 1089-1104 [2022-05-10; online 2022-04-21]

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Orthotopic Transplantation of Human Paediatric High-Grade Glioma in Zebrafish Larvae.

Larsson S, Kettunen P, Carén H

Brain Sci 12 (5) - [2022-05-10; online 2022-05-10]

Integrated Microscopy Technologies Gothenburg [Service]

Hepatocyte Thorns, A Novel Drug-Induced Stress Response in Human and Mouse Liver Spheroids.

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Cell Rep 39 (6) 110798 [2022-05-10; online 2022-05-12]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Speciation and population divergence in a mutualistic seed dispersing bird.

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Commun Biol 5 (1) 429 [2022-05-09; online 2022-05-09]

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Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.

Laber CP, Pontiller B, Bunse C, ..., Pinhassi J, Farnelid H

Front Microbiol 13 (-) 828459 [2022-05-09; online 2022-05-09]

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Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.

Kierczak M, Rafati N, Höglund J, ..., Karlsson T, Johansson Å

Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]

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Association between systemic inflammation and experimental pain sensitivity in subjects with pain and painless neuropathy after traumatic nerve injuries.

Miclescu AA, Granlund P, Butler S, Gordh T

Scand J Pain - (-) - [2022-05-09; online 2022-05-09]

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy.

Sun H, Yamada P, Paetow A, ..., Dominguez-Bello MG, Young BK

Sci Rep 12 (1) 7509 [2022-05-07; online 2022-05-07]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

A Fatty Diet Induces a Jejunal Ketogenesis Which Inhibits Local SGLT1-Based Glucose Transport via an Acetylation Mechanism-Results from a Randomized Cross-Over Study between Iso-Caloric High-Fat versus High-Carbohydrate Diets in Healthy Volunteers.

Elebring E, Wallenius V, Casselbrant A, ..., Marschall HU, Fändriks L

Nutrients 14 (9) - [2022-05-07; online 2022-05-07]

Integrated Microscopy Technologies Gothenburg [Service]

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Nucleic Acids Res. 50 (8) 4372-4388 [2022-05-06; online 2022-04-08]

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Evaluating metagenomic assembly approaches for biome-specific gene catalogues.

Delgado LF, Andersson AF

Microbiome 10 (1) 72 [2022-05-06; online 2022-05-06]

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Birth weight and young adult body mass index for predicting the risk of developing adult heart failure in men.

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Eur J Prev Cardiol 29 (6) 971-978 [2022-05-06; online 2021-12-16]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro.

Dube F, Hinas A, Roy S, ..., Svärd S, Tydén E

Parasit Vectors 15 (1) 158 [2022-05-05; online 2022-05-05]

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"ON THE IMPORTANCE OF VARIATION OF ALKALISATION CONDITIONS ON CELLULOSE ETHER SYNTHESIS"

REYES FORSBERG DC, SUNDMAN O

Cellulose Chem. Technol. 56 (3-4) 227-238 [2022-05-05; online 2022-05-05]

Real-time evaluation of glioblastoma growth in patient-specific zebrafish xenografts.

Almstedt E, Rosén E, Gloger M, ..., Krona C, Nelander S

Neuro-oncology 24 (5) 726-738 [2022-05-04; online 2021-12-18]

Genome Engineering Zebrafish [Service]

FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.

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Front Immunol 13 (-) 880668 [2022-05-04; online 2022-05-04]

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Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.

Darolti I, Almeida P, Wright AE, Mank JE

J. Evol. Biol. 35 (12) 1646-1658 [2022-05-04; online 2022-05-04]

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Wolf M, de Jong M, Halldórsson SD, Árnason Ú, Janke A

Mol. Biol. Evol. 39 (5) - [2022-05-03; online 2022-05-06]

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Genetic Landscape of the ACE2 Coronavirus Receptor.

Yang Z, Macdonald-Dunlop E, Chen J, ..., Wilson JF, Shen X

Circulation 145 (18) 1398-1411 [2022-05-03; online 2022-04-07]

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Combined Transcriptomic and Protein Array Cytokine Profiling of Human Stem Cells from Dental Apical Papilla Modulated by Oral Bacteria.

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Int J Mol Sci 23 (9) 5098 [2022-05-03; online 2022-05-03]

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Factors Associated With Serological Response to SARS-CoV-2 Vaccination in Patients With Multiple Sclerosis Treated With Rituximab.

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JAMA Netw Open 5 (5) e2211497 [2022-05-02; online 2022-05-02]

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Mol. Biol. Cell 33 (5) br7 [2022-05-01; online 2022-03-02]

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Hepatocyte growth factor, colony-stimulating factor 1, CD40, and 11 other inflammation-related proteins are associated with pain in diabetic neuropathy: exploration and replication serum data from the Pain in Neuropathy Study.

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Stem Cell Research 61 (-) 102752 [2022-05-00; online 2022-05-00]

The outcome of targeted NGS screening in patients with syndromic forms of sagittal and pansynostosis - IL11RA is an emerging core-gene for pansynostosis.

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Eur J Med Genet 65 (5) 104476 [2022-05-00; online 2022-03-21]

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Tetraspanins distinguish separate extracellular vesicle subpopulations in human serum and plasma - Contributions of platelet extracellular vesicles in plasma samples.

Karimi N, Dalirfardouei R, Dias T, Lötvall J, Lässer C

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Mol. Immunol. 145 (-) 17-26 [2022-05-00; online 2022-05-00]

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Soil phosphorus forms show only minor changes across a 5000-year-old boreal wildfire chronosequence

Vincent AG, Schleucher J, Giesler R, Wardle DA

Biogeochemistry 159 (1) 15-32 [2022-05-00; online 2022-02-27]

Re: Chen Dong, Sung-Lang Chen, and Wen-Wei Sung's Letter to the Editor re: Karin Welén, Ebba Rosendal, Magnus Gisslén, et al. A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data. Eur Urol. 2022;81:285-93.

Welen K, Rosendal E, Freyhult E, ..., Överby AK, Josefsson A

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Polymorphisms in alpha 7 nicotinic acetylcholine receptor gene, CHRNA7, and its partially duplicated gene, CHRFAM7A, associate with increased inflammatory response in human peripheral mononuclear cells.

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FASEB J. 36 (5) e22271 [2022-05-00; online 2022-03-29]

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Plaque Evaluation by Ultrasound and Transcriptomics Reveals BCLAF1 as a Regulator of Smooth Muscle Cell Lipid Transdifferentiation in Atherosclerosis.

Rykaczewska U, Zhao Q, Saliba-Gustafsson P, ..., Hedin U, Matic L

Arterioscler. Thromb. Vasc. Biol. 42 (5) 659-676 [2022-05-00; online 2022-03-24]

Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.

Nilsson E, Li K, Hoetzinger M, Holmfeldt K

Environ. Microbiol. 24 (5) 2270-2281 [2022-05-00; online 2022-01-26]

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Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not.

Fataftah N, Edlund E, Lihavainen J, ..., Näsholm T, Jansson S

Physiol Plantarum 174 (3) e13690 [2022-05-00; online 2022-04-24]

Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate.

Bradley F, Franzén Boger M, Kaldhusdal V, ..., Tjernlund A, Broliden K

PLoS Pathog. 18 (5) e1010494 [2022-05-00; online 2022-05-09]

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Microbial functional genes influenced by short-term experimental drought across European agricultural fields

Kozjek K, Manoharan L, Ahrén D, Hedlund K

Soil Biology and Biochemistry 168 (-) 108650 [2022-05-00; online 2022-05-00]

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Metagenomic evidence of a novel family of anammox bacteria in a subsea environment.

Suarez C, Dalcin Martins P, Jetten MSM, ..., Hermansson M, Persson F

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Mechanical removal of biofilm on titanium discs: An in vitro study.

Ichioka Y, Derks J, Dahlén G, Berglundh T, Larsson L

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Interleukin-10 regulates goblet cell numbers through Notch signaling in the developing zebrafish intestine.

Morales RA, Rabahi S, Diaz OE, ..., Hernández PP, Villablanca EJ

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Hormone-sensitive lipase is localized at synapses and is necessary for normal memory functioning in mice.

Skoug C, Holm C, Duarte JMN

J. Lipid Res. 63 (5) 100195 [2022-05-00; online 2022-03-15]

HLA variants associated with azathioprine-induced pancreatitis in patients with Crohn's disease.

Ås J, Bertulyte I, Eriksson N, ..., Wadelius M, Hallberg P

Clin Transl Sci 15 (5) 1249-1256 [2022-05-00; online 2022-02-20]

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Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.

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Author Correction: The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.

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A starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels.

Nilholm C, Manoharan L, Roth B, D'Amato M, Ohlsson B

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A modeling-based proposal for safe and efficacious reintroduction of bedaquiline after dose interruption: A population pharmacokinetics study.

Keutzer L, Akhondipour Salehabad Y, Davies Forsman L, Simonsson USH

CPT Pharmacometrics Syst Pharmacol 11 (5) 628-639 [2022-05-00; online 2022-02-16]

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"Randomized phase II study of azacitidine ± lenalidomide in higher-risk myelodysplastic syndromes and acute myeloid leukemia with a karyotype including Del(5q)".

Rasmussen B, Göhring G, Bernard E, ..., Möllgård L, Hellström-Lindberg E

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Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A

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RpuS/R Is a Novel Two-Component Signal Transduction System That Regulates the Expression of the Pyruvate Symporter MctP in Sinorhizobium fredii NGR234.

Ramos AL, Aquino M, García G, ..., Lupas AN, Sepulveda E

Front Microbiol 13 (-) 871077 [2022-04-29; online 2022-04-29]

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Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis.

Bronge M, Högelin KA, Thomas OG, ..., Olsson T, Grönlund H

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Cancer cells use self-inflicted DNA breaks to evade growth limits imposed by genotoxic stress.

Larsen BD, Benada J, Yung PYK, ..., Bartek J, Sørensen CS

Science 376 (6592) 476-483 [2022-04-29; online 2022-04-28]

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Langen B, Vorontsov E, Spetz J, ..., Helou K, Forssell-Aronsson E

Sci Rep 12 (1) 7000 [2022-04-29; online 2022-04-29]

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Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.

Rojas L, Grüttner J, Ma'ayeh S, Xu F, Svärd SG

Front. Cell. Infect. Microbiol. 12 (-) 862211 [2022-04-27; online 2022-04-27]

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Wastewater effluent affects behaviour and metabolomic endpoints in damselfly larvae.

Späth J, Fick J, McCallum E, ..., Nording ML, Brodin T

Sci Rep 12 (1) 6830 [2022-04-26; online 2022-04-26]

Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.

Lu X, Maturi NP, Jarvius M, ..., Uhrbom L, Chen X

Nat Commun 13 (1) 2236 [2022-04-25; online 2022-04-25]

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Auxin boosts energy generation pathways to fuel pollen maturation in barley.

Amanda D, Frey FP, Neumann U, ..., Ljung K, Acosta IF

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Auxilin is a novel susceptibility gene for congenital heart block which directly impacts fetal heart function.

Meisgen S, Hedlund M, Ambrosi A, ..., Sonesson S, Wahren-Herlenius M

Ann. Rheum. Dis. 81 (8) 1151-1161 [2022-04-25; online 2022-04-25]

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The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies.

Moškrič A, Marinč A, Ferk P, ..., Soler L, Prešern J

Insects 13 (5) 403 [2022-04-22; online 2022-04-22]

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Comprehensive Target Screening and Cellular Profiling of the Cancer-Active Compound b-AP15 Indicate Abrogation of Protein Homeostasis and Organelle Dysfunction as the Primary Mechanism of Action.

Gubat J, Selvaraju K, Sjöstrand L, ..., Linder S, D'Arcy P

Front Oncol 12 (-) 852980 [2022-04-22; online 2022-04-22]

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Kelly JJ, Tranter D, Pardon E, ..., Huiskonen JT, Yue WW

Nat. Struct. Mol. Biol. - (-) - [2022-04-21; online 2022-04-21]

Characterization of the ganglioside recognition profile of Escherichia coli heat-labile enterotoxin LT-IIc.

Zalem D, Juhás M, Terrinoni M, ..., Connell TD, Teneberg S

Glycobiology 32 (5) 391-403 [2022-04-21; online 2022-01-02]

App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden.

Kennedy B, Fitipaldi H, Hammar U, ..., Franks PW, Fall T

Nat Commun 13 (1) 2110 [2022-04-21; online 2022-04-21]

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Advances in the development of new biomarkers for Alzheimer's disease.

Klyucherev TO, Olszewski P, Shalimova AA, ..., Syvänen S, Schiöth HB

Transl Neurodegener 11 (1) 25 [2022-04-21; online 2022-04-21]

Baseline Pro-Inflammatory Cytokine Levels Moderate Psychological Inflexibility in Behavioral Treatment for Chronic Pain.

Karshikoff B, Åström J, Holmström L, ..., Kemani MK, Wicksell RK

J Clin Med 11 (9) - [2022-04-20; online 2022-04-20]

Systems analysis shows a role of cytophilic antibodies in shaping innate tolerance to malaria.

Lautenbach MJ, Yman V, Silva CS, ..., Färnert A, Sundling C

Cell Rep 39 (3) 110709 [2022-04-19; online 2022-04-21]

Silencing of STE20-type kinase STK25 in human aortic endothelial and smooth muscle cells is atheroprotective.

Cansby E, Kumari S, Caputo M, ..., Goncalves I, Mahlapuu M

Commun Biol 5 (1) 379 [2022-04-19; online 2022-04-19]

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Interaction of Bartonella henselae with Fibronectin Represents the Molecular Basis for Adhesion to Host Cells.

Vaca DJ, Thibau A, Leisegang MS, ..., Happonen L, Kempf VAJ

Microbiol Spectr - (-) e0059822 [2022-04-18; online 2022-04-18]

Impact of SARS-CoV-2 infection on vaccine-induced immune responses over time.

Havervall S, Marking U, Greilert-Norin N, ..., Åberg M, Thålin C

Clin Transl Immunology 11 (4) e1388 [2022-04-18; online 2022-04-18]

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The Effects of High Fiber Rye, Compared to Refined Wheat, on Gut Microbiota Composition, Plasma Short Chain Fatty Acids, and Implications for Weight Loss and Metabolic Risk Factors (the RyeWeight Study).

Iversen KN, Dicksved J, Zoki C, ..., Langton M, Landberg R

Nutrients 14 (8) - [2022-04-17; online 2022-04-17]

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Multi-omics protein-coding units as massively parallel Bayesian networks: Empirical validation of causality structure.

Zenere A, Rundquist O, Gustafsson M, Altafini C

iScience 25 (4) 104048 [2022-04-15; online 2022-03-11]

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Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.

Shakeri Yekta S, Elreedy A, Liu T, ..., Fujii M, Schnürer A

Sci. Total Environ. 817 (-) 152967 [2022-04-15; online 2022-01-10]

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Evaluation of polarity switching for untargeted lipidomics using liquid chromatography coupled to high resolution mass spectrometry.

Carlsson H, Vaivade A, Emami Khoonsari P, Burman J, Kultima K

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Early Detection of Oral Potentially Malignant Disorders: A Review on Prospective Screening Methods with Regard to Global Challenges

Haj-Hosseini N, Lindblad J, Hasséus B, ..., Subramaniam N, Hirsch JM

J. Maxillofac. Oral Surg. - (-) - [2022-04-15; online 2022-04-15]

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Design and development of photoswitchable DFG-Out RET kinase inhibitors.

Xu Y, Gao C, Andreasson M, ..., Andréasson J, Grøtli M

Eur J Med Chem 234 (-) 114226 [2022-04-15; online 2022-03-10]

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Pharmacodynamic Evaluation of Zoliflodacin Treatment of Neisseria gonorrhoeae Strains With Amino Acid Substitutions in the Zoliflodacin Target GyrB Using a Dynamic Hollow Fiber Infection Model.

Jacobsson S, Golparian D, Oxelbark J, ..., Drusano G, Unemo M

Front Pharmacol 13 (-) 874176 [2022-04-14; online 2022-04-14]

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HPA-axis dysregulation is not associated with accelerated epigenetic aging in patients with hypersexual disorder.

Boström ADE, Andersson P, Chatzittofis A, ..., Arver S, Jokinen J

Psychoneuroendocrinology 141 (-) 105765 [2022-04-14; online 2022-04-14]

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Broad-spectrum antidote discovery by untangling the reactivation mechanism of nerve agent inhibited acetylcholinesterase.

Lindgren C, Forsgren N, Hoster N, ..., Ekström F, Linusson A

Chemistry - (-) - [2022-04-14; online 2022-04-14]

Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals.

Svensson Akusjärvi S, Krishnan S, Jütte BB, ..., Sönnerborg A, Neogi U

Commun Biol 5 (1) 357 [2022-04-13; online 2022-04-13]

Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.

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Basal ganglia neuropeptides show abnormal processing associated with L-DOPA-induced dyskinesia.

Hulme H, Fridjonsdottir E, Vallianatou T, ..., Bezard E, Andrén PE

NPJ Parkinsons Dis 8 (1) 41 [2022-04-13; online 2022-04-13]

Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models.

Al Jewari C, Baldauf SL

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Molecular Organisation of Tick-Borne Encephalitis Virus.

Pulkkinen LIA, Barrass SV, Domanska A, ..., Anastasina M, Butcher SJ

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Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.

Lewerentz J, Johansson A, Larsson J, Stenberg P

BMC Genomics 23 (1) 276 [2022-04-07; online 2022-04-07]

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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation.

Raine A, Lundmark A, Annett A, ..., Bergin C, Nordlund J

Sci Rep 12 (1) 5772 [2022-04-06; online 2022-04-06]

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Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics.

Crowe-McAuliffe C, Murina V, Turnbull KJ, ..., Wilson DN, Hauryliuk V

Nat Commun 13 (1) 1860 [2022-04-06; online 2022-04-06]

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Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.

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Direct measurements of mRNA translation kinetics in living cells.

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SLC38A10 Regulate Glutamate Homeostasis and Modulate the AKT/TSC2/mTOR Pathway in Mouse Primary Cortex Cells.

Tripathi R, Aggarwal T, Lindberg FA, Klemm AH, Fredriksson R

Front Cell Dev Biol 10 (-) 854397 [2022-04-05; online 2022-04-05]

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Well-Plate μFASP for Proteomic Analysis of Single Pancreatic Islets.

Sandbaumhüter FA, Nezhyva M, Eriksson O, ..., Andrén PE, Jansson ET

J. Proteome Res. 21 (4) 1167-1174 [2022-04-01; online 2022-03-16]

Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.

von Grothusen C, Frisendahl C, Modhukur V, ..., Boggavarapu NR, Gemzell-Danielsson K

Hum. Reprod. 37 (4) 734-746 [2022-04-01; online 2022-02-12]

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Induction of Mitochondrial Fragmentation and Mitophagy after Neonatal Hypoxia-Ischemia.

Nair S, Leverin AL, Rocha-Ferreira E, ..., Mallard C, Hagberg H

Cells 11 (7) - [2022-04-01; online 2022-04-01]

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Glycoproteomic and Phenotypic Elucidation of B4GALNT2 Expression Variants in the SID Histo-Blood Group System.

Stenfelt L, Nilsson J, Hellberg Å, ..., Larson G, Olsson ML

Int J Mol Sci 23 (7) - [2022-04-01; online 2022-04-01]

Two structural types of dithiocarbamato-chlorido complexes of mercury(II): Preparation, supramolecular self-assembly, solid-state 13C and 15N NMR characterisation and thermal behaviour of pseudo-polymeric compounds of [Hg2(S2CNBu2)2Cl2] and [Hg4(S2CNiBu2)6][Hg2Cl6]

Loseva OV, Rodina TA, Shah FU, ..., Antzutkin ON, Ivanov AV

Inorganica Chimica Acta 533 (-) 120786 [2022-04-00; online 2022-04-00]

Timing is everything - obtaining accurate measures of plant uptake of amino acids.

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Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.

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Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]

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Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.

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Adv Sci (Weinh) 9 (11) e2104373 [2022-04-00; online 2022-02-07]

Multidisciplinary investigation reveals an individual of West African origin buried in a Portuguese Mesolithic shell midden four centuries ago

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Journal of Archaeological Science: Reports 42 (-) 103370 [2022-04-00; online 2022-04-00]

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Metabolism is a major driver of hydrogen isotope fractionation recorded in tree-ring glucose of Pinus nigra.

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Laurén I, Havervall S, Ng H, ..., Thålin C, Mangsbo S

Immun Inflamm Dis 10 (4) e595 [2022-04-00; online 2022-03-30]

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Long-Term Follow-Up of Newborns with 22q11 Deletion Syndrome and Low TRECs

Framme JL, Lundqvist C, Lundell AC, ..., Oskarsdóttir S, Ekwall O

J Clin Immunol 42 (3) 618-633 [2022-04-00; online 2022-01-26]

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Inherited IFNAR1 Deficiency in a Child with Both Critical COVID-19 Pneumonia and Multisystem Inflammatory Syndrome

Abolhassani H, Landegren N, Bastard P, ..., Hammarström L, Pan-Hammarström Q

J Clin Immunol 42 (3) 471-483 [2022-04-00; online 2022-01-28]

Gastrointestinal mucus in dog: Physiological characteristics, composition, and structural properties.

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Eur J Pharm Biopharm 173 (-) 92-102 [2022-04-00; online 2022-02-25]

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Mucosal Immunol 15 (4) 717-729 [2022-04-00; online 2022-04-00]

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Characterization of novel nonacid glycosphingolipids as biomarkers of human gastric adenocarcinoma.

Jin C, Teneberg S

J. Biol. Chem. 298 (4) 101732 [2022-04-00; online 2022-02-15]

Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro.

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Reprod Toxicol 109 (-) 19-30 [2022-04-00; online 2022-02-24]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Acute sleep loss alters circulating fibroblast growth factor 21 levels in humans: A randomised crossover trial.

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J Sleep Res 31 (2) e13472 [2022-04-00; online 2021-09-02]

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ADP-ribosylating adjuvant reveals plasticity in cDC1 cells that drive mucosal Th17 cell development and protection against influenza virus infection.

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Mucosal Immunol 15 (4) 745-761 [2022-04-00; online 2022-04-13]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution.

Agback P, Lesovoy DM, Han X, ..., Achour A, Orekhov VY

Biomol NMR Assign 16 (1) 135-145 [2022-04-00; online 2022-02-12]

Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy.

Thörnqvist L, Sjöberg R, Greiff L, van Hage M, Ohlin M

Front. Allergy 3 (-) 859126 [2022-03-31; online 2022-03-31]

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Coupling Lipid Nanoparticle Structure and Automated Single Particle Composition Analysis to Design Phospholipase Responsive Nanocarriers.

Barriga HMG, Pence IJ, Holme MN, ..., Carroni M, Stevens MM

Adv Mater - (-) e2200839 [2022-03-31; online 2022-03-31]

Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia.

Arimide DA, Szojka ZI, Zealiyas K, ..., Björkman P, Medstrand P

Viruses 14 (4) - [2022-03-30; online 2022-03-30]

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Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer.

Gyllensten U, Hedlund-Lindberg J, Svensson J, ..., Åberg M, Enroth S

Cancers (Basel) 14 (7) - [2022-03-30; online 2022-03-30]

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Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines.

Leo IR, Aswad L, Stahl M, ..., Vesterlund M, Jafari R

Nat Commun 13 (1) 1691 [2022-03-30; online 2022-03-30]

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Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing

Kaimal JM, Tampere M, Le TH, ..., Östling P, Stadler C

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An inverse association between plasma benzoxazinoid metabolites and PSA after rye intake in men with prostate cancer revealed with a new method.

Nordin E, Steffensen SK, Laursen BB, ..., Fomsgaard IS, Landberg R

Sci Rep 12 (1) 5260 [2022-03-28; online 2022-03-28]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Genetics of age-at-onset in major depression.

Harder A, Nguyen TD, Pasman JA, ..., Hägg S, Lu Y

Transl Psychiatry 12 (1) 124 [2022-03-26; online 2022-03-26]

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Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies.

Hanke L, Sheward DJ, Pankow A, ..., McInerney GM, Murrell B

Sci Adv 8 (12) eabm0220 [2022-03-25; online 2022-03-25]

Inflammation and neutrophil extracellular traps in cerebral cavernous malformation.

Yau ACY, Globisch MA, Onyeogaziri FC, ..., Dejana E, Magnusson PU

Cell. Mol. Life Sci. 79 (4) 206 [2022-03-25; online 2022-03-25]

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Temporal patterns of inflammation-related proteins measured in the cerebrospinal fluid of patients with aneurysmal subarachnoid hemorrhage using multiplex Proximity Extension Assay technology.

Vlachogiannis P, Hillered L, Enblad P, Ronne-Engström E

PLoS ONE 17 (3) e0263460 [2022-03-24; online 2022-03-24]

A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias.

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Front Med (Lausanne) 9 (-) 842507 [2022-03-24; online 2022-03-24]

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Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity

Garcia SL, Nuy JK, Mehrshad M, ..., Hawkes J, Bertilsson S

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Microbial Single Cell Genomics [Technology development]

Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence.

Martín-Hernández GC, Müller B, Brandt C, ..., Viehweger A, Passoth V

JoF 8 (4) - [2022-03-22; online 2022-03-22]

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A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines.

Feola S, Chiaro J, Martins B, ..., Lehtiö J, Cerullo V

Elife 11 (-) - [2022-03-22; online 2022-03-22]

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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation.

Martín-Rodríguez AJ, Higdon SM, Thorell K, ..., Krell T, Römling U

mSystems - (-) e0151821 [2022-03-21; online 2022-03-21]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Small Molecule Screening of Primary Human Acute Myeloid Leukemia Using Co-culture and Multiplexed FACS Analysis.

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BIO-PROTOCOL 12 (6) e4353 [2022-03-20; online 2022-03-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Periodontal Disease Augments Cardiovascular Disease Risk Biomarkers in Rheumatoid Arthritis.

Panezai J, Ghaffar A, Altamash M, ..., Larsson A, Engström PE

Biomedicines 10 (3) - [2022-03-19; online 2022-03-19]

GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.

Rezaei S, Uffenorde J, Gimm O, ..., Guerrero-Bosagna C, Pértille F

STAR Protoc 3 (1) 101202 [2022-03-18; online 2022-03-03]

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Deficits in attention, motor control and perception childhood to age 30 years: prospective case-control study of outcome predictors.

Landgren V, Fernell E, Gillberg C, Landgren M, Johnson M

BMJ Open 12 (3) e054424 [2022-03-17; online 2022-03-17]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

The Molecular Chaperone CCT Sequesters Gelsolin and Protects it from Cleavage by Caspase-3.

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J. Mol. Biol. 434 (5) 167399 [2022-03-15; online 2021-12-09]

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Structural Analysis of the Black-Legged Tick Saliva Protein Salp15.

Chaves-Arquero B, Persson C, Merino N, ..., Anguita J, Blanco FJ

Int J Mol Sci 23 (6) - [2022-03-15; online 2022-03-15]

Extracellular endosulfatase Sulf-2 harbors a chondroitin/dermatan sulfate chain that modulates its enzyme activity.

El Masri R, Seffouh A, Roelants C, ..., Filhol O, Vivès RR

Cell Rep 38 (11) 110516 [2022-03-15; online 2022-03-17]

Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis.

Eriksson K, Lundmark A, Delgado LF, ..., Andersson AF, Yucel-Lindberg T

Front. Cell. Infect. Microbiol. 12 (-) 841139 [2022-03-14; online 2022-03-14]

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Norway spruce postglacial recolonization of Fennoscandia.

Nota K, Klaminder J, Milesi P, ..., Suyama Y, Parducci L

Nat Commun 13 (1) 1333 [2022-03-14; online 2022-03-14]

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Five Hours Total Sleep Deprivation Does Not Affect CA1 Dendritic Length or Spine Density.

Brodin ATS, Gabulya S, Wellfelt K, Karlsson TE

Front. Synaptic Neurosci. 14 (-) 854160 [2022-03-14; online 2022-03-14]

Integrated Microscopy Technologies Stockholm [Service]

High throughput screen in a co-culture model to uncover therapeutic strategies to potentiate the cancer-inhibiting properties of the tumor-stroma in pancreatic cancer

Mason J, Cumming J, Eriksson AU, ..., Chorell E, Öhlund D

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Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Mixed-mode chromatography-mass spectrometry enables targeted and untargeted screening of carboxylic acids in biological samples.

Hodek O, Argemi-Muntadas L, Khan A, Moritz T

Anal. Methods 14 (10) 1015-1022 [2022-03-10; online 2022-03-10]

Swedish Metabolomics Centre (SMC) [Technology development]

A "spindle and thread" mechanism unblocks p53 translation by modulating N-terminal disorder.

Kaldmäe M, Vosselman T, Zhong X, ..., Lane DP, Landreh M

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Control of NK cell tolerance in MHC class I-deficiency by regulated SHP-1 localization to the activating immune synapse

Schmied L, Luu TT, Søndergaard JN, ..., Saeed MB, Höglund P

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Weakened resilience of benthic microbial communities in the face of climate change

Seidel L, Ketzer M, Broman E, ..., Hylander S, Dopson M

ISME COMMUN. 2 (1) - [2022-03-08; online 2022-03-08]

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Elevated mid-pregnancy plasma levels of angiotensin-converting enzyme 2 in women prior to the development of preeclampsia.

Junus K, Björk Ragnarsdóttir I, Nordlöf Callbo P, ..., Lager S, Wikström AK

Sci Rep 12 (1) 4109 [2022-03-08; online 2022-03-08]

Downregulation and Hypermethylation of GABPB1 Is Associated with Aggressive Thyroid Cancer Features.

Xing X, Mu N, Yuan X, ..., Neo SY, Xu D

Cancers (Basel) 14 (6) - [2022-03-08; online 2022-03-08]

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Computational Modeling of O-Linked Glycan Biosynthesis in CHO Cells.

Kouka T, Akase S, Sogabe I, ..., Karlsson NG, Aoki-Kinoshita KF

Molecules 27 (6) - [2022-03-08; online 2022-03-08]

Alterations in Self-Aggregating Neuropeptides in Cerebrospinal Fluid of Patients with Parkinsonian Disorders.

Zhu S, Bäckström D, Forsgren L, Trupp M

J Parkinsons Dis 12 (4) 1169-1189 [2022-03-08; online 2022-03-08]

Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated by 1H NMR and All-Atom Molecular Dynamics Simulations.

Hjalte J, Hossain S, Hugerth A, ..., Larsson P, Lundberg D

Mol. Pharm. 19 (3) 904-917 [2022-03-07; online 2022-02-01]

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Visible-Light Mediated Oxidative Fragmentation of Ethers and Acetals by Means of Fe(III) Catalysis.

Lindroth R, Ondrejková A, Wallentin CJ

Org. Lett. 24 (8) 1662-1667 [2022-03-04; online 2022-02-22]

Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells.

Rosa FF, Pires CF, Kurochkin I, ..., Scheding S, Pereira CF

Sci Immunol 7 (69) eabg5539 [2022-03-04; online 2022-03-04]

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Effect of the Aza-N-Bridge and Push-Pull Moieties: A Comparative Study between BODIPYs and Aza-BODIPYs.

Schäfer C, Mony J, Olsson T, Börjesson K

J. Org. Chem. 87 (5) 2569-2579 [2022-03-04; online 2022-02-21]

Broad anti-SARS-CoV-2 antibody immunity induced by heterologous ChAdOx1/mRNA-1273 vaccination.

Kaku CI, Champney ER, Normark J, ..., Forsell MNE, Walker LM

Science 375 (6584) 1041-1047 [2022-03-04; online 2022-02-10]

Autoimmunity and Serology Profiling [Collaborative]

The respiratory supercomplex from C. glutamicum.

Moe A, Kovalova T, Król S, ..., Högbom M, Brzezinski P

Structure 30 (3) 338-349.e3 [2022-03-03; online 2021-12-14]

Improvements in Body Composition after a Proposed Anti-Inflammatory Diet Are Modified by Employment Status in Weight-Stable Patients with Rheumatoid Arthritis, a Randomized Controlled Crossover Trial.

Hulander E, Lindqvist HM, Wadell AT, ..., Winkvist A, Bärebring L

Nutrients 14 (5) - [2022-03-02; online 2022-03-02]

Structural Modifications and Biological Evaluations of Rift Valley Fever Virus Inhibitors Identified from Chemical Library Screening.

Islam K, Carlsson M, Enquist PA, ..., Ahlm C, Evander M

ACS Omega 7 (8) 6854-6868 [2022-03-01; online 2022-02-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics.

Olausson J, Brunet S, Vracar D, ..., Jakobsson HE, Tang K

Sci Rep 12 (1) 3378 [2022-03-01; online 2022-03-01]

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Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.

Stenudd M, Sabelström H, Llorens-Bobadilla E, ..., Barnabé-Heider F, Frisén J

Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]

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GWAS in people of Middle Eastern descent reveals a locus protective of kidney function-a cross-sectional study.

Mohamed SA, Fernadez-Tajes J, Franks PW, Bennet L

BMC Med 20 (1) 76 [2022-03-01; online 2022-03-01]

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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.

Viluma A, Flagstad Ø, Åkesson M, ..., Wabakken P, Ellegren H

Genome Res. 32 (3) 449-458 [2022-03-00; online 2022-02-08]

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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern.

Ernst M, Jønsson KA, Ericson PGP, Blom MPK, Irestedt M

Heredity (Edinb) 128 (3) 159-168 [2022-03-00; online 2022-01-26]

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The era of reference genomes in conservation genomics.

Formenti G, Theissinger K, Fernandes C, ..., Bálint M, European Reference Genome Atlas (ERGA) Consortium

Trends Ecol Evol 37 (3) 197-202 [2022-03-00; online 2022-01-24]

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The chemical composition and antioxidant activity of mandaçaia (melipona quadrifasciata) geopropolis varies more due to region than month of collection.

Gabriel MB, Carneiro MJ, de Camargo RCR, Sawaya ACHF

Nat Prod Res 36 (6) 1626-1630 [2022-03-00; online 2021-03-10]

The Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum.

Mahjani B, Klei L, Mattheisen M, ..., Devlin B, Grice DE

Am J Psychiatry 179 (3) 216-225 [2022-03-00; online 2021-11-18]

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Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.

Stsiapanava A, Xu C, Nishio S, ..., Wu B, Jovine L

Nat. Struct. Mol. Biol. 29 (3) 190-193 [2022-03-00; online 2022-03-10]

Pseudouridine-modified tRNA fragments repress aberrant protein synthesis and predict leukaemic progression in myelodysplastic syndrome.

Guzzi N, Muthukumar S, Cieśla M, ..., Dimitriou M, Bellodi C

Nat Cell Biol 24 (3) 299-306 [2022-03-00; online 2022-03-15]

Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?

Ljungström V, Mattisson J, Halvardson J, ..., Baliakas P, Forsberg LA

Leukemia 36 (3) 889-891 [2022-03-00; online 2021-11-01]

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Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.

Mueller JC, Botero-Delgadillo E, Espíndola-Hernández P, ..., Gruselius J, Kempenaers B

Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]

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Hypoxia induces radioresistance, epithelial‑mesenchymal transition, cancer stem cell‑like phenotype and changes in genes possessing multiple biological functions in head and neck squamous cell carcinoma.

Wiechec E, Matic N, Ali A, Roberg K

Oncol. Rep. 47 (3) - [2022-03-00; online 2022-01-21]

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Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris).

Kardum Hjort C, Paris JR, Olsson P, ..., Dudaniec RY, Smith HG

Evol Appl 15 (3) 365-382 [2022-03-00; online 2022-03-14]

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Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.

Eshghi Sahraei S, Furneaux B, Kluting K, ..., Hytteborn H, Rosling A

Ecol Evol 12 (3) e8676 [2022-03-00; online 2022-03-08]

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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.

Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J

Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]

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Blood protein profiles related to preterm birth and retinopathy of prematurity.

Danielsson H, Tebani A, Zhong W, ..., Uhlén M, Hellström A

Pediatr. Res. 91 (4) 937-946 [2022-03-00; online 2021-04-24]

Bioproduction of (Z,E)-9,12-tetradecadienyl acetate (ZETA), the major pheromone component of Plodia, Ephestia, and Spodoptera species in yeast.

Ding BJ, Wang HL, Al-Saleh MA, Löfstedt C, Antony B

Pest Manag Sci 78 (3) 1048-1059 [2022-03-00; online 2021-12-06]

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Associations between biomarkers of multimorbidity burden and mortality risk among patients with acute dyspnea.

Wessman T, Tofik R, Ruge T, Melander O

Intern Emerg Med 17 (2) 559-567 [2022-03-00; online 2021-08-20]

ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.

Widmark A, Sagredo EA, Karlström V, ..., Daniel C, Öhman M

J. Biol. Chem. 298 (3) 101682 [2022-03-00; online 2022-02-03]

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In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation.

Martinell M, Andersson T, Mannsverk SS, ..., Lindh J, Kaden R

Viruses 14 (3) - [2022-02-28; online 2022-02-28]

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Salivary biomarkers in children with juvenile idiopathic arthritis and healthy age-matched controls: a prospective observational study.

Collin M, Ernberg M, Christidis N, Hedenberg-Magnusson B

Sci Rep 12 (1) 3240 [2022-02-25; online 2022-02-25]

Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia: Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up.

Arimide DA, Esquivel-Gómez LR, Kebede Y, ..., Kühnert D, Medstrand P

Front Microbiol 13 (-) 821006 [2022-02-25; online 2022-02-25]

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Duration of SARS-CoV-2 Immune Responses Up to Six Months Following Homologous or Heterologous Primary Immunization with ChAdOx1 nCoV-19 and BNT162b2 mRNA Vaccines.

Marking U, Havervall S, Greilert-Norin N, ..., Åberg M, Thålin C

Vaccines (Basel) 10 (3) - [2022-02-24; online 2022-02-24]

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Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.

Luttens A, Gullberg H, Abdurakhmanov E, ..., Danielson UH, Carlsson J

J. Am. Chem. Soc. 144 (7) 2905-2920 [2022-02-23; online 2022-02-10]

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A complementary chemical probe approach towards customized studies of G-quadruplex DNA structures in live cells.

Prasad B, Doimo M, Andréasson M, ..., Chorell E, Wanrooij S

Chem. Sci. 13 (8) 2347-2354 [2022-02-23; online 2022-02-01]

The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids.

Rajer F, Sandegren L

MBio 13 (1) e0355221 [2022-02-22; online 2022-01-18]

NanoSIMS Imaging Reveals the Impact of Ligand-ASO Conjugate Stability on ASO Subcellular Distribution.

Kay E, Stulz R, Becquart C, ..., Andersson S, Kurczy M

Pharmaceutics 14 (2) 463 [2022-02-21; online 2022-02-21]

Integrated Microscopy Technologies Gothenburg [Collaborative]

TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

Börjesson V, Martinez-Monleon A, Fransson S, ..., Milosevic J, López MD

BMC Genomics 23 (1) 149 [2022-02-20; online 2022-02-20]

Clinical Genomics [Technology development] Clinical Genomics Gothenburg [Technology development]

Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

Nguyen D, Peona V, Unneberg P, ..., Jern P, Johannesson H

Fungal Genetics Reports 66 (1) - [2022-02-18; online 2022-02-18]

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Nontarget mass spectrometry and in silico molecular characterization of air pollution from the Indian subcontinent

Papazian S, D’Agostino LA, Sadiktsis I, ..., Gustafsson Ö, Martin JW

Commun Earth Environ 3 (1) - [2022-02-18; online 2022-02-18]

The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.

Sturk-Andreaggi K, Ring JD, Ameur A, ..., Marshall C, Allen M

Int J Mol Sci 23 (4) - [2022-02-17; online 2022-02-17]

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Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.

André D, Zambrano JA, Zhang B, ..., Marcon A, Nilsson O

Front Plant Sci 13 (-) 823019 [2022-02-17; online 2022-02-17]

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Longitudinal Serum Metabolomics in Extremely Premature Infants: Relationships With Gestational Age, Nutrition, and Morbidities.

Nilsson AK, Tebani A, Malmodin D, ..., Uhlén M, Hellström A

Front. Neurosci. 16 (-) 830884 [2022-02-17; online 2022-02-17]

Semi-supervised learning with natural language processing for right ventricle classification in echocardiography-a scalable approach.

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Comput Biol Med 143 (-) 105282 [2022-02-15; online 2022-02-15]

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Zhao S, Zhang Y, Hallgrimsdottir S, ..., Grigelioniene G, Wu N

npj Genom. Med. 7 (1) 11 [2022-02-15; online 2022-02-15]

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Production of Exopolysaccharides by Cultivation of Halotolerant Bacillus atrophaeus BU4 in Glucose- and Xylose-Based Synthetic Media and in Hydrolysates of Quinoa Stalks

Chambi D, Lundqvist J, Nygren E, ..., Jönsson LJ, Martín C

Fermentation 8 (2) 79 [2022-02-14; online 2022-02-14]

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Hartvigsson O, Barman M, Savolainen O, ..., Sandberg AS, Brunius C

Metabolites 12 (2) 175 [2022-02-13; online 2022-02-13]

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Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]

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The spatial transcriptomic landscape of the healing mouse intestine following damage.

Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ

Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]

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Scavenger receptor CD36 governs recruitment of myeloid cells to the blood-CSF barrier after stroke in neonatal mice.

Rayasam A, Mottahedin A, Faustino J, Mallard C, Vexler ZS

J Neuroinflammation 19 (1) 47 [2022-02-11; online 2022-02-11]

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Sci Data 9 (1) 47 [2022-02-10; online 2022-02-10]

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Haghikia A, Zimmermann F, Schumann P, ..., Haghikia A, Landmesser U

Eur. Heart J. 43 (6) 518-533 [2022-02-10; online 2021-10-02]

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NMR Backbone Assignment of VIM-2 and Identification of the Active Enantiomer of a Potential Inhibitor

Wieske LHE, Bogaerts J, Leding AAM, ..., Bayer A, Erdélyi M

ACS Med Chem Lett 13 (2) 257-261 [2022-02-10; online 2022-01-28]

Fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs), but not gluten, elicit modest symptoms of irritable bowel syndrome: a double-blind, placebo-controlled, randomized three-way crossover trial.

Nordin E, Brunius C, Landberg R, Hellström PM

Am. J. Clin. Nutr. 115 (2) 344-352 [2022-02-09; online 2021-10-08]

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Acta Orthop 93 (-) 317-326 [2022-02-08; online 2022-02-08]

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Nadeem A, Berg A, Pace H, ..., Uhlin BE, Wai SN

Elife 11 (-) - [2022-02-08; online 2022-02-08]

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Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters.

Palica K, Vorácová M, Skagseth S, ..., Andersson H, Erdélyi M

ACS Omega 7 (5) 4550-4562 [2022-02-08; online 2022-01-25]

Larsson M, Rudqvist NP, Spetz J, ..., Helou K, Forssell-Aronsson E

Sci Rep 12 (1) 2107 [2022-02-08; online 2022-02-08]

A serum proteomic study of two case-control cohorts identifies novel biomarkers for bipolar disorder.

Göteson A, Isgren A, Sparding T, ..., Pålsson E, Landén M

Transl Psychiatry 12 (1) 55 [2022-02-08; online 2022-02-08]

The role of caspase-1, caspase-4 and NLRP3 in regulating the host cell response evoked by uropathogenic Escherichia coli.

Lindblad A, Johansson C, Persson K, Demirel I

Sci Rep 12 (1) 2005 [2022-02-07; online 2022-02-07]

Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids.

Hou XQ, Zhang DD, Powell D, ..., Andersson MN, Löfstedt C

BMC Biol. 20 (1) 34 [2022-02-07; online 2022-02-07]

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Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

Umer HM, Audain E, Zhu Y, ..., Branca RM, Perez-Riverol Y

Bioinformatics 38 (5) 1470-1472 [2022-02-07; online 2021-12-15]

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Rauschmeier R, Reinhardt A, Gustafsson C, ..., Busslinger M, Kreslavsky T

J. Exp. Med. 219 (2) - [2022-02-07; online 2021-12-17]

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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.

Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A

Front Genet 12 (-) 803683 [2022-02-04; online 2022-02-04]

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Mutation analysis of disease causing genes in patients with early onset or familial forms of Alzheimer's disease and frontotemporal dementia.

Pagnon de la Vega M, Näslund C, Brundin R, ..., Ingelsson M, Giedraitis V

BMC Genomics 23 (1) 99 [2022-02-04; online 2022-02-04]

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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.

Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T

Sci Adv 8 (5) eabl6496 [2022-02-04; online 2022-02-04]

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A Sparse Model-Inspired Deep Thresholding Network for Exponential Signal Reconstruction--Application in Fast Biological Spectroscopy.

Wang Z, Guo D, Tu Z, ..., Orekhov V, Qu X

IEEE Trans Neural Netw Learn Syst PP (-) - [2022-02-04; online 2022-02-04]

The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.

Oliver C, Annacondia ML, Wang Z, ..., Köhler C, Martinez G

Plant Cell 34 (2) 784-801 [2022-02-03; online 2021-11-11]

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The involvement of cyclotides in mutual interactions of violets and the two-spotted spider mite.

Slazak B, Jędrzejska A, Badyra B, ..., Göransson U, Kiełkiewicz M

Sci Rep 12 (1) 1914 [2022-02-03; online 2022-02-03]

PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data.

Abrahamsson S, Eiengård F, Rohlin A, Dávila López M

BMC Bioinformatics 23 (1) 59 [2022-02-03; online 2022-02-03]

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Pyruvate metabolism guides definitive lineage specification during hematopoietic emergence.

Oburoglu L, Mansell E, Canals I, ..., Soneji S, Woods NB

EMBO Rep. 23 (2) e54384 [2022-02-03; online 2021-12-16]

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Urinary Metabolomic Changes Accompanying Albuminuria Remission following Gastric Bypass Surgery for Type 2 Diabetic Kidney Disease.

Martin WP, Malmodin D, Pedersen A, ..., le Roux CW, Docherty NG

Metabolites 12 (2) 139 [2022-02-02; online 2022-02-22]

Comprehensive Peak Characterization (CPC) in Untargeted LC-MS Analysis.

Pirttilä K, Balgoma D, Rainer J, ..., Hedeland M, Brunius C

Metabolites 12 (2) - [2022-02-02; online 2022-02-02]

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Höijer I, Emmanouilidou A, Östlund R, ..., den Hoed M, Ameur A

Nat Commun 13 (1) 627 [2022-02-02; online 2022-02-02]

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PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides.

Rush JS, Parajuli P, Ruda A, ..., Widmalm G, Korotkova N

Nat Commun 13 (1) 590 [2022-02-01; online 2022-02-01]

ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal.

Jalalvand E, Alvelid J, Coceano G, ..., Grillner S, Testa I

Elife 11 (-) - [2022-02-01; online 2022-02-01]

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Heppler LN, Attarha S, Persaud R, ..., Page BDG, Frank DA

J. Biol. Chem. 298 (2) 101531 [2022-02-00; online 2021-12-23] Open Access

The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.

Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J

Nat Cancer 3 (2) 251-261 [2022-02-00; online 2022-02-24]

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Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2.

Matsuoka R, Fudim R, Jung S, ..., Beckstein O, Drew D

Nat. Struct. Mol. Biol. 29 (2) 108-120 [2022-02-00; online 2022-02-16]

Structural amyloid plaque polymorphism is associated with distinct lipid accumulations revealed by trapped ion mobility mass spectrometry imaging.

Michno W, Wehrli PM, Koutarapu S, ..., Hopf C, Hanrieder J

J. Neurochem. 160 (4) 482-498 [2022-02-00; online 2021-12-26]

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Prog Neurobiol 209 (-) 102199 [2022-02-00; online 2021-12-15]

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Quasiperiodic Van der Waals Heterostructures of Graphene and Hexagonal Boron Nitride

Bhandary S, Haldar S, Sanyal B

Physica Status Solidi (b) 259 (2) - [2022-02-00; online 2021-11-21]

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Proteomic characterisation of polyglucosan bodies in skeletal muscle in RBCK1 deficiency.

Thomsen C, Malfatti E, Jovanovic A, ..., Lindberg C, Oldfors A

Neuropathol Appl Neurobiol 48 (1) e12761 [2022-02-00; online 2021-09-12]

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Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.

Hernandez-Castro LE, Villacís AG, Jacobs A, ..., Llewellyn MS, Grijalva MJ

PLoS Genet. 18 (2) e1010019 [2022-02-00; online 2022-02-04]

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Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation

Sparreman Mikus M, Kolmert J, Andersson LI, ..., Dahlén SE, James A

Eur Respir J 59 (2) 2100142 [2022-02-00; online 2021-11-04]

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Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress.

Bonagas N, Gustafsson NMS, Henriksson M, ..., Homan EJ, Helleday T

Nat Cancer 3 (2) 156-172 [2022-02-00; online 2022-02-28]

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LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases.

Ronkainen J, Nedelec R, Atehortua A, ..., Juola T, Sebert S

Environ Epidemiol 6 (1) e184 [2022-02-00; online 2021-12-28]

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Links between boreal forest management, soil fungal communities and below‐ground carbon sequestration

Jörgensen K, Granath G, Strengbom J, Lindahl BD

Functional Ecology 36 (2) 392-405 [2022-02-00; online 2021-12-22]

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Impaired phosphocreatine metabolism in white adipocytes promotes inflammation.

Maqdasy S, Lecoutre S, Renzi G, ..., Mejhert N, Rydén M

Nat Metab 4 (2) 190-202 [2022-02-00; online 2022-02-14]

Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.

Edvardsen RB, Wallerman O, Furmanek T, ..., Norberg B, Rubin CJ

PLoS Genet. 18 (2) e1010011 [2022-02-00; online 2022-02-08]

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Genomic differentiation within East Asian Helicobacter pylori.

You Y, Thorell K, He L, ..., Falush D, Zhang J

Microb Genom 8 (2) - [2022-02-00; online 2022-02-22]

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Genetically proxied therapeutic inhibition of antihypertensive drug targets and risk of common cancers: A mendelian randomization analysis.

Yarmolinsky J, Díez-Obrero V, Richardson TG, ..., Martin RM, Moreno V

PLoS Med. 19 (2) e1003897 [2022-02-00; online 2022-02-03]

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Contribution of Rare Genetic Variation to Disease Susceptibility in a Large Scandinavian Myositis Cohort.

Bianchi M, Kozyrev SV, Notarnicola A, ..., Lindblad-Toh K, Lundberg IE

Arthritis & rheumatology (Hoboken, N.J.) 74 (2) 342-352 [2022-02-00; online 2021-12-23]

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Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C.

Thysell E, Köhn L, Semenas J, ..., Bergh A, Wikström P

Mol Oncol 16 (4) 846-859 [2022-02-00; online 2021-12-27]

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Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development.

Habicher J, Varshney GK, Waldmann L, ..., Burgess SM, Ledin J

PLoS Genet. 18 (2) e1010067 [2022-02-00; online 2022-02-22]

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Autosomal recessive congenital hereditary corneal dystrophy associated with a novel SLC4A11 mutation in two consanguineous Tunisian families.

Chibani Z, Abid IZ, Söderkvist P, Feki J, Aifa MH

Br J Ophthalmol 106 (2) 281-287 [2022-02-00; online 2021-04-20]

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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.

Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT

Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]

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A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene.

Rafiei V, Ruffino A, Persson Hodén K, ..., Dubey M, Tzelepis G

Mol. Plant Pathol. 23 (2) 291-303 [2022-02-00; online 2021-11-26]

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In situ 13 C solid-state polarization transfer NMR to follow starch transformations in food.

Nowacka-Perrin A, Steglich T, Topgaard D, Bernin D

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Longitudinal analyses of development of the immune system during the first five years of life in relation to lifestyle.

Olin A, Acevedo N, Lakshmikanth T, ..., Scheynius A, Brodin P

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Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter.

Chaptal V, Zampieri V, Wiseman B, ..., Boumendjel A, Falson P

Sci Adv 8 (4) eabg9215 [2022-01-28; online 2022-01-26]

Spatial Statistics for Understanding Tissue Organization.

Behanova A, Klemm A, Wählby C

Front Physiol 13 (-) 832417 [2022-01-28; online 2022-01-28]

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Sequence specificity in DNA binding is mainly governed by association.

Marklund E, Mao G, Yuan J, ..., Deindl S, Elf J

Science 375 (6579) 442-445 [2022-01-28; online 2022-01-27]

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Intramolecular carbon isotope signals reflect metabolite allocation in plants.

Wieloch T, Sharkey TD, Werner RA, Schleucher J

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16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds

Rissanen A, Buck M, Peura S

Aquat. Microb. Ecol. 88 (-) 25-30 [2022-01-27; online 2022-01-27]

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Medications Activating Tubular Fatty Acid Oxidation Enhance the Protective Effects of Roux-en-Y Gastric Bypass Surgery in a Rat Model of Early Diabetic Kidney Disease.

Martin WP, Chuah YHD, Abdelaal M, ..., le Roux CW, Docherty NG

Front Endocrinol (Lausanne) 12 (-) 757228 [2022-01-26; online 2022-01-26]

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Standards recommendations for the Earth BioGenome Project.

Lawniczak MKN, Durbin R, Flicek P, ..., Lewin HA, Richards S

Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-20]

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Occasional paternal inheritance of the germline-restricted chromosome in songbirds.

Pei Y, Forstmeier W, Ruiz-Ruano FJ, ..., Suh A, Kempenaers B

Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]

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Method To Visualize the Intratumor Distribution and Impact of Gemcitabine in Pancreatic Ductal Adenocarcinoma by Multimodal Imaging.

Strittmatter N, Richards FM, Race AM, ..., Goodwin RJA, Jodrell DI

Anal. Chem. 94 (3) 1795-1803 [2022-01-25; online 2022-01-10]

Massive genome inversion drives coexistence of divergent morphs in common quails.

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Curr. Biol. 32 (2) 462-469.e6 [2022-01-24; online 2021-11-29]

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Single-Cell Transcriptomics reveals relaxed evolutionary constraint of spermatogenesis in two passerine birds as compared to mammals

Segami JC, Semon M, Cunha C, ..., Mugal CF, Qvarnström A

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Region-Specific and Age-Dependent Multitarget Effects of Acetylcholinesterase Inhibitor Tacrine on Comprehensive Neurotransmitter Systems.

Fridjonsdottir E, Vallianatou T, Mantas I, ..., Svenningsson P, Andrén PE

ACS Chem. Biol. 17 (1) 147-158 [2022-01-21; online 2021-12-21]

Integrative proteo-transcriptomic and immunophenotyping signatures of HIV-1 elite control phenotype: A cross-talk between glycolysis and HIF signaling.

Akusjärvi SS, Ambikan AT, Krishnan S, ..., Sönnerborg A, Neogi U

iScience 25 (1) 103607 [2022-01-21; online 2021-12-10]

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Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.

Berggren H, Tibblin P, Yıldırım Y, ..., Lundin D, Forsman A

Front Microbiol 12 (-) 767770 [2022-01-21; online 2022-01-21]

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Overexpression of the SARS-CoV-2 receptor angiotensin converting enzyme 2 in cardiomyocytes of failing hearts.

Vukusic K, Thorsell A, Muslimovic A, ..., Sandstedt J, Hammarsten O

Sci Rep 12 (1) 965 [2022-01-19; online 2022-01-19]

Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort

Carapito R, Li R, Helms J, ..., Chittenden TW, Bahram S

Sci. Transl. Med. 14 (628) eabj7521 [2022-01-19; online 2022-01-19]

An Image-Analysis-Based Method for the Prediction of Recombinant Protein Fiber Tensile Strength.

Bäcklund FG, Schmuck B, Miranda GHB, ..., Rydén J, Rising A

Materials (Basel) 15 (3) - [2022-01-18; online 2022-01-18]

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Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt.

de Miranda JR, Brettell LE, Chejanovsky N, ..., Martin SJ, Ball BV

Virol J 19 (1) 12 [2022-01-15; online 2022-01-15]

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Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.

Öhlund P, Delhomme N, Hayer J, Hesson JC, Blomström AL

Int J Mol Sci 23 (2) - [2022-01-14; online 2022-01-14]

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Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.

Ghadamgahi F, Tarighi S, Taheri P, ..., Ortiz R, Vetukuri RR

Biology (Basel) 11 (1) - [2022-01-14; online 2022-01-14]

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3D Microvascularized Tissue Models by Laser-Based Cavitation Molding of Collagen.

Enrico A, Voulgaris D, Östmans R, ..., Herland A, Stemme G

Adv Mater - (-) e2109823 [2022-01-14; online 2022-01-14]

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First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016.

Hadad R, Golparian D, Velicko I, ..., Engstrand L, Unemo M

Front Microbiol 12 (-) 820998 [2022-01-13; online 2022-01-13]

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Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer.

Thomas CE, Dahl L, Byström S, ..., Schwenk JM, Gabrielson M

Transl Oncol 17 (-) 101339 [2022-01-13; online 2022-01-13]

The formation of avian montane diversity across barriers and along elevational gradients.

Pujolar JM, Blom MPK, Reeve AH, ..., Irestedt M, Jønsson KA

Nat Commun 13 (1) 268 [2022-01-12; online 2022-01-12]

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SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection.

Havervall S, Jernbom Falk A, Klingström J, ..., Nilsson P, Thålin C

PLoS ONE 17 (1) e0262169 [2022-01-12; online 2022-01-12]

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Developmental origins of cell heterogeneity in the human lung

Sountoulidis A, Salas SM, Braun E, ..., Nilsson M, Samakovlis C

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Anaplerotic flux into the Calvin-Benson cycle: hydrogen isotope evidence for in vivo occurrence in C3 metabolism.

Wieloch T, Augusti A, Schleucher J

New Phytol. - (-) - [2022-01-12; online 2022-01-12]

Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.

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Blood Adv 6 (1) 152-164 [2022-01-11; online 2021-10-08]

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Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection.

Mikaeloff F, Svensson Akusjärvi S, Ikomey GM, ..., Benfeitas R, Neogi U

Commun Biol 5 (1) 27 [2022-01-11; online 2022-01-11]

Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.

Westmeijer G, Mehrshad M, Turner S, ..., Bertilsson S, Dopson M

Commun Biol 5 (1) 37 [2022-01-11; online 2022-01-11]

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Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.

Chachoua I, Tzelepis I, Dai H, ..., Mehmood R, Göndör A

Nat Commun 13 (1) 204 [2022-01-11; online 2022-01-11]

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Characterization of surface markers on extracellular vesicles isolated from lymphatic exudate from patients with breast cancer.

Ekström K, Crescitelli R, Pétursson HI, ..., Lässer C, Olofsson Bagge R

BMC Cancer 22 (1) 50 [2022-01-10; online 2022-01-10]

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Fungal Perspective of Pine and Oak Colonization in Mediterranean Degraded Ecosystems

Adamo I, Dashevskaya S, Alday JG

Forests 13 (1) 88 [2022-01-08; online 2022-01-08]

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Vegan Diet Is Associated With Favorable Effects on the Metabolic Performance of Intestinal Microbiota: A Cross-Sectional Multi-Omics Study.

Prochazkova M, Budinska E, Kuzma M, ..., Gojda J, Cahova M

Front Nutr 8 (-) 783302 [2022-01-07; online 2022-01-07]

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Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.

Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T

Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]

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MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome".

Das SK, Kuzin V, Cameron DP, ..., Levens D, Baranello L

Mol. Cell 82 (1) 140-158.e12 [2022-01-06; online 2021-12-09]

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.

Romdhane S, Spor A, Banerjee S, ..., Saghai A, Philippot L

Environ Microbiome 17 (1) 1 [2022-01-06; online 2022-01-06]

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Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas.

Tabebi M, Łysiak M, Dutta RK, ..., Gimm O, Söderkvist P

Cancers (Basel) 14 (2) - [2022-01-06; online 2022-01-06]

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A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.

Johansson PA, Brattås PL, Douse CH, ..., Eichler EE, Jakobsson J

Cell Stem Cell 29 (1) 52-69.e8 [2022-01-06; online 2021-10-07]

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TRAPing Ghrelin-Activated Circuits: A Novel Tool to Identify, Target and Control Hormone-Responsive Populations in TRAP2 Mice.

Stoltenborg I, Peris-Sampedro F, Schéle E, ..., Adan RAH, Dickson SL

Int J Mol Sci 23 (1) - [2022-01-05; online 2022-01-05]

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Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.

Mennuni M, Filograna R, Felser A, ..., Lytovchenko O, Larsson N

EMBO Rep. 23 (1) e53054 [2022-01-05; online 2021-11-15]

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Loss of SDHB Induces a Metabolic Switch in the hPheo1 Cell Line toward Enhanced OXPHOS.

Tabebi M, Kumar Dutta R, Skoglund C, Söderkvist P, Gimm O

Int J Mol Sci 23 (1) - [2022-01-05; online 2022-01-05]

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Backbone chemical shift assignment and dynamics of the N-terminal domain of ClpB from Francisella tularensis type VI secretion system.

Mushtaq AU, Ådén J, Alam A, Sjöstedt A, Gröbner G

Biomol NMR Assign - (-) - [2022-01-05; online 2022-01-05]

Risk of Revision After Arthroplasty Associated with Specific Gene Loci: A Genomewide Association Study of Single-Nucleotide Polymorphisms in 1,130 Twins Treated with Arthroplasty.

Brüggemann A, Eriksson N, Michaëlsson K, Hailer NP

J Bone Joint Surg Am 104 (7) 610-620 [2022-01-04; online 2022-01-04]

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In Silico-Based Experiments on Mechanistic Interactions between Several Intestinal Permeation Enhancers with a Lipid Bilayer Model.

Kneiszl R, Hossain S, Larsson P

Mol. Pharm. 19 (1) 124-137 [2022-01-03; online 2021-12-16]

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CRISPR/Cas9-Induced DNA Damage Enriches for Mutations in a p53-Linked Interactome: Implications for CRISPR-Based Therapies.

Jiang L, Ingelshed K, Shen Y, ..., Lane DP, Wermeling F

Cancer Res. 82 (1) 36-45 [2022-01-01; online 2021-11-18]

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Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.

Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L

Mol. Ecol. 31 (2) 498-511 [2022-01-00; online 2021-11-15]

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Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.

Skaftason A, Qu Y, Abdulla M, ..., Rosenquist R, Mansouri L

Genes Chromosomes Cancer 61 (1) 27-36 [2022-01-00; online 2021-10-23]

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The Sulawesi Thrush ( Cataponera turdoides ; Aves: Passeriformes) belongs to the genus Turdus

Reeve AH, Blom MPK, Zahl Marki P, ..., Irestedt M, Jønsson KA

Zool Scr 51 (1) 32-40 [2022-01-00; online 2021-11-04]

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Sustained Response to Entrectinib in an Infant With a Germline ALKAL2 Variant and Refractory Metastatic Neuroblastoma With Chromosomal 2p Gain and Anaplastic Lymphoma Kinase and Tropomyosin Receptor Kinase Activation.

Treis D, Umapathy G, Fransson S, ..., Martinsson T, Kogner P

JCO Precision Oncology 6 (6) e2100271 [2022-01-00; online 2022-01-28]

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Super-Resolution Imaging of the Filtration Barrier Suggests a Role for Podocin R229Q in Genetic Predisposition to Glomerular Disease.

Butt L, Unnersjö-Jess D, Höhne M, ..., Schermer B, Benzing T

J. Am. Soc. Nephrol. 33 (1) 138-154 [2022-01-00; online 2021-12-01]

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Salivary IgG to SARS-CoV-2 indicates seroconversion and correlates to serum neutralization in mRNA-vaccinated immunocompromised individuals

Healy K, Pin E, Chen P, ..., Aleman S, Chen MS

Med - (-) - [2022-01-00; online 2022-01-00]

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Robust humoral and cellular immune responses and low risk for reinfection at least 8 months following asymptomatic to mild COVID-19.

Havervall S, Ng H, Jernbom Falk A, ..., Hober S, Thålin C

J. Intern. Med. 291 (1) 72-80 [2022-01-00; online 2021-09-27]

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Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.

Benz C, Ali M, Krystkowiak I, ..., Davey NE, Ivarsson Y

Mol. Syst. Biol. 18 (1) e10584 [2022-01-00; online 2022-01-20]

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Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells

Hühn D, Martí‐Rodrigo P, Mouron S, ..., Carreras‐Puigvert J, Fernandez‐Capetillo O

Mol Oncol 16 (1) 148-165 [2022-01-00; online 2021-08-29]

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Phytophthora infestans Ago1-associated miRNA promotes potato late blight disease.

Hu X, Persson Hodén K, Liao Z, Åsman A, Dixelius C

New Phytol. 233 (1) 443-457 [2022-01-00; online 2021-10-27]

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Oxygen‐deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments

Capo E, Broman E, Bonaglia S, ..., Nascimento FJA, Björn E

Limnol Oceanogr 67 (1) 135-146 [2022-01-00; online 2021-11-18]

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Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.

Yang M, Johnsson P, Bräutigam L, ..., Cao Y, Höiom V

Genet Med 24 (1) 157-169 [2022-01-00; online 2021-11-30]

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Metabolomics reveals changes in metabolite profiles due to growth and metamorphosis during the ontogeny of the northern damselfly.

Späth J, Brodin T, McCallum E, ..., Fick J, Nording ML

J Insect Physiol 136 (-) 104341 [2022-01-00; online 2021-11-27]

Influence of lipid extraction and processing conditions on hydrothermal conversion of microalgae feedstocks – Effect on hydrochar composition, secondary char formation and phytotoxicity

Benavente V, Lage S, Gentili FG, Jansson S

Chemical Engineering Journal 428 (-) 129559 [2022-01-00; online 2022-01-00]

Improved breast cancer histological grading using deep learning.

Wang Y, Acs B, Robertson S, ..., Hartman J, Rantalainen M

Ann. Oncol. 33 (1) 89-98 [2022-01-00; online 2021-09-29]

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Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors.

Brem J, Panduwawala T, Hansen JU, ..., Walsh TR, Schofield CJ

Nat Chem 14 (1) 15-24 [2022-01-00; online 2021-12-13]

Gut microbiome alterations in the crustacean Pacifastacus leniusculus exposed to environmental concentrations of antibiotics and effects on susceptibility to bacteria challenges.

Hernández-Pérez A, Zamora-Briseño JA, Söderhäll K, Söderhäll I

Dev. Comp. Immunol. 126 (-) 104181 [2022-01-00; online 2021-06-24]

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Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I.

Petersen G, Shyama Prasad Rao R, Anderson B, ..., Rasmusson AG, Max Møller I

Mitochondrion 62 (-) 1-12 [2022-01-00; online 2021-11-02]

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Fibroblast growth factor 23 is associated with risk of intracerebral hemorrhage.

Svensson EH, Söderholm M

Eur. J. Neurol. 29 (1) 114-120 [2022-01-00; online 2021-08-31]

Exploiting low-grade waste heat to produce electricity through supercapacitor containing carbon electrodes and ionic liquid electrolytes

Haque M, Abdurrokhman I, Idström A, ..., Lundgren P, Enoksson P

Electrochimica Acta 403 (-) 139640 [2022-01-00; online 2022-01-00]

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity.

Fallerini C, Picchiotti N, Baldassarri M, ..., Renieri A, Furini S

Hum. Genet. 141 (1) 147-173 [2022-01-00; online 2021-12-10]

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Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.

Gao W, Gallardo-Dodd CJ, Kutter C

Genome Res. 32 (1) 97-110 [2022-01-00; online 2021-12-02]

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Amplification of ERBB2 (HER2) in embryonal rhabdomyosarcoma: A potential treatment target in rare cases?

Mitra S, Sydow S, Magnusson L, ..., Gisselsson D, Mertens F

Genes Chromosomes Cancer 61 (1) 5-9 [2022-01-00; online 2021-09-01]

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A genome-wide scan to locate regions associated with familial vesicoureteral reflux.

Bartik Z, Sillén U, Östensson M, ..., Sjöberg R, Martinsson T

Exp Ther Med 23 (1) 92 [2022-01-00; online 2021-11-28]

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A 3D deep learning model to predict the diagnosis of dementia with Lewy bodies, Alzheimer's disease, and mild cognitive impairment using brain 18F-FDG PET.

Etminani K, Soliman A, Davidsson A, ..., Garibotto V, Ochoa-Figueroa M

Eur J Nucl Med Mol Imaging 49 (2) 563-584 [2022-01-00; online 2021-07-30]

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Vacancy assisted growth of copper tantalum sulfide nanocrystals

Haque A, Ershadrad S, Chonamada TD, ..., Sanyal B, Santra PK

J. Mater. Chem. A 10 (37) 19925-19934 [2022-00-00; online 2022-00-00]

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Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution

Zhang X, Lytovchenko O, Lundström S, Zubarev R, Gaetani M

BIO-PROTOCOL 12 (22) - [2022-00-00; online 2022-00-00]

Metabolomics analysis of cerebrospinal fluid suggests citric acid cycle aberrations in bipolar disorder

Smedler E, Salehi AM, Pelanis A, ..., Sparding T, Landén M

Neuroscience Applied 1 (-) 100108 [2022-00-00; online 2022-00-00]

Design of a green chemoenzymatic cascade for scalable synthesis of bio-based styrene alternatives

Petermeier P, Bittner JP, Müller S, Byström E, Kara S

Green Chem. - (-) - [2022-00-00; online 2022-00-00]

Batch Processing Methods in ImageJ

Klemm A, Miura K

Springer - (-) 7-27 [2022-00-00; online 2022-09-29]

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Alfa-Synuclein-induced deformation of small unilamellar vesicles

Makasewicz K, Wennmalm S, Linse S, Sparr E

QRB Discovery 3 (-) - [2022-00-00; online 2022-07-25]

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Streptococcus bovis-bacteremia: subspecies distribution and association with colorectal cancer: a retrospective cohort study

Öberg J, Rasmussen M, Buchwald P, Nilson B, Inghammar M

Epidemiol. Infect. 150 (-) - [2022-00-00; online 2021-11-26]

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In situ monitoring of cellulose etherification in solution: probing the impact of solvent composition on the synthesis of 3-allyloxy-2-hydroxypropyl-cellulose in aqueous hydroxide systems

Naserifar S, Kuijpers PF, Wojno S, ..., Bernin D, Hasani M

Polym. Chem. 13 (28) 4111-4123 [2022-00-00; online 2022-00-00]

Global CO2 fertilization of Sphagnum peat mosses via suppression of photorespiration during the twentieth century.

Serk H, Nilsson MB, Bohlin E, ..., Pancotto V, Schleucher J

Sci Rep 11 (1) 24517 [2021-12-31; online 2021-12-31]

Endogenous Levels of Gamma Amino-Butyric Acid Are Correlated to Glutamic-Acid Decarboxylase Antibody Levels in Type 1 Diabetes.

Hill H, Elksnis A, Lundkvist P, ..., Carlsson PO, Espes D

Biomedicines 10 (1) - [2021-12-31; online 2021-12-31]

Biased TCR gene usage in citrullinated Tenascin C specific T-cells in rheumatoid arthritis.

Sharma RK, Boddul SV, Yoosuf N, ..., Klareskog L, Malmström V

Sci Rep 11 (1) 24512 [2021-12-31; online 2021-12-31]

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Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera).

Ghanavi HR, Twort VG, Duplouy A

Sci Rep 11 (1) 24499 [2021-12-30; online 2021-12-30]

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Immunoprofiling of active and inactive systemic juvenile idiopathic arthritis reveals distinct biomarkers: a single-center study.

Qu H, Sundberg E, Aulin C, ..., Olsson M, Harris HE

Pediatr Rheumatol Online J 19 (1) 173 [2021-12-28; online 2021-12-28]

Whole-Exome Sequencing of HPV Positive Tonsillar and Base of Tongue Squamous Cell Carcinomas Reveals a Global Mutational Pattern along with Relapse-Specific Somatic Variants.

Ährlund-Richter A, Holzhauser S, Dalianis T, Näsman A, Mints M

Cancers (Basel) 14 (1) - [2021-12-24; online 2021-12-24]

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Structure and ion-release mechanism of PIB-4-type ATPases.

Grønberg C, Hu Q, Mahato DR, ..., Wang K, Gourdon P

Elife 10 (-) - [2021-12-24; online 2021-12-24]

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CD105+CD90+CD13+ identifies a clonogenic subset of adventitial lung fibroblasts.

Kadefors M, Rolandsson Enes S, Åhrman E, ..., Scheding S, Westergren-Thorsson G

Sci Rep 11 (1) 24417 [2021-12-24; online 2021-12-24]

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Structural Analysis of Botulinum Neurotoxins Type B and E by Cryo-EM.

Košenina S, Martínez-Carranza M, Davies JR, Masuyer G, Stenmark P

Toxins (Basel) 14 (1) - [2021-12-23; online 2021-12-23]

Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice.

López-Pérez A, Norlin S, Steneberg P, ..., Edlund H, Hörnblad A

Sci Rep 11 (1) 24410 [2021-12-23; online 2021-12-23]

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Localization and Absolute Quantification of Dopamine in Discrete Intravesicular Compartments Using NanoSIMS Imaging.

Rabasco S, Nguyen TDK, Gu C, ..., Phan NTN, Ewing AG

Int J Mol Sci 23 (1) - [2021-12-23; online 2021-12-23]

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Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord.

Pontiller B, Pérez-Martínez C, Bunse C, ..., Lundin D, Pinhassi J

mSystems 6 (6) e0057521 [2021-12-21; online 2021-12-14]

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Immune-Proteome Profiling in Classical Hodgkin Lymphoma Tumor Diagnostic Tissue.

Gholiha AR, Hollander P, Löf L, ..., Kamali-Moghaddam M, Enblad G

Cancers (Basel) 14 (1) 9 [2021-12-21; online 2021-12-21]

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Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast.

Malina C, Yu R, Björkeroth J, Kerkhoven EJ, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 118 (51) - [2021-12-21; online 2021-12-15]

Chitinase 3 like 1 is a regulator of smooth muscle cell physiology and atherosclerotic lesion stability.

Tsantilas P, Lao S, Wu Z, ..., Maegdefessel L, Leeper NJ

Cardiovasc. Res. 117 (14) 2767-2780 [2021-12-17; online 2021-01-21]

Characterization of backbone dynamics using solution NMR spectroscopy to discern the functional plasticity of structurally analogous proteins.

Kawale AA, Burmann BM

STAR Protoc 2 (4) 100919 [2021-12-17; online 2021-10-29]

C3a Receptor Signaling Inhibits Neurodegeneration Induced by Neonatal Hypoxic-Ischemic Brain Injury.

Pozo-Rodrigálvarez A, Li Y, Stokowska A, ..., Pekny M, Pekna M

Front Immunol 12 (-) 768198 [2021-12-17; online 2021-12-17]

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Childhood Kaposi sarcoma related to hypomorphic severe combined immunodeficiency caused by a novel CORO1A mutation.

Muleviciene A, Sekine T, Zondag T, ..., Tesi B, Rascon J

Pediatr Blood Cancer - (-) e29487 [2021-12-16; online 2021-12-16] Open Access

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Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities.

Albert S, Hedberg P, Motwani NH, ..., Winder M, Nascimento FJA

Sci Rep 11 (1) 24033 [2021-12-15; online 2021-12-15]

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Identification of Novel Neurocircuitry Through Which Leptin Targets Multiple Inputs to the Dopamine System to Reduce Food Reward Seeking.

Omrani A, de Vrind VAJ, Lodder B, ..., Meye FJ, Adan RAH

Biol. Psychiatry 90 (12) 843-852 [2021-12-15; online 2021-02-23]

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A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data.

Welén K, Rosendal E, Gisslén M, ..., Överby AK, Josefsson A

Eur. Urol. - (-) - [2021-12-15; online 2021-12-15]

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Rapid genome editing by CRISPR-Cas9-POLD3 fusion

Reint G, Li Z, Labun K, ..., Taipale J, Haapaniemi E

Elife 10 (-) - [2021-12-13; online 2021-12-13] Open Access

CRISPR Functional Genomics [Collaborative]

A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells.

Riaz M, Mattisson J, Polekhina G, ..., Forsberg LA, Lacaze P

Cell Biosci 11 (1) 205 [2021-12-12; online 2021-12-12]

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Structural basis of DegP protease temperature-dependent activation.

Šulskis D, Thoma J, Burmann BM

Sci Adv 7 (50) eabj1816 [2021-12-10; online 2021-12-08]

Causal effects of inflammatory protein biomarkers on inflammatory diseases.

Ek WE, Karlsson T, Höglund J, Rask-Andersen M, Johansson Å

Sci Adv 7 (50) eabl4359 [2021-12-10; online 2021-12-08]

Unraveling complex magnetism in two-dimensional <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub>FeS2</mml:msub></mml:math>

Wang D, Chen X, Sanyal B

Phys. Rev. B 104 (24) - [2021-12-09; online 2021-12-09]

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Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount (Book chapter)

Gaetani_M_and_Zubarev_RA

Methods in Molecular Biology in press (-) - [2021-12-09]

Plasma Metabolite Markers of Parkinson’s Disease and Atypical Parkinsonism

Pathan M, Wu J, Lakso HÅ, Forsgren L, Öhman A

Metabolites 11 (12) 860 [2021-12-09; online 2021-12-09]

Meta-analyses identify DNA methylation associated with kidney function and damage.

Schlosser P, Tin A, Matias-Garcia PR, ..., Köttgen A, Teumer A

Nat Commun 12 (1) 7174 [2021-12-09; online 2021-12-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus.

Tin A, Schlosser P, Matias-Garcia PR, ..., Teumer A, Köttgen A

Nat Commun 12 (1) 7173 [2021-12-09; online 2021-12-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural basis for transthyretin amyloid formation in vitreous body of the eye.

Iakovleva I, Hall M, Oelker M, ..., Anan I, Sauer-Eriksson AE

Nat Commun 12 (1) 7141 [2021-12-08; online 2021-12-08]

Cryo-EM [Collaborative] Structural Proteomics [Service]

Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes.

Carravilla P, Dasgupta A, Zhurgenbayeva G, ..., Sezgin E, Eggeling C

Biophysical Reports 1 (2) None [2021-12-08; online 2021-12-08]

Integrated Microscopy Technologies Stockholm [Service]

Genome-wide spatial expression profiling in formalin-fixed tissues.

Gracia Villacampa E, Larsson L, Mirzazadeh R, ..., Carlson J, Lundeberg J

Cell Genomics 1 (3) 100065 [2021-12-08; online 2021-12-08]

NGI Short read [Service] NGI Spatial omics [Service] National Genomics Infrastructure [Service]

Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection

Bauer W, Weber M, Diehl-Wiesenecker E, ..., Micke P, Kappert K

Viruses 13 (12) 2456 [2021-12-07; online 2021-12-07] Open Access

Male-biased migration from East Africa introduced pastoralism into southern Africa.

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BMC Biol. 19 (1) 259 [2021-12-07; online 2021-12-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The SEQC2 epigenomics quality control (EpiQC) study.

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Genome Biol. 22 (1) 332 [2021-12-06; online 2021-12-06]

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Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation.

Engström K, Mandakh Y, Garmire L, ..., Erlandsson L, Hansson SR

Toxics 9 (12) 338 [2021-12-06; online 2021-12-06]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Three-Dimensional Super-Resolved Imaging of Paraffin-Embedded Kidney Samples

Unnersjö-Jess D, Ramdedovic A, Höhne M, ..., Schermer B, Benzing T

Kidney360 - (-) 10.34067/KID.0005882021 [2021-12-03; online 2021-12-03]

Integrated Microscopy Technologies Stockholm [Technology development]

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

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F1000Res 10 (-) 1238 [2021-12-03; online 2021-12-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history.

Seidel L, Broman E, Turner S, Ståhle M, Dopson M

Sci Rep 11 (1) 23384 [2021-12-03; online 2021-12-03]

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Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis.

Haytural H, Benfeitas R, Schedin-Weiss S, ..., Frykman S, Tjernberg LO

Sci Data 8 (1) 312 [2021-12-03; online 2021-12-03]

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Improved Peripheral and Hepatic Insulin Sensitivity after Lifestyle Interventions in Type 2 Diabetes Is Associated with Specific Metabolomic and Lipidomic Signatures in Skeletal Muscle and Plasma.

Chorell E, Otten J, Stomby A, ..., Svensson M, Olsson T

Metabolites 11 (12) 834 [2021-12-03; online 2021-12-03]

Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver.

Hildebrandt F, Andersson A, Saarenpää S, ..., Lundeberg J, Ankarklev J

Nat Commun 12 (1) 7046 [2021-12-02; online 2021-12-02]

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Holistic Characterization of a Salmonella Typhimurium Infection Model Using Integrated Molecular Imaging.

Strittmatter N, Kanvatirth P, Inglese P, ..., Goodwin RJA, Mastroeni P

J. Am. Soc. Mass Spectrom. 32 (12) 2791-2802 [2021-12-01; online 2021-11-12]

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Thaduri S, Marupakula S, Terenius O, ..., Locke B, de Miranda JR

Sci Rep 11 (1) 23214 [2021-12-01; online 2021-12-01]

The power of genetic diversity in genome-wide association studies of lipids.

Graham SE, Clarke SL, Wu KH, ..., Sun YV, Willer CJ

Nature 600 (7890) 675-679 [2021-12-00; online 2021-12-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The genomics of heart failure: design and rationale of the HERMES consortium.

Lumbers RT, Shah S, Lin H, ..., Vasan RS, Smith JG

ESC Heart Failure 8 (6) 5531-5541 [2021-12-00; online 2021-09-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

TUBB3 Arg262His causes a recognizable syndrome including CFEOM3, facial palsy, joint contractures, and early-onset peripheral neuropathy

Whitman MC, Barry BJ, Robson CD, ..., Manoli I, Engle EC

Hum Genet 140 (12) 1709-1731 [2021-12-00; online 2021-10-15]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.

Boehm U, Nelson G, Brown CM, ..., Swedlow JR, Nitschke R

Nat. Methods 18 (12) 1423-1426 [2021-12-00; online 2021-05-23]

Integrated Microscopy Technologies Gothenburg [Collaborative]

Pyramiding of scald resistance genes in four spring barley MAGIC populations.

Hautsalo J, Novakazi F, Jalli M, ..., Bengtsson T, PPP Barley Consortium

Theor. Appl. Genet. 134 (12) 3829-3843 [2021-12-00; online 2021-08-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Physiological properties, composition and structural profiling of porcine gastrointestinal mucus.

Barmpatsalou V, Dubbelboer IR, Rodler A, ..., Pedersen BL, Bergström CAS

Eur J Pharm Biopharm 169 (-) 156-167 [2021-12-00; online 2021-10-20]

Global Proteomics and Proteogenomics [Service] Integrated Microscopy Technologies Umeå [Service] Swedish Metabolomics Centre (SMC) [Service]

Perfluorooctane sulfonate (PFOS) exposure of bovine oocytes affects early embryonic development at human-relevant levels in an in vitro model.

Hallberg I, Persson S, Olovsson M, ..., Rüegg J, Sjunnesson YCB

Toxicology 464 (-) 153028 [2021-12-00; online 2021-11-08]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Novel Mutation of the TGF-β 3 Protein (Loeys-Dietz Type 5) Associated With Aortic and Carotid Dissections: Case Report.

Hussein D, Olsson C, Lagerstedt-Robinson K, Moreira T

Neurol Genet 7 (6) e625 [2021-12-00; online 2021-09-14]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Multiplexed single‐cell mass cytometry reveals distinct inhibitory effects on intracellular phosphoproteins by midostaurin in combination with chemotherapy in AML cells

Rörby E, Adolfsson J, Hultin E, ..., Cammenga J, Jönsson JI

Exp Hematol Oncol 10 (1) 7 [2021-12-00; online 2021-02-02]

Cellular Immunomonitoring [Service]

Melphalan flufenamide inhibits osteoclastogenesis by suppressing proliferation of monocytes.

Byrgazov K, Lind T, Rasmusson AJ, ..., Larsson R, Fryknäs M

Bone Rep 15 (-) 101098 [2021-12-00; online 2021-06-07]

Drug Discovery and Development (DDD)

Lowered nutritional quality of plankton caused by global environmental changes.

Lau DCP, Jonsson A, Isles PDF, Creed IF, Bergström AK

Glob Chang Biol 27 (23) 6294-6306 [2021-12-00; online 2021-09-30]

Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought

Kozjek K, Kundel D, Kushwaha SK, ..., Birkhofer K, Hedlund K

Applied Soil Ecology 168 (-) 104140 [2021-12-00; online 2021-12-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Identification of Endothelial Proteins in Plasma Associated With Cardiovascular Risk Factors.

Iglesias MJ, Kruse LD, Sanchez-Rivera L, ..., Odeberg J, Butler LM

Arterioscler. Thromb. Vasc. Biol. 41 (12) 2990-3004 [2021-12-00; online 2021-10-28]

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).

Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, ..., Moodley Y, Gilbert MTP

Mol. Ecol. 30 (23) 6355-6369 [2021-12-00; online 2021-07-07]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.

Beale MA, Marks M, Cole MJ, ..., Fifer H, Thomson NR

Nat Microbiol 6 (12) 1549-1560 [2021-12-00; online 2021-11-24]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Genetic variants at the RTP4/MASP1 locus are associated with fatigue in Scandinavian patients with primary Sjögren's syndrome.

Norheim KB, Imgenberg-Kreuz J, Alexsson A, ..., Ronnblom L, Omdal R

RMD Open 7 (3) - [2021-12-00; online 2021-12-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis.

Mäkinen A, Nikkilä A, Mehtonen J, ..., Paavonen T, Lohi O

Pathology 53 (7) 875-882 [2021-12-00; online 2021-05-26]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolutionary history of the extinct Sardinian dhole

Ciucani MM, Jensen JK, Sinding MHS, ..., Gilbert MTP, Gopalakrishnan S

Current Biology 31 (24) 5571-5579.e6 [2021-12-00; online 2021-12-00]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Differences in risk for SARS-CoV-2 infection among healthcare workers.

Elfström KM, Blomqvist J, Nilsson P, ..., Lundgren KC, Dillner J

Prev Med Rep 24 (-) 101518 [2021-12-00; online 2021-08-21]

Differences in biomarker concentrations and predictions of long-term outcome in patients with ST-elevation and non-ST-elevation myocardial infarction.

Hjort M, Eggers KM, Lindhagen L, ..., Spaak J, Lindahl B

Clin. Biochem. 98 (-) 17-23 [2021-12-00; online 2021-09-05]

Clustered sparsity and Poisson-gap sampling.

Kasprzak P, Urbańczyk M, Kazimierczuk K

J. Biomol. NMR 75 (10-12) 401-416 [2021-12-00; online 2021-11-05]

Cerebrospinal fluid proteomics targeted for central nervous system processes in bipolar disorder.

Göteson A, Isgren A, Jonsson L, ..., Holmén-Larsson J, Landén M

Mol. Psychiatry 26 (12) 7446-7453 [2021-12-00; online 2021-08-04]

Aqueous N,N-dimethylmorpholinium hydroxide as a novel solvent for cellulose

Naserifar S, Swensson B, Bernin D, Hasani M

European Polymer Journal 161 (-) 110822 [2021-12-00; online 2021-12-00]

An atlas of the Norway spruce needle seasonal transcriptome.

Bag P, Lihavainen J, Delhomme N, ..., Robinson KM, Jansson S

Plant J. 108 (6) 1815-1829 [2021-12-00; online 2021-10-21]

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Altered ceramide metabolism is a feature in the extracellular vesicle-mediated spread of alpha-synuclein in Lewy body disorders.

Kurzawa-Akanbi M, Tammireddy S, Fabrik I, ..., Whitfield PD, Morris CM

Acta Neuropathol. 142 (6) 961-984 [2021-12-00; online 2021-09-13]

Adult-Onset Ataxia With Neuropathy and White Matter Abnormalities Due to a Novel SAMD9L Variant.

Paucar M, Tesi B, Eshtad S, ..., Bryceson YT, Svenningsson P

Neurol Genet 7 (6) e628 [2021-12-00; online 2021-10-28]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health.

Marabita F, James T, Karhu A, ..., Sallinen R, Kallioniemi O

Cell Syst - (-) - [2021-11-30; online 2021-11-30]

Autoimmunity and Serology Profiling [Service] Swedish Metabolomics Centre (SMC) [Collaborative]

Safety and efficacy of the mRNA BNT162b2 vaccine against SARS-CoV-2 in five groups of immunocompromised patients and healthy controls in a prospective open-label clinical trial.

Bergman P, Blennow O, Hansson L, ..., Aleman S, COVAXID-collaborator group (shown separately)

EBioMedicine 74 (-) 103705 [2021-11-29; online 2021-11-29]

Autoimmunity and Serology Profiling [Collaborative]

Changes in the Proteome in the Development of Chronic Human Papillomavirus Infection-A Prospective Study in HIV Positive and HIV Negative Rwandan Women.

Bienvenu E, Mukanyangezi MF, Rulisa S, ..., Tobin G, Giglio D

Cancers (Basel) 13 (23) - [2021-11-28; online 2021-11-28]

Fed-batch production assessment of a tetravalent bispecific antibody: A case study on piggyBac stably transfected HEK293 cells.

Napoleone A, Laurén I, Linkgreim T, ..., Lord M, Mangsbo S

N Biotechnol 65 (-) 9-19 [2021-11-25; online 2021-07-15]

Drug Discovery and Development (DDD) [Collaborative]

ATR inhibition enables complete tumour regression in ALK-driven NB mouse models.

Szydzik J, Lind DE, Arefin B, ..., Hallberg B, Palmer RH

Nat Commun 12 (1) 6813 [2021-11-24; online 2021-11-24]

A multi-scale map of cell structure fusing protein images and interactions.

Qin Y, Huttlin EL, Winsnes CF, ..., Lundberg E, Ideker T

Nature - (-) - [2021-11-24; online 2021-11-24]

THCz: Small molecules with antimicrobial activity that block cell wall lipid intermediates.

Reithuber E, Wixe T, Ludwig KC, ..., Almqvist F, Mellroth P

Proc. Natl. Acad. Sci. U.S.A. 118 (47) - [2021-11-23; online 2021-11-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

In vitro evaluation of chemical decontamination of titanium discs.

Ichioka Y, Derks J, Dahlén G, Berglundh T, Larsson L

Sci Rep 11 (1) 22753 [2021-11-23; online 2021-11-23]

Integrated Microscopy Technologies Gothenburg [Technology development]

High Dimensional Immune Profiling Reveals Different Response Patterns in Active and Latent Tuberculosis Following Stimulation With Mycobacterial Glycolipids.

Silva CS, Sundling C, Folkesson E, ..., Correia-Neves M, Källenius G

Front Immunol 12 (-) 727300 [2021-11-23; online 2021-11-23]

Affinity Proteomics Stockholm [Service] Cellular Immunomonitoring [Collaborative]

Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials.

Johnson A, Högfors-Rönnholm E, Engblom S, ..., Åström M, Dopson M

Sci. Total Environ. - (-) 151864 [2021-11-23; online 2021-11-23]

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A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion.

Nadeem A, Nagampalli R, Toh E, ..., Wai SN, Persson K

Proc. Natl. Acad. Sci. U.S.A. 118 (47) - [2021-11-23; online 2021-11-21]

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.

Hickey JW, Neumann EK, Radtke AJ, ..., Kelleher NL, Saka SK

Nat. Methods - (-) - [2021-11-22; online 2021-11-22]

Spatial Proteomics [Collaborative]

Tracking the ATP-binding response in adenylate kinase in real time.

Orädd F, Ravishankar H, Goodman J, ..., Wolf-Watz M, Andersson M

Sci Adv 7 (47) eabi5514 [2021-11-19; online 2021-11-17]

Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.

Zerdes I, Simonetti M, Matikas A, ..., Crosetto N, Foukakis T

NPJ Breast Cancer 7 (1) 144 [2021-11-19; online 2021-11-19]

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In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain.

Uçkun E, Wolfstetter G, Anthonydhason V, ..., Fuchs J, Palmer RH

J. Mol. Biol. 433 (23) 167282 [2021-11-19; online 2021-10-06]

Genetic Characterization of Staphylococcus aureus From Subclinical Mastitis Cases in Dairy Cows in Rwanda.

Ndahetuye JB, Leijon M, Båge R, Artursson K, Persson Y

Front Vet Sci 8 (-) 751229 [2021-11-18; online 2021-11-18]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.

Schön ME, Zlatogursky VV, Singh RP, ..., Wideman JG, Burki F

Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]

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Root traits and soil microorganisms as drivers of plant‐soil feedbacks within the sub‐arctic tundra meadow

Spitzer CM, Wardle DA, Lindahl BD, ..., Fanin N, Kardol P

J Ecol - (-) - [2021-11-17; online 2021-11-17]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Exciton Delocalization Counteracts the Energy Gap: A New Pathway toward NIR-Emissive Dyes.

Cravcenco A, Yu Y, Edhborg F, ..., Albinsson B, Börjesson K

J. Am. Chem. Soc. 143 (45) 19232-19239 [2021-11-17; online 2021-11-08]

Comparison of EM-seq and PBAT methylome library methods for low-input DNA.

Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, ..., Needhamsen M, Jagodic M

Epigenetics 17 (10) 1195-1204 [2021-11-17; online 2021-11-17]

NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.

Grosche S, Marenholz I, Esparza-Gordillo J, ..., Xu C, Lee Y

Nat Commun 12 (1) 6618 [2021-11-16; online 2021-11-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Polyoxoniobates as molecular building blocks in thin films.

Rambaran MA, Gorzsás A, Holmboe M, Ohlin CA

Dalton Trans 50 (44) 16030-16038 [2021-11-16; online 2021-11-16]

Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium.

Sáinz-Jaspeado M, Smith RO, Plunde O, ..., Bäck M, Claesson-Welsh L

Circulation 144 (20) 1629-1645 [2021-11-16; online 2021-10-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.

Kang W, Fromm B, Houben AJ, ..., Biryukova I, Friedländer MR

Cell Rep 37 (7) 110015 [2021-11-16; online 2021-11-18]

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Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids.

van Husen LS, Katsori A, Meineke B, ..., Schedin-Weiss S, Elsässer SJ

ChemBioChem 22 (22) 3208-3213 [2021-11-16; online 2021-09-13]

Integrated Microscopy Technologies Stockholm [Service]

Towards understanding kraft lignin depolymerisation under hydrothermal conditions

Ahlbom A, Maschietti M, Nielsen R, Hasani M, Theliander H

- 0 (0) - [2021-11-15; online 2021-11-15]

MTH1 Inhibitor TH1579 Induces Oxidative DNA Damage and Mitotic Arrest in Acute Myeloid Leukemia.

Sanjiv K, Calderón-Montaño JM, Pham TM, ..., Helleday T, Warpman Berglund U

Cancer Res. 81 (22) 5733-5744 [2021-11-15; online 2021-09-30]

Bioinformatics Support for Computational Resources [Service]

Limited benefit in patients with MDS receiving venetoclax and azacitidine as a bridge to allogeneic stem cell transplantation.

Jädersten M, Boriskina K, Lindholm C, ..., Mielke S, Tobiasson M

Leuk. Lymphoma - (-) 1-4 [2021-11-15; online 2021-11-15]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system.

Baniol M, Murganti F, Smialowska A, ..., Derks W, Bergmann O

Exp. Cell Res. 408 (2) 112880 [2021-11-15; online 2021-10-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes.

Anderson BM, Krause K, Petersen G

BMC Genomics 22 (1) 816 [2021-11-12; online 2021-11-12]

Bioinformatics Support for Computational Resources [Service]

Different Responses to Neoadjuvant Chemotherapy in Urothelial Carcinoma Molecular Subtypes.

Sjödahl G, Abrahamsson J, Holmsten K, ..., Ullén A, Liedberg F

Eur. Urol. - (-) - [2021-11-12; online 2021-11-12]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

Sabatier P, Beusch CM, Saei AA, ..., Rodin S, Zubarev RA

Nat Commun 12 (1) 6558 [2021-11-12; online 2021-11-12] Open Access

A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification.

Eriksson P, Marzouka NA, Sjödahl G, ..., Liedberg F, Höglund M

Bioinformatics - (-) - [2021-11-12; online 2021-11-12]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Proteins associated with incident metabolic syndrome in population-based cohorts.

Lind L, Sundström J, Ärnlöv J

Diabetol Metab Syndr 13 (1) 131 [2021-11-10; online 2021-11-10]

Elevated circulating follistatin associates with an increased risk of type 2 diabetes.

Wu C, Borné Y, Gao R, ..., Groop L, De Marinis Y

Nat Commun 12 (1) 6486 [2021-11-10; online 2021-11-10]

Affinity Proteomics Stockholm [Collaborative] Affinity Proteomics Uppsala [Service]

Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.

Zhao Y, Fang LT, Shen T, ..., Hong H, Xiao W

Sci Data 8 (1) 296 [2021-11-09; online 2021-11-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

The role of circulating galectin-1 in type 2 diabetes and chronic kidney disease: evidence from cross-sectional, longitudinal and Mendelian randomisation analyses.

Drake I, Fryk E, Strindberg L, ..., Orho-Melander M, Jansson PA

Diabetologia - (-) - [2021-11-07; online 2021-11-07]

Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.

Abreha KB, Alexandersson E, Resjö S, ..., Levander F, Andreasson E

Int J Mol Sci 22 (21) - [2021-11-06; online 2021-11-06]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.

Chattopadhyay S, Karlsson J, Valind A, Andersson N, Gisselsson D

Brief. Bioinformatics 22 (6) - [2021-11-05; online 2021-08-04]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multiomics Profiling of Alzheimer's Disease Serum for the Identification of Autoantibody Biomarkers.

San Segundo-Acosta P, Montero-Calle A, Jernbom-Falk A, ..., Nilsson P, Barderas R

J. Proteome Res. 20 (11) 5115-5130 [2021-11-05; online 2021-10-10]

Autoimmunity and Serology Profiling [Collaborative]

Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain.

Szykowska A, Chen Y, Smith TB, ..., Burgess-Brown NA, Bullock AN

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Global Proteomics and Proteogenomics [Technology development]

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Glycoproteomics and MS Proteomics [Technology development]

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BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]

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Automating classification of osteoarthritis according to Kellgren-Lawrence in the knee using deep learning in an unfiltered adult population.

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Presenting artificial intelligence, deep learning, and machine learning studies to clinicians and healthcare stakeholders: an introductory reference with a guideline and a Clinical AI Research (CAIR) checklist proposal.

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Cell Genomics 1 (1) 100002 [2021-10-00; online 2021-10-00]

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Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes.

Ilumäe AM, Post H, Flores R, ..., Rootsi S, Villems R

Eur. J. Hum. Genet. 29 (10) 1510-1519 [2021-10-00; online 2021-05-07]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life

Twort VG, Minet J, Wheat CW, Wahlberg N

Systematic Entomology 46 (4) 926-937 [2021-10-00; online 2021-07-08]

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Milligram scale expression, refolding, and purification of Bombyx mori cocoonase using a recombinant E. coli system.

Phoeurk C, Mushtaq AU, Rogne P, Wolf-Watz M

Protein Expression and Purification 186 (-) 105919 [2021-10-00; online 2021-05-24]

Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.

Juras A, Ehler E, Chyleński M, ..., Jakobsson M, Dabert M

Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]

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Inflammatory proteins and miRNA-144-5p in patients with depression, anxiety, or stress- and adjustment disorders after psychological treatment.

Sundquist K, Memon AA, Palmér K, Sundquist J, Wang X

Cytokine 146 (-) 155646 [2021-10-00; online 2021-07-27]

Immune responses against oxidized LDL as possible targets for prevention of atherosclerosis in systemic lupus erythematosus.

Yao Mattisson I, Rattik S, Björkbacka H, ..., Nilsson J, Wigren M

Vascul Pharmacol 140 (-) 106863 [2021-10-00; online 2021-04-15]

Hyperglycaemia-associated Caspase-3 predicts diabetes and coronary artery disease events.

Sun J, Singh P, Österlund J, ..., Engström G, Edsfeldt A

J. Intern. Med. 290 (4) 855-865 [2021-10-00; online 2021-07-26]

High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.

Hammarsjö A, Pettersson M, Chitayat D, ..., Lindstrand A, Grigelioniene G

J. Hum. Genet. 66 (10) 995-1008 [2021-10-00; online 2021-04-20]

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Genome-wide association study of liver enzyme elevation in rheumatoid arthritis patients starting methotrexate.

Sundbaum JK, Baecklund E, Eriksson N, ..., Wadelius M, Hallberg P

Pharmacogenomics 22 (15) 973-982 [2021-10-00; online 2021-09-15]

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Ecologically coherent population structure of uncultivated bacterioplankton.

Sjöqvist C, Delgado LF, Alneberg J, Andersson AF

ISME J 15 (10) 3034-3049 [2021-10-00; online 2021-05-05]

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Differential effects of estradiol and progesterone on human T cell activation in vitro.

Papapavlou G, Hellberg S, Raffetseder J, ..., Jenmalm MC, Ernerudh J

Eur. J. Immunol. 51 (10) 2430-2440 [2021-10-00; online 2021-07-26]

DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha.

Lagercrantz U, Billhardt A, Rousku SN, ..., Reza SH, Eklund DM

New Phytol. 232 (2) 595-609 [2021-10-00; online 2021-08-19]

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Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.

Zeybel M, Altay O, Arif M, ..., Borén J, Mardinoglu A

Mol. Syst. Biol. 17 (10) e10459 [2021-10-00; online 2021-10-26]

Carotid atherosclerosis, changes in tissue remodeling and repair in patients with aortic coarctation.

Hlebowicz J, Holm J, Lindstedt S, Goncalves I, Nilsson J

Atherosclerosis 335 (-) 47-52 [2021-10-00; online 2021-09-21]

Broadening the roles of UDP-glycosyltransferases in auxin homeostasis and plant development.

Mateo-Bonmatí E, Casanova-Sáez R, Šimura J, Ljung K

New Phytol. 232 (2) 642-654 [2021-10-00; online 2021-08-10]

A single sulfatase is required to access colonic mucin by a gut bacterium.

Luis AS, Jin C, Pereira GV, ..., Cartmell A, Martens EC

Nature 598 (7880) 332-337 [2021-10-00; online 2021-10-06]

ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression.

Naboulsi R, Larsson M, Andersson L, Younis S

Sci Rep 11 (1) 19484 [2021-09-30; online 2021-09-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Design and development of a photoswitchable DFG-out kinase inhibitor.

Xu Y, Gao C, Håversen L, ..., Andréasson J, Grøtli M

Chem. Commun. (Camb.) 57 (78) 10043-10046 [2021-09-30; online 2021-09-30]

Chemical Biology Consortium Sweden (CBCS) [Service]

An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses.

Mangsbo SM, Havervall S, Laurén I, ..., Klingström J, Thålin C

PLoS ONE 16 (9) e0258041 [2021-09-30; online 2021-09-30]

Autoimmunity and Serology Profiling [Technology development]

In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A

Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]

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Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.

Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C

Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Composition and Seasonality of Membrane Transporters in Marine Picoplankton.

Hagström Å, Zweifel UL, Sundh J, ..., Müller-Karulis B, Pinhassi J

Front Microbiol 12 (-) 714732 [2021-09-28; online 2021-09-28]

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Association between cardiovascular disease- and inflammation-related serum biomarkers and poor lung function in elderly.

Egervall K, Rosso A, Elmståhl S

Clin Proteomics 18 (1) 23 [2021-09-28; online 2021-09-28]

A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma.

Milon B, Shulman ED, So KS, ..., Elkon R, Hertzano R

Cell Rep 36 (13) 109758 [2021-09-28; online 2021-10-01]

Eukaryotic Single Cell Genomics (ESCG) [Service]

The localization of amyloid precursor protein to ependymal cilia in vertebrates and its role in ciliogenesis and brain development in zebrafish.

Chebli J, Rahmati M, Lashley T, ..., Zetterberg H, Abramsson A

Sci Rep 11 (1) 19115 [2021-09-27; online 2021-09-27]

Integrated Microscopy Technologies Gothenburg [Service]

Saturation mutagenesis charts the functional landscape of Salmonella ProQ and reveals a gene regulatory function of its C-terminal domain.

Rizvanovic A, Kjellin J, Söderbom F, Holmqvist E

Nucleic Acids Res. 49 (17) 9992-10006 [2021-09-27; online 2021-08-28]

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Covid-19 in patients with chronic lymphocytic leukemia: clinical outcome and B- and T-cell immunity during 13 months in consecutive patients.

Blixt L, Bogdanovic G, Buggert M, ..., Hansson L, Österborg A

Leukemia - (-) - [2021-09-25; online 2021-09-25]

Development of humoral and cellular immunological memory against SARS-CoV-2 despite B cell depleting treatment in multiple sclerosis.

Asplund Högelin K, Ruffin N, Pin E, ..., Piehl F, Al Nimer F

iScience 24 (9) 103078 [2021-09-24; online 2021-09-02]

Autoimmunity and Serology Profiling [Collaborative]

Glycemic Control and Metabolic Adaptation in Response to High-Fat versus High-Carbohydrate Diets-Data from a Randomized Cross-Over Study in Healthy Subjects.

Wallenius V, Elebring E, Casselbrant A, ..., Marschall HU, Fändriks L

Nutrients 13 (10) - [2021-09-23; online 2021-09-23]

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.

Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K

Sci Rep 11 (1) 18822 [2021-09-22; online 2021-09-22]

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Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.

Arroyo Mühr LS, Dillner J, Ure AE, Sundström K, Hultin E

Sci Rep 11 (1) 18852 [2021-09-22; online 2021-09-22]

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Sulfation of O-glycans on Mucin-type Proteins From Serous Ovarian Epithelial Tumors.

Thomsson KA, Vitiazeva V, Mateoiu C, ..., Sundfeldt K, Karlsson NG

Mol. Cell Proteomics 20 (-) 100150 [2021-09-21; online 2021-09-21]

Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.

Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B

Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]

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Long-Term Elevated Inflammatory Protein Levels in Asymptomatic SARS-CoV-2 Infected Individuals.

Tserel L, Jõgi P, Naaber P, ..., Lutsar I, Peterson P

Front Immunol 12 (-) 709759 [2021-09-17; online 2021-09-17]

BioID-Screening Identifies PEAK1 and SHP2 as Components of the ALK Proximitome in Neuroblastoma Cells.

Uçkun E, Siaw JT, Guan J, ..., Hallberg B, Palmer RH

J. Mol. Biol. 433 (19) 167158 [2021-09-17; online 2021-07-15]

Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.

Li D, Cheng S, Pei Y, ..., Deng Q, Xu Landén N

J. Invest. Dermatol. - (-) - [2021-09-16; online 2021-09-16]

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Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP

Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]

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Nontypeable Haemophilus influenzae P5 Binds Human C4b-Binding Protein, Promoting Serum Resistance.

Thofte O, Bettoni S, Su Y, ..., Blom AM, Riesbeck K

J. Immunol. 207 (6) 1566-1577 [2021-09-15; online 2021-08-25]

Integrated Microscopy Technologies Umeå [Collaborative]

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.

Glaros V, Rauschmeier R, Artemov AV, ..., Busslinger M, Kreslavsky T

Immunity 54 (9) 2005-2023.e10 [2021-09-14; online 2021-09-16]

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Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.

Sandholt AKS, Wattrang E, Lilja T, ..., Svärd SG, Söderlund R

BMC Genomics 22 (1) 660 [2021-09-14; online 2021-09-14]

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The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.

Peona V, Palacios-Gimenez OM, Blommaert J, ..., Jern P, Suh A

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1833) 20200186 [2021-09-13; online 2021-07-26]

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Autoantibody profiles associated with clinical features in psychotic disorders.

Jernbom Falk A, Galletly C, Just D, ..., Månberg A, Schubert KO

Transl Psychiatry 11 (1) 474 [2021-09-13; online 2021-09-13]

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PubMed

Increased antibody reactivity against insulin receptor-A and insulin like growth factor 1 receptor and their ligands in cerebrospinal fluid and serum of patients with schizophrenia or related psychosis.

Melkersson K, Bensing S

Neuro Endocrinol. Lett. 42 (5) 339-358 [2021-09-10; online 2021-09-10]

The liver-alpha-cell axis after a mixed meal and during weight loss in type 2 diabetes.

Otten J, Stomby A, Waling M, ..., Holst JJ, Olsson T

Endocr Connect 10 (9) 1101-1110 [2021-09-09; online 2021-09-09]

Proteoglycan profiling of human, rat and mouse insulin-secreting cells.

Nikpour M, Nilsson J, Persson A, ..., Vorontsov E, Larson G

Glycobiology 31 (8) 916-930 [2021-09-09; online 2021-05-18]

A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.

Powell D, Groβe-Wilde E, Krokene P, ..., Andersson MN, Schlyter F

Commun Biol 4 (1) 1059 [2021-09-09; online 2021-09-09]

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Temporally balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring.

Durland E, De Wit P, Langdon C

Proc. Biol. Sci. 288 (1958) 20203223 [2021-09-08; online 2021-09-01]

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Selection on accessible chromatin regions in Capsella grandiflora.

Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T

Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]

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Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin.

Bäckdahl J, Franzén L, Massier L, ..., Ståhl PL, Mejhert N

Cell Metab. 33 (9) 1869-1882.e6 [2021-09-07; online 2021-08-10]

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Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.

Bedoya-Reina OC, Li W, Arceo M, ..., Kogner P, Schlisio S

Nat Commun 12 (1) 5309 [2021-09-07; online 2021-09-07]

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Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion.

Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P

Nat Commun 12 (1) 5277 [2021-09-06; online 2021-09-06]

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome.

Bacic L, Gaullier G, Sabantsev A, ..., Boulton SJ, Deindl S

Elife 10 (-) - [2021-09-06; online 2021-09-06]

Allogeneic Hematopoietic Stem Cell Transplantation for Chronic Myelomonocytic Leukemia: Clinical and Molecular Genetic Prognostic Factors in a Nordic Population.

Wedge E, Hansen JW, Dybedal I, ..., Ljungman P, Friis LS

Transplant Cell Ther - (-) - [2021-09-06; online 2021-09-06]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.

Zhao Y, Lindberg BG, Esfahani SS, ..., Piazza S, Engström Y

BMC Biol. 19 (1) 185 [2021-09-03; online 2021-09-03]

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Neuropharmacokinetic visualization of regional and subregional unbound antipsychotic drug transport across the blood-brain barrier.

Luptáková D, Vallianatou T, Nilsson A, ..., Loryan I, Andrén PE

Mol. Psychiatry - (-) - [2021-09-03; online 2021-09-03]

Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma.

Cao X, Sandberg A, Araújo JE, ..., Eriksson LE, Pernemalm M

J. Proteome Res. 20 (9) 4610-4620 [2021-09-03; online 2021-07-28]

Global Proteomics and Proteogenomics [Technology development]

Immunoglobulin A Autoreactivity toward Brain Enriched and Apoptosis-Regulating Proteins in Saliva of Athletes after Acute Concussion and Subconcussive Impacts.

Pin E, Petricoin EF, Cortes N, ..., Nilsson P, Caswell SV

J. Neurotrauma 38 (17) 2373-2383 [2021-09-01; online 2021-05-24]

Autoimmunity and Serology Profiling [Collaborative]

Genetic Variant Score and Arrhythmogenic Right Ventricular Cardiomyopathy Phenotype in Plakophilin-2 Mutation Carriers.

Svensson A, Platonov PG, Haugaa KH, ..., Svendsen JH, Gunnarsson C

Cardiology 146 (6) 763-771 [2021-09-01; online 2021-09-01]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Anorexia and Fat Aversion Induced by Vertical Sleeve Gastrectomy Is Attenuated in Neurotensin Receptor 1-Deficient Mice.

Ratner C, Shin JH, Dwibedi C, ..., Seeley RJ, Holst B

Endocrinology 162 (9) - [2021-09-01; online 2021-07-01]

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Using Deep Learning to Emulate the Use of an External Contrast Agent in Cardiovascular 4D Flow MRI.

Bustamante M, Viola F, Carlhäll CJ, Ebbers T

J Magn Reson Imaging 54 (3) 777-786 [2021-09-00; online 2021-02-25]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.

Xiao W, Ren L, Chen Z, ..., Wang C, Shi L

Nat. Biotechnol. 39 (9) 1141-1150 [2021-09-00; online 2021-09-09]

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The microRNA response associated with methyl jasmonate-induced resistance in Norway spruce bark

Wilkinson SW, Vivian-Smith A, Krokene P, Mageroy MH

Plant Gene 27 (-) 100301 [2021-09-00; online 2021-09-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels.

Axelsson E, Ljungvall I, Bhoumik P, ..., Häggström J, Lindblad-Toh K

PLoS Genet. 17 (9) e1009726 [2021-09-00; online 2021-09-02]

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Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Matalonga L, Hernández-Ferrer C, Piscia D, ..., Beltran S, Solve-RD Consortia

Eur. J. Hum. Genet. 29 (9) 1337-1347 [2021-09-00; online 2021-06-01]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Soil physico-chemical properties have a greater effect on soil fungi than host species in Mediterranean pure and mixed pine forests

Adamo I, Castaño C, Bonet JA, ..., Martínez de Aragón J, Alday JG

Soil Biology and Biochemistry 160 (-) 108320 [2021-09-00; online 2021-09-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Screening of biomarkers for prediction of multisite artery disease in patients with recent myocardial infarction.

Jönelid B, Christersson C, Hedberg P, ..., Oldgren J, Siegbahn A

Scand J Clin Lab Invest 81 (5) 353-360 [2021-09-00; online 2021-08-04]

Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage.

Ylänne H, Madsen RL, Castaño C, Metcalfe DB, Clemmensen KE

Glob Chang Biol 27 (18) 4254-4268 [2021-09-00; online 2021-06-14]

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Regulatory T cells reduce endothelial neutral sphingomyelinase 2 to prevent T-cell migration into tumors.

Akeus P, Szeponik L, Langenes V, ..., Slusher BS, Quiding-Järbrink M

Eur. J. Immunol. 51 (9) 2317-2329 [2021-09-00; online 2021-07-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Q-space trajectory imaging with positivity constraints (QTI+).

Herberthson M, Boito D, Haije TD, ..., Westin CF, Özarslan E

Neuroimage 238 (-) 118198 [2021-09-00; online 2021-05-21]

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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.

Chase MA, Ellegren H, Mugal CF

Evolution 75 (9) 2179-2196 [2021-09-00; online 2021-05-03]

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Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change.

Chattopadhyay B, Forcina G, Garg KM, ..., Barbanera F, Rheindt FE

Genomics 113 (5) 3430-3438 [2021-09-00; online 2021-08-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mitochondrial dysfunction in adult midbrain dopamine neurons triggers an early immune response.

Filograna R, Lee S, Tiklová K, ..., Perlmann T, Larsson NG

PLoS Genet. 17 (9) e1009822 [2021-09-00; online 2021-09-27]

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Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus.

Reid S, Hagberg N, Sandling JK, ..., Rönnblom L, Leonard D

Ann. Rheum. Dis. 80 (9) 1183-1189 [2021-09-00; online 2021-03-25]

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Impact of Different Synthesis Methods on the Low-Temperature Deactivation of Cu/SAPO-34 for NH3-SCR Reaction

Woo J, Wang A, Bernin D, ..., Zammit M, Olsson L

Emiss. Control Sci. Technol. 7 (3) 198-209 [2021-09-00; online 2021-08-03]

Genomic and transcriptomic characterization of desmoplastic small round cell tumors.

Sydow S, Versleijen-Jonkers YMH, Hansson M, ..., Flucke UE, Mertens F

Genes Chromosomes Cancer 60 (9) 595-603 [2021-09-00; online 2021-05-17]

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Genetic deletion of the ghrelin receptor (GHSR) impairs growth and blunts endocrine response to fasting in Ghsr-IRES-Cre mice.

Peris-Sampedro F, Stoltenborg I, Le May MV, ..., Adan RAH, Dickson SL

Mol Metab 51 (-) 101223 [2021-09-00; online 2021-03-31]

Integrated Microscopy Technologies Gothenburg [Service]

Evaluation of 92 cardiovascular proteins in dried blood spots collected under field-conditions: Off-the-shelf affinity-based multiplexed assays work well, allowing for simplified sample collection.

Broberg K, Svensson J, Grahn K, ..., Selander J, Enroth S

Bioessays 43 (9) e2000299 [2021-09-00; online 2021-02-15]

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Fang LT, Zhu B, Zhao Y, ..., Xiao W, Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium

Nat. Biotechnol. 39 (9) 1151-1160 [2021-09-00; online 2021-09-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Efficacy of EBL-1003 (apramycin) against Acinetobacter baumannii lung infections in mice.

Becker K, Aranzana-Climent V, Cao S, ..., Hobbie SN, ENABLE consortium

Clin. Microbiol. Infect. 27 (9) 1315-1321 [2021-09-00; online 2020-12-11]

Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient

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J Ecol 109 (9) 3195-3210 [2021-09-00; online 2020-11-26]

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Distinct plasma biomarkers confirm the diagnosis of mastocytosis and identify increased risk of anaphylaxis.

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J. Allergy Clin. Immunol. 148 (3) 889-894 [2021-09-00; online 2021-03-02]

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Adv Sci (Weinh) 8 (17) e2101222 [2021-09-00; online 2021-06-28]

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New Phytol. 231 (5) 1770-1783 [2021-09-00; online 2021-06-18]

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Limnol Oceanogr 66 (9) 3523-3534 [2021-09-00; online 2021-07-30]

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Branched-chain amino acid metabolism is regulated by ERRα in primary human myotubes and is further impaired by glucose loading in type 2 diabetes.

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Diabetologia 64 (9) 2077-2091 [2021-09-00; online 2021-06-16]

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In Situ Sequencing (ISS) [Collaborative] Spatial Proteomics

A novel silver(I) di-iso-butyldithiocarbamate: Unusually complicated 1-D polymeric structure, multiple ligand-supported Ag–Ag interactions and its capability to bind gold(III). Preparation, structural organisation and (13C, 15N) CP-MAS NMR of [Ag6(S2CNiBu2)6] and [Au(S2CNiBu2)2][AgCl2]

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A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.

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Nat. Genet. 53 (9) 1276-1282 [2021-09-00; online 2021-09-07]

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A genome-wide association study of the frailty index highlights brain pathways in ageing.

Atkins JL, Jylhävä J, Pedersen NL, ..., Williams DM, Pilling LC

Aging Cell 20 (9) e13459 [2021-09-00; online 2021-08-25]

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A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis.

de Boer E, Ockeloen CW, Matalonga L, ..., Verloes A, Vissers LELM

Eur. J. Hum. Genet. 29 (9) 1359-1368 [2021-09-00; online 2021-06-01]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures.

Deiana M, Mosser M, Le Bahers T, ..., Monnereau C, Guy L

Nanoscale 13 (32) 13795-13808 [2021-08-28; online 2021-08-04]

Novel Microdialysis Technique Reveals a Dramatic Shift in Metabolite Secretion during the Early Stages of the Interaction between the Ectomycorrhizal Fungus Pisolithus microcarpus and Its Host Eucalyptus grandis.

Plett KL, Buckley S, Plett JM, ..., Lundberg-Felten J, Jämtgård S

Microorganisms 9 (9) - [2021-08-26; online 2021-08-26]

Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.

Martin F, Halvarsson P, Delhomme N, Höglund J, Tydén E

International Journal for Parasitology: Drugs and Drug Resistance 17 (-) 84-91 [2021-08-26; online 2021-08-26]

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Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia.

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Front Oncol 11 (-) 740083 [2021-08-26; online 2021-08-26]

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Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.

Grochowski CM, Krepischi ACV, Eisfeldt J, ..., Lindstrand A, Carvalho CMB

Front Genet 12 (-) 708348 [2021-08-26; online 2021-08-26]

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Amnion signals are essential for mesoderm formation in primates.

Yang R, Goedel A, Kang Y, ..., Niu Y, Chien KR

Nat Commun 12 (1) 5126 [2021-08-26; online 2021-08-26]

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A genetic titration of membrane composition in Caenorhabditis elegans reveals its importance for multiple cellular and physiological traits.

Devkota R, Kaper D, Bodhicharla R, ..., Borén J, Pilon M

Genetics 219 (1) - [2021-08-26; online 2021-06-15]

Integrated Microscopy Technologies Gothenburg [Service]

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Lepzien R, Nie M, Czarnewski P, ..., Grunewald J, Smed-Sörensen A

J Leukoc Biol - (-) - [2021-08-25; online 2021-08-25]

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Interleukin 6 and Cardiovascular Outcomes in Patients With Chronic Kidney Disease and Chronic Coronary Syndrome.

Batra G, Ghukasyan Lakic T, Lindbäck J, ..., Wallentin L, STABILITY Investigators

JAMA Cardiol - (-) - [2021-08-25; online 2021-08-25]

The Amot/integrin protein complex transmits mechanical forces required for vascular expansion.

Zhang Y, Zhang Y, Kameishi S, ..., Cavallo F, Holmgren L

Cell Rep 36 (8) 109616 [2021-08-24; online 2021-08-26]

The Accessibility of the Cell Wall in Scots Pine (Pinus sylvestris L.) Sapwood to Colloidal Fe3O4 Nanoparticles.

Garskaite E, Stoll SL, Forsberg F, ..., Liu K, Sandberg D

ACS Omega 6 (33) 21719-21729 [2021-08-24; online 2021-08-10]

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.

Mahboubi A, Delhomme N, Häggström S, Hanson J

Plant Methods 17 (1) 92 [2021-08-24; online 2021-08-24]

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Genomic Epidemiology of Azithromycin-Nonsusceptible Neisseria gonorrhoeae, Argentina, 2005-2019.

Gianecini RA, Poklepovich T, Golparian D, ..., Galarza P, Gonococcal Antimicrobial Susceptibility Surveillance Programme—Argentina1

Emerg. Infect. Dis. 27 (9) 2369-2378 [2021-08-24; online 2021-08-24]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Comprehensive in situ mapping of human cortical transcriptomic cell types.

Langseth CM, Gyllborg D, Miller JA, ..., Hilscher MM, Nilsson M

Commun Biol 4 (1) 998 [2021-08-24; online 2021-08-24]

Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.

Westbury MV, Le Duc D, Duchêne DA, ..., Schöneberg T, Hofreiter M

Mol. Biol. Evol. 38 (9) 3884-3897 [2021-08-23; online 2021-08-25]

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RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system.

Takada H, Crowe-McAuliffe C, Polte C, ..., Wilson DN, Hauryliuk V

Nucleic Acids Res. 49 (14) 8355-8369 [2021-08-20; online 2021-07-14]

A Minimalistic Coumarin Turn-On Probe for Selective Recognition of Parallel G-Quadruplex DNA Structures.

Deiana M, Obi I, Andreasson M, ..., Chorell E, Sabouri N

ACS Chem. Biol. 16 (8) 1365-1376 [2021-08-20; online 2021-07-30]

X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19.

Asano T, Boisson B, Onodi F, ..., Zhang Q, Casanova JL

Sci Immunol 6 (62) - [2021-08-19; online 2021-08-21]

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Transcriptomic markers of fungal growth, respiration and carbon-use efficiency.

Hasby FA, Barbi F, Manzoni S, Lindahl BD

FEMS Microbiol. Lett. 368 (15) - [2021-08-19; online 2021-08-03]

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The broad role of Nkx3.2 in the development of the zebrafish axial skeleton.

Waldmann L, Leyhr J, Zhang H, ..., Allalou A, Haitina T

PLoS ONE 16 (8) e0255953 [2021-08-19; online 2021-08-19]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Genome Engineering Zebrafish [Service]

Community composition of aquatic fungi across the thawing Arctic.

Kluge M, Wurzbacher C, Wauthy M, ..., Stenlid J, Peura S

Sci Data 8 (1) 221 [2021-08-19; online 2021-08-19]

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A simple pressure-assisted method for MicroED specimen preparation.

Zhao J, Xu H, Lebrette H, ..., Högbom M, Zou X

Nat Commun 12 (1) 5036 [2021-08-19; online 2021-08-19]

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Roghanian M, Van Nerom K, Takada H, ..., Garcia-Pino A, Hauryliuk V

Mol. Cell 81 (16) 3310-3322.e6 [2021-08-19; online 2021-08-21]

Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.

Houtman M, Hesselberg E, Rönnblom L, ..., Malmström V, Padyukov L

Front Immunol 12 (-) 707217 [2021-08-17; online 2021-08-17]

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Association of Variants Near the Bradykinin Receptor B2 Gene With Angioedema in Patients Taking ACE Inhibitors.

Ghouse J, Ahlberg G, Andreasen L, ..., Bundgaard H, Olesen MS

J. Am. Coll. Cardiol. 78 (7) 696-709 [2021-08-17; online 2021-08-14]

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Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community.

Singh A, Moestedt J, Berg A, Schnürer A

Front Microbiol 12 (-) 700256 [2021-08-16; online 2021-08-16]

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Metabolomics profiling predicts outcome of tocilizumab in rheumatoid arthritis: an exploratory study.

Murillo-Saich JD, Diaz-Torne C, Ortiz MA, ..., Vidal S, Guma M

Metabolomics 17 (9) 74 [2021-08-16; online 2021-08-16]

Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey.

Rahimi Y, Ingvarsson PK, Bihamta MR, ..., Taleei A, Khoshnoodi Jabar Abadi S

Front Plant Sci 12 (-) 710867 [2021-08-16; online 2021-08-16]

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Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells.

Hühn D, Martí-Rodrigo P, Mouron S, ..., Carreras-Puigvert J, Fernandez-Capetillo O

Mol Oncol - (-) - [2021-08-15; online 2021-08-15]

Chemical Biology Consortium Sweden (CBCS) [Service]

Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods.

Freire RVM, Pillco-Valencia Y, da Hora GCA, ..., Soares TA, Salentinig S

Journal of Colloid and Interface Science 596 (-) 352-363 [2021-08-15; online 2021-03-16]

Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.

Lindholm Carlström E, Niazi A, Etemadikhah M, ..., Nilsson B, Feuk L

Genes 12 (8) - [2021-08-13; online 2021-08-13]

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Site-Dependent Relationships Between Fungal Community Composition, Plant Genotypic Diversity and Environmental Drivers in a Salix Biomass System

Hoeber S, Baum C, Weih M, Manzoni S, Fransson P

Front. Fungal Biol. 2 (-) - [2021-08-13; online 2021-08-13]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.

Ma J, Tibbitt CA, Georén SK, ..., Bachert C, Coquet JM

Sci Immunol 6 (62) - [2021-08-13; online 2021-08-15]

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Expanding the Chondroitin Sulfate Glycoproteome - But How Far?

Noborn F, Nikpour M, Persson A, Nilsson J, Larson G

Front Cell Dev Biol 9 (-) 695970 [2021-08-13; online 2021-08-13]

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.

Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S

Front Microbiol 12 (-) 669937 [2021-08-12; online 2021-08-12]

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Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.

Bellenberg S, Salas B, Ganji S, ..., Dopson M, Vera M

Sci Rep 11 (1) 16275 [2021-08-11; online 2021-08-11]

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Sensitive Measurement of Drug-Target Engagement by a Cellular Thermal Shift Assay with Multiplex Proximity Extension Readout.

Al-Amin RA, Gallant CJ, Muthelo PM, Landegren U

Anal. Chem. 93 (31) 10999-11009 [2021-08-10; online 2021-07-28]

A Super-Resolved View of the Alzheimer's Disease-Related Amyloidogenic Pathway in Hippocampal Neurons.

Yu Y, Gao Y, Winblad B, Tjernberg LO, Schedin-Weiss S

J. Alzheimers Dis. 83 (2) 833-852 [2021-08-10; online 2021-08-10]

Integrated Microscopy Technologies Stockholm [Service]

Genome assemblies of three closely related leaf beetle species (Galerucella spp.).

Yang X, Slotte T, Dainat J, Hambäck PA

G3 (Bethesda) 11 (8) - [2021-08-07; online 2021-12-02]

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Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.

Sayyab S, Lundmark A, Larsson M, ..., Nordlund J, Syvänen A

Sci Rep 11 (1) 15988 [2021-08-06; online 2021-08-06]

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High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins.

Niksirat H, Siino V, Steinbach C, Levander F

J. Proteome Res. 20 (8) 4075-4088 [2021-08-06; online 2021-06-29]

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Shifts in gene expression variability in the blood-stage of Plasmodium relictum.

Kalbskopf V, Ahrén D, Valkiūnas G, Palinauskas V, Hellgren O

Gene 792 (-) 145723 [2021-08-05; online 2021-05-18]

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Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae.

Tellgren-Roth C, Thorell K, Galperin MY, ..., Sjöling Å, Martín-Rodríguez AJ

Microbiol Resour Announc 10 (31) e0055921 [2021-08-05; online 2021-08-05]

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Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.

Natarajan K, Eisfeldt J, Hammond M, ..., Öijerstedt L, Graff C

Acta Neuropathol Commun 9 (1) 132 [2021-08-03; online 2021-08-03]

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PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.

Seyfferth C, Wessels BA, Vahala J, ..., Tuominen H, Lundberg-Felten J

Cells 10 (8) 1971 [2021-08-03; online 2021-08-03]

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Persisting Salivary IgG Against SARS-CoV-2 at 9 Months After Mild COVID-19: A Complementary Approach to Population Surveys.

Alkharaan H, Bayati S, Hellström C, ..., Pin E, Sällberg Chen M

J. Infect. Dis. 224 (3) 407-414 [2021-08-02; online 2021-05-13]

Autoimmunity and Serology Profiling [Collaborative]

Three weeks of interrupting sitting lowers fasting glucose and glycemic variability, but not glucose tolerance, in free-living women and men with obesity.

Smith JAB, Savikj M, Sethi P, ..., Zierath JR, Näslund E

Am J Physiol Endocrinol Metab 321 (2) E203-E216 [2021-08-01; online 2021-06-21]

Single-cell atlas reveals meningeal leukocyte heterogeneity in the developing mouse brain.

Zelco A, Börjesson V, de Kanter JK, ..., Holstege FCP, Wang X

Genes Dev. 35 (15-16) 1190-1207 [2021-08-01; online 2021-07-22]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Genome-wide estrogen receptor β chromatin binding in human colon cancer cells reveals its tumor suppressor activity.

Indukuri R, Jafferali MH, Song D, ..., Archer A, Williams C

Int. J. Cancer 149 (3) 692-706 [2021-08-01; online 2021-04-05]

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Transcriptional study reveals a potential leptin-dependent gene regulatory network in zebrafish brain.

Ahi EP, Tsakoumis E, Brunel M, Schmitz M

Fish Physiol Biochem 47 (4) 1283-1298 [2021-08-00; online 2021-07-08]

Genome Engineering Zebrafish [Service]

The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.

Kanellis DC, Espinoza JA, Zisi A, ..., Lindström MS, Bartek J

Sci Adv 7 (32) - [2021-08-00; online 2021-08-04]

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The effects of chemical and structural factors on the enzymatic saccharification of Eucalyptus sp. samples pre-treated by various technologies

Thoresen M, Malgas S, Gandla ML, ..., Sithole B, Pletschke BI

Industrial Crops and Products 166 (-) 113449 [2021-08-00; online 2021-08-00]

The Babytwins Study Sweden (BATSS): A Multi-Method Infant Twin Study of Genetic and Environmental Factors Influencing Infant Brain and Behavioral Development.

Falck-Ytter T, Hamrefors L, Siqueiros Sanches M, ..., Tammimies K, Ronald A

Twin Res Hum Genet 24 (4) 217-227 [2021-08-00; online 2021-09-15]

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Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).

Figueroa D, Capo E, Lindh MV, ..., Pinhassi J, Andersson A

Environ. Microbiol. 23 (8) 4200-4213 [2021-08-00; online 2021-06-01]

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Strong Associations Between Early Tubular Damage and Urinary Cytokine, Chemokine, and Growth Factor Levels in Elderly Males and Females.

Fellström B, Helmersson-Karlqvist J, Lind L, ..., Kultima K, Larsson A

Journal of Interferon & Cytokine Research 41 (8) 283-290 [2021-08-00; online 2021-08-20]

Serum profiling of anorexia nervosa: A 1H NMR-based metabolomics study.

Salehi M A, Nilsson IA, Figueira J, ..., Bulik CM, Landén M

Eur Neuropsychopharmacol 49 (-) 1-10 [2021-08-00; online 2021-03-18]

SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.

Guo M, Goudarzi KM, Abedi S, ..., Nistér M, Hägerstrand D

Oncogene 40 (32) 5066-5080 [2021-08-00; online 2021-05-21]

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SARS-CoV-2 infections amongst personnel providing home care services for older persons in Stockholm, Sweden.

Hassan SS, Seigerud Å, Abdirahman R, ..., Conneryd Lundgren K, Dillner J

J. Intern. Med. 290 (2) 430-436 [2021-08-00; online 2021-04-12]

Quantitative proteomic analysis to identify differentially expressed proteins in patients with epilepsy.

Banote RK, Larsson D, Berger E, Kumlien E, Zelano J

Epilepsy Res 174 (-) 106674 [2021-08-00; online 2021-05-15]

Plasma proteome alterations by MAPK inhibitors in BRAFV600-mutated metastatic cutaneous melanoma.

Babačić H, Eriksson H, Pernemalm M

Neoplasia 23 (8) 783-791 [2021-08-00; online 2021-07-08]

Optimization of droplet digital PCR assays for the type-specific detection and quantification of five HPV genotypes, including additional data on viral loads of nine different HPV genotypes in cervical carcinomas.

Malin K, Louise BM, Gisela H, Mats KG, Gabriella L

J Virol Methods 294 (-) 114193 [2021-08-00; online 2021-05-19]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Molecular architecture of the developing mouse brain.

La Manno G, Siletti K, Furlan A, ..., Lönnerberg P, Linnarsson S

Nature 596 (7870) 92-96 [2021-08-00; online 2021-07-28]

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Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.

Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M

Mol Ecol Resour 21 (6) 1833-1849 [2021-08-00; online 2021-05-06]

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Human MAIT cells endowed with HBV specificity are cytotoxic and migrate towards HBV-HCC while retaining antimicrobial functions.

Healy K, Pavesi A, Parrot T, ..., Bertoletti A, Sällberg Chen M

JHEP Rep 3 (4) 100318 [2021-08-00; online 2021-06-11]

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Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).

Nadachowska-Brzyska K, Dutoit L, Smeds L, ..., Gustafsson L, Ellegren H

Mol. Ecol. 30 (16) 3965-3973 [2021-08-00; online 2021-07-01]

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Genetic insights into biological mechanisms governing human ovarian ageing.

Ruth KS, Day FR, Hussain J, ..., Roig I, Perry JRB

Nature 596 (7872) 393-397 [2021-08-00; online 2021-08-04]

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Founder effects facilitate the use of a genotyping-based approach to molecular diagnosis in Swedish patients with familial hypercholesterolaemia.

Benedek P, Jiao H, Duvefelt K, ..., Eriksson M, Angelin B

J. Intern. Med. 290 (2) 404-415 [2021-08-00; online 2021-05-06]

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Electrochemical N2 reduction at ambient condition – Overcoming the selectivity issue via control of reactants’ availabilities

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International Journal of Hydrogen Energy 46 (59) 30366-30372 [2021-08-00; online 2021-08-00]

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Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

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Transl Oncol 14 (8) 101149 [2021-08-00; online 2021-06-09]

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Marco Salas S, Gyllborg D, Mattsson Langseth C, Nilsson M

BMC Bioinformatics 22 (1) 391 [2021-07-31; online 2021-07-31]

High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.

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Transl Psychiatry 11 (1) 413 [2021-07-30; online 2021-07-30]

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Bacterial Composition and Metabolomics of Dental Plaque From Adolescents.

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Neuroinflammation and Alzheimer's Disease: A Machine Learning Approach to CSF Proteomics.

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Complex population structure of the Atlantic puffin revealed by whole genome analyses.

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Commun Biol 4 (1) 922 [2021-07-29; online 2021-07-29]

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Unraveling negative biotic interactions determining soil microbial community assembly and functioning.

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Strong Associations between Plasma Osteopontin and Several Inflammatory Chemokines, Cytokines, and Growth Factors.

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Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.

Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC

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Metabolomics analysis for diagnosis and biomarker discovery of transthyretin amyloidosis.

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Amyloid - (-) 1-9 [2021-07-28; online 2021-07-28]

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Cell Death Dis 12 (8) 739 [2021-07-27; online 2021-07-27]

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Genome-scale metabolic network reconstruction of model animals as a platform for translational research.

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Proc. Natl. Acad. Sci. U.S.A. 118 (30) e2102344118 [2021-07-27; online 2021-07-21]

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Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy.

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Front Mol Biosci 8 (-) 713608 [2021-07-26; online 2021-07-26]

Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood.

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Sci Rep 11 (1) 15160 [2021-07-26; online 2021-07-26]

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Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.

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Curr. Biol. 31 (14) 2973-2983.e9 [2021-07-26; online 2021-05-18]

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Association between Cardiorespiratory Fitness and Circulating Proteins in 50-Year-Old Swedish Men and Women: a Cross-Sectional Study.

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Sports Med Open 7 (1) 52 [2021-07-26; online 2021-07-26]

The enigmatic RNase MRP of kinetoplastids.

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RNA Biol - (-) 1-9 [2021-07-25; online 2021-07-25]

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Identification of Novel Positive Allosteric Modulators of Neurotrophin Receptors for the Treatment of Cognitive Dysfunction.

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Cells 10 (8) - [2021-07-23; online 2021-07-23]

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The Promotor and Poison Effects of the Inorganic Elements of Kraft Lignin during Hydrotreatment over NiMoS Catalyst

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Catalysts 11 (8) 874 [2021-07-21; online 2021-07-21]

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Biochemistry 60 (28) 2246-2258 [2021-07-20; online 2021-07-12]

A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients.

Wendt C, Muranen TA, Mielikäinen L, ..., Borg Å, Lindblom A

Sci Rep 11 (1) 14763 [2021-07-20; online 2021-07-20]

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Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.

Hober S, Hellström C, Olofsson J, ..., Hedhammar M, Nilsson P

Clin Transl Immunology 10 (7) e1312 [2021-07-19; online 2021-07-19]

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DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome.

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Front Immunol 12 (-) 702037 [2021-07-16; online 2021-07-16]

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Large-scale serum analysis identifies unique systemic biomarkers in psoriasis and hidradenitis suppurativa.

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Br J Dermatol - (-) - [2021-07-13; online 2021-07-13]

Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis.

Grankvist A, Jaén-Luchoro D, Wass L, Sikora P, Wennerås C

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Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.

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Nat Commun 12 (1) 4253 [2021-07-12; online 2021-07-12]

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Computing the orientational-average of diffusion-weighted MRI signals: a comparison of different techniques.

Afzali M, Knutsson H, Özarslan E, Jones DK

Sci Rep 11 (1) 14345 [2021-07-12; online 2021-07-12]

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Wide-Ranging Effects on the Brain Proteome in a Transgenic Mouse Model of Alzheimer's Disease Following Treatment with a Brain-Targeting Somatostatin Peptide.

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ACS Chem Neurosci 12 (13) 2529-2541 [2021-07-07; online 2021-06-25]

Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy.

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Cancers (Basel) 13 (14) - [2021-07-07; online 2021-07-07]

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Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations.

Kerzeli IK, Lord M, Doroszko M, ..., Segersten U, Mangsbo SM

PLoS ONE 16 (7) e0253178 [2021-07-07; online 2021-07-07]

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Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.

Calleja-Rodriguez A, Chen Z, Suontama M, Pan J, Wu HX

Front Plant Sci 12 (-) 666820 [2021-07-07; online 2021-07-07]

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Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.

Kundu S, Ali MA, Handin N, ..., Globisch D, Sjöblom T

J. Exp. Clin. Cancer Res. 40 (1) 225 [2021-07-07; online 2021-07-07]

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The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades.

Hiltunen M, Ament-Velásquez SL, Johannesson H

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-05-30]

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Pharmacological activation of p53 triggers viral mimicry response thereby abolishing tumor immune evasion and promoting anti-tumor immunity.

Zhou X, Singh M, Sanz Santos G, ..., Johnsen JI, Selivanova G

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High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.

Zhang L, Steward RA, Wheat CW, Reed RD

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-07-21]

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Comparative Genomics Reveals Factors Associated with Phenotypic Expression of Wolbachia.

Baião GC, Janice J, Galinou M, Klasson L

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-05-19]

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Chick fetal organ spheroids as a model to study development and disease.

Dakhel S, Davies WIL, Joseph JV, ..., Remeseiro S, Gunhaga L

BMC Mol Cell Biol 22 (1) 37 [2021-07-05; online 2021-07-05]

Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.

Haas JC, Vergara A, Serrano AR, ..., Hurry V, Street NR

Tree Physiol 41 (7) 1230-1246 [2021-07-05; online 2021-01-09]

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Metabolic Profiling of Plasma in Patients with Irritable Bowel Syndrome after a 4-Week Starch- and Sucrose-Reduced Diet.

Stenlund H, Nilholm C, Chorell E, ..., D'Amato M, Ohlsson B

Metabolites 11 (7) - [2021-07-04; online 2021-07-04]

Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires.

Elfstrand M, Chen J, Cleary M, ..., Stadler M, Durling MB

BMC Genomics 22 (1) 503 [2021-07-04; online 2021-07-04]

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Real-world effectiveness of vedolizumab in inflammatory bowel disease: week 52 results from the Swedish prospective multicentre SVEAH study.

Eriksson C, Rundquist S, Lykiardopoulos V, ..., Halfvarson J, SWIBREG SVEAH Study Group

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Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer.

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Mol. Med. 27 (1) 68 [2021-07-03; online 2021-07-03]

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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.

Éliás S, Schmidt A, Gomez-Cabrero D, Tegnér J

J Immunol Res 2021 (-) 8880585 [2021-07-03; online 2021-07-03]

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High Amounts of SARS-CoV-2 Precede Sickness Among Asymptomatic Health Care Workers.

Dillner J, Elfström KM, Blomqvist J, ..., Arroyo Mühr LS, Lundgren KC

J. Infect. Dis. 224 (1) 14-20 [2021-07-02; online 2021-02-14]

TAAR1-Dependent and -Independent Actions of Tyramine in Interaction With Glutamate Underlie Central Effects of Monoamine Oxidase Inhibition.

Mantas I, Vallianatou T, Yang Y, ..., Andrén PE, Svenningsson P

Biol. Psychiatry 90 (1) 16-27 [2021-07-01; online 2020-12-19]

Structural determinants of multimerization and dissociation in 2-Cys peroxiredoxin chaperone function.

Troussicot L, Burmann BM, Molin M

Structure 29 (7) 640-654 [2021-07-01; online 2021-05-03]

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.

Jensen A, Lillie M, Bergström K, Larsson P, Höglund J

Heredity (Edinb) 127 (1) 79-91 [2021-07-00; online 2021-05-07]

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Variants in BANK1 are associated with lupus nephritis of European ancestry.

Bolin K, Imgenberg-Kreuz J, Leonard D, ..., Rönnblom L, Nordmark G

Genes Immun. 22 (3) 194-202 [2021-07-00; online 2021-06-14]

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Thermal proteome profiling identifies PIP4K2A and ZADH2 as off-targets of Polo-like kinase 1 inhibitor volasertib.

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Sci Adv 7 (27) - [2021-07-00; online 2021-07-02]

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The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.

Bakovic V, Martin Cerezo ML, Höglund A, ..., Hargeby A, Wright D

Mol. Ecol. 30 (14) 3530-3547 [2021-07-00; online 2021-06-08]

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The IgGFc-binding protein FCGBP is secreted with all GDPH sequences cleaved but maintained by interfragment disulfide bonds.

Ehrencrona E, van der Post S, Gallego P, ..., Hansson GC, Johansson MEV

J. Biol. Chem. 297 (1) 100871 [2021-07-00; online 2021-06-11]

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Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death.

Adolfsson E, Qvick A, Gréen H, ..., Jonasson J, Gréen A

Forensic Sci Int Genet 53 (-) 102522 [2021-07-00; online 2021-04-26]

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Synthetic bacterial vesicles combined with tumour extracellular vesicles as cancer immunotherapy.

Park KS, Svennerholm K, Crescitelli R, ..., Gribonika I, Lötvall J

J Extracell Vesicles 10 (9) e12120 [2021-07-00; online 2021-07-03]

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Spatial visualization of comprehensive brain neurotransmitter systems and neuroactive substances by selective in situ chemical derivatization mass spectrometry imaging.

Shariatgorji R, Nilsson A, Fridjonsdottir E, ..., Odell LR, Andrén PE

Nat Protoc 16 (7) 3298-3321 [2021-07-00; online 2021-06-02]

Single‐cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs

Pfisterer U, Bräunig J, Brattås P, ..., Karlsson G, Fioretos T

Genes Chromosomes Cancer 60 (7) 504-524 [2021-07-00; online 2021-03-15]

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Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.

Bartosovic M, Kabbe M, Castelo-Branco G

Nat. Biotechnol. 39 (7) 825-835 [2021-07-00; online 2021-04-12]

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Severe COVID-19 in an APS1 patient with interferon autoantibodies treated with plasmapheresis

Lemarquis A, Campbell T, Aranda-Guillén M, ..., Berg S, Ekwall O

Journal of Allergy and Clinical Immunology 148 (1) 96-98 [2021-07-00; online 2021-07-00]

STED and parallelized RESOLFT optical nanoscopy of the tubular endoplasmic reticulum and its mitochondrial contacts in neuronal cells

Damenti M, Coceano G, Pennacchietti F, Bodén A, Testa I

Neurobiology of Disease 155 (-) 105361 [2021-07-00; online 2021-07-00]

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Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.

Izabel-Shen D, Albert S, Winder M, Farnelid H, Nascimento FJA

Mol. Ecol. 30 (14) 3515-3529 [2021-07-00; online 2021-06-11]

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Plasma S1P (Sphingosine-1-Phosphate) Links to Hypertension and Biomarkers of Inflammation and Cardiovascular Disease: Findings From a Translational Investigation.

Jujic A, Matthes F, Vanherle L, ..., Magnusson M, Meissner A

Hypertension 78 (1) 195-209 [2021-07-00; online 2021-05-17]

On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).

Bachmann JA, Tedder A, Fracassetti M, ..., Köhler C, Slotte T

Heredity (Edinb) 127 (1) 124-134 [2021-07-00; online 2021-04-19]

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Non-uniform sampling for NOESY? A case study on spiramycin.

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Nicotinamide provides neuroprotection in glaucoma by protecting against mitochondrial and metabolic dysfunction.

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Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.

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Eur. Respir. J. 58 (1) 2003468 [2021-07-00; online 2021-07-22]

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Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin.

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J Extracell Vesicles 10 (9) e12128 [2021-07-00; online 2021-07-22]

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Trends Genet. 37 (7) 682-683 [2021-07-00; online 2021-05-11]

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Lack of diagnostic-escape mutants of group B streptococcus in Slovenia.

Perme T, Golparian D, Unemo M, Jeverica S

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Insights into the multitrophic interactions between the biocontrol agent Bacillus subtilis MBI 600, the pathogen Botrytis cinerea and their plant host.

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Microbiol Res 248 (-) 126752 [2021-07-00; online 2021-04-02]

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Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease.

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Am J Respir Cell Mol Biol 65 (1) 103-113 [2021-07-00; online 2021-04-01]

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High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.

Broman E, Bonaglia S, Norkko A, Creer S, Nascimento FJA

Mol. Ecol. 30 (13) 3023-3039 [2021-07-00; online 2020-08-19]

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HIV-Infected Individuals on ART With Impaired Immune Recovery Have Altered Plasma Metabolite Profiles.

Nyström S, Govender M, Yap SH, ..., Rajasuriar R, Larsson M

Open Forum Infect Dis 8 (7) ofab288 [2021-07-00; online 2021-06-02]

Genomic signatures of rapid adaptive divergence in a tropical montane species.

Ericson PGP, Irestedt M, She H, Qu Y

Biol. Lett. 17 (7) 20210089 [2021-07-00; online 2021-07-28]

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Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector.

Sekar V, Rivero A, Pigeault R, ..., Ahren D, Hellgren O

Genomics 113 (4) 2327-2337 [2021-07-00; online 2021-05-21]

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FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response.

Bogatyrova O, Mattsson JSM, Ross EM, ..., Esdar C, Micke P

Eur. J. Cancer 151 (-) 136-149 [2021-07-00; online 2021-05-10]

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Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish.

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Nat Ecol Evol 5 (7) 939-948 [2021-07-00; online 2021-05-06]

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Exercise training improves mitochondrial respiration and is associated with an altered intramuscular phospholipid signature in women with obesity.

Mendham AE, Goedecke JH, Zeng Y, ..., Olsson T, Chorell E

Diabetologia 64 (7) 1642-1659 [2021-07-00; online 2021-03-26]

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Cell 184 (15) 3884-3898.e11 [2021-07-00; online 2021-07-00]

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An ARHGAP25 variant links aberrant Rac1 function to early-onset skeletal fragility.

Mäkitie RE, Henning P, Jiu Y, ..., Lappalainen P, Mäkitie O

JBMR Plus 5 (7) e10509 [2021-07-00; online 2021-06-07]

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Sci Adv 7 (31) eabh2169 [2021-07-00; online 2021-07-28]

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A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest.

Lindahl BD, Kyaschenko J, Varenius K, ..., Karltun E, Stendahl J

Ecol. Lett. 24 (7) 1341-1351 [2021-07-00; online 2021-05-02]

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Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.

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Front Microbiol 12 (-) 693615 [2021-06-30; online 2021-06-30]

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DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.

Novotny A, Zamora-Terol S, Winder M

Proc. Biol. Sci. 288 (1953) 20210908 [2021-06-30; online 2021-06-16]

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Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells.

Huoman J, Martínez-Enguita D, Olsson E, ..., Gustafsson M, Jenmalm MC

Clin Epigenetics 13 (1) 135 [2021-06-30; online 2021-06-30]

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Proteomic Profiling of Tissue Exosomes Indicates Continuous Release of Malignant Exosomes in Urinary Bladder Cancer Patients, Even with Pathologically Undetectable Tumour.

Eldh M, Mints M, Hiltbrunner S, ..., Sherif A, Gabrielsson S

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Maccarana M, Tykesson E, Pera EM, ..., Ghiselli G, Li J

Glycobiology - (-) - [2021-06-29; online 2021-06-29]

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Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis.

Khademi SMH, Gabrielaite M, Paulsson M, ..., Marvig RL, Påhlman LI

mSystems - (-) e0052321 [2021-06-29; online 2021-06-29]

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Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging.

McCartney DL, Min JL, Richmond RC, ..., Horvath S, Marioni RE

Genome Biol. 22 (1) 194 [2021-06-29; online 2021-06-29]

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An Hsp90 co-chaperone links protein folding and degradation and is part of a conserved protein quality control.

Eisele F, Eisele-Bürger AM, Hao X, ..., Liu B, Nyström T

Cell Rep 35 (13) 109328 [2021-06-29; online 2021-07-01]

A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids.

Jhun M, Mendelson M, Wilson R, ..., Irvin MR, Assimes TL

Nat Commun 12 (1) 3987 [2021-06-28; online 2021-06-28]

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Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.

Bai X, Narayanan A, Nowak P, ..., Neogi U, Sönnerborg A

Front Microbiol 12 (-) 667718 [2021-06-25; online 2021-06-25]

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Li P, Wang K, Salustros N, Grønberg C, Gourdon P

Nat Commun 12 (1) 3973 [2021-06-25; online 2021-06-25]

Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.

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Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.

Chen J, Bi H, Pettersson ME, ..., Scheerer P, Andersson L

Commun Biol 4 (1) 795 [2021-06-25; online 2021-06-25]

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Does Anatomical Contextual Information Improve 3D U-Net-Based Brain Tumor Segmentation?

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Rasmusson AJ, Gallwitz M, Soltanabadi B, ..., Schiöth HB, Cunningham JL

Transl Psychiatry 11 (1) 371 [2021-06-24; online 2021-06-24]

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Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.

Singh A, Müller B, Schnürer A

Sci Rep 11 (1) 13298 [2021-06-24; online 2021-06-24]

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COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.

Simonetti M, Zhang N, Harbers L, ..., Ghisetti V, Crosetto N

Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]

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The γ-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.

Corvaisier M, Zhou J, Malycheva D, ..., Lindström L, Alvarado-Kristensson M

Commun Biol 4 (1) 767 [2021-06-22; online 2021-06-22]

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Characterization of Individual Projections Reveal That Neuromasts of the Zebrafish Lateral Line are Innervated by Multiple Inhibitory Efferent Cells.

Manuel R, Iglesias Gonzalez AB, Habicher J, Koning HK, Boije H

Front Neuroanat 15 (-) 666109 [2021-06-21; online 2021-06-21]

Genome Engineering Zebrafish

A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism.

Melo GA, Abreu IN, de Oliveira MB, ..., Pimenta MAS, Moritz T

Sci Rep 11 (1) 12933 [2021-06-21; online 2021-06-21]

Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion.

Sork H, Conceicao M, Corso G, ..., El Andaloussi S, Mäger I

Cells 10 (6) 1543 [2021-06-18; online 2021-06-18]

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Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici.

Samils B, Andersson B, Edin E, ..., Hellin P, Kildea S

Front Microbiol 12 (-) 692845 [2021-06-18; online 2021-06-18]

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Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.

Roxhed N, Bendes A, Dale M, ..., Fredolini C, Schwenk JM

Nat Commun 12 (1) 3695 [2021-06-17; online 2021-06-17]

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Cooperativity of α-Synuclein Binding to Lipid Membranes.

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ACS Chem Neurosci 12 (12) 2099-2109 [2021-06-16; online 2021-06-02]

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Hartvigsson O, Barman M, Rabe H, ..., Brunius C, Sandberg AS

Sci Rep 11 (1) 12706 [2021-06-16; online 2021-06-16]

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Transcription factor FOXP2 is a flow-induced regulator of collecting lymphatic vessels.

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EMBO J. 40 (12) e107192 [2021-06-15; online 2021-05-02]

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Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury.

Abu Hamdeh S, Ciuculete DM, Sarkisyan D, ..., Schiöth HB, Marklund N

J. Neurotrauma 38 (12) 1679-1688 [2021-06-15; online 2021-01-08]

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Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data.

Khakzad H, Happonen L, Malmström J, Malmström L

Bioinformatics - (-) - [2021-06-15; online 2021-06-15]

Guve, Ygle och Rane DNA-analyser löser frågan om släktskap

Arcini C, Hedvall R

Arkeologi i Östergötland - (1) 46-47 [2021-06-14]

Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.

Morris ERA, Boyle AG, Riihimäki M, ..., Pringle J, Cohen ND

PLoS ONE 16 (6) e0252804 [2021-06-14; online 2021-06-14]

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Cyclotide host-defense tailored for species and environments in violets from the Canary Islands.

Slazak B, Kaltenböck K, Steffen K, ..., Andrén PE, Göransson U

Sci Rep 11 (1) 12452 [2021-06-14; online 2021-06-14]

Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.

Chen ZQ, Zan Y, Milesi P, ..., Lascoux M, Wu HX

Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]

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Impaired Luminal Control of Intestinal Macrophage Maturation in Patients With Ulcerative Colitis During Remission.

Maasfeh L, Härtlova A, Isaksson S, ..., Öhman L, Magnusson MK

Cellular and Molecular Gastroenterology and Hepatology 12 (4) 1415-1432 [2021-06-12; online 2021-06-12]

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Bead-Based Assays for Validating Proteomic Profiles in Body Fluids.

Bendes A, Dale M, Mattsson C, ..., Schwenk JM, Fredolini C

Methods Mol. Biol. 2344 (-) 65-78 [2021-06-12; online 2021-06-12]

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Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.

Crowe-McAuliffe C, Murina V, Turnbull KJ, ..., Hauryliuk V, Wilson DN

Nat Commun 12 (1) 3577 [2021-06-11; online 2021-06-11]

Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa.

Meidl P, Furneaux B, Tchan KI, ..., Yorou NS, Rosling A

MycoKeys 81 (-) 45-68 [2021-06-11; online 2021-06-11]

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DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).

Krali O, Palle J, Bäcklin CL, ..., Zeller B, Nordlund J

Genes 12 (6) 895 [2021-06-10; online 2021-06-10]

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Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies.

Begnini F, Poongavanam V, Atilaw Y, ..., Schiesser S, Kihlberg J

ACS Med Chem Lett 12 (6) 983-990 [2021-06-10; online 2021-05-18]

A Distinct Faecal Microbiota and Metabolite Profile Linked to Bowel Habits in Patients with Irritable Bowel Syndrome.

Ahluwalia B, Iribarren C, Magnusson MK, ..., Simrén M, Öhman L

Cells 10 (6) - [2021-06-10; online 2021-06-10]

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Silica Particles Trigger the Exopolysaccharide Production of Harsh Environment Isolates of Growth-Promoting Rhizobacteria and Increase Their Ability to Enhance Wheat Biomass in Drought-Stressed Soils.

Fetsiukh A, Conrad J, Bergquist J, Timmusk S

Int J Mol Sci 22 (12) 6201 [2021-06-08; online 2021-06-08]

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.

Gustafsson J, Robinson J, Nielsen J, Pachter L

Genome Biol. 22 (1) 174 [2021-06-08; online 2021-06-08]

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Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

Yaka R, Mapelli I, Kaptan D, ..., Özer F, Somel M

Curr. Biol. 31 (11) 2455-2468.e18 [2021-06-07; online 2021-04-14]

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Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation.

Karampelias C, Rezanejad H, Rosko M, ..., Korbutt GS, Andersson O

Nat Commun 12 (1) 3362 [2021-06-07; online 2021-06-07]

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Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.

de Rojas I, Moreno-Grau S, Tesi N, ..., van der Lee SJ, Ruiz A

Nat Commun 12 (1) 3417 [2021-06-07; online 2021-06-07]

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Osteoprotegerin predicts cardiovascular events in patients treated with hemodialysis.

Wu PH, Glerup RI, Svensson MHS, ..., Ljunggren Ö, Fellström B

Nephrol Dial Transplant - (-) - [2021-06-04; online 2021-06-04]

Machine learning for cell classification and neighborhood analysis in glioma tissue.

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Cytometry A - (-) - [2021-06-04; online 2021-06-04]

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Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing.

Walcher L, Kistenmacher AK, Sommer C, ..., Dünkel A, Fricke S

Front Immunol 12 (-) 684052 [2021-06-04; online 2021-06-04]

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CryoEM reveals BIN1 (isoform 8) does not bind to single actin filaments in vitro.

Wang Z, Mim C

MicroPubl Biol 2021 (-) - [2021-06-04; online 2021-06-04]

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172.

Tõlgo M, Hüttner S, Rugbjerg P, ..., Larsbrink J, Olsson L

Biotechnol Biofuels 14 (1) 131 [2021-06-03; online 2021-06-03]

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EBF1 and PAX5 control pro-B cell expansion via opposing regulation of the Myc gene.

Somasundaram R, Jensen CT, Tingvall-Gustafsson J, ..., Ungerbäck J, Sigvardsson M

Blood 137 (22) 3037-3049 [2021-06-03; online 2021-02-24]

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Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.

Friess L, Cheray M, Keane L, Grabert K, Joseph B

Mol Brain 14 (1) 87 [2021-06-03; online 2021-06-03]

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RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.

Avican K, Aldahdooh J, Togninalli M, ..., Rhen M, Fällman M

Nat Commun 12 (1) 3282 [2021-06-02; online 2021-06-02]

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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).

Eriksson JS, Bacon CD, Bennett DJ, ..., Oxelman B, Antonelli A

BMC Ecol Evol 21 (1) 107 [2021-06-02; online 2021-06-02]

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B Lymphocyte Specification Is Preceded by Extensive Epigenetic Priming in Multipotent Progenitors.

Strid T, Okuyama K, Tingvall-Gustafsson J, ..., Ungerbäck J, Sigvardsson M

J. Immunol. 206 (11) 2700-2713 [2021-06-01; online 2021-05-21]

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Variation in the SERPINA6/SERPINA1 locus alters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expression in peripheral tissues, and risk of cardiovascular disease.

Crawford AA, Bankier S, Altmaier E, ..., Walker BR, CORtisol NETwork (CORNET) consortium

J. Hum. Genet. 66 (6) 625-636 [2021-06-00; online 2021-01-20]

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Urokinase, CX3CL1, CCL2, TRAIL and IL-18 induced by interferon-β treatment.

Zhukovsky C, Herman S, Wiberg A, ..., Kultima K, Burman J

Acta Neurol. Scand. 143 (6) 602-607 [2021-06-00; online 2021-02-24]

The trans-ancestral genomic architecture of glycemic traits.

Chen J, Spracklen CN, Marenne G, ..., Barroso I, Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC)

Nat. Genet. 53 (6) 840-860 [2021-06-00; online 2021-05-31]

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The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases.

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Targeting the NS2B-NS3 protease of tick-borne encephalitis virus with pan-flaviviral protease inhibitors.

Akaberi D, Båhlström A, Chinthakindi PK, ..., Lundkvist Å, Lennerstrand J

Antiviral Res. 190 (-) 105074 [2021-06-00; online 2021-04-16]

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Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells

Mathew NR, Jayanthan JK, Smirnov IV, ..., Bemark M, Angeletti D

Cell Rep 35 (12) 109286 [2021-06-00; online 2021-06-00]

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Krzewińska M, Rodríguez-Varela R, Ahlström Arcini C, ..., Storå J, Götherström A

Journal of Archaeological Science: Reports 37 (-) 102939 [2021-06-00; online 2021-06-00]

RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children.

Chen D, Camponeschi A, Nordlund J, ..., Fogelstrand L, Mårtensson IL

Cancer Med 10 (12) 3997-4003 [2021-06-00; online 2021-05-13]

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Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.

Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Kular L

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Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress.

Mishra LS, Kim SY, Caddell DF, Coleman-Derr D, Funk C

Physiol Plantarum 172 (2) 1045-1058 [2021-06-00; online 2020-12-16]

Large-scale identification of protein histidine methylation in human cells.

Kapell S, Jakobsson ME

NAR Genom Bioinform 3 (2) lqab045 [2021-06-00; online 2021-05-22]

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JAK/STAT inhibition augments soleus muscle function in a rat model of critical illness myopathy via regulation of complement C3/3R.

Addinsall AB, Cacciani N, Akkad H, ..., Kirkland JL, Larsson L

J Physiol 599 (11) 2869-2886 [2021-06-00; online 2021-05-02]

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High Sensitivity Detection of a Solubility Limiting Surface Transformation of Drug Particles by DNP SENS.

Viger-Gravel J, Pinon AC, Björgvinsdóttir S, ..., Schantz S, Emsley L

J Pharm Sci 110 (6) 2452-2456 [2021-06-00; online 2021-01-06]

Genomic and fitness consequences of inbreeding in an endangered carnivore.

Hasselgren M, Dussex N, von Seth J, ..., Dalén L, Norén K

Mol. Ecol. 30 (12) 2790-2799 [2021-06-00; online 2021-05-20]

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Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.

Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A

Mar Biotechnol (NY) 23 (3) 402-416 [2021-06-00; online 2021-05-01]

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Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.

de Las Fuentes L, Sung YJ, Noordam R, ..., Rao DC, Fornage M

Mol. Psychiatry 26 (6) 2111-2125 [2021-06-00; online 2020-05-05]

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Following spatial Aβ aggregation dynamics in evolving Alzheimer's disease pathology by imaging stable isotope labeling kinetics.

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Sci Adv 7 (25) - [2021-06-00; online 2021-06-16]

Integrated Microscopy Technologies Gothenburg [Collaborative]

ENABLE: an engine for European antibacterial drug discovery and development.

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DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan.

van Dongen J, Hagenbeek FA, Suderman M, ..., Bartels M, Boomsma DI

Mol. Psychiatry 26 (6) 2148-2162 [2021-06-00; online 2021-01-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Correction to: Deciphering the genetic and epidemiological landscape of mitochondrial DNA abundance.

Hägg S, Jylhävä J, Wang Y, Czene K, Grassmann F

Hum. Genet. 140 (6) 863 [2021-06-00; online 2021-02-07]

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Combinations of dietary calcium intake and mediterranean-style diet on risk of hip fracture: A longitudinal cohort study of 82,000 women and men.

Warensjö Lemming E, Byberg L, Höijer J, ..., Wolk A, Michaëlsson K

Clin Nutr 40 (6) 4161-4170 [2021-06-00; online 2021-02-05]

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Cancer diagnostics based on plasma protein biomarkers: hard times but great expectations.

Landegren U, Hammond M

Mol Oncol 15 (6) 1715-1726 [2021-06-00; online 2020-11-17]

CO2 fertilization of Sphagnum peat mosses is modulated by water table level and other environmental factors.

Serk H, Nilsson MB, Figueira J, Wieloch T, Schleucher J

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Jabbar KS, Dolan B, Eklund L, ..., Simren M, Hansson GC

Gut 70 (6) 1117-1129 [2021-06-00; online 2020-11-11]

Integrated Microscopy Technologies Gothenburg [Service]

Klevebro S, Björkander S, Ekström S, ..., Bergström A, Melén E

Sci Rep 11 (1) 11391 [2021-05-31; online 2021-05-31]

NK cells integrate signals over large areas when building immune synapses but require local stimuli for degranulation.

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Sci Signal 14 (684) eabe2740 [2021-05-25; online 2021-05-25]

Integrated Microscopy Technologies Stockholm [Service]

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.

Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F

Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.

Mold JE, Modolo L, Hård J, ..., Michaëlsson J, Frisén J

Cell Rep 35 (8) 109174 [2021-05-25; online 2021-05-27]

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A combined approach for single-cell mRNA and intracellular protein expression analysis.

Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ

Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]

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Trailblazing precision medicine in Europe: A joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany.

Stenzinger A, Edsjö A, Ploeger C, ..., Rosenquist R, GMS working groups and ZPM working groups

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Clinical Genomics [Service] Clinical Genomics Lund [Service] Clinical Genomics Stockholm [Collaborative] Clinical Genomics Uppsala [Collaborative]

Crystal structure of a homotrimeric verrucomicrobial exo-β-1,4-mannosidase active in the hindgut of the wood-feeding termite Reticulitermes flavipes.

Kalyani DC, Reichenbach T, Keskitalo MM, ..., Aspeborg H, Divne C

Journal of Structural Biology: X 5 (-) 100048 [2021-05-24; online 2021-05-24]

Adsorption of bio-organic eco-corona molecules reduces the toxic response to metallic nanoparticles in Daphnia magna.

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Sci Rep 11 (1) 10784 [2021-05-24; online 2021-05-24]

Stromal Heterogeneity in the Human Proliferative Endometrium-A Single-Cell RNA Sequencing Study.

Queckbörner S, von Grothusen C, Boggavarapu NR, ..., Davies LC, Gemzell-Danielsson K

J Pers Med 11 (6) - [2021-05-22; online 2021-05-22]

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Towards a bioengineered uterus: bioactive sheep uterus scaffolds are effectively recellularized by enzymatic preconditioning.

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NPJ Regen Med 6 (1) 26 [2021-05-21; online 2021-05-21]

Integrated Microscopy Technologies Gothenburg [Service]

Pharmacodynamic Evaluation of Dosing, Bacterial Kill, and Resistance Suppression for Zoliflodacin Against Neisseria gonorrhoeae in a Dynamic Hollow Fiber Infection Model.

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Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry.

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Front Vet Sci 8 (-) 642085 [2021-05-20; online 2021-05-20]

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Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe.

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Nat Commun 12 (1) 2983 [2021-05-20; online 2021-05-20]

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Complement-Opsonized HIV Modulates Pathways Involved in Infection of Cervical Mucosal Tissues: A Transcriptomic and Proteomic Study.

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Front Immunol 12 (-) 625649 [2021-05-20; online 2021-05-20]

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Which image-based phenotypes are most promising for using AI to understand cellular functions and why?

Lundberg E, Funke J, Uhlmann V, ..., Carpenter A, Coehlo LP

Cell Syst 12 (5) 384-387 [2021-05-19; online 2021-05-21]

Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex.

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Mol. Biol. Evol. 38 (6) 2475-2492 [2021-05-19; online 2021-02-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Integration of Mass Spectrometry Imaging and Machine Learning Visualizes Region-Specific Age-Induced and Drug-Target Metabolic Perturbations in the Brain.

Vallianatou T, Shariatgorji R, Nilsson A, ..., Svenningsson P, Andrén PE

ACS Chem Neurosci 12 (10) 1811-1823 [2021-05-19; online 2021-05-03]

X-chromosome variants are associated with aldosterone producing adenomas.

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Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18]

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Symptoms and Functional Impairment Assessed 8 Months After Mild COVID-19 Among Health Care Workers.

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JAMA 325 (19) 2015-2016 [2021-05-18; online 2021-04-08]

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Factors Affecting Detoxification of Softwood Enzymatic Hydrolysates Using Sodium Dithionite

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Processes 9 (5) 887 [2021-05-18; online 2021-05-18]

Phage Biocontrol of Pseudomonas aeruginosa in Water.

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Viruses 13 (5) 928 [2021-05-17; online 2021-05-17]

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Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.

Jönsson E, Ljung L, Norrman E, ..., Dahlqvist J, Dahlqvist SR

Rheumatology (Oxford) - (-) - [2021-05-16; online 2021-05-16]

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A plasma lipid signature predicts incident coronary artery disease.

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Int. J. Cardiol. 331 (-) 249-254 [2021-05-15; online 2021-02-03]

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Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.

Buck M, Garcia SL, Fernandez L, ..., Bertilsson S, Peura S

Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium.

Salvà-Serra F, Donoso RA, Cho KH, ..., Moore ERB, Pérez-Pantoja D

Microbiol Resour Announc 10 (19) - [2021-05-13; online 2021-05-13]

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Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.

Wojewodzic MW, Leithaug M, Lauritzen M, ..., Grotmol T, Rounge TB

Clin Epigenetics 13 (1) 107 [2021-05-12; online 2021-05-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy.

Hellberg S, Raffetseder J, Rundquist O, ..., Ernerudh J, Gustafsson M

Front Immunol 12 (-) 672168 [2021-05-12; online 2021-05-12]

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Highly Permeable Fluorinated Polymer Nanocomposites for Plasmonic Hydrogen Sensing.

Östergren I, Pourrahimi AM, Darmadi I, ..., Langhammer C, Müller C

ACS Appl Mater Interfaces 13 (18) 21724-21732 [2021-05-12; online 2021-04-28]

Integrated Microscopy Technologies Gothenburg [Service]

Dynamics of Auxin and Cytokinin Metabolism during Early Root and Hypocotyl Growth in Theobroma cacao.

Mboene Noah A, Casanova-Sáez R, Makondy Ango RE, ..., Niemenak N, Ljung K

Plants (Basel) 10 (5) - [2021-05-12; online 2021-05-12]

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.

Garcia SL, Mehrshad M, Buck M, ..., Greening C, Peura S

mSystems 6 (3) - [2021-05-11; online 2021-05-11]

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PubMed

[Precision diagnostics and therapy in hematological malignancies].

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Lakartidningen 118 (-) - [2021-05-10; online 2021-05-10]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP.

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BMC Biol. 19 (1) 98 [2021-05-10; online 2021-05-10]

African and Asian leopards are highly differentiated at the genomic level.

Paijmans JLA, Barlow A, Becker MS, ..., Manica A, Hofreiter M

Curr. Biol. 31 (9) 1872-1882.e5 [2021-05-10; online 2021-04-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Genomic Architecture and Evolutionary Fates of Supergenes.

Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-20]

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The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan.

Hollfelder N, Babiker H, Granehäll L, Schlebusch CM, Jakobsson M

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]

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The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.

Boman J, Mugal CF, Backström N

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]

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Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance.

De Marchi T, Pyl PT, Sjöström M, ..., Malmström L, Niméus E

J. Proteome Res. 20 (5) 2983-3001 [2021-05-07; online 2021-04-15]

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Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.

Morgell A, Reisz JA, Ateeb Z, ..., Chen MS, D'Alessandro A

J. Proteome Res. 20 (5) 2725-2738 [2021-05-07; online 2021-03-15]

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INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.

Yadav VK, Santos-González J, Köhler C

Nucleic Acids Res. 49 (8) 4371-4385 [2021-05-07; online 2021-03-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality.

Schunk SJ, Kleber ME, März W, ..., eQTLGen consortium , BIOS consortium

Eur. Heart J. 42 (18) 1742-1756 [2021-05-07; online 2021-03-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).

Celorio-Mancera MP, Rastas P, Steward RA, Nylin S, Wheat CW

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-23]

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Serine Protease HTRA1 as a Novel Target Antigen in Primary Membranous Nephropathy.

Al-Rabadi LF, Caza T, Trivin-Avillach C, ..., Larsen C, Beck LH

J. Am. Soc. Nephrol. 32 (7) 1666-1681 [2021-05-05; online 2021-05-05]

Plasma Protein Profile of Carotid Artery Atherosclerosis and Atherosclerotic Outcomes: Meta-Analyses and Mendelian Randomization Analyses.

Lind L, Gigante B, Borné Y, ..., Engström G, Mälarstig A

Arterioscler. Thromb. Vasc. Biol. 41 (5) 1777-1788 [2021-05-05; online 2021-03-04]

The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns.

Seeger C, Dyrhage K, Mahajan M, ..., Lind SB, Andersson SGE

Front Microbiol 12 (-) 643045 [2021-05-04; online 2021-05-04]

How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent.

Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ

Mol. Biol. Evol. 38 (5) 1715-1730 [2021-05-04; online 2020-11-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.

Talibov VO, Fabini E, FitzGerald EA, ..., Del Rio A, Danielson UH

ChemBioChem 22 (9) 1597-1608 [2021-05-04; online 2021-02-11]

False Positive Results in SARS-CoV-2 Serological Tests for Samples From Patients With Chronic Inflammatory Diseases.

Kharlamova N, Dunn N, Bedri SK, ..., Fink K, Fogdell-Hahn A

Front Immunol 12 (-) 666114 [2021-05-03; online 2021-05-03]

Activation of endogenous retroviruses during brain development causes an inflammatory response.

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EMBO J. 40 (9) e106423 [2021-05-03; online 2021-03-01]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Lund [Service]

The transcriptome-wide landscape of molecular subtype-specific mRNA expression profiles in acute myeloid leukemia.

Mou T, Pawitan Y, Stahl M, ..., Lehtiö J, Vu TN

Am. J. Hematol. 96 (5) 580-588 [2021-05-01; online 2021-03-10]

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Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.

Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J

Cell Res 31 (5) 554-568 [2021-05-00; online 2021-01-08]

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The association between genetically determined ABO blood types and major depressive disorder.

Garvert L, Baune BT, Berger K, ..., Grabe HJ, Van der Auwera S

Psychiatry Res 299 (-) 113837 [2021-05-00; online 2021-02-24]

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The Enterprise, a massive transposon carrying Spok meiotic drive genes.

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Genome Res. 31 (5) 789-798 [2021-05-00; online 2021-04-19]

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Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals.

Lihavainen J, Edlund E, Björkén L, ..., Robinson KM, Jansson S

Physiol Plantarum 172 (1) 201-217 [2021-05-00; online 2021-01-07]

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Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.

Kameneva P, Artemov AV, Kastriti ME, ..., Kharchenko PV, Adameyko I

Nat. Genet. 53 (5) 694-706 [2021-05-00; online 2021-04-08]

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Serum metabolomic profiling correlated with ISS and clinical outcome for multiple myeloma patients treated with high-dose melphalan and autologous stem cell transplantation.

Veskovski L, Andersson PO, Turesson I, ..., Pedersen A, Mellqvist UH

Exp Hematol 97 (-) 79-88.e8 [2021-05-00; online 2021-02-18]

Self-generation of low ash carbon microspheres from the hydrothermal supernatant of anaerobic digestate: Formation insights and supercapacitor performance

Latham KG, Kozyatnyk I, Figueira J, ..., Rosenbaum E, Jansson S

Chemical Engineering Journal Advances 6 (-) 100097 [2021-05-00; online 2021-05-00]

Prediction of complex phenotypes using the Drosophila melanogaster metabolome.

Rohde PD, Kristensen TN, Sarup P, Muñoz J, Malmendal A

Heredity (Edinb) 126 (5) 717-732 [2021-05-00; online 2021-01-28]

Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.

Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S

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In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.

Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O

Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]

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ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.

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Curr Protoc 1 (5) e89 [2021-05-00; online 2021-05-27]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Ibrutinib Has Time-dependent On- and Off-target Effects on Plasma Biomarkers and Immune Cells in Chronic Lymphocytic Leukemia.

Mulder TA, Peña-Pérez L, Berglöf A, ..., Smith CIE, Palma M

Hemasphere 5 (5) e564 [2021-05-00; online 2021-04-26]

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Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.

Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A

Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]

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Histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes.

Granlund L, Hedin A, Wahlhütter M, ..., Skog O, Lundberg M

BMJ Open Diabetes Res Care 9 (1) - [2021-05-00; online 2021-05-26]

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Genetic basis of lacunar stroke: a pooled analysis of individual patient data and genome-wide association studies.

Traylor M, Persyn E, Tomppo L, ..., UK DNA Lacunar Stroke Study Investigators , International Stroke Genetics Consortium

Lancet Neurol 20 (5) 351-361 [2021-05-00; online 2021-03-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Examination of how variations in lignin properties from Kraft and organosolv extraction influence the physicochemical characteristics of hydrothermal carbon

Latham KG, Matsakas L, Figueira J, ..., Christakopoulos P, Jansson S

Journal of Analytical and Applied Pyrolysis 155 (-) 105095 [2021-05-00; online 2021-05-00]

Evidence for discrete modes of YAP1 signaling via mRNA splice isoforms in development and diseases.

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Effects of liraglutide on the metabolism of triglyceride‐rich lipoproteins in type 2 diabetes

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Diabetes Obes Metab 23 (5) 1191-1201 [2021-05-00; online 2021-03-05]

Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.

Sandholt AKS, Xu F, Söderlund R, ..., Svärd SG, Wattrang E

Parasitology 148 (6) 712-725 [2021-05-00; online 2021-02-04]

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Dissolution of wood components during hot water extraction of birch

Wojtasz-Mucha J, Hasani M, Theliander H

Wood Sci Technol 55 (3) 811-835 [2021-05-00; online 2021-04-05]

Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.

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Thromb. Haemost. 121 (5) 573-583 [2021-05-00; online 2020-11-17]

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Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes.

Sahlén P, Spalinskas R, Asad S, ..., Bradley M, Tapia-Páez I

J. Allergy Clin. Immunol. 147 (5) 1742-1752 [2021-05-00; online 2020-10-16]

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Binding of the human antioxidation protein α1-microglobulin (A1M) to heparin and heparan sulfate. Mapping of binding site, molecular and functional characterization, and co-localization in vivo and in vitro.

Bergwik J, Kristiansson A, Larsson J, ..., Åkerström B, Allhorn M

Redox Biol 41 (-) 101892 [2021-05-00; online 2021-02-10]

Association of Epicardial Fat Volume With the Extent of Coronary Atherosclerosis and Cardiovascular Adverse Events in Asymptomatic Patients With Diabetes.

Venuraju SM, Lahiri A, Jeevarethinam A, ..., Shah PK, Nilsson J

Angiology 72 (5) 442-450 [2021-05-00; online 2021-01-20]

Association between inflammasome-related polymorphisms and psoriatic arthritis.

Juneblad K, Kastbom A, Johansson L, ..., Söderkvist P, Alenius G

Scand. J. Rheumatol. 50 (3) 206-212 [2021-05-00; online 2020-12-10]

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An amylin and calcitonin receptor agonist modulates alcohol behaviors by acting on reward-related areas in the brain.

Kalafateli AL, Satir TM, Vallöf D, Zetterberg H, Jerlhag E

Prog Neurobiol 200 (-) 101969 [2021-05-00; online 2020-12-02]

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A chemical screen for modulators of mRNA translation identifies a distinct mechanism of toxicity for sphingosine kinase inhibitors.

Corman A, Kanellis DC, Michalska P, ..., Carreras-Puigvert J, Fernandez-Capetillo O

PLoS Biol. 19 (5) e3001263 [2021-05-00; online 2021-05-25]

Chemical Biology Consortium Sweden (CBCS) [Service]

Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists.

Martins GG, Cordelières FP, Colombelli J, ..., Tinevez JY, Miura K

F1000Res 10 (-) 334 [2021-04-30; online 2021-04-30]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden.

Saxenborn P, Baxter J, Tilevik A, ..., Enroth H, Tilevik D

Front Microbiol 12 (-) 640408 [2021-04-30; online 2021-04-30]

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Subcellular proteomics.

Christopher JA, Stadler C, Martin CE, ..., Emili A, Lilley KS

Nat Rev Methods Primers 1 (1) - [2021-04-29; online 2021-04-29]

Immune-Associated Proteins Are Enriched in Lung Tissue-Derived Extracellular Vesicles during Allergen-Induced Eosinophilic Airway Inflammation.

Lässer C, Kishino Y, Park KS, ..., Rådinger M, Lötvall J

Int J Mol Sci 22 (9) - [2021-04-29; online 2021-04-29]

Complete Genome Sequence of an Antimicrobial-Producing Bacillus velezensis Sam8H1 Isolate from the Makgadikgadi Saltpans of Botswana.

Modikwe G, Manoharan L, Mabutho G, ..., Lebogang L, Zhou N

Microbiol Resour Announc 10 (17) - [2021-04-29; online 2021-04-29]

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Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain.

Säll O, Stenmark B, Jacobsson S, ..., Sundqvist M, Mölling P

Epidemiol. Infect. 149 (-) e126 [2021-04-29; online 2021-04-29]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

How Does Liquid-Liquid Phase Separation in Model Membranes Reflect Cell Membrane Heterogeneity?

Sych T, Gurdap CO, Wedemann L, Sezgin E

Membranes 11 (5) 323 [2021-04-28; online 2021-04-28]

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Genome-wide CRISPR screens reveal synthetic lethal interaction between CREBBP and EP300 in diffuse large B-cell lymphoma.

Nie M, Du L, Ren W, ..., Zhang F, Pan-Hammarström Q

Cell Death Dis 12 (5) 419 [2021-04-28; online 2021-04-28]

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Cyanophage Diversity and Community Structure in Dead Zone Sediments.

Broman E, Holmfeldt K, Bonaglia S, Hall POJ, Nascimento FJA

mSphere 6 (2) - [2021-04-28; online 2021-04-28]

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Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.

Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]

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Neutron reflectometry and NMR spectroscopy of full-length Bcl-2 protein reveal its membrane localization and conformation.

Mushtaq AU, Ådén J, Clifton LA, ..., Sparrman T, Gröbner G

Commun Biol 4 (1) 507 [2021-04-27; online 2021-04-27]

An introgressed gene causes meiotic drive in Neurospora sitophila.

Svedberg J, Vogan AA, Rhoades NA, ..., Hammond TM, Johannesson H

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2026605118 [2021-04-27; online 2021-04-21]

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Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.

Barlow A, Paijmans JLA, Alberti F, ..., Baryshnikov G, Hofreiter M

Curr. Biol. 31 (8) 1771-1779.e7 [2021-04-26; online 2021-02-15]

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Live Cell FRET Imaging Reveals Amyloid β-Peptide Oligomerization in Hippocampal Neurons.

Gao Y, Wennmalm S, Winblad B, Schedin-Weiss S, Tjernberg LO

Int J Mol Sci 22 (9) 4530 [2021-04-26; online 2021-04-26]

Integrated Microscopy Technologies Stockholm [Service]

Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.

von Seth J, Dussex N, Díez-Del-Molino D, ..., Götherström A, Dalén L

Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]

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Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C.

Wallerstein J, Ekberg V, Ignjatović MM, ..., Ryde U, Akke M

JACS Au 1 (4) 484-500 [2021-04-26; online 2021-04-01]

Bioimage analysis workflows: community resources to navigate through a complex ecosystem.

Paul-Gilloteaux P, Tosi S, Hériché JK, ..., Miura K, Colombelli J

F1000Res 10 (-) 320 [2021-04-26; online 2021-04-26]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy.

Seguin-Orlando A, Costedoat C, Der Sarkissian C, ..., Signoli M, Orlando L

iScience 24 (4) 102383 [2021-04-23; online 2021-03-31]

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Divergent airway microbiomes in lung transplant recipients with or without pulmonary infection.

Påhlman LI, Manoharan L, Aspelund AS

Respir. Res. 22 (1) 118 [2021-04-23; online 2021-04-23]

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Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.

Mattsson L, Sörenson E, Capo E, ..., Lindehoff E, Legrand C

Front Bioeng Biotechnol 9 (-) 651895 [2021-04-22; online 2021-04-22]

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Epigenome-wide association study of level and change in cognitive abilities from midlife through late life.

Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Pedersen NL

Clin Epigenetics 13 (1) 85 [2021-04-21; online 2021-04-21]

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Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture.

Wahlgren WY, Golonka D, Westenhoff S, Möglich A

Front Plant Sci 12 (-) 663751 [2021-04-21; online 2021-04-21]

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Alternative redox forms of ASNA-1 separate insulin signaling from tail-anchored protein targeting and cisplatin resistance in C. elegans.

Raj D, Billing O, Podraza-Farhanieh A, ..., Kao G, Naredi P

Sci Rep 11 (1) 8678 [2021-04-21; online 2021-04-21]

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smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites.

Persson Hodén K, Hu X, Martinez G, Dixelius C

Int J Mol Sci 22 (8) 4267 [2021-04-20; online 2021-04-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders.

Gillentine MA, Wang T, Hoekzema K, ..., Bernier RA, Eichler EE

Genome Med 13 (1) 63 [2021-04-19; online 2021-04-19]

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Phenological shifts in lake stratification under climate change.

Woolway RI, Sharma S, Weyhenmeyer GA, ..., Thiery W, Jennings E

Nat Commun 12 (1) 2318 [2021-04-19; online 2021-04-19]

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A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.

Sánchez-Busó L, Yeats CA, Taylor B, ..., Unemo M, Aanensen DM

Genome Med 13 (1) 61 [2021-04-19; online 2021-04-19]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

Gong B, Li D, Kusko R, ..., Jones W, Xu J

Genome Biol. 22 (1) 109 [2021-04-16; online 2021-04-16]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function.

Nyström EEL, Martinez-Abad B, Arike L, ..., Hansson GC, Johansson MEV

Science 372 (6539) - [2021-04-16; online 2021-04-17]

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Metabolomic profiling reveals plasma GlycA and GlycB as a potential biomarkers for treatment efficiency in rheumatoid arthritis.

Dudka I, Chachaj A, Sebastian A, ..., Gröbner G, Szuba A

Journal of Pharmaceutical and Biomedical Analysis 197 (-) 113971 [2021-04-15; online 2021-02-17]

Swedish Metabolomics Centre (SMC) [Collaborative] Swedish NMR Centre (SNC) [Collaborative]

Loss of RET Promotes Mesenchymal Identity in Neuroblastoma Cells.

Siaw JT, Gabre JL, Uçkun E, ..., Palmer RH, Guan J

Cancers (Basel) 13 (8) - [2021-04-15; online 2021-04-15]

Estimating divergence times from DNA sequences.

Sjödin P, McKenna J, Jakobsson M

Genetics 217 (4) - [2021-04-15; online 2021-03-27]

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Active DNRA and denitrification in oxic hypereutrophic waters.

Broman E, Zilius M, Samuiloviene A, ..., Nascimento FJA, Bonaglia S

Water Res. 194 (-) 116954 [2021-04-15; online 2021-02-21]

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A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.

Rosengren MK, Sigurðardóttir H, Eriksson S, ..., Solé M, Lindgren G

BMC Genomics 22 (1) 267 [2021-04-14; online 2021-04-14]

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A Combined Theoretical and Experimental Study of the Polymer Matrix-Mediated Stress Transfer in a Cellulose Nanocomposite

Peterson A, Mehandzhiyski AY, Svenningsson L, ..., Zozoulenko I, Müller C

Macromolecules 54 (7) 3507-3516 [2021-04-13; online 2021-03-19]

DNA methylation in cord blood in association with prenatal depressive symptoms.

Kallak TK, Bränn E, Fransson E, ..., Lyle R, Skalkidou A

Clin Epigenetics 13 (1) 78 [2021-04-12; online 2021-04-12]

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Sex-differences in circulating biomarkers during acute myocardial infarction: An analysis from the SWEDEHEART registry.

Eggers KM, Lindhagen L, Baron T, ..., Spaak J, Lindahl B

PLoS ONE 16 (4) e0249830 [2021-04-08; online 2021-04-08]

CA10 regulates neurexin heparan sulfate addition via a direct binding in the secretory pathway.

Montoliu-Gaya L, Tietze D, Kaminski D, ..., Tietze AA, Sterky FH

EMBO Rep. 22 (4) e51349 [2021-04-07; online 2021-02-15]

Glycoproteomics and MS Proteomics [Collaborative] Swedish NMR Centre (SNC) [Service]

A spinal organ of proprioception for integrated motor action feedback.

Picton LD, Bertuzzi M, Pallucchi I, ..., Shearing PR, El Manira A

Neuron 109 (7) 1188-1201.e7 [2021-04-07; online 2021-02-11]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial.

Chantzichristos D, Svensson PA, Garner T, ..., Stevens A, Johannsson G

Elife 10 (-) - [2021-04-06; online 2021-04-06]

Variants That Differentiate Wolf and Dog Populations Are Enriched in Regulatory Elements.

Sahlén P, Yanhu L, Xu J, ..., Wang GD, Savolainen P

Genome Biol Evol 13 (4) - [2021-04-05; online 2021-05-01]

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Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds.

Ottenburghs J, Geng K, Suh A, Kutter C

Genome Biol Evol 13 (4) - [2021-04-05; online 2021-02-04]

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Serum proteins associated with periodontitis relapse post-surgery: A pilot study.

Esberg A, Isehed C, Holmlund A, Lindquist S, Lundberg P

J Periodontol - (-) - [2021-04-04; online 2021-04-04]

Using RELION software within the Scipion framework.

Sharov G, Morado DR, Carroni M, de la Rosa-Trevín JM

Acta Crystallogr D Struct Biol 77 (4) 403-410 [2021-04-01; online 2021-03-30]

Cryo-EM [Technology development]

Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.

Fatima A, Hoeber J, Schuster J, ..., Klar J, Dahl N

Am. J. Hum. Genet. 108 (4) 739-748 [2021-04-01; online 2021-03-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Chemical Biology Consortium Sweden; Experiences in academic and industry partnerships – forging a path to translational drug discovery. - Book chapter

Gustavsson A, Chorell E

Burger's Medicinal Chemistry, Drug Discovery and Development, Volumes 1 - 8 Volume 3 (chapter 2) - [2021-04-01]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Artificial intelligence for the classification of fractures around the knee in adults according to the 2018 AO/OTA classification system.

Lind A, Akbarian E, Olsson S, ..., Razavian AS, Gordon M

PLoS ONE 16 (4) e0248809 [2021-04-01; online 2021-04-01]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

A draft transcriptome of a parasite Neocamacolaimus parasiticus (Camacolaimidae, Plectida).

Ahmed M, Adedidran F, Holovachov O

J Nematol 53 (-) - [2021-04-01; online 2021-04-01]

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Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size.

Tyson Y, Hillman C, Majenburg N, ..., Mohaddes M, Hailer NP

Acta Orthop 92 (2) 143-150 [2021-04-00; online 2020-11-12]

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The heart microbiome of insectivorous bats from Central and South Eastern Europe.

Corduneanu A, Mihalca AD, Sándor AD, ..., Viso NP, Bongcam-Rudloff E

Comp Immunol Microbiol Infect Dis 75 (-) 101605 [2021-04-00; online 2021-01-07]

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The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation.

Thörn F, Rödin-Mörch P, Cortazar-Chinarro M, ..., Laurila A, Höglund J

Heredity (Edinb) 126 (4) 656-667 [2021-04-00; online 2021-02-09]

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The C. elegans PAQR-2 and IGLR-2 membrane homeostasis proteins are uniquely essential for tolerating dietary saturated fats.

Devkota R, Henricsson M, Borén J, Pilon M

Biochim Biophys Acta Mol Cell Biol Lipids 1866 (4) 158883 [2021-04-00; online 2021-01-11]

Integrated Microscopy Technologies Gothenburg [Service]

Severe congenital lactic acidosis and hypertrophic cardiomyopathy caused by an intronic variant in NDUFB7.

Correia SP, Moedas MF, Naess K, ..., Wedell A, Wredenberg A

Hum. Mutat. 42 (4) 378-384 [2021-04-00; online 2021-02-04]

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PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS.

Abdulla M, Alexsson A, Sundström C, ..., Hollander P, Amini RM

Acta Oncol 60 (4) 531-538 [2021-04-00; online 2021-02-12]

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Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.

Bruhn H, Samuelsson K, Schober FA, ..., Wedell A, Wredenberg A

Neurol Genet 7 (2) e566 [2021-04-00; online 2021-03-15]

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Modulation of Arabidopsis root growth by specialized triterpenes.

Bai Y, Fernández-Calvo P, Ritter A, ..., Goossens A, Pollier J

New Phytol. 230 (1) 228-243 [2021-04-00; online 2021-01-19]

Swedish Metabolomics Centre (SMC)

Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline.

Gorski M, Jung B, Li Y, ..., Pattaro C, Heid IM

Kidney Int. 99 (4) 926-939 [2021-04-00; online 2020-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Machine learning-based investigation of the cancer protein secretory pathway.

Saghaleyni R, Sheikh Muhammad A, Bangalore P, Nielsen J, Robinson JL

PLoS Comput. Biol. 17 (4) e1008898 [2021-04-00; online 2021-04-05]

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Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.

Lind L, Sundström J, Ärnlöv J, ..., Lumbers RT, Lampa E

Circ Genom Precis Med 14 (2) e002963 [2021-04-00; online 2021-02-26]

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Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.

Coutinho A, Malmström H, Edlund H, ..., Schlebusch CM, Jakobsson M

Am. J. Phys. Anthropol. 174 (4) 701-713 [2021-04-00; online 2021-02-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

LY6K-AS lncRNA is a lung adenocarcinoma prognostic biomarker and regulator of mitotic progression.

Ali MM, Di Marco M, Mahale S, ..., Kanduri M, Kanduri C

Oncogene 40 (13) 2463-2478 [2021-04-00; online 2021-03-05]

Integrated Microscopy Technologies Gothenburg [Service]

Integrating omics to characterize eco-physiological adaptations: How moose diet and metabolism differ across biogeographic zones.

Fohringer C, Dudka I, Spitzer R, ..., Ericsson G, Singh NJ

Ecol Evol 11 (7) 3159-3183 [2021-04-00; online 2021-03-04]

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.

Dumanski JP, Halvardson J, Davies H, ..., Ryś J, Forsberg LA

Cell. Mol. Life Sci. 78 (8) 4019-4033 [2021-04-00; online 2021-04-10]

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Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics.

Gnann C, Cesnik AJ, Lundberg E

Trends Cancer 7 (4) 278-282 [2021-04-00; online 2021-01-10]

Function of the pseudo phosphotransfer proteins has diverged between rice and Arabidopsis.

Vaughan-Hirsch J, Tallerday EJ, Burr CA, ..., Bishopp A, Kieber JJ

Plant J. 106 (1) 159-173 [2021-04-00; online 2021-02-08]

Extensive transcription mis-regulation and membrane defects in AdipoR2-deficient cells challenged with saturated fatty acids.

Ruiz M, Palmgren H, Henricsson M, ..., Borén J, Pilon M

Biochim Biophys Acta Mol Cell Biol Lipids 1866 (4) 158884 [2021-04-00; online 2021-01-11]

Integrated Microscopy Technologies Gothenburg [Service]

Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root.

Abdelfattah A, Wisniewski M, Schena L, Tack AJM

Environ. Microbiol. 23 (4) 2199-2214 [2021-04-00; online 2021-01-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Direct observation of hyperpolarization breaking through the spin diffusion barrier.

Stern Q, Cousin SF, Mentink-Vigier F, ..., Cala O, Jannin S

Sci Adv 7 (18) - [2021-04-00; online 2021-04-30]

Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.

Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX

Mol Ecol Resour 21 (3) 880-896 [2021-04-00; online 2020-12-02]

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Correction to: High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways.

Circ Genom Precis Med 14 (2) e000081 [2021-04-00; online 2021-03-02]

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Burden of rare variants in synaptic genes in patients with severe tinnitus: An exome based extreme phenotype study.

Amanat S, Gallego-Martinez A, Sollini J, ..., Cederroth CR, Lopez-Escamez JA

EBioMedicine 66 (-) 103309 [2021-04-00; online 2021-04-01]

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Autoantibodies against the C-terminus of Lipopolysaccharide binding protein are elevated in young adults with psychiatric disease.

Just D, Rasmusson AJ, Nilsson P, ..., Månberg A, Cunningham JL

Psychoneuroendocrinology 126 (-) 105162 [2021-04-00; online 2021-02-04]

A modified protein marker panel to identify four consensus molecular subtypes in colorectal cancer using immunohistochemistry.

Li X, Larsson P, Ljuslinder I, ..., Edin S, Palmqvist R

Pathol Res Pract 220 (-) 153379 [2021-04-00; online 2021-03-05]

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A fast and simple clearing and swelling protocol for 3D in-situ imaging of the kidney across scales.

Unnersjö-Jess D, Butt L, Höhne M, ..., Brismar H, Blom H

Kidney Int. 99 (4) 1010-1020 [2021-04-00; online 2020-12-05]

Integrated Microscopy Technologies Stockholm [Technology development]

Deletions on Chromosome Y and Downregulation of the SRY Gene in Tumor Tissue Are Associated with Worse Survival of Glioblastoma Patients.

Łysiak M, Smits A, Roodakker KR, ..., Söderkvist P, Malmström A

Cancers (Basel) 13 (7) - [2021-03-31; online 2021-03-31]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.

Qu Y, Chen C, Chen X, ..., Zhang YE, Lei F

Proc. Natl. Acad. Sci. U.S.A. 118 (13) e2012398118 [2021-03-30; online 2021-03-24]

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The associations between red cell distribution width and plasma proteins in a general population.

Pan J, Borné Y, Orho-Melander M, ..., Melander O, Engström G

Clin Proteomics 18 (1) 12 [2021-03-30; online 2021-03-30]

Multiple migrations to the Philippines during the last 50,000 years.

Larena M, Sanchez-Quinto F, Sjödin P, ..., Endicott P, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 118 (13) - [2021-03-30; online 2021-03-24]

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Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.

Indukuri R, Hases L, Archer A, Williams C

Front Endocrinol (Lausanne) 12 (-) 650625 [2021-03-30; online 2021-03-30]

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TLR4-Associated IRF-7 and NFκB Signaling Act as a Molecular Link Between Androgen and Metformin Activities and Cytokine Synthesis in the PCOS Endometrium.

Hu M, Zhang Y, Li X, ..., Shao LR, Billig H

J. Clin. Endocrinol. Metab. 106 (4) 1022-1040 [2021-03-25; online 2021-01-01]

Integrated Microscopy Technologies Gothenburg [Service]

High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer.

Ku A, Fredsøe J, Sørensen KD, ..., Lilja H, Ceder Y

Front Oncol 11 (-) 631021 [2021-03-25; online 2021-03-25]

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Case Report: A Novel Mutation in the Mitochondrial MT-ND5 Gene Is Associated With Leber Hereditary Optic Neuropathy (LHON).

Engvall M, Kawasaki A, Carelli V, ..., Wedell A, Träisk F

Front Neurol 12 (-) 652590 [2021-03-25; online 2021-03-25]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids.

Strassert JFH, Irisarri I, Williams TA, Burki F

Nat Commun 12 (1) 1879 [2021-03-25; online 2021-03-25]

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Methodological considerations for identifying multiple plasma proteins associated with all-cause mortality in a population-based prospective cohort.

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Sci Rep 11 (1) 6734 [2021-03-24; online 2021-03-24]

CytoBrowser: a browser-based collaborative annotation platform for whole slide images

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F1000Res 10 (-) 226 [2021-03-22; online 2021-03-22]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus).

Pappas F, Palaiokostas C

Animals (Basel) 11 (3) - [2021-03-21; online 2021-03-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans.

Persson A, Nikpour M, Vorontsov E, Nilsson J, Larson G

Mol. Cell Proteomics 20 (-) 100074 [2021-03-20; online 2021-03-20]

SOCS3 Expression by Thymic Stromal Cells Is Required for Normal T Cell Development.

Gao Y, Liu R, He C, ..., Carow B, Rottenberg ME

Front Immunol 12 (-) 642173 [2021-03-18; online 2021-03-18]

Global Proteomics and Proteogenomics [Collaborative]

Proteomic blood profiling in mild, severe and critical COVID-19 patients.

Patel H, Ashton NJ, Dobson RJB, ..., Gisslen M, Zetterberg H

Sci Rep 11 (1) 6357 [2021-03-18; online 2021-03-18]

Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex.

Stenmark B, Eriksson L, Thulin Hedberg S, ..., Roberts RJ, Mölling P

Sci Rep 11 (1) 6239 [2021-03-18; online 2021-03-18]

Clinical Genomics [Technology development] Clinical Genomics Örebro [Technology development]

Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis.

Öz R, Wang JL, Guerois R, ..., Strick TR, Westerlund F

Nucleic Acids Res. 49 (5) 2629-2641 [2021-03-18; online 2021-02-17]

Integrated Microscopy Technologies Gothenburg [Service]

PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.

He L, Jones J, He W, ..., Wen J, Dai Q

Development 148 (6) - [2021-03-17; online 2021-03-17]

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Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients.

Stranneheim H, Lagerstedt-Robinson K, Magnusson M, ..., Lindstrand A, Wedell A

Genome Med 13 (1) 40 [2021-03-17; online 2021-03-17]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.

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PeerJ 9 (-) e10947 [2021-03-16; online 2021-03-16]

NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood.

Brownlie D, Scharenberg M, Mold JE, ..., Marquardt N, Michaëlsson J

Proc. Natl. Acad. Sci. U.S.A. 118 (11) e2016580118 [2021-03-16; online 2021-04-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Effects of Lactobacillus reuteri supplementation on the gut microbiota in extremely preterm infants in a randomized placebo-controlled trial.

Martí M, Spreckels JE, Ranasinghe PD, ..., Jenmalm MC, Abrahamsson T

Cell Reports Medicine 2 (3) 100206 [2021-03-16; online 2021-02-22]

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COVIDENZA - A prospective, multicenter, randomized PHASE II clinical trial of enzalutamide treatment to decrease the morbidity in patients with Corona virus disease 2019 (COVID-19): a structured summary of a study protocol for a randomised controlled trial.

Welén K, Överby AK, Ahlm C, ..., Gisslén M, Josefsson A

Trials 22 (1) 209 [2021-03-16; online 2021-03-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma.

Mitra S, Muralidharan SV, Di Marco M, ..., Mondal T, Kanduri C

Cancer Res. 81 (6) 1457-1471 [2021-03-15; online 2020-12-28]

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Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast.

Yu R, Vorontsov E, Sihlbom C, Nielsen J

Elife 10 (-) - [2021-03-15; online 2021-03-15]

Circulating proteins associated with allergy development in infants-an exploratory analysis.

Stockfelt M, Hong M, Hesselmar B, ..., Lundell A, Rudin A

Clin Proteomics 18 (1) 11 [2021-03-15; online 2021-03-15]

3D-printing of solid lipid tablets from emulsion gels.

Johannesson J, Khan J, Hubert M, Teleki A, Bergström CAS

Int J Pharm 597 (-) 120304 [2021-03-15; online 2021-02-01]

Transcriptional analysis of islets of Langerhans from organ donors of different ages.

Seiron P, Stenwall A, Hedin A, ..., Lundberg M, Skog O

PLoS ONE 16 (3) e0247888 [2021-03-12; online 2021-03-12]

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Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions.

Golparian D, Sánchez-Busó L, Cole M, Unemo M

J. Antimicrob. Chemother. 76 (4) 940-944 [2021-03-12; online 2021-01-08]

Clinical Genomics [Technology development] Clinical Genomics Örebro [Technology development]

The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.

Holmfeldt K, Nilsson E, Simone D, ..., Bertilsson S, Dopson M

Commun Biol 4 (1) 307 [2021-03-08; online 2021-03-08]

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Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.

Kupari J, Usoskin D, Parisien M, ..., Diatchenko L, Ernfors P

Nat Commun 12 (1) 1510 [2021-03-08; online 2021-03-08]

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Insight into Functional Membrane Proteins by Solution NMR: The Human Bcl-2 Protein-A Promising Cancer Drug Target.

Ul Mushtaq A, Ådén J, Sparrman T, Hedenström M, Gröbner G

Molecules 26 (5) 1467 [2021-03-08; online 2021-03-08]

Chemical Biology Consortium Sweden (CBCS) [Service] Swedish NMR Centre (SNC) [Service]

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

Seguin-Orlando A, Donat R, Der Sarkissian C, ..., Guilaine J, Orlando L

Curr. Biol. 31 (5) 1072-1083.e10 [2021-03-08; online 2021-01-13]

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Albumin Urinary Excretion Is Associated with Increased Levels of Urinary Chemokines, Cytokines, and Growth Factors Levels in Humans.

Fellström B, Helmersson-Karlqvist J, Lind L, ..., Kultima K, Larsson A

Biomolecules 11 (3) - [2021-03-08; online 2021-03-08]

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model.

Pértille F, Alvarez-Rodriguez M, da Silva AN, ..., Guerrero-Bosagna C, Rodriguez-Martinez H

Int J Mol Sci 22 (5) 2679 [2021-03-06; online 2021-03-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prevalence of germline pathogenic variants in 22 cancer susceptibility genes in Swedish pediatric cancer patients.

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Sci Rep 11 (1) 5307 [2021-03-05; online 2021-03-05]

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OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons.

Willforss J, Siino V, Levander F

BMC Bioinformatics 22 (1) 107 [2021-03-04; online 2021-03-04]

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NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2.

Zhou S, Pettersson P, Huang J, ..., Mäler L, Ädelroth P

Structure 29 (3) 275-283.e4 [2021-03-04; online 2020-09-08]

Expanding functional protein sequence spaces using generative adversarial networks

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Nat Mach Intell 3 (4) 324-333 [2021-03-04; online 2021-03-04]

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Effluent solids recirculation to municipal sludge digesters enhances long-chain fatty acids degradation capacity.

Shakeri Yekta S, Liu T, Mendes Anacleto T, ..., Björn A, Schnürer A

Biotechnol Biofuels 14 (1) 56 [2021-03-04; online 2021-03-04]

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Antibodies to SARS-CoV-2 and risk of past or future sick leave.

Dillner J, Elfström KM, Blomqvist J, ..., Mühr LSA, Conneryd Lundgren K

Sci Rep 11 (1) 5160 [2021-03-04; online 2021-03-04]

A two-tiered targeted proteomics approach to identify pre-diagnostic biomarkers of colorectal cancer risk.

Harlid S, Harbs J, Myte R, ..., Liu X, Van Guelpen B

Sci Rep 11 (1) 5151 [2021-03-04; online 2021-03-04]

Extracellular Vesicles for the Treatment of Radiation-Induced Normal Tissue Toxicity in the Lung.

Montay-Gruel P, Zhu Y, Petit B, ..., Vozenin MC, Limoli CL

Front Oncol 10 (-) 602763 [2021-03-02; online 2021-03-02]

A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases.

Kmezik C, Mazurkewich S, Meents T, ..., Brändén G, Larsbrink J

J. Biol. Chem. 296 (-) 100500 [2021-03-02; online 2021-03-02]

Chalmers Mass Spectrometry Infrastructure [Service]

Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.

Zhong X, Lundberg M, Råberg L

Genome Biol Evol 13 (3) - [2021-03-01; online 2021-02-11]

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Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study.

Sutton L, Ljungström V, Enjuanes A, ..., Stamatopoulos K, Rosenquist R

Haematologica 106 (3) 682-691 [2021-03-01; online 2021-03-01]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.

Smeds L, Aspi J, Berglund J, ..., Tirronen K, Ellegren H

Evol Appl 14 (3) 721-734 [2021-03-00; online 2020-11-09]

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

Muus C, Luecken MD, Eraslan G, ..., NHLBI LungMap Consortium , Human Cell Atlas Lung Biological Network

Nat. Med. 27 (3) 546-559 [2021-03-00; online 2021-03-02]

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Serum choline in extremely preterm infants declines with increasing parenteral nutrition.

Nilsson AK, Pedersen A, Malmodin D, ..., Pupp IH, Hellström A

Eur J Nutr 60 (2) 1081-1089 [2021-03-00; online 2020-06-25]

RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite.

Barragán CE, Márquez MA, Dopson M, Montoya D

Extremophiles 25 (2) 143-158 [2021-03-00; online 2021-02-22]

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Plasma oxylipin levels associated with preterm birth in preterm labor✰.

Svenvik M, Raffetseder J, Brudin L, ..., Ernerudh J, Nording ML

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 166 (-) 102251 [2021-03-00; online 2021-01-23]

Plasma metabolomics of presymptomatic PSEN1-H163Y mutation carriers: a pilot study.

Natarajan K, Ullgren A, Khoshnood B, ..., Blennow K, Graff C

Ann Clin Transl Neurol 8 (3) 579-591 [2021-03-00; online 2021-01-21]

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Million-year-old DNA sheds light on the genomic history of mammoths.

van der Valk T, Pečnerová P, Díez-Del-Molino D, ..., Götherström A, Dalén L

Nature 591 (7849) 265-269 [2021-03-00; online 2021-02-17]

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Isolation and characterization of extracellular vesicle subpopulations from tissues.

Crescitelli R, Lässer C, Lötvall J

Nat Protoc 16 (3) 1548-1580 [2021-03-00; online 2021-01-25]

Glycoproteomics and MS Proteomics [Service] Integrated Microscopy Technologies Gothenburg [Collaborative]

Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO2.

Walker AP, De Kauwe MG, Bastos A, ..., Whelan ME, Zuidema PA

New Phytol. 229 (5) 2413-2445 [2021-03-00; online 2020-10-21]

Inflammatory bowel disease and risk of severe COVID-19: A nationwide population-based cohort study in Sweden.

Ludvigsson JF, Axelrad J, Halfvarson J, ..., Söderling J, Olén O

United European Gastroenterol J 9 (2) 177-192 [2021-03-00; online 2021-03-11]

Experimental evolution of adaptive divergence under varying degrees of gene flow.

Tusso S, Nieuwenhuis BPS, Weissensteiner B, Immler S, Wolf JBW

Nat Ecol Evol 5 (3) 338-349 [2021-03-00; online 2021-01-11]

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Evaluation of the prognostic value of GDF-15, ABC-AF-bleeding score and ABC-AF-death score in patients with atrial fibrillation across different geographical areas.

Pol T, Hijazi Z, Lindbäck J, ..., Siegbahn A, Wallentin L

Open Heart 8 (1) - [2021-03-00; online 2021-03-21]

Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions.

Wäneskog M, Halvorsen T, Filek K, ..., Poole SJ, Koskiniemi S

Microb Genom 7 (3) - [2021-03-00; online 2021-03-01]

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Decadal nitrogen addition alters chemical composition of soil organic matter in a boreal forest

Hasegawa S, Marshall J, Sparrman T, Näsholm T

Geoderma 386 (-) 114906 [2021-03-00; online 2021-03-00]

Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate PLK1.

Silva Cascales H, Burdova K, Middleton A, ..., Macurek L, Lindqvist A

Life Sci. Alliance 4 (3) e202000980 [2021-03-00; online 2021-01-05]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Combined Use of Detergents and Ultrasonication for Generation of an Acellular Pig Larynx.

Nayakawde NB, Methe K, Premaratne GU, Banerjee D, Olausson M

Tissue Eng Part A 27 (5-6) 362-371 [2021-03-00; online 2020-09-10]

Integrated Microscopy Technologies Gothenburg [Collaborative]

Changes in Circulating Cytokines and Adipokines After RYGB in Patients with and without Type 2 Diabetes.

Katsogiannos P, Kamble PG, Pereira MJ, ..., Eriksson JW, Espes D

Obesity (Silver Spring) 29 (3) 535-542 [2021-03-00; online 2021-02-25]

Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy

Mikus M, Zandian A, Sjöberg R, ..., van Hage M, Ohlin M

Journal of Allergy and Clinical Immunology 147 (3) 1077-1086 [2021-03-00; online 2021-03-00]

Autoimmunity and Serology Profiling [Collaborative]

Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.

Kjellin J, Avesson L, Reimegård J, ..., Schaap P, Söderbom F

Genome Res. 31 (3) 436-447 [2021-03-00; online 2021-01-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

System-wide identification and prioritization of enzyme substrates by thermal analysis.

Saei AA, Beusch CM, Sabatier P, ..., Schüler H, Zubarev RA

Nat Commun 12 (1) 1296 [2021-02-26; online 2021-02-26] Open Access

Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses.

Flatt JW, Domanska A, Seppälä AL, Butcher SJ

Commun Biol 4 (1) 250 [2021-02-26; online 2021-02-26]

Highly Soluble CsPbBr3 Perovskite Quantum Dots for Solution-Processed Light-Emission Devices

Liu Y, Tang S, Fan J, ..., Edman L, Wang J

ACS Appl. Nano Mater. 4 (2) 1162-1174 [2021-02-26; online 2021-01-13]

Peptidoglycan-Binding Anchor Is a Pseudomonas aeruginosa OmpA Family Lipoprotein With Importance for Outer Membrane Vesicles, Biofilms, and the Periplasmic Shape.

Paulsson M, Kragh KN, Su YC, ..., Bjarnsholt T, Riesbeck K

Front Microbiol 12 (-) 639582 [2021-02-25; online 2021-02-25]

Vibrio cholerae cytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy.

Corkery DP, Nadeem A, Aung KM, ..., Wai SN, Wu Y

J. Cell. Sci. 134 (5) jcs.252015 [2021-02-23; online 2021-02-23]

Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks.

Mihai IS, Das D, Maršalkaite G, Henriksson J

Genes 12 (2) - [2021-02-23; online 2021-02-23]

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Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML.

Mareschal S, Palau A, Lindberg J, ..., Grönberg H, Lehmann S

Blood Adv 5 (4) 1003-1016 [2021-02-23; online 2021-02-17]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes.

Johansson H, Søndergaard JN, Jorns C, Kutter C, Ellis ECS

Front Endocrinol (Lausanne) 11 (-) 554922 [2021-02-22; online 2021-02-22]

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Single-Cell Analysis of Blood-Brain Barrier Response to Pericyte Loss.

Mäe MA, He L, Nordling S, ..., Keller A, Betsholtz C

Circ. Res. 128 (4) e46-e62 [2021-02-19; online 2020-12-30]

Bioinformatics Support for Computational Resources [Service]

Mechanism of membrane-tethered mitochondrial protein synthesis.

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Science 371 (6531) 846-849 [2021-02-19; online 2021-02-20]

Continuous human uterine NK cell differentiation in response to endometrial regeneration and pregnancy.

Strunz B, Bister J, Jönsson H, ..., Ivarsson MA, Björkström NK

Sci Immunol 6 (56) eabb7800 [2021-02-19; online 2021-02-19]

Cellular Immunomonitoring [Service]

Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia.

Harzandi A, Lee S, Bidkhori G, ..., Shoaie S, Sharpe CC

iScience 24 (2) 102046 [2021-02-19; online 2021-01-09]

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Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds.

Halvarsson P, Höglund J

Parasit Vectors 14 (1) 114 [2021-02-18; online 2021-02-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer.

Kaminska K, Akrap N, Staaf J, ..., Bosch A, Honeth G

Breast Cancer Res. 23 (1) 26 [2021-02-18; online 2021-02-18]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.

Zaghlool A, Niazi A, Björklund ÅK, ..., Ameur A, Feuk L

Sci Rep 11 (1) 4076 [2021-02-18; online 2021-02-18]

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Elastin-like recombinamers-based hydrogel modulates post-ischemic remodeling in a non-transmural myocardial infarction in sheep.

Contessotto P, Orbanić D, Da Costa M, ..., Rodríguez-Cabello JC, Pandit A

Sci Transl Med 13 (581) - [2021-02-17; online 2021-02-19]

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees.

Gandla ML, Mähler N, Escamez S, ..., Tuominen H, Jönsson LJ

Biotechnol Biofuels 14 (1) 43 [2021-02-16; online 2021-02-16]

Mode of Action of Disinfection Chemicals on the Bacterial Spore Structure and Their Raman Spectra.

Malyshev D, Dahlberg T, Wiklund K, ..., Henriksson S, Andersson M

Anal. Chem. 93 (6) 3146-3153 [2021-02-16; online 2021-02-01]

Integrated Microscopy Technologies Umeå [Collaborative]

IL-22 promotes the formation of a MUC17 glycocalyx barrier in the postnatal small intestine during weaning.

Layunta E, Jäverfelt S, Dolan B, Arike L, Pelaseyed T

Cell Rep 34 (7) 108757 [2021-02-16; online 2021-02-18]

Integrated Microscopy Technologies Gothenburg [Service]

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.

Schneider AN, Sundh J, Sundström G, ..., Hurry V, Street NR

mSystems 6 (1) - [2021-02-16; online 2021-02-16]

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Biological and therapeutic implications of a unique subtype of NPM1 mutated AML.

Mer AS, Heath EM, Madani Tonekaboni SA, ..., Schimmer AD, Haibe-Kains B

Nat Commun 12 (1) 1054 [2021-02-16; online 2021-02-16]

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Time-Dependent Effects of Oral Contraceptive Use on Breast, Ovarian, and Endometrial Cancers.

Karlsson T, Johansson T, Höglund J, Ek WE, Johansson Å

Cancer Res. 81 (4) 1153-1162 [2021-02-15; online 2020-12-17]

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Functional and Neurochemical Identification of Ghrelin Receptor (GHSR)-Expressing Cells of the Lateral Parabrachial Nucleus in Mice.

Le May MV, Peris-Sampedro F, Stoltenborg I, ..., Adan RAH, Dickson SL

Front. Neurosci. 15 (-) 633018 [2021-02-15; online 2021-02-15]

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Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.

Wu H, Petitpré C, Fontanet P, ..., Hadjab S, Lallemend F

Nat Commun 12 (1) 1026 [2021-02-15; online 2021-02-15]

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Disassociated molecular orientation distributions of a composite cellulose-lignin carbon fiber precursor: A study by rotor synchronized NMR spectroscopy and X-ray scattering.

Svenningsson L, Bengtsson J, Jedvert K, ..., Theliander H, Evenäs L

Carbohydr Polym 254 (-) 117293 [2021-02-15; online 2020-11-08]

Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge.

Modrzyński JJ, Aamand J, Wittorf L, ..., Hallin S, Albers CN

Water Res. 190 (-) 116669 [2021-02-15; online 2020-11-25]

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Asymmetric introgression reveals the genetic architecture of a plumage trait.

Semenov GA, Linck E, Enbody ED, ..., Andersson L, Taylor SA

Nat Commun 12 (1) 1019 [2021-02-15; online 2021-02-15]

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Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns.

Ugalde-Morales E, Grassmann F, Humphreys K, ..., Hall P, Czene K

Int. J. Cancer 148 (4) 884-894 [2021-02-15; online 2020-09-05]

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Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass.

Sörenson E, Capo E, Farnelid H, Lindehoff E, Legrand C

Front Microbiol 12 (-) 607601 [2021-02-11; online 2021-02-11]

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GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility.

Eriksson D, Røyrvik EC, Aranda-Guillén M, ..., Kämpe O, Husebye ES

Nat Commun 12 (1) 959 [2021-02-11; online 2021-02-11]

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Using Isopropanol as a Capping Agent in the Hydrothermal Liquefaction of Kraft Lignin in Near-Critical Water

Ahlbom A, Maschietti M, Nielsen R, ..., Hasani M, Theliander H

Energies 14 (4) 932 [2021-02-10; online 2021-02-10]

Neuromesodermal progenitor origin of trunk neural crest in vivo

Lukoseviciute M, Mayes S, Sauka-Spengler T

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Circulating tight-junction proteins are potential biomarkers for blood-brain barrier function in a model of neonatal hypoxic/ischemic brain injury.

Andersson EA, Mallard C, Ek CJ

Fluids Barriers CNS 18 (1) 7 [2021-02-10; online 2021-02-10]

Integrated Microscopy Technologies Gothenburg [Service]

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.

Wang C, Wallerman O, Arendt ML, ..., Meadows JRS, Lindblad-Toh K

Commun Biol 4 (1) 185 [2021-02-10; online 2021-02-10]

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Major alterations in the mononuclear phagocyte landscape associated with COVID-19 severity.

Kvedaraite E, Hertwig L, Sinha I, ..., Svensson M, Karolinska KI/K COVID-19 Study Group

Proc. Natl. Acad. Sci. U.S.A. 118 (6) e2018587118 [2021-02-09; online 2021-01-23]

Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.

Stratmann S, Yones SA, Mayrhofer M, ..., Cavelier L, Holmfeldt L

Blood Adv 5 (3) 900-912 [2021-02-09; online 2021-02-10]

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Distinct developmental pathways from blood monocytes generate human lung macrophage diversity.

Evren E, Ringqvist E, Tripathi KP, ..., Villablanca EJ, Willinger T

Immunity 54 (2) 259-275.e7 [2021-02-09; online 2020-12-30]

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Chromaffin Cells with Sympathoblast Signature: Too Similar to Keep Apart?

Bedoya-Reina OC, Schlisio S

Cancer Cell 39 (2) 134-135 [2021-02-08; online 2020-12-31]

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The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms.

Hasan M, Khakzad H, Happonen L, ..., Malmström A, Tykesson E

Chem. Sci. 12 (5) 1869-1885 [2021-02-07; online 2020-12-08]

multiclassPairs: An R package to train multiclass pairbased classifier.

Marzouka NA, Eriksson P

Bioinformatics - (-) - [2021-02-05; online 2021-02-05]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Transport Properties and Local Structure of an Imidazole/Protic Ionic Liquid Mixture Confined in the Mesopores of Hydrophobic Silica

Vavra S, Elamin K, Evenäs L, Martinelli A

J. Phys. Chem. C 125 (4) 2607-2618 [2021-02-04; online 2021-01-27]

Signaling Mechanism of Phytochromes in Solution.

Isaksson L, Gustavsson E, Persson C, ..., Orekhov V, Westenhoff S

Structure 29 (2) 151-160.e3 [2021-02-04; online 2020-09-10]

Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients.

Wallander K, Eisfeldt J, Lindblad M, ..., Liedén A, Tham E

PLoS ONE 16 (2) e0245488 [2021-02-04; online 2021-02-04]

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Sex Disparities in MGMT Promoter Methylation and Survival in Glioblastoma: Further Evidence from Clinical Cohorts.

Smits A, Lysiak M, Magnusson A, ..., Söderkvist P, Malmström A

J Clin Med 10 (4) - [2021-02-03; online 2021-02-03]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Plasma proteome profiling of cardiotoxicity in patients with diffuse large B-cell lymphoma.

Mörth C, Sabaa AA, Freyhult E, ..., Eriksson A, Enblad G

Cardiooncology 7 (1) 6 [2021-02-03; online 2021-02-03]

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Halophytophthora fluviatilis Pathogenicity and Distribution along a Mediterranean-Subalpine Gradient.

Caballol M, Štraus D, Macia H, ..., Redondo MÁ, Oliva J

JoF 7 (2) 112 [2021-02-03; online 2021-02-03]

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Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae.

Bendixsen DP, Gettle N, Gilchrist C, Zhang Z, Stelkens R

Genome Biol Evol 13 (2) - [2021-02-03; online 2021-01-13]

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Soluble TatA forms oligomers that interact with membranes: Structure and insertion studies of a versatile protein transporter.

Pettersson P, Patrick J, Jakob M, ..., Wennmalm S, Mäler L

Biochimica et Biophysica Acta (BBA) - Biomembranes 1863 (2) 183529 [2021-02-01; online 2020-12-03]

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Mapping the energy landscape of protein-ligand binding via linear free energy relationships determined by protein NMR relaxation dispersion.

Stenström O, Diehl C, Modig K, Nilsson UJ, Akke M

RSC Chem Biol 2 (1) 259-265 [2021-02-01; online 2020-12-23]

Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts.

Stegmayr J, Alsafadi HN, Langwiński W, ..., Leigh ND, Wagner DE

Am J Physiol Lung Cell Mol Physiol 320 (2) L232-L240 [2021-02-01; online 2020-10-28]

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Genetic and clinical basis for two distinct subtypes of primary Sjögren's syndrome.

Thorlacius GE, Hultin-Rosenberg L, Sandling JK, ..., Wahren-Herlenius M, Nordmark G

Rheumatology (Oxford) 60 (2) 837-848 [2021-02-01; online 2020-09-06]

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Genetic Risk Score for Serum 25-Hydroxyvitamin D Concentration Helps to Guide Personalized Vitamin D Supplementation in Healthy Finnish Adults.

Sallinen RJ, Dethlefsen O, Ruotsalainen S, ..., Kaunisto MA, Kallioniemi O

J. Nutr. 151 (2) 281-292 [2021-02-01; online 2021-01-01]

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ALK ligand ALKAL2 potentiates MYCN-driven neuroblastoma in the absence of ALK mutation.

Borenäs M, Umapathy G, Lai WY, ..., Hallberg B, Palmer RH

EMBO J. 40 (3) e105784 [2021-02-01; online 2021-01-07]

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The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.

Schober FA, Moore D, Atanassov I, ..., Freyer C, Wredenberg A

Sci Adv 7 (8) - [2021-02-00; online 2021-02-19]

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Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians.

Sjöstrand AE, Sjödin P, Hegay T, ..., Heyer E, Jakobsson M

Eur. J. Hum. Genet. 29 (2) 325-337 [2021-02-00; online 2020-10-01]

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Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.

Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E

Nature 590 (7847) 649-654 [2021-02-00; online 2021-02-24]

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Small-scale population divergence is driven by local larval environment in a temperate amphibian.

Rödin-Mörch P, Palejowski H, Cortazar-Chinarro M, ..., Höglund J, Laurila A

Heredity (Edinb) 126 (2) 279-292 [2021-02-00; online 2020-09-21]

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Single nucleus transcriptomics data integration recapitulates the major cell types in human liver.

Diamanti K, Inda Díaz JS, Raine A, ..., Wadelius C, Cavalli M

Hepatol Res 51 (2) 233-238 [2021-02-00; online 2020-11-28]

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Sea‐ice microbial communities in the Central Arctic Ocean: Limited responses to short‐term <scp> pCO 2 </scp> perturbations

Torstensson A, Margolin AR, Showalter GM, ..., Bolinesi F, Deming JW

Limnol Oceanogr 66 (S1) - [2021-02-00; online 2021-01-20]

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Root trait-microbial relationships across tundra plant species.

Spitzer CM, Lindahl B, Wardle DA, ..., Fanin N, Kardol P

New Phytol. 229 (3) 1508-1520 [2021-02-00; online 2020-10-30]

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Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress.

Liu S, de Jonge J, Trejo-Arellano MS, ..., Köhler C, Hennig L

New Phytol. 229 (4) 2238-2250 [2021-02-00; online 2020-11-22]

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Proactive Construction of an Annotated Imaging Database for Artificial Intelligence Training.

Stadler CB, Lindvall M, Lundström C, ..., Woisetschläger M, Forsberg D

J Digit Imaging 34 (1) 105-115 [2021-02-00; online 2020-11-11]

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Measuring Domain Shift for Deep Learning in Histopathology.

Stacke K, Eilertsen G, Unger J, Lundstrom C

IEEE J Biomed Health Inform 25 (2) 325-336 [2021-02-00; online 2021-02-05]

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MAP3K6 Mutations in a Neurovascular Disease Causing Stroke, Cognitive Impairment, and Tremor.

Ilinca A, Englund E, Samuelsson S, ..., Lindgren AG, Puschmann A

Neurol Genet 7 (1) e548 [2021-02-00; online 2021-01-21]

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Increased apoptosis, reduced Wnt/β-catenin signaling, and altered tail development in zebrafish embryos exposed to a human-relevant chemical mixture.

Smirnova A, Mentor A, Ranefall P, ..., Mattsson A, Jönsson M

Chemosphere 264 (1) 128467 [2021-02-00; online 2020-09-30]

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Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells.

Niklasson CU, Fredlund E, Monni E, ..., Bronner ME, Mohlin S

Dev. Dyn. 250 (2) 191-236 [2021-02-00; online 2020-09-26]

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Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.

Dziasek K, Simon L, Lafon-Placette C, ..., Slotte T, Köhler C

PLoS Genet. 17 (2) e1009370 [2021-02-00; online 2021-02-11]

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Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.

Rengefors K, Gollnisch R, Sassenhagen I, ..., Bassham S, Ahrén D

Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]

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Elastin-like hydrogel stimulates angiogenesis in a severe model of critical limb ischemia (CLI): An insight into the glyco-host response.

Marsico G, Jin C, Abbah SA, ..., McCullagh KJA, Pandit A

Biomaterials 269 (-) 120641 [2021-02-00; online 2021-01-04]

Effects of Evolocumab on the Postprandial Kinetics of Apo (Apolipoprotein) B100- and B48-Containing Lipoproteins in Subjects With Type 2 Diabetes.

Taskinen MR, Björnson E, Kahri J, ..., Packard CJ, Borén J

Arterioscler. Thromb. Vasc. Biol. 41 (2) 962-975 [2021-02-00; online 2020-12-24]

Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales).

Broberg M, Dubey M, Iqbal M, ..., Brandström Durling M, Karlsson M

Evol Appl 14 (2) 476-497 [2021-02-00; online 2020-09-28]

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Chondrodysplasia and growth failure in children after early hematopoietic stem cell transplantation for non-oncologic disorders.

Botto LD, Meeths M, Campos-Xavier B, ..., Unger S, Superti-Furga A

Am. J. Med. Genet. A 185 (2) 517-527 [2021-02-00; online 2021-01-04]

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CD8+ T cells in the central nervous system of mice with herpes simplex infection are highly activated and express high levels of CCR5 and CXCR3.

Lind L, Svensson A, Thörn K, Krzyzowska M, Eriksson K

J Neurovirol 27 (1) 145-153 [2021-02-00; online 2021-01-25]

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Building a high-quality Human Cell Atlas.

Rozenblatt-Rosen O, Shin JW, Rood JE, ..., Regev A, Heyn H

Nat. Biotechnol. 39 (2) 149-153 [2021-02-00; online 2021-01-28]

A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes.

Pruisscher P, Nylin S, Wheat CW, Gotthard K

Evolution 75 (2) 490-500 [2021-02-00; online 2020-12-27]

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A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.

Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U

Mol. Microbiol. 115 (2) 255-271 [2021-02-00; online 2020-10-12]

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A novel heterozygous variant in FGF9 associated with previously unreported features of multiple synostosis syndrome 3.

Thuresson AC, Croft B, Hailer YD, ..., Harley VR, Stattin EL

Clin. Genet. 99 (2) 325-329 [2021-02-00; online 2020-11-12]

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The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers.

Hases L, Ibrahim A, Chen X, ..., Hartman J, Williams C

Int J Mol Sci 22 (3) 1354 [2021-01-29; online 2021-01-29]

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Acute systemic LPS-exposure impairs perivascular CSF distribution in mice.

Manouchehrian O, Ramos M, Bachiller S, Lundgaard I, Deierborg T

J Neuroinflammation 18 (1) 34 [2021-01-29; online 2021-01-29]

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SMAD4 haploinsufficiency in small intestinal neuroendocrine tumors.

Hofving T, Elias E, Rehammar A, ..., Nilsson O, Arvidsson Y

BMC Cancer 21 (1) 101 [2021-01-28; online 2021-01-28]

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Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.

Norin U, Rintisch C, Meng L, ..., Bäckdahl L, Holmdahl R

Nat Commun 12 (1) 610 [2021-01-27; online 2021-01-27]

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Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes.

Rissanen AJ, Saarela T, Jäntti H, ..., Elvert M, Nykänen H

FEMS Microbiol. Ecol. 97 (2) - [2021-01-26; online 2020-12-15]

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Ecological adaptation in European eels is based on phenotypic plasticity.

Enbody ED, Pettersson ME, Sprehn CG, ..., Wickström H, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 118 (4) e2022620118 [2021-01-26; online 2021-01-23]

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Umbilical cord blood metabolome differs in relation to delivery mode, birth order and sex, maternal diet and possibly future allergy development in rural children.

Ross AB, Barman M, Hartvigsson O, ..., Wold AE, Sandberg AS

PLoS ONE 16 (1) e0242978 [2021-01-25; online 2021-01-25]

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Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide.

Heidler TV, Ernits K, Ziolkowska A, Claesson R, Persson K

Commun Biol 4 (1) 106 [2021-01-25; online 2021-01-25]

Divergence and Remarkable Diversity of the Y Chromosome in Guppies.

Almeida P, Sandkam BA, Morris J, ..., Breden F, Mank JE

Mol. Biol. Evol. 38 (2) 619-633 [2021-01-23; online 2020-10-07]

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Diet intervention improves cardiovascular profile in patients with rheumatoid arthritis: results from the randomized controlled cross-over trial ADIRA.

Hulander E, Bärebring L, Turesson Wadell A, ..., Winkvist A, Lindqvist HM

Nutr J 20 (1) 9 [2021-01-23; online 2021-01-23]

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep.

Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R

PLoS ONE 16 (1) e0244408 [2021-01-22; online 2021-01-22]

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Telomeric double-strand DNA-binding proteins DTN-1 and DTN-2 ensure germline immortality in Caenorhabditis elegans.

Yamamoto I, Zhang K, Zhang J, Vorontsov E, Shibuya H

Elife 10 (-) - [2021-01-21; online 2021-01-21]

Porphyromonas gingivalis Produce Neutrophil Specific Chemoattractants Including Short Chain Fatty Acids.

Dahlstrand Rudin A, Khamzeh A, Venkatakrishnan V, ..., Christenson K, Bylund J

Front. Cell. Infect. Microbiol. 10 (-) 620681 [2021-01-19; online 2021-01-19]

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LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.

Herdenberg C, Mutie PM, Billing O, ..., Franks PW, Hedman H

Commun Biol 4 (1) 90 [2021-01-19; online 2021-01-19]

Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46.

Persson BD, John L, Rafie K, ..., Carlson LA, Arnberg N

Proc. Natl. Acad. Sci. U.S.A. 118 (3) - [2021-01-19; online 2021-01-02]

Aging and CMV discordance are associated with increased immune diversity between monozygotic twins.

Yan Z, Maecker HT, Brodin P, ..., Nadeau KC, Andorf S

Immun Ageing 18 (1) 5 [2021-01-18; online 2021-01-18]

A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens.

Vella P, Rudraraju RS, Lundbäck T, ..., Schneider G, Schnell R

Bioorg. Med. Chem. 30 (-) 115898 [2021-01-15; online 2020-12-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Structure of a full-length bacterial polysaccharide co-polymerase.

Wiseman B, Nitharwal RG, Widmalm G, Högbom M

Nat Commun 12 (1) 369 [2021-01-14; online 2021-01-14]

Ygle, Guve och Rane i Skänninge DNA-analyser löste frågan om deras släktskap

Ahlström Arcini C, Hedvall R, Lundgren M

Fornvännen 115 (4) 274-278 [2021-01-12]

The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals.

Strawbridge RJ, Johnston KJA, Bailey MES, ..., Sennblad B, Smith DJ

Sci Rep 11 (1) 632 [2021-01-12; online 2021-01-12]

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In Situ Assembly of Choline Acetyltransferase Ligands by a Hydrothiolation Reaction Reveals Key Determinants for Inhibitor Design.

Wiktelius D, Allgardsson A, Bergström T, ..., Linusson A, Ekström F

Angew. Chem. Int. Ed. Engl. 60 (2) 813-819 [2021-01-11; online 2020-11-20]

DNA-Metabarcoding of Belowground Fungal Communities in Bare-Root Forest Nurseries: Focus on Different Tree Species.

Marčiulynienė D, Marčiulynas A, Lynikienė J, ..., Gedminas A, Menkis A

Microorganisms 9 (1) - [2021-01-11; online 2021-01-11]

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