Publications

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]

A model of photosynthetic <scp> CO 2 </scp> assimilation in <scp> C 3 </scp> leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway

Wieloch T, Augusti A, Schleucher J

New Phytol - (-) - [2023-05-23; online 2023-05-23]

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]

The dynamics of touch-responsive gene expression in cereals.

Darwish E, Ghosh R, Bentzer J, ..., Sirijovski N, Van Aken O

Plant J. - (-) - [2023-05-09; online 2023-05-09]

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

The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots

Lazarian G, Leroy B, Theves F, ..., Soussi T, None

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]

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 - (-) e2191 [2023-05-08; online 2023-05-08]

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]

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

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]

Exposomics [Collaborative]

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]

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

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]

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

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]

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]

Characterization of the Mitochondrial Genetic Landscape in Abdominal Aortic Aneurysm.

Vats S, Sundquist K, Li Y, ..., Gottsäter A, Memon AA

J Am Heart Assoc 12 (8) e029248 [2023-04-18; online 2023-04-07]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19.

Yu M, Charles A, Cagigi A, ..., Loré K, Smed-Sörensen A

Nat Commun 14 (1) 2164 [2023-04-15; online 2023-04-15]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

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]

SHP-1 localization to the activating immune synapse promotes NK cell tolerance in MHC class I deficiency.

Schmied L, Luu TT, Søndergaard JN, ..., Saeed MB, Höglund P

Sci Signal 16 (780) eabq0752 [2023-04-11; online 2023-04-11]

Integrated Microscopy Technologies Stockholm [Service]

Type I interferon shapes brain distribution and tropism of tick-borne flavivirus.

Chotiwan N, Rosendal E, Willekens SMA, ..., Marcellino D, Överby AK

Nat Commun 14 (1) 2007 [2023-04-10; online 2023-04-10]

Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service]

Lymphoscintigraphic alterations in lower limbs in women with lipedema in comparison to women with overweight/obesity.

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]

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]

NGI Long read [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 [2023-04-07; online 2023-04-07]

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†

Circ Genom Precis Med - (-) e003710 [2023-04-06; online 2023-04-06]

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

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]

Red clover root-associated microbiota is shaped by geographic location and choice of farming system.

Jambagi S, Hodén KP, Öhlund L, Dixelius C

J Appl Microbiol 134 (4) - [2023-04-03; online 2023-04-04]

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

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]

Stratified Genetic Analysis Reveals Sex Differences In MPO-ANCA-associated Vasculitis.

Ekman D, Sennblad B, Knight A, ..., Lindblad-Toh K, Dahlqvist J

Rheumatology (Oxford) - (-) - [2023-04-02; online 2023-04-02]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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 - (-) - [2023-04-00; online 2023-04-00]

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]

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]

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

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 Support, Infrastructure and Training [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]

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

Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Support, Infrastructure and Training [Service]

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]

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 - (-) e2167 [2023-03-26; online 2023-03-26]

Clinical Genomics Stockholm [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]

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

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]

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 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]

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]

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. - (-) - [2023-03-13; online 2023-03-13]

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]

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]

VEGF-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. - (-) - [2023-03-03; online 2023-03-03]

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

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]

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

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]

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

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]

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]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

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]

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

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]

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

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]

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

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]

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]

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]

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

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]

Chemical Proteomics [Service]

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]

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]

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

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]

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

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]

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]

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]

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]

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

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]

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]

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

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]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Larval transcriptomes reflect the evolutionary history of plant-insect associations.

de la Paz Celorio-Mancera M, Steward RA, Pruisscher P, ..., Wheat CW, Nylin S

Evolution 77 (2) 519-533 [2023-02-04; online 2023-01-11]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative.

Johannesson K, Leder EH, André C, ..., Thorndyke M, Blomberg A

Evol Appl 16 (2) 530-541 [2023-02-00; online 2023-01-07]

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

Migratory behaviour is positively associated with genetic diversity in butterflies.

García-Berro A, Talla V, Vila R, ..., Backström N, Talavera G

Mol. Ecol. 32 (3) 560-574 [2023-02-00; online 2022-11-23]

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

Inactivation of RB1, CDKN2A, and TP53 have distinct effects on genomic stability at side-by-side comparison in karyotypically normal cells.

Andersson N, Saba KH, Magnusson L, ..., Nord KH, Gisselsson D

Genes Chromosomes Cancer 62 (2) 93-100 [2023-02-00; online 2022-09-30]

Hypercomplex Low Rank Reconstruction for NMR Spectroscopy

Guo Y, Zhan J, Tu Z, ..., Qu X, Guo D

Signal Processing 203 (-) 108809 [2023-02-00; online 2023-02-00]

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]

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]

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]

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

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.

Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C

Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]

BioImage Informatics [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis.

van Creij J, Auxier B, An J, ..., Pan Z, Limpens E

BMC Genomics 24 (1) 53 [2023-01-28; online 2023-01-28]

Microbial Single Cell Genomics [Service]

Inversions maintain differences between migratory phenotypes of a songbird.

Lundberg M, Mackintosh A, Petri A, Bensch S

Nat Commun 14 (1) 452 [2023-01-27; online 2023-01-27]

NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).

Höök L, Näsvall K, Vila R, Wiklund C, Backström N

Chromosome Res. 31 (1) 2 [2023-01-20; online 2023-01-20]

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

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]

Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.

Wang B, Hu H, Bishop K, ..., Bertilsson S, Bravo AG

J Hazard Mater 442 (-) 130057 [2023-01-15; online 2022-09-23]

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

A hypomorphic variant in the translocase of the outer mitochondrial membrane complex subunit TOMM7 causes short stature and developmental delay.

Young C, Batkovskyte D, Kitamura M, ..., Grigelioniene G, Kobayashi T

HGG Adv 4 (1) 100148 [2023-01-12; online 2022-10-04]

Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.

Nishimura K, Yang S, Lee KW, ..., Linnarsson S, Arenas E

Stem Cell Reports 18 (1) 337-353 [2023-01-10; online 2022-11-17]

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

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 (-) - [2023-01-10; online 2023-01-10]

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.

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Curr. Biol. 33 (1) 41-57.e15 [2023-01-09; online 2022-12-08]

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

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]

Deep Learning on Ultrasound Images Visualizes the Femoral Nerve with Good Precision.

Berggreen J, Johansson A, Jahr J, Möller S, Jansson T

Healthcare (Basel) 11 (2) - [2023-01-07; online 2023-01-07]

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]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

The genetic history of Scandinavia from the Roman Iron Age to the present.

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Cell 186 (1) 32-46.e19 [2023-01-05; online 2023-01-08]

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

Solid-phase capture and profiling of open chromatin by spatial ATAC.

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Nat. Biotechnol. - (-) - [2023-01-05; online 2023-01-05]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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. - (-) - [2023-01-04; online 2023-01-04]

Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression.

Sokolov AV, Manu DM, Nordberg DOT, ..., Jokinen J, Schiöth HB

Clin Epigenetics 15 (1) 1 [2023-01-04; online 2023-01-04]

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

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.

Alaei Kakhki N, Schweizer M, Lutgen D, ..., Schielzeth H, Burri R

Mol. Biol. Evol. 40 (1) - [2023-01-04; online 2022-12-30]

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

Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.

Allesøe RL, Lundgaard AT, Hernández Medina R, ..., Brunak S, IMI DIRECT Consortium

Nat. Biotechnol. - (-) - [2023-01-02; online 2023-01-02]

The path to immortalization of cells starts by managing stress through gene duplications.

Lewerentz J, Johansson AM, Stenberg P

Exp. Cell Res. 422 (1) 113431 [2023-01-01; online 2022-11-21]

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

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]

Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.

Wen J, Trost B, Engchuan W, ..., Yuen RKC, Szatkiewicz JP

Mol. Psychiatry 28 (1) 475-482 [2023-01-00; online 2022-11-16]

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

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]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [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 Long-term Support WABI [Collaborative] 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]

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 - (-) - [2022-12-30; online 2022-12-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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]

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.

Hauser J, Dale M, Beck O, ..., Fredolini C, Roxhed N

Anal. Chem. - (-) - [2022-12-22; online 2022-12-22]

Affinity Proteomics Stockholm [Technology development]

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]

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

Scand J Urol - (-) 1-8 [2022-12-20; online 2022-12-20]

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

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] Drug Discovery and Development (DDD) [Service]

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 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 [Service]

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]

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]

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

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]

Autoantigenic properties of the aminoacyl tRNA synthetase family in idiopathic inflammatory myopathies.

Preger C, Notarnicola A, Hellström C, ..., Gräslund S, Jakobsson PJ

J. Autoimmun. 134 (-) 102951 [2022-12-02; online 2022-12-02]

Autoimmunity and Serology Profiling [Service] Drug Discovery and Development (DDD) [Service]

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]

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]

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 emerging landscape of spatial profiling technologies.

Moffitt JR, Lundberg E, Heyn H

Nat. Rev. Genet. 23 (12) 741-759 [2022-12-00; online 2022-07-20]

Spatial Proteomics [Service]

Screening patients with autoimmune endocrine disorders for cytokine autoantibodies reveals monogenic immune deficiencies.

Sjøgren T, Bratland E, Røyrvik EC, ..., Husebye ES, Wolff ASB

J. Autoimmun. 133 (-) 102917 [2022-12-00; online 2022-09-30]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [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]

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 Compute and Storage [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]

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.

Akhter S, Westrin KJ, Zivi N, ..., Emanuelsson O, Sundström JF

New Phytol. 236 (5) 1951-1963 [2022-12-00; online 2022-09-16]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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 Compute and Storage [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 Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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 - (-) - [2022-11-25; online 2022-11-25]

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

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]

Affinity Proteomics Uppsala [Collaborative]

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]

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]

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]

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]

Enantioselective CE-MS analysis of ketamine metabolites in urine.

Sandbaumhüter FA, Aerts JT, Theurillat R, ..., Thormann W, Jansson ET

Electrophoresis - (-) - [2022-11-18; online 2022-11-18]

A comprehensive characterisation of patients diagnosed with post-COVID-19 condition in Sweden 16 months after the introduction of the ICD-10 diagnosis code (U09.9): a population-based cohort study.

Bygdell M, Leach S, Lundberg L, ..., Gisslén M, Nyberg F

Int J Infect Dis - (-) - [2022-11-18; online 2022-11-18]

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]

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 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]

Widespread CNS pathology in amyotrophic lateral sclerosis homozygous for the D90A SOD1 mutation

Forsberg KM, Graffmo KS, Stenvall E, ..., Brännström T, Andersen PM

Acta Neuropathol - (-) - [2022-11-16; online 2022-11-16]

Integrated Microscopy Technologies Umeå [Service]

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 - (-) - [2022-11-16; online 2022-11-16]

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]

Bioinformatics Compute and Storage [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]

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]

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

MS2Tox Machine Learning Tool for Predicting the Ecotoxicity of Unidentified Chemicals in Water by Nontarget LC-HRMS.

Peets P, Wang WC, MacLeod M, ..., Martin JW, Kruve A

Environ. Sci. Technol. 56 (22) 15508-15517 [2022-11-15; online 2022-10-21]

Exposomics [Technology development]

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]

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]

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]

Integrated Microscopy Technologies Umeå [Service]

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) - (-) - [2022-11-11; online 2022-11-11]

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]

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

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 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 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]

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 - (-) - [2022-11-08; online 2022-11-08]

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 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]

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 Linköping [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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 Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] 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]

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

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 C

Sci Data 9 (1) 667 [2022-11-03; online 2022-11-03]

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

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]

Chemical Proteomics [Collaborative]

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]

Chemical Proteomics [Technology development]

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]

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]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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 Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] 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]

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

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]

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

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]

In Situ Sequencing (ISS) [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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 <scp>non‐Alzheimer</scp> ʼs 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 Applications) [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]

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 - (-) 105652 [2022-11-00; online 2022-11-00]

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]

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]

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]

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]

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

medRxiv - (-) - [2022-10-25; online 2022-10-25]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

NGI Short read [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]

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 Compute and Storage [Service] 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]

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]

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 [2022-10-17; online 2022-10-17]

Resistance of subarctic soil fungal and invertebrate communities to disruption of below‐ground carbon supply

Parker TC, Chomel M, Clemmensen KE, ..., Subke J, Wookey PA

J Ecol - (-) - [2022-10-17; online 2022-10-17]

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

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]

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

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]

Bioinformatics Compute and Storage [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]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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

- - (-) - [2022-10-11; online 2022-10-11]

Integrated Microscopy Technologies Stockholm [Service]

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]

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]

Drug repurposing screens identifies compounds that inhibit α-synuclein oligomers’ membrane disruption and block antibody interactions

Somavarapu AK, Kleijwegt G, Nagaraj M, ..., Nielsen J, Otzen D

- - (-) - [2022-10-07; online 2022-10-07]

Chemical Biology Consortium Sweden (CBCS) [Service]

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 - (-) - [2022-10-07; online 2022-10-07]

Integrated Microscopy Technologies Gothenburg [Service]

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]

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]

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 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]

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]

Chemical Proteomics [Technology development]

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]

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]

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]

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 Compute and Storage [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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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 Umeå [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]

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 Gothenburg [Collaborative] Clinical Genomics Linköping [Service] 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 Compute and Storage [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 Compute and Storage [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]

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]

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]

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]

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]

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

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]

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]

Accurate genotype-based demultiplexing of single cell RNA sequencing samples from non-human animals

Cardiello JF, Araus AJ, Giatrellis S, Simon A, Leigh ND

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Eukaryotic Single Cell Genomics (ESCG) [Service]

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]

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]

Exposomics [Technology development]

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]

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 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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Gothenburg [Service]

Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.

Marklund M, Schultz N, Friedrich S, ..., Sonnhammer E, Lundeberg J

Nat Commun 13 (1) 5475 [2022-09-17; online 2022-09-17]

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

Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.

Stenberg H, Hellman S, Lindström L, ..., Hayer J, Malmberg M

BMC Vet Res 18 (1) 348 [2022-09-16; online 2022-09-16]

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

Treatment of periprosthetic joint infections guided by minimum biofilm eradication concentration (MBEC) in addition to minimum inhibitory concentration (MIC): protocol for a prospective randomised clinical trial.

Tillander JAN, Rilby K, Svensson Malchau K, ..., Rolfson O, Trobos M

BMJ Open 12 (9) e058168 [2022-09-15; online 2022-09-15]

Modification of xylan via an oxidation-reduction reaction.

Palasingh C, Nakayama K, Abik F, ..., Ström A, Nypelö T

Carbohydr Polym 292 (-) 119660 [2022-09-15; online 2022-05-27]

Swedish NMR Centre (SNC)

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.

Golparian D, Pleininger S, Jacobsson S, Indra A, Unemo M

Microbiol Resour Announc 11 (9) e0074422 [2022-09-15; online 2022-08-25]

Anosmia, mild cognitive impairment, and biomarkers of brain aging in older adults.

Dong Y, Li Y, Liu K, ..., Du Y, Qiu C

Alzheimers Dement - (-) - [2022-09-15; online 2022-09-15]

Distinct subcellular autophagy impairments in induced neurons from patients with Huntington's disease.

Pircs K, Drouin-Ouellet J, Horváth V, ..., Barker RA, Jakobsson J

Brain 145 (9) 3035-3057 [2022-09-14; online 2021-12-23]

Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.

Peña-Pérez L, Frengen N, Hauenstein J, ..., Lindstrand A, Månsson R

Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]

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

Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination.

Gao Y, Cai C, Wullimann D, ..., Aleman S, Buggert M

Immunity 55 (9) 1732-1746.e5 [2022-09-13; online 2022-07-19]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Autoantibodies targeting malondialdehyde-modifications in rheumatoid arthritis regulate osteoclasts via inducing glycolysis and lipid biosynthesis.

Sakuraba K, Krishnamurthy A, Sun J, ..., Catrina AI, Réthi B

J. Autoimmun. 133 (-) 102903 [2022-09-13; online 2022-09-13]

How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus.

Zhang Z, Kryvokhyzha D, Orsucci M, ..., Milesi P, Lascoux M

New Phytol. - (-) - [2022-09-12; online 2022-09-12]

Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species.

Fischer F, Vorontsov E, Turlin E, ..., Vinella D, De Reuse H

Metallomics 14 (9) - [2022-09-12; online 2022-08-25]

Sialic Acid and Fucose Residues on the SARS-CoV-2 Receptor-Binding Domain Modulate IgG Antibody Reactivity.

Samuelsson E, Mirgorodskaya E, Nyström K, ..., Liljeqvist JÅ, Nordén R

ACS Infect Dis 8 (9) 1883-1893 [2022-09-09; online 2022-08-18]

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).

Thureborn O, Razafimandimbison SG, Wikström N, Rydin C

Front Plant Sci 13 (-) 967456 [2022-09-08; online 2022-09-08]

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

Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice.

Hases L, Birgersson M, Indukuri R, Archer A, Williams C

Int J Mol Sci 23 (18) - [2022-09-08; online 2022-09-08]

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

ATP6V0C variants impair vacuolar V-ATPase causing a neurodevelopmental disorder often associated with epilepsy.

Mattison KA, Tossing G, Mulroe F, ..., Campeau PM, Escayg A

Brain - (-) - [2022-09-08; online 2022-09-08]

AI-based prostate analysis system trained without human supervision to predict patient outcome from tissue samples.

Walhagen P, Bengtsson E, Lennartz M, Sauter G, Busch C

J Pathol Inform 13 (-) 100137 [2022-09-08; online 2022-09-08]

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 - (-) - [2022-09-05; online 2022-09-05]

CRISPR Functional Genomics [Service] Chemical Biology Consortium Sweden (CBCS) [Service]

Human CD38 regulates B cell antigen receptor dynamic organization in normal and malignant B cells.

Camponeschi A, Kläsener K, Sundell T, ..., Reth M, Mårtensson IL

J. Exp. Med. 219 (9) - [2022-09-05; online 2022-07-12]

Three Adult Cases of STAT1 Gain-of-Function with Chronic Mucocutaneous Candidiasis Treated with JAK Inhibitors.

Borgström EW, Edvinsson M, Pérez LP, ..., Brodin P, Bergman P

J Clin Immunol - (-) - [2022-09-02; online 2022-09-02]

Cellular Immunomonitoring [Collaborative] Clinical Genomics Stockholm [Service]

Distinct metabolic hallmarks of WHO classified adult glioma subtypes.

Björkblom B, Wibom C, Eriksson M, ..., Sandström M, Melin B

Neuro-oncology 24 (9) 1454-1468 [2022-09-01; online 2022-02-15]

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.

Nilsson T, Waraky A, Östlund A, ..., Abrahamsson J, Palmqvist L

Int. J. Cancer 151 (5) 770-782 [2022-09-01; online 2022-06-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Gothenburg [Technology development]

A small molecule screen for paqr-2 suppressors identifies Tyloxapol as a membrane fluidizer for C. elegans and mammalian cells.

Ruiz M, Svensk E, Einarsson E, Grahn EP, Pilon M

Biochimica et Biophysica Acta (BBA) - Biomembranes 1864 (9) 183959 [2022-09-01; online 2022-05-17]

Integrated Microscopy Technologies Gothenburg [Service]

Valorization of hydrolysis lignin from a spruce-based biorefinery by applying γ-valerolactone treatment.

Momayez F, Hedenström M, Stagge S, Jönsson LJ, Martín C

Bioresour. Technol. 359 (-) 127466 [2022-09-00; online 2022-06-13]

The role of Gdf5 in the development of the zebrafish fin endoskeleton.

Waldmann L, Leyhr J, Zhang H, ..., Öhman-Mägi C, Haitina T

Dev. Dyn. 251 (9) 1535-1549 [2022-09-00; online 2021-07-29]

BioImage Informatics [Collaborative] Genome Engineering Zebrafish [Service]

Temporal brain transcriptome analysis reveals key pathological events after germinal matrix hemorrhage in neonatal rats.

Song J, Nilsson G, Xu Y, ..., Zhu C, Wang X

J. Cereb. Blood Flow Metab. 42 (9) 1632-1649 [2022-09-00; online 2022-05-01]

Integrated Microscopy Technologies Gothenburg [Service]

Spatial profiling of chromatin accessibility in mouse and human tissues.

Deng Y, Bartosovic M, Ma S, ..., Castelo-Branco G, Fan R

Nature 609 (7926) 375-383 [2022-09-00; online 2022-08-17]

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

Sir2 and Reb1 antagonistically regulate nucleosome occupancy in subtelomeric X-elements and repress TERRAs by distinct mechanisms.

Bauer SL, Grochalski TNT, Smialowska A, Åström SU

PLoS Genet. 18 (9) e1010419 [2022-09-00; online 2022-09-22]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Seroprevalence of SARS-CoV-2 antibodies among public transport workers in Sweden

Sjörs Dahlman A, Anund A

Journal of Transport & Health - (-) 101508 [2022-09-00; online 2022-09-00]

Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles.

Lischnig A, Bergqvist M, Ochiya T, Lässer C

Mol. Cell Proteomics 21 (9) 100273 [2022-09-00; online 2022-07-30]

Pupil size and pupillary light reflex in early infancy: heritability and link to genetic liability to schizophrenia.

Portugal AM, Taylor MJ, Viktorsson C, ..., Ronald A, Falck-Ytter T

J Child Psychol Psychiatry 63 (9) 1068-1077 [2022-09-00; online 2021-12-23]

Plasma proteome profiling of healthy individuals across the life span in a Sicilian cohort with long-lived individuals.

Siino V, Ali A, Accardi G, ..., Levander F, Vasto S

Aging Cell 21 (9) e13684 [2022-09-00; online 2022-08-06]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.

Wikström T, Abrahamsson S, Bengtsson-Palme J, ..., Valentin L, Hagberg H

Clin Transl Med 12 (9) e1023 [2022-09-00; online 2022-09-15]

Impact of temperature and residence time on the hydrothermal carbonization of organosolv lignin

Latham KG, Matsakas L, Figueira J, ..., Christakopoulos P, Jansson S

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.

Arnardottir H, Pawelzik SC, Sarajlic P, ..., Wheelock CE, Bäck M

Clin Transl Med 12 (9) e895 [2022-09-00; online 2022-09-20]

Glycosaminoglycan linkage region of urinary bikunin as a potentially useful biomarker for β3GalT6-deficient spondylodysplastic Ehlers-Danlos syndrome.

Nikpour M, Noborn F, Nilsson J, ..., Malfait F, Larson G

JIMD Rep 63 (5) 462-467 [2022-09-00; online 2022-06-28]

Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.

Parrett JM, Chmielewski S, Aydogdu E, ..., Konczal M, Radwan J

Nat Ecol Evol 6 (9) 1330-1342 [2022-09-00; online 2022-07-18]

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

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]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

Enhanced cytotoxicity of a novel family of ATPase inhibitors in colorectal cancer cells with high NAT2 activity.

Zhang X, Akcan E, Correia M, ..., Globisch D, Sjöblom T

Biochem. Pharmacol. 203 (-) 115184 [2022-09-00; online 2022-07-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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.

Sköld C, Kultima K, Freyhult E, ..., Hailer NP, Mallmin H

Osteoporos Int 33 (9) 1-8 [2022-09-00; online 2022-05-24]

Effect of perfluoroalkyl exposure in pregnancy and infancy on intrauterine and childhood growth and anthropometry. Sub study from COPSAC2010 birth cohort.

Sevelsted A, Gürdeniz G, Rago D, ..., Bisgaard H, Chawes B

EBioMedicine 83 (-) 104236 [2022-09-00; online 2022-08-26]

Exposomics [Collaborative]

Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties.

Ragaller F, Andronico L, Sykora J, ..., Vattulainen I, Sezgin E

Open Biol 12 (9) 220175 [2022-09-00; online 2022-09-14]

Integrated Microscopy Technologies Stockholm [Service]

Automated detection of vascular remodeling in tumor-draining lymph nodes by the deep-learning tool HEV-finder.

Bekkhus T, Avenel C, Hanna S, ..., Wählby C, Ulvmar MH

J. Pathol. 258 (1) 4-11 [2022-09-00; online 2022-07-12]

BioImage Informatics [Technology development]

Advances in spatial mass spectrometry enable in-depth neuropharmacodynamics.

Baijnath S, Kaya I, Nilsson A, Shariatgorji R, Andrén PE

Trends Pharmacol. Sci. 43 (9) 740-753 [2022-09-00; online 2022-07-05]

Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses.

Munke A, Kimura K, Tomaru Y, ..., Hongo Y, Okamoto K

MBio 13 (4) e0015622 [2022-08-30; online 2022-07-20]

Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae.

Dharamshi JE, Gaarslev N, Steffen K, ..., Sipkema D, Ettema TJG

ISME J - (-) - [2022-08-30; online 2022-08-30]

Glioblastoma CD105+ cells define a SOX2- cancer stem cell-like subpopulation in the pre-invasive niche.

Li J, Ek F, Olsson R, Belting M, Bengzon J

Acta Neuropathol Commun 10 (1) 126 [2022-08-29; online 2022-08-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Clinical Genomics Lund [Service]

Uncovering the genomic basis of an extraordinary plant invasion.

Bieker VC, Battlay P, Petersen B, ..., Hodgins KA, Martin MD

Sci Adv 8 (34) eabo5115 [2022-08-26; online 2022-08-24]

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

PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.

Toskas K, Yaghmaeian-Salmani B, Skiteva O, ..., Perlmann T, Holmberg J

Sci Adv 8 (34) eabo1543 [2022-08-26; online 2022-08-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Methylation associated with long- or short-term survival in glioblastoma patients from the Nordic phase 3 trial.

Łysiak M, Das J, Malmström A, Söderkvist P

Front Genet 13 (-) 934519 [2022-08-25; online 2022-08-25]

Bioinformatics Compute and Storage [Service] Clinical Genomics Linköping [Service]

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]

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

Electroactive Covalent Organic Framework Enabling Photostimulus-Responsive Devices.

Yang Y, Sandra AP, Idström A, ..., Evenäs L, Börjesson K

J. Am. Chem. Soc. - (-) - [2022-08-25; online 2022-08-25]

Mapping the GALNT1 substrate landscape with versatile proteomics tools

Saei AA, Lundström SL, Lyu H, ..., Gygi SP, Zubarev RA

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Chemical Proteomics [Technology development]

Epigenetic clock indicates accelerated aging in glial cells of progressive multiple sclerosis patients.

Kular L, Klose D, Urdánoz-Casado A, ..., Needhamsen M, Jagodic M

Front Aging Neurosci 14 (-) 926468 [2022-08-24; online 2022-08-24]

A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.

Ericson PGP, Irestedt M, Zuccon D, ..., Werdelin L, Qu Y

Commun Biol 5 (1) 857 [2022-08-23; online 2022-08-23]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

Increased expression and accumulation of GDF15 in IPF extracellular matrix contribute to fibrosis.

Radwanska A, Cottage CT, Piras A, ..., Hogaboam CM, Murray LA

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.

Eisfeldt J, Schuy J, Stattin EL, ..., Feuk L, Lindstrand A

Int J Mol Sci 23 (16) - [2022-08-20; online 2022-08-20]

Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.

van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L

iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]

Bioinformatics Compute and Storage [Service] 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]

Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.

Söderhäll I, Fasterius E, Ekblom C, Söderhäll K

iScience 25 (8) 104850 [2022-08-19; online 2022-08-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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.

Bier RL, Vass M, Székely AJ, Langenheder S

ISME J 16 (12) 2635-2643 [2022-08-18; online 2022-08-18]

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

Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield.

Osterholz H, Turner S, Alakangas LJ, ..., Kalinowski BE, Dopson M

Nat Commun 13 (1) 4837 [2022-08-17; online 2022-08-17]

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

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]

Affinity Proteomics Uppsala [Service] Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]

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]

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

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]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Feasibility and reliability of measures of bioactive lipids in human plasma and nasal mucosa.

Claeson AS, Lindberg RH, Gouveia-Figueira S, Nording ML

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.

Liu R, Pisco AO, Braun E, Linnarsson S, Zou J

J. Mol. Biol. 434 (15) 167606 [2022-08-15; online 2022-04-27]

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

A method for Boolean analysis of protein interactions at a molecular level.

Raykova D, Kermpatsou D, Malmqvist T, ..., Kampf C, Söderberg O

Nat Commun 13 (1) 4755 [2022-08-13; online 2022-08-13]

BioImage Informatics [Collaborative]

Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility.

Qiao C, Debiasi-Anders G, Mir-Sanchis I

Nucleic Acids Res. 50 (14) 8349-8362 [2022-08-12; online 2022-07-25]

agoTRIBE detects miRNA-target interactions transcriptome-wide in single cells

Sekar V, Mármol-Sánchez E, Kalogeropoulos P, ..., Biryukova I, Friedländer MR

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Eukaryotic Single Cell Genomics (ESCG) [Service]

Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis.

Baltrušis P, Halvarsson P, Höglund J

Parasit Vectors 15 (1) 290 [2022-08-11; online 2022-08-11]

Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.

Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S

Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]

Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.

Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H

Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.

Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B

Am. J. Respir. Crit. Care Med. - (-) - [2022-08-10; online 2022-08-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

Detailed Characterization of the Cell Wall Structure and Composition of Nordic Green Microalgae.

Spain O, Funk C

J. Agric. Food Chem. 70 (31) 9711-9721 [2022-08-10; online 2022-07-27]

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.

Dahn HA, Mountcastle J, Balacco J, ..., Jarvis ED, Fedrigo O

Gigascience 11 (-) - [2022-08-10; online 2022-08-11]

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

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]

Bioinformatics Compute and Storage [Service] 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]

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]

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]

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

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]

A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.

Ramdas S, Judd J, Graham SE, ..., Zhu X, Brown CD

Am. J. Hum. Genet. 109 (8) 1366-1387 [2022-08-04; online 2022-08-06]

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

Single, but not dual, attack by a biotrophic pathogen and a sap-sucking insect affects the oak leaf metabolome.

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]

Cryo-EM [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

Swedish Metabolomics Centre (SMC) [Technology development]

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]

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

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]

In Situ Sequencing (ISS) [Collaborative]

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]

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]

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

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]

Drug Discovery and Development (DDD) [Collaborative]

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 I

IEEE J Biomed Health Inform 26 (8) 4079-4089 [2022-08-00; online 2022-08-11]

BioImage Informatics [Technology development]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

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]

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

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

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]

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

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]

Spatial Proteomics [Service]

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]

BioImage Informatics [Technology development] In Situ Sequencing (ISS) [Collaborative]

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]

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

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]

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]

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

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]

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]

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Cholleti H, de Jong J, Blomström AL, Berg M

Viruses 14 (8) - [2022-07-28; online 2022-07-28]

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

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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.

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Proc. Biol. Sci. 289 (1979) 20220968 [2022-07-27; online 2022-07-20]

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

Mobilization of systemic CCL4 following HIV pre-exposure prophylaxis in young men in Africa.

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Front Immunol 13 (-) 965214 [2022-07-27; online 2022-07-27]

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Front Microbiol 13 (-) 809166 [2022-07-27; online 2022-07-27]

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

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Khatri B, Tessneer KL, Rasmussen A, ..., Nordmark G, Lessard CJ

Nat Commun 13 (1) 4287 [2022-07-27; online 2022-07-27]

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

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Proliferation and Immune Response Gene Signatures Associated with Clinical Outcome to Immunotherapy and Targeted Therapy in Metastatic Cutaneous Malignant Melanoma.

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

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Elife 11 (-) - [2022-07-21; online 2022-07-21]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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Pol T, Hijazi Z, Lindbäck J, ..., Siegbahn A, Wallentin L

Cardiovasc. Res. 118 (9) 2112-2123 [2022-07-20; online 2021-08-07]

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Martinez-Monleon A, Kryh Öberg H, Gaarder J, ..., Fransson S, Martinsson T

Sci Rep 12 (1) 12420 [2022-07-20; online 2022-07-20]

The Influence of Plant Stress Hormones and Biotic Elicitors on Cyclotide Production in Viola uliginosa Cell Suspension Cultures.

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Spatial Mass Spectrometry [Collaborative]

Sensitive Protein Detection Using Site-Specifically Oligonucleotide-Conjugated Nanobodies.

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Anal. Chem. 94 (28) 10054-10061 [2022-07-19; online 2022-07-05]

Drug Discovery and Development (DDD) [Collaborative]

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]

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

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Soták M, Rajan MR, Clark M, ..., Lange S, Börgeson E

iScience 25 (7) 104602 [2022-07-15; online 2022-06-11]

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

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Galectin-9 and Interferon-Gamma Are Released by Natural Killer Cells upon Activation with Interferon-Alpha and Orchestrate the Suppression of Hepatitis C Virus Infection.

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Chemical Proteomics [Collaborative]

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Nat Commun 13 (1) 4092 [2022-07-14; online 2022-07-14]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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FEBS Lett. - (-) - [2022-07-14; online 2022-07-14]

BioImage Informatics [Collaborative]

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Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Clinical Genomics Uppsala [Collaborative]

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]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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) - [2022-07-11; online 2022-07-11]

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

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]

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]

Integrated Microscopy Technologies Gothenburg [Service]

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]

Autoimmunity and Serology Profiling [Collaborative]

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Kobialka P, Sabata H, Vilalta O, ..., Castillo SD, Graupera M

EMBO Mol Med 14 (7) e15619 [2022-07-07; online 2022-06-13]

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]

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

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]

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]

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]

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]

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]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]

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]

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

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]

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]

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 [Service] 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]

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

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) - [2022-07-00; online 2022-06-03]

Integrated Microscopy Technologies Stockholm [Collaborative]

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]

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]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Affinity Proteomics Uppsala [Service] Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service]

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]

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]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

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]

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]

Integrated Microscopy Technologies Gothenburg [Service]

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

Chemical Proteomics [Service]

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]

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]

BioImage Informatics [Collaborative] Genome Engineering Zebrafish [Service]

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 2022-06-00]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Spatial Proteomics [Service]

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]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Immune gene expression in the mosquito vector Culex quinquefasciatus during an avian malaria infection

García-Longoria L, Ahrén D, Berthomieu A, ..., Rivero A, Hellgren O

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Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

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]

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

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]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Clinical Genomics Uppsala [Technology development]

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]

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]

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]

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

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]

Cryo-EM [Technology development]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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 Y

J. Am. Soc. Mass Spectrom. 33 (6) 917-931 [2022-06-01; online 2022-05-02]

Clinical Genomics Gothenburg [Collaborative] Glycoproteomics [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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]

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

PatientMatcher: A customizable Python-based open-source tool for matching undiagnosed rare disease patients via the Matchmaker Exchange network.

Rasi C, Nilsson D, Magnusson M, ..., Wirta V, Stranneheim H

Hum. Mutat. 43 (6) 708-716 [2022-06-00; online 2022-03-07]

Clinical Genomics Stockholm [Technology development]

No association in maternal serum levels of TMAO and its precursors in pre-eclampsia and in non-complicated pregnancies.

Jääskeläinen T, Kärkkäinen O, Heinonen S, Hanhineva K, Laivuori H

Pregnancy Hypertens 28 (-) 74-80 [2022-06-00; online 2022-02-26]

Metabolomic profiles of mid-trimester amniotic fluid are not associated with subsequent spontaneous preterm delivery or gestational duration at delivery.

Hallingström M, Barman M, Savolainen O, ..., Brunius C, Jacobsson B

J Matern Fetal Neonatal Med 35 (11) 2054-2062 [2022-06-00; online 2020-06-16]

Chalmers Mass Spectrometry Infrastructure [Service]

Mechanism of mitoribosomal small subunit biogenesis and preinitiation.

Itoh Y, Khawaja A, Laptev I, ..., Rorbach J, Amunts A

Nature 606 (7914) 603-608 [2022-06-00; online 2022-06-08]

Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]

Loss of Nexilin function leads to a recessive lethal fetal cardiomyopathy characterized by cardiomegaly and endocardial fibroelastosis.

Johansson J, Frykholm C, Ericson K, ..., Bondeson ML, Wilbe M

Am. J. Med. Genet. A 188 (6) 1676-1687 [2022-06-00; online 2022-02-15]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] 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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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]

Dataset on seston and zooplankton fatty-acid compositions, zooplankton and phytoplankton biomass, and environmental conditions of coastal and offshore waters of the northern Baltic Sea.

Bandara T, Brugel S, Andersson A, Lau DCP

Data Brief 42 (-) 108158 [2022-06-00; online 2022-04-10]

Dataset for suppressors of amyloid-β toxicity and their functions in recombinant protein production in yeast.

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]

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

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]

Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.

Rodrigues Soares AE, Boroffka N, Schröder O, ..., Benecke N, Günther T

R. Soc. open sci. 9 (6) 220104 [2022-06-00; online 2022-06-15]

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

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]

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.

Stenfors N, Persson H, Tutt A, ..., Ainegren M, Hanstock HG

Eur J Appl Physiol 122 (6) 1473-1484 [2022-06-00; online 2022-04-07]

Development of gut microbiota during the first 2 years of life.

Wernroth ML, Peura S, Hedman AM, ..., Dicksved J, Fall T

Sci Rep 12 (1) 9080 [2022-05-31; online 2022-05-31]

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

An empirical evaluation of genotype imputation of ancient DNA.

Ausmees K, Sanchez-Quinto F, Jakobsson M, Nettelblad C

G3 (Bethesda) 12 (6) - [2022-05-30; online 2022-04-29]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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 Compute and Storage [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.

Fineschi S, Klar J, Gustafsson KA, ..., Karlsson B, Dahl N

Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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 [2022-05-25; online 2022-05-25]

In Situ Sequencing (ISS) [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

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 [2022-05-19; online 2022-05-19]

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]

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]

In Situ Sequencing (ISS) [Collaborative]

Generalisation effects of predictive uncertainty estimation in deep learning for digital pathology.

Pocevičiūtė M, Eilertsen G, Jarkman S, Lundström C

Sci Rep 12 (1) 8329 [2022-05-18; online 2022-05-18]

DGAT1 activity synchronises with mitophagy to protect cells from metabolic rewiring by iron depletion.

Long M, Sanchez-Martinez A, Longo M, ..., Whitworth AJ, McWilliams TG

EMBO J. 41 (10) e109390 [2022-05-16; online 2022-04-12]

A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases.

Rozman Grinberg I, Martínez-Carranza M, Bimai O, ..., Sjöberg BM, Stenmark P

Nat Commun 13 (1) 2700 [2022-05-16; online 2022-05-16]

A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases

Rozman Grinberg I, Martínez-Carranza M, Bimai O, ..., Sjöberg BM, Stenmark P

Nat Commun 13 (1) - [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.

De Jager V, Gupte N, Nunes S, ..., Diacon AH, Dooley KE

Am. J. Respir. Crit. Care Med. 205 (10) 1228-1235 [2022-05-15; online 2022-03-09]

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]

Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.

Lee H, Marco Salas S, Gyllborg D, Nilsson M

Sci Rep 12 (1) 7976 [2022-05-13; online 2022-05-13]

In Situ Sequencing (ISS) [Technology development]

Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts.

Resl P, Bujold AR, Tagirdzhanova G, ..., Willis LM, Spribille T

Nat Commun 13 (1) 2634 [2022-05-12; online 2022-05-12]

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]

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

Competitive ability depends on mating system and ploidy level across Capsella species.

Orsucci M, Yang X, Vanikiotis T, ..., Lascoux M, Glémin S

Ann. Bot. 129 (6) 697-708 [2022-05-12; online 2022-03-25]

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]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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.

Pridgeon CS, Bolhuis DP, Milosavljević F, ..., Jukić MM, Ingelman-Sundberg M

Cells 11 (10) - [2022-05-10; online 2022-05-10]

Chemical Proteomics [Service]

Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction.

Safi F, Dhapola P, Warsi S, ..., Thakur RK, Karlsson G

Cell Rep 39 (6) 110798 [2022-05-10; online 2022-05-12]

Speciation and population divergence in a mutualistic seed dispersing bird.

de Raad J, Päckert M, Irestedt M, ..., Neuschulz EL, Nilsson MA

Commun Biol 5 (1) 429 [2022-05-09; online 2022-05-09]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression.

Faucillion M, Johansson A, Larsson J

Nucleic Acids Res. 50 (8) 4372-4388 [2022-05-06; online 2022-04-08]

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

Evaluating metagenomic assembly approaches for biome-specific gene catalogues.

Delgado LF, Andersson AF

Microbiome 10 (1) 72 [2022-05-06; online 2022-05-06]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Birth weight and young adult body mass index for predicting the risk of developing adult heart failure in men.

Bygdell M, Ohlsson C, Lilja L, ..., Rosengren A, Kindblom JM

Eur J Prev Cardiol 29 (6) 971-978 [2022-05-06; online 2021-12-16]

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]

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

"ON THE IMPORTANCE OF VARIATION OF ALKALISATION CONDITIONS ON CELLULOSE ETHER SYNTHESIS"

REYES FORSBERG DC, None , SUNDMAN O, None

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.

Peña-Pérez L, Kharazi S, Frengen N, ..., Luc S, Månsson R

Front Immunol 13 (-) 880668 [2022-05-04; online 2022-05-04]

Bioinformatics Compute and Storage [Service] 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]

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]

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

Genomic Impact of Whaling in North Atlantic Fin Whales.

Wolf M, de Jong M, Halldórsson SD, Árnason Ú, Janke A

Mol. Biol. Evol. 39 (5) - [2022-05-03; online 2022-05-06]

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

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]

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

Combined Transcriptomic and Protein Array Cytokine Profiling of Human Stem Cells from Dental Apical Papilla Modulated by Oral Bacteria.

Zymovets V, Razghonova Y, Rakhimova O, ..., Landström M, Romani Vestman N

Int J Mol Sci 23 (9) 5098 [2022-05-03; online 2022-05-03]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Factors Associated With Serological Response to SARS-CoV-2 Vaccination in Patients With Multiple Sclerosis Treated With Rituximab.

Tolf A, Wiberg A, Müller M, ..., Mangsbo S, Burman J

JAMA Netw Open 5 (5) e2211497 [2022-05-02; online 2022-05-02]

The microtubule plus-end tracking protein Bik1 is required for chromosome congression.

Julner A, Abbasi M, Menéndez-Benito V

Mol. Biol. Cell 33 (5) br7 [2022-05-01; online 2022-03-02]

BioImage Informatics [Service]

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.

Bäckryd E, Themistocleous A, Larsson A, ..., Bennett DL, Gerdle B

Pain 163 (5) 897-909 [2022-05-01; online 2021-08-27]

[Correlation between intake of fish or supplements containing omega-3 fatty acids and early pregnancy plasma concentrations.].

Tryggvadottir EA, Halldorsson TI, Birgisdottir BE, ..., Hardardottir H, Gunnarsdottir I

Laeknabladid 108 (5) 238-243 [2022-05-00; online 2022-05-03]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

The proteome signature of cord blood plasma with high hematopoietic stem and progenitor cell count.

Nilsson AK, Rydbeck H, Thorsell A, ..., Lundgren P, Hellström A

Stem Cell Res 61 (-) 102752 [2022-05-00; online 2022-03-14]

The outcome of targeted NGS screening in patients with syndromic forms of sagittal and pansynostosis - IL11RA is an emerging core-gene for pansynostosis.

Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L

Eur J Med Genet 65 (5) 104476 [2022-05-00; online 2022-03-21]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

J Extracell Vesicles 11 (5) e12213 [2022-05-00; online 2022-05-08]

Stratification of COVID-19 patients based on quantitative immune-related gene expression in whole blood.

Persson J, Andersson B, van Veen S, ..., Andersson L, Harandi AM

Mol. Immunol. 145 (-) 17-26 [2022-05-00; online 2022-03-04]

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]

Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study.

England-Mason G, Merrill SM, Gladish N, ..., Dewey D, APrON Study Team

Environ Int 163 (-) 107183 [2022-05-00; online 2022-03-21]

Exposomics [Collaborative]

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.

Pattanaik B, Hammarlund M, Mjörnstedt F, ..., Bergström G, Johansson ME

FASEB J. 36 (5) e22271 [2022-05-00; online 2022-03-29]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

BioImage Informatics [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Metagenomic evidence of a novel family of anammox bacteria in a subsea environment.

Suarez C, Dalcin Martins P, Jetten MSM, ..., Hermansson M, Persson F

Environ. Microbiol. 24 (5) 2348-2360 [2022-05-00; online 2022-04-18]

Mechanical removal of biofilm on titanium discs: An in vitro study.

Ichioka Y, Derks J, Dahlén G, Berglundh T, Larsson L

J. Biomed. Mater. Res. Part B Appl. Biomater. 110 (5) 1044-1055 [2022-05-00; online 2021-12-13]

Integrated Microscopy Technologies Gothenburg [Service]

Interleukin-10 regulates goblet cell numbers through Notch signaling in the developing zebrafish intestine.

Morales RA, Rabahi S, Diaz OE, ..., Hernández PP, Villablanca EJ

Mucosal Immunol 15 (5) 940-951 [2022-05-00; online 2022-07-15]

Genome Engineering Zebrafish [Service]

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]

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

Evolution, geographic spreading, and demographic distribution of Enterovirus D68.

Hodcroft EB, Dyrdak R, Andrés C, ..., Neher RA, Albert J

PLoS Pathog. 18 (5) e1010515 [2022-05-00; online 2022-05-31]

Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.

Eroglu E, Yen CYT, Tsoi Y, ..., Simon A, Chien KR

Nat Cell Biol 24 (5) 645-658 [2022-05-00; online 2022-05-12]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Author Correction: 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 (5) 649 [2022-05-00; online 2022-04-23]

Global Proteomics and Proteogenomics [Technology development]

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

United European Gastroenterol J 10 (4) 363-375 [2022-05-00; online 2022-04-28]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Satellite DNA evolution in Corvoidea inferred from short and long reads.

Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A

Mol. Ecol. - (-) - [2022-04-30; online 2022-04-30]

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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]

Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis.

Bronge M, Högelin KA, Thomas OG, ..., Olsson T, Grönlund H

Sci Adv 8 (17) eabn1823 [2022-04-29; online 2022-04-27]

Autoimmunity and Serology Profiling [Collaborative]

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]

Age and sex effects across the blood proteome after ionizing radiation exposure can bias biomarker screening and risk assessment.

Langen B, Vorontsov E, Spetz J, ..., Helou K, Forssell-Aronsson E

Sci Rep 12 (1) 7000 [2022-04-29; online 2022-04-29]

Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.

Sigeman H, Sinclair B, Hansson B

BMC Genomics 23 (1) 328 [2022-04-27; online 2022-04-27]

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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]

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

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]

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

Auxin boosts energy generation pathways to fuel pollen maturation in barley.

Amanda D, Frey FP, Neumann U, ..., Ljung K, Acosta IF

Curr. Biol. 32 (8) 1798-1811.e8 [2022-04-25; online 2022-03-21]

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]

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

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

Snapshots of actin and tubulin folding inside the TRiC chaperonin.

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Glycoproteomics [Service] Systems Biology [Collaborative]

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]

Affinity Proteomics Uppsala [Collaborative] Autoimmunity and Serology Profiling [Collaborative]

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]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

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]

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

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]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish NMR Centre (SNC) [Collaborative]

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

Journal of Chromatography B 1195 (-) 123200 [2022-04-15; online 2022-02-28]

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

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]

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]

Chemical Biology Consortium Sweden (CBCS) [Service]

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]

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]

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

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]

Drug Discovery and Development (DDD) [Service]

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.

Dehasque M, Pečnerová P, Kempe Lagerholm V, ..., Vartanyan S, Dalén L

Genes 13 (4) - [2022-04-13; online 2022-04-13]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

Syst. Biol. - (-) - [2022-04-12; online 2022-04-12]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics NGI Single cell [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

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]

Bioinformatics Compute and Storage [Service] Cryo-EM [Service]

Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.

Meijer M, Agirre E, Kabbe M, ..., Malhotra D, Castelo-Branco G

Neuron 110 (7) 1193-1210.e13 [2022-04-06; online 2022-01-31]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Direct measurements of mRNA translation kinetics in living cells.

Metelev M, Lundin E, Volkov IL, ..., Elf J, Johansson M

Nat Commun 13 (1) 1852 [2022-04-06; online 2022-04-06]

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]

Autoimmunity and Serology Profiling [Service] Swedish Metabolomics Centre (SMC) [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Integrated Microscopy Technologies Gothenburg [Service]

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.

Svennerstam H, Jämtgård S

New Phytol. 234 (1) 311-318 [2022-04-00; online 2022-02-02]

Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.

Ferreira PdL, Batista R, Andermann T, ..., Bacon CD, Antonelli A

Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]

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

Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.

Zeybel M, Arif M, Li X, ..., Borén J, Mardinoglu A

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

Peyroteo-Stjerna R, Simões LG, Fernandes R, ..., Günther T, Jakobsson M

Journal of Archaeological Science: Reports 42 (-) 103370 [2022-04-00; online 2022-04-00]

Metabolism is a major driver of hydrogen isotope fractionation recorded in tree-ring glucose of Pinus nigra.

Wieloch T, Grabner M, Augusti A, ..., Yu J, Schleucher J

New Phytol. 234 (2) 449-461 [2022-04-00; online 2022-02-26]

Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology.

Laurén I, Havervall S, Ng H, ..., Thålin C, Mangsbo S

Immun Inflamm Dis 10 (4) e595 [2022-04-00; online 2022-03-30]

Autoimmunity and Serology Profiling [Collaborative]

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]

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.

Dubbelboer IR, Barmpatsalou V, Rodler A, ..., Häggström J, Bergström CAS

Eur J Pharm Biopharm 173 (-) 92-102 [2022-04-00; online 2022-02-25]

Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity

Omokanye A, Ong LC, Lebrero-Fernandez C, ..., Czarnewski P, Lycke N

Mucosal Immunol 15 (4) 717-729 [2022-04-00; online 2022-04-00]

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

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.

Hallberg I, Persson S, Olovsson M, ..., Rüegg J, Sjunnesson YCB

Reprod Toxicol 109 (-) 19-30 [2022-04-00; online 2022-02-24]

BioImage Informatics [Collaborative]

Acute sleep loss alters circulating fibroblast growth factor 21 levels in humans: A randomised crossover trial.

Mateus Brandão LE, Espes D, Westholm JO, ..., Benedict C, Cedernaes J

J Sleep Res 31 (2) e13472 [2022-04-00; online 2021-09-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

ADP-ribosylating adjuvant reveals plasticity in cDC1 cells that drive mucosal Th17 cell development and protection against influenza virus infection.

Arabpour M, Lebrero-Fernandez C, Schön K, ..., Agace W, Lycke N

Mucosal Immunol 15 (4) 745-761 [2022-04-00; online 2022-04-13]

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 (-) - [2022-03-31; online 2022-03-31]

Autoimmunity and Serology Profiling [Collaborative]

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]

Cryo-EM [Collaborative]

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]

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]

Affinity Proteomics Uppsala [Collaborative] NGI Proteomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 - (-) - [2022-03-29; online 2022-03-29]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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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Spatial Proteomics

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]

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]

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

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.

Berglund E, Barbany G, Orsmark-Pietras C, ..., Fioretos T, Rosenquist R

Front Med (Lausanne) 9 (-) 842507 [2022-03-24; online 2022-03-24]

Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Umeå [Service] Clinical Genomics Uppsala [Collaborative]

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]

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

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]

Global Proteomics and Proteogenomics [Technology development]

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.

Baudet A, Hultmark S, Ek F, Magnusson M

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]

Affinity Proteomics Uppsala [Collaborative]

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]

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

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]

The Molecular Chaperone CCT Sequesters Gelsolin and Protects it from Cleavage by Caspase-3.

Cuéllar J, Vallin J, Svanström A, ..., Valpuesta JM, Grantham J

J. Mol. Biol. 434 (5) 167399 [2022-03-15; online 2021-12-09]

Integrated Microscopy Technologies Gothenburg [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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

Structure - (-) - [2022-03-10; online 2022-03-10]

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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Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

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]

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

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]

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]

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]

Swedish NMR Centre (SNC)

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Gothenburg [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Cryo-EM [Collaborative]

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]