Publications 2023

UROSCAN and UROSCANSEQ: a large-scale multicenter effort towards translation of molecular bladder cancer subtypes into clinical practice – from biobank to RNA-sequencing in real time

Liedberg F, Abrahamsson J, Bernardo C, ..., Sjödahl G, Eriksson P

Scandinavian Journal of Urology 57 (1-6) 2-9 [2023-11-02; online 2022-12-20]

Clinical Genomics Lund [Collaborative]

Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation.

Mengal K, Kor G, Siino V, ..., Levander F, Niksirat H

Dev. Comp. Immunol. 147 (-) 104760 [2023-10-00; online 2023-06-16]

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

PLK1 as a cooperating partner for BCL2-mediated antiapoptotic program in leukemia.

Shah K, Nasimian A, Ahmed M, ..., Lock RB, Kazi JU

Blood Cancer J 13 (1) 139 [2023-09-07; online 2023-09-07]

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

Large-scale proximity extension assay reveals CSF midkine and DOPA decarboxylase as supportive diagnostic biomarkers for Parkinson's disease.

Paslawski W, Khosousi S, Hertz E, ..., Boxer A, Svenningsson P

Transl Neurodegener 12 (1) 42 [2023-09-04; online 2023-09-04]

Verticillium longisporum phospholipase VlsPLA2 is a virulence factor that targets host nuclei and modulates plant immunity.

Rafiei V, Vélëz H, Piombo E, Dubey M, Tzelepis G

Mol. Plant Pathol. 24 (9) 1078-1092 [2023-09-00; online 2023-05-12]

Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.

Shaw D, Abad R, Amin-Chowdhury Z, ..., Zhou F, Brueggemann AB

Lancet Digit Health 5 (9) e582-e593 [2023-09-00; online 2023-07-27]

Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis

Hung SW, Gaetani M, Li Y, ..., Zubarev RA, Wang CC

Journal of Pharmaceutical Analysis - (-) - [2023-09-00; online 2023-09-00]

Chemical Proteomics [Service]

An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants.

Tran HC, Schmitt V, Lama S, ..., Delannoy E, Van Aken O

Science 381 (6661) eadg0995 [2023-09-00; online 2023-09-01]

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

Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles.

Seeger C, Dyrhage K, Näslund K, Andersson SGE

Microlife 4 (-) uqad037 [2023-08-29; online 2023-08-29]

Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor.

Cowgill J, Fan C, Haloi N, ..., Howard RJ, Lindahl E

Neuron - (-) - [2023-08-25; online 2023-08-25]

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).

Steffen K, Proux-Wéra E, Soler L, ..., Sundh J, Cárdenas P

G3 (Bethesda) - (-) - [2023-08-24; online 2023-08-24]

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

Long-read whole-genome analysis of human single cells.

Hård J, Mold JE, Eisfeldt J, ..., Michaëlsson J, Ameur A

Nat Commun 14 (1) 5164 [2023-08-24; online 2023-08-24]

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

Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen AC

Arthritis & rheumatology (Hoboken, N.J.) - (-) - [2023-08-23; online 2023-08-23]

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

Bacterial bioindicators enable biological status classification along the continental Danube river.

Fontaine L, Pin L, Savio D, ..., Farnleitner AH, Eiler A

Commun Biol 6 (1) 862 [2023-08-18; online 2023-08-18]

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

An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver.

Fernández Moro C, Geyer N, Harrizi S, ..., Bozóky B, Gerling M

Nat Commun 14 (1) 5024 [2023-08-18; online 2023-08-18]

CRISPR Functional Genomics [Service]

Sustained Transmission of Neisseria gonorrhoeae Strains with High-Level Azithromycin Resistance (MIC ≥ 256 μg/mL) in Argentina, 2018 to 2022.

Gianecini RA, Poklepovich T, Golparian D, ..., Campos J, Galarza P

Microbiol Spectr 11 (4) e0097023 [2023-08-17; online 2023-06-20]

Amyloids of α-Synuclein Promote Chemical Transformations of Neuronal Cell Metabolites.

Horvath I, Mohamed KA, Kumar R, Wittung-Stafshede P

Int J Mol Sci 24 (16) - [2023-08-16; online 2023-08-16]

Pantothenate Kinase 4 controls efficient skeletal muscle energy substrate metabolism via acetyl-CoA

Miranda-Cervantes A, Fritzen AM, Raun SH, ..., Richter EA, Kleinert M

- - (-) - [2023-08-14; online 2023-08-14]

Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase.

Andriianov A, Trigüis S, Drobiazko A, ..., Severinov K, Isaev A

Cell Rep 42 (8) 112972 [2023-08-13; online 2023-08-13]

Complementarity-determining region clustering may cause CAR-T cell dysfunction.

Sarén T, Saronio G, Marti Torrell P, ..., Yu D, Essand M

Nat Commun 14 (1) 4732 [2023-08-10; online 2023-08-10]

Drug Discovery and Development (DDD) [Service]

Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.

Mattila TM, Svensson EM, Juras A, ..., Malmström H, Jakobsson M

Commun Biol 6 (1) 793 [2023-08-09; online 2023-08-09]

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

A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing.

Johansson J, Lidéus S, Höijer I, ..., Bondeson ML, Wilbe M

Sci Rep 13 (1) 12856 [2023-08-08; online 2023-08-08]

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

Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.

Almamoun R, Pierozan P, Manoharan L, Karlsson O

Ecotoxicol Environ Saf 262 (-) 115321 [2023-08-05; online 2023-08-05]

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

Single-cell RNA analysis reveals cell-intrinsic functions of CAR-T cells correlating with response in a phase II study of lymphoma patients.

Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M

Clin. Cancer Res. - (-) - [2023-08-04; online 2023-08-04]

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

The development of blood protein profiles in extremely preterm infants follows a stereotypic evolution pattern.

Zhong W, Danielsson H, Brusselaers N, ..., Uhlén M, Hellström A

Commun Med (Lond) 3 (1) 107 [2023-08-02; online 2023-08-02]

Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20.

Kakooza F, Golparian D, Matoga M, ..., Wi T, Unemo M

J. Antimicrob. Chemother. 78 (8) 1982-1991 [2023-08-02; online 2023-06-23]

Genetic insights into resting heart rate and its role in cardiovascular disease.

van de Vegte YJ, Eppinga RN, van der Ende MY, ..., Verweij N, van der Harst P

Nat Commun 14 (1) 4646 [2023-08-02; online 2023-08-02]

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

Alternating L4 loop architecture of the bacterial polysaccharide co-polymerase WzzE.

Wiseman B, Widmalm G, Högbom M

Commun Biol 6 (1) 802 [2023-08-02; online 2023-08-02]

N-terminal proteoforms may engage in different protein complexes.

Bogaert A, Fijalkowska D, Staes A, ..., Calderwood MA, Gevaert K

Life Sci. Alliance 6 (8) - [2023-08-00; online 2023-06-14]

Spatial Proteomics [Collaborative]

A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing

Plaza DF, Zerebinski J, Broumou I, ..., Sundling C, Färnert A

Cell Reports Methods - (-) 100574 [2023-08-00; online 2023-08-00]

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

Transposable element insertions in 1000 Swedish individuals.

Bilgrav Saether K, Nilsson D, Thonberg H, ..., Eisfeldt J, Lindstrand A

PLoS ONE 18 (7) e0289346 [2023-07-28; online 2023-07-28]

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

Combined GLUT1 and OXPHOS inhibition eliminates acute myeloid leukemia cells by restraining their metabolic plasticity.

Rodriguez-Zabala M, Ramakrishnan R, Reinbach K, ..., Woods NB, Järås M

Blood Adv - (-) - [2023-07-28; online 2023-07-28]

An Okinawan-Based Nordic Diet Leads to Profound Effects on Gut Microbiota and Plasma Metabolites Linked to Glucose and Lipid Metabolism.

Manoharan L, Roth B, Bang C, Stenlund H, Ohlsson B

Nutrients 15 (14) - [2023-07-24; online 2023-07-24]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Vegetation, topography, and soil depth drive microbial community structure in two Swedish grasslands.

Guasconi D, Juhanson J, Clemmensen KE, ..., Roth N, Fransson P

FEMS Microbiol. Ecol. 99 (8) - [2023-07-21; online 2023-07-21]

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

Endophytic Beauveria bassiana induces biosynthesis of flavonoids in oilseed rape following both seed inoculation and natural colonization.

Muola A, Birge T, Helander M, ..., Saikkonen K, Fuchs B

Pest Manag Sci - (-) - [2023-07-19; online 2023-07-19]

Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature.

Lihavainen J, Šimura J, Bag P, ..., Ljung K, Jansson S

Nat Commun 14 (1) 4288 [2023-07-18; online 2023-07-18]

Phospholipid Removal for Enhanced Chemical Exposomics in Human Plasma

Sdougkou K, Xie H, Papazian S, ..., Bergdahl IA, Martin JW

Environ. Sci. Technol. 57 (28) 10173-10184 [2023-07-18; online 2023-07-03]

Exposomics [Collaborative]

Historical RNA expression profiles from the extinct Tasmanian tiger.

Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR

Genome Res. - (-) - [2023-07-18; online 2023-07-18]

Bioinformatics Support, Infrastructure and Training [Collaborative]

Impact of xylan on field productivity and wood saccharification properties in aspen.

Derba-Maceluch M, Sivan P, Donev EN, ..., Jönsson LJ, Mellerowicz EJ

Front Plant Sci 14 (-) 1218302 [2023-07-17; online 2023-07-17]

Extensive transcriptome sex-reversal later in life, after developmental low-dose bisphenol A exposure

Dunder L, Lejonklou M, Lind M, ..., Lind L, Lind T

- - (-) - [2023-07-07; online 2023-07-07]

High-level in vitro resistance to gentamicin acquired in a stepwise manner in Neisseria gonorrhoeae.

Golparian D, Jacobsson S, Holley CL, Shafer WM, Unemo M

J. Antimicrob. Chemother. 78 (7) 1769-1778 [2023-07-05; online 2023-05-30]

Arabinoxylan supplemented bread: From extraction of fibers to effect of baking, digestion, and fermentation.

Zhang D, Rudjito RC, Pietiäinen S, ..., Vilaplana F, Jiménez-Quero A

Food Chem 413 (-) 135660 [2023-07-01; online 2023-02-10]

Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.

Adolfsson E, Kling D, Gunnarsson C, ..., Gréen H, Gréen A

Int J Legal Med 137 (4) 1215-1234 [2023-07-00; online 2022-11-08]

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]

Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.

Kluting K, Strid Y, Six D, Rosling A

Microb. Ecol. 86 (1) 224-239 [2023-07-00; online 2022-07-13]

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

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.

Lauterbur ME, Cavassim MIA, Gladstein AL, ..., Schrider DR, Gronau I

Elife 12 (-) - [2023-06-21; online 2023-06-21]

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

Microbial Profiling of Amniotic Fluid, Umbilical Blood and Placenta of the Foaling Mare.

Hemberg E, Niazi A, Guo Y, ..., Morrell JM, Kútvölgyi G

Animals (Basel) 13 (12) - [2023-06-18; online 2023-06-18]

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

A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function

Schlesinger D, Dirks C, Luzon CN, ..., Eirich J, Elsässer SJ

- - (-) - [2023-06-13; online 2023-06-13]

CRISPR Functional Genomics [Service]

High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler.

Sych T, Schlegel J, Barriga HMG, ..., Stevens MM, Sezgin E

Nat. Biotechnol. - (-) - [2023-06-12; online 2023-06-12]

Integrated Microscopy Technologies Stockholm [Service]

Adipokines and risk of rheumatoid arthritis: A two-sample multivariable Mendelian randomisation study.

Vasileiadis GK, Sayols S, Zhao SS, Fatima T, Maglio C

PLoS ONE 18 (6) e0286981 [2023-06-09; online 2023-06-09]

Clinical Genomics Gothenburg [Service]

Epidemiology, validation, and clinical characteristics of inflammatory bowel disease: the ABIS birth cohort study.

Östensson M, Björkqvist O, Guo A, ..., Mårild K, Ludvigsson J

BMC Gastroenterol 23 (1) 199 [2023-06-08; online 2023-06-08]

RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.

Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM

BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]

BioImage Informatics [Service]

Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions.

Johansson J, Lidéus S, Frykholm C, ..., Wilbe M, Bondeson ML

Eur. J. Hum. Genet. - (-) - [2023-06-05; online 2023-06-05]

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

Small molecule-mediated disruption of ribosome biogenesis synergizes with FGFR inhibitors to suppress glioma cell growth

Zisi A, Kanellis DC, Moussaud S, ..., Bartek J, Lindström MS

Neuro-oncology 25 (6) 1058-1072 [2023-06-02; online 2022-12-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Creation of distinctive Bax-lipid complexes at mitochondrial membrane surfaces drives pore formation to initiate apoptosis.

Clifton LA, Wacklin-Knecht HP, Ådén J, ..., Sparrman T, Gröbner G

Sci Adv 9 (22) eadg7940 [2023-06-02; online 2023-06-02]

Role of myeloid cells in system-level immunometabolic dysregulation during prolonged successful HIV-1 treatment.

Svensson Akusjärvi S, Krishnan S, Ambikan AT, ..., Sönnerborg A, Neogi U

AIDS 37 (7) 1023-1033 [2023-06-01; online 2023-03-21]

An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).

Peona V, Palacios-Gimenez OM, Lutgen D, ..., Suh A, Burri R

G3 (Bethesda) 13 (6) - [2023-06-01; online 2023-04-25]

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

Transcriptome and metabolome profiling identify factors potentially involved in pro-vitamin A accumulation in cassava landraces.

Olayide P, Alexandersson E, Tzfadia O, ..., Gisel A, Stavolone L

Plant Physiol Biochem 199 (-) 107713 [2023-06-00; online 2023-04-24]

The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus).

Fuentes-Pardo AP, Farrell ED, Pettersson ME, Sprehn CG, Andersson L

Evol Appl 16 (6) 1201-1219 [2023-06-00; online 2023-06-06]

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

The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.

Yazdi HP, Olito C, Kawakami T, ..., Hansson B, Cornwallis CK

PLoS Genet. 19 (6) e1010801 [2023-06-00; online 2023-06-30]

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

Retention of essential fatty acids in fish differs by species, habitat use and nutritional quality of prey.

Bandara T, Brugel S, Andersson A, Lau DCP

Ecol Evol 13 (6) e10158 [2023-06-00; online 2023-06-01]

Directionality of developing skeletal muscles is set by mechanical forces.

Sunadome K, Erickson AG, Kah D, ..., Fried K, Adameyko I

Nat Commun 14 (1) 3060 [2023-05-27; online 2023-05-27]

Integrated Microscopy Technologies Stockholm [Service]

The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.

Díaz de Ståhl T, Shamikh A, Mayrhofer M, ..., Sandgren J, Nistér M

J Transl Med 21 (1) 342 [2023-05-23; online 2023-05-23]

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]

A model of photosynthetic CO2 assimilation in C3 leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway.

Wieloch T, Augusti A, Schleucher J

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

Variation in fatty acid content among benthic invertebrates in a seasonally driven system

Hedberg P, Lau DCP, Albert S, Winder M

Limnol Oceanogr Letters - (-) - [2023-05-22; online 2023-05-22]

Cross-reactive EBNA1 immunity targets alpha-crystallin B and is associated with multiple sclerosis.

Thomas OG, Bronge M, Tengvall K, ..., Olsson T, Kockum I

Sci Adv 9 (20) eadg3032 [2023-05-19; online 2023-05-17]

Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.

Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å

Front Microbiol 14 (-) 1159811 [2023-05-18; online 2023-05-18]

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

Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.

Ahlstrom CA, Woksepp H, Sandegren L, Ramey AM, Bonnedahl J

Appl. Environ. Microbiol. - (-) e0031923 [2023-05-17; online 2023-05-17]

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

Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.

Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P

J. Am. Chem. Soc. 145 (19) 10700-10711 [2023-05-17; online 2023-05-04]

The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis.

Kokkinou E, Soini T, Pandey RV, ..., Rolandsdotter H, Mjösberg J

Cell Reports Medicine 4 (5) 101038 [2023-05-16; online 2023-05-08]

Bioinformatics Support, Infrastructure and Training [Collaborative]

Development of a machine learning framework for radiation biomarker discovery and absorbed dose prediction.

Andersson B, Langen B, Liu P, Dávila López M

Front Oncol 13 (-) 1156009 [2023-05-15; online 2023-05-15]

Clinical Genomics Gothenburg [Technology development]

The impact of immunomodulating treatment on the immunogenicity of COVID-19 vaccines in patients with immune-mediated inflammatory rheumatic diseases compared to healthy controls. A Swedish nationwide study (COVID19-REUMA).

Frodlund M, Nived P, Chatzidionysiou A, ..., Klareskog L, Kapetanovic MC

Vaccine 41 (20) 3247-3257 [2023-05-11; online 2023-04-04]

Glycan Stability and Flexibility: Thermodynamic and Kinetic Characterization of Nonconventional Hydrogen Bonding in Lewis Antigens.

Kwon J, Ruda A, Azurmendi HF, ..., Widmalm G, Freedberg DI

J. Am. Chem. Soc. 145 (18) 10022-10034 [2023-05-10; online 2023-04-26]

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, ..., Baran-Marszak F, Soussi T

Hum. Mutat. 2023 (-) 1-17 [2023-05-09; online 2023-05-09]

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

CRISPR-Cas9 knockout screen identifies novel treatment targets in childhood high-grade glioma.

Wenger A, Karlsson I, Kling T, Carén H

Clin Epigenetics 15 (1) 80 [2023-05-09; online 2023-05-09]

CRISPR Functional Genomics [Service]

Reduced binding of apoE4 to complement factor H promotes amyloid-β oligomerization and neuroinflammation.

Chernyaeva L, Ratti G, Teirilä L, ..., Nissilä E, Haapasalo K

EMBO Rep. - (-) e56467 [2023-05-08; online 2023-05-08]

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]

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

Imaging Radial Distribution Functions of Complex Particles by Relayed Dynamic Nuclear Polarization.

Berruyer P, Cibaka-Ndaya C, Pinon A, ..., Drisko GL, Emsley L

J. Am. Chem. Soc. 145 (17) 9700-9707 [2023-05-03; online 2023-04-19]

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]

Resolution enhancement of NMR by decoupling with the low-rank Hankel model.

Qiu T, Jahangiri A, Han X, ..., Qu X, Orekhov V

Chem. Commun. (Camb.) 59 (36) 5475-5478 [2023-05-02; online 2023-05-02]

Nontarget Analysis of Polluted Surface Waters in Bangladesh Using Open Science Workflows

Bonnefille B, Karlsson O, Rian MB, ..., Islam MS, Martin JW

Environ. Sci. Technol. 57 (17) 6808-6824 [2023-05-02; online 2023-04-21]

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]

Structural elucidation of 3-nitrophenylhydrazine derivatives of tricarboxylic acid cycle acids and optimization of their fragmentation to boost sensitivity in liquid chromatography-mass spectrometry.

Hodek O, Henderson J, Argemi-Muntadas L, Khan A, Moritz T

Journal of Chromatography B 1222 (-) 123719 [2023-05-01; online 2023-04-11]

Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.

Mosquera KD, Nilsson LKJ, de Oliveira MR, ..., de Souza AQL, Terenius O

Parasit Vectors 16 (1) 156 [2023-05-01; online 2023-05-01]

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]

TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data.

Pielawski N, Andersson A, Avenel C, ..., Solorzano L, Wählby C

Heliyon 9 (5) e15306 [2023-05-00; online 2023-04-17]

BioImage Informatics [Technology development]

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.

Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E

Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]

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

Overweight in childhood and young adulthood increases the risk for adult thromboembolic events.

Lilja L, Bygdell M, Martikainen J, ..., Kindblom JM, Ohlsson C

J. Intern. Med. 293 (5) 615-623 [2023-05-00; online 2023-03-01]

Insulin thermostability in a real-world setting.

Pendsey S, James S, Garrett TJ, ..., Forsander G, Ogle GD

Lancet Diabetes Endocrinol 11 (5) 310-312 [2023-05-00; online 2023-03-29]

Full activation of thermogenesis in brown adipocytes requires Basigin action.

Rupar K, Isidor MS, Argemi-Muntadas L, ..., Moritz T, Emanuelli B

FEBS J. 290 (10) 2673-2691 [2023-05-00; online 2023-01-14]

Flexible Organic Electronic Ion Pump for Flow-Free Phytohormone Delivery into Vasculature of Intact Plants.

Bernacka-Wojcik I, Talide L, Abdel Aziz I, ..., Niittylä T, Stavrinidou E

Adv Sci (Weinh) 10 (14) e2206409 [2023-05-00; online 2023-03-19]

B4GALNT3 regulates glycosylation of sclerostin and bone mass.

Movérare-Skrtic S, Voelkl J, Nilsson KH, ..., Henning P, Ohlsson C

EBioMedicine 91 (-) 104546 [2023-05-00; online 2023-04-04]

Prominent epigenetic and transcriptomic changes in CD4+ and CD8+ T cells during and after pregnancy in women with multiple sclerosis and controls.

Zenere A, Hellberg S, Papapavlou Lingehed G, ..., Gustafsson M, Ernerudh J

J Neuroinflammation 20 (1) 98 [2023-04-27; online 2023-04-27]

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

Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.

Rosenbaum A, Dahlin AM, Andersson U, ..., Wibom C, Melin B

Sci Rep 13 (1) 6777 [2023-04-25; online 2023-04-25]

Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.

Majumdar S, Emmerich A, Krakovka S, ..., Svärd SG, Sanyal S

Nucleic Acids Res. 51 (7) 3436-3451 [2023-04-24; online 2023-03-14]

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

Transcriptomics unravels molecular changes associated with cilia and COVID-19 in chronic rhinosinusitis with nasal polyps.

Torinsson Naluai Å, Östensson M, Fowler PC, ..., Harandi AM, Bende M

Sci Rep 13 (1) 6592 [2023-04-21; online 2023-04-21]

Identification of three bacterial species associated with increased appendicular lean mass: the HUNT study.

Grahnemo L, Nethander M, Coward E, ..., Hveem K, Ohlsson C

Nat Commun 14 (1) 2250 [2023-04-20; online 2023-04-20]

Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.

Koskela von Sydow A, Lindqvist CM, Asghar N, ..., Mölling P, Stenmark B

Sci Rep 13 (1) 6461 [2023-04-20; online 2023-04-20]

Clinical Genomics Örebro [Technology development]

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]

Data Processing Methods: Fourier and Beyond

Orekhov V, Kasprzak P, Kazimierczuk K

- - (-) 19-46 [2023-04-14; online 2023-04-21]

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]

Molecular profiling of high-level athlete skeletal muscle after acute exercise – a systems biology approach

Reitzner SM, Emanuelsson EB, Arif M, ..., Chapman MA, Sundberg CJ

- - (-) - [2023-04-11; online 2023-04-11]

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]

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

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]

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

Comparing plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells.

Boussardon C, Carrie C, Keech O

J. Exp. Bot. - (-) - [2023-04-07; online 2023-04-07]

Global Proteomics and Proteogenomics [Service]

Serum metabolomic profiling identifies potential biomarkers in arthritis in older adults: an exploratory study.

Cedeno M, Murillo-Saich J, Coras R, ..., Martinez-Morillo M, Guma M

Metabolomics 19 (4) 37 [2023-04-06; online 2023-04-06]

Cross-Sectional Gene-Smoking Interaction Analysis in Relation to Subclinical Atherosclerosis-Results From the IMPROVE Study.

Maitusong B, Laguzzi F, Strawbridge RJ, ..., Leander K, IMPROVE Study group†

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]

Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.

Magoulopoulou A, Salas SM, Tiklová K, ..., Hilscher MM, Nilsson M

Annu Rev Genomics Hum Genet - (-) - [2023-04-05; online 2023-04-05]

In Situ Sequencing (ISS) [Technology development]

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) 62 (9) 3213-3218 [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]

Metabolomics of early myocardial ischemia.

Hasselbalch RB, Kristensen JH, Strandkjær N, ..., Malmendal A, Iversen KK

Metabolomics 19 (4) 33 [2023-04-01; online 2023-04-01]

Microbial gene activity in straw residue amendments reveals carbon sequestration mechanisms in agricultural soils

Kozjek K, Manoharan L, Urich T, Ahrén D, Hedlund K

Soil Biology and Biochemistry 179 (-) 108994 [2023-04-00; online 2023-04-00]

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

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]

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

Formate overflow drives toxic folate trapping in MTHFD1 inhibited cancer cells.

Green AC, Marttila P, Kiweler N, ..., Henriksson M, Meiser J

Nat Metab 5 (4) 642-659 [2023-04-00; online 2023-04-03]

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]

Effect of alkalinity on the diffusion of solvent-fractionated lignin through cellulose membranes

Ghaffari R, Almqvist H, Idström A, ..., Lawoko M, Larsson A

Cellulose 30 (6) 3685-3698 [2023-04-00; online 2023-02-28]

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]

C-type lectin receptor agonists elicit functional IL21-expressing Tfh cells and induce primary B cell responses in neonates.

Vono M, Mastelic-Gavillet B, Mohr E, ..., Lambert PH, Siegrist CA

Front Immunol 14 (-) 1155200 [2023-03-31; online 2023-03-31]

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] Swedish Metabolomics Centre (SMC) [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]

Temperature-dependent regulation ofArabidopsis thalianagrowth and development byLSM7

Nardeli SM, Zacharaki V, Rojas-Murcia N, ..., Schmid M, Goretti D

- - (-) - [2023-03-29; online 2023-03-29]

On the hydrothermal depolymerisation of kraft lignin using glycerol as a capping agent

Ahlbom A, Maschietti M, Nielsen R, Hasani M, Theliander H

- 77 (3) 159-169 [2023-03-28; online 2023-01-26]

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]

Insights into Photosensitized Reactions for Upgrading Lignin

Riddell A, Hynynen J, Baena-Moreno F, ..., Parkås J, Bernin D

ACS Sustainable Chem. Eng. 11 (12) 4850-4859 [2023-03-27; online 2023-03-15]

Deep learning-based segmentation and quantification of podocyte foot process morphology suggests differential patterns of foot process effacement across kidney pathologies.

Unnersjö-Jess D, Butt L, Höhne M, ..., Bozek K, Benzing T

Kidney Int. - (-) - [2023-03-27; online 2023-03-27]

Integrated Microscopy Technologies Stockholm [Collaborative]

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]

Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants.

Mäkelä AR, Uğurlu H, Hannula L, ..., Rissanen I, Saksela K

Nat Commun 14 (1) 1637 [2023-03-24; online 2023-03-24]

New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus.

Durcik M, Cotman AE, Toplak Ž, ..., Tomašič T, Peterlin Mašič L

J. Med. Chem. 66 (6) 3968-3994 [2023-03-23; online 2023-03-06]

Drug Discovery and Development (DDD) [Service]

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]

Complete Reference Genome Sequence of the Clinical Neisseria gonorrhoeae Strain H035, with Resistance to the Novel Antimicrobial Zoliflodacin, Identified in Japan in 2000.

Golparian D, Jacobsson S, Ohnishi M, Unemo M

Microbiol Resour Announc 12 (3) e0113022 [2023-03-16; online 2023-02-28]

Rapid and accurate determination of protein content in North Atlantic seaweed by NIR and FTIR spectroscopies.

Niemi C, Mortensen AM, Rautenberger R, ..., Gorzsás A, Gentili FG

Food Chem 404 (Pt B) 134700 [2023-03-15; online 2022-10-19]

Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis.

Geroldinger-Simić M, Bayati S, Pohjanen E, ..., Nilsson P, Pin E

Int J Mol Sci 24 (6) - [2023-03-15; online 2023-03-15]

Autoimmunity and Serology Profiling [Collaborative]

A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena.

Conde E Silva N, Leguilloux M, Bellec A, ..., Berges H, Deveaux Y

J. Exp. Bot. 74 (5) 1448-1459 [2023-03-13; online 2022-12-14]

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

Proteome integral solubility alteration high-throughput proteomics assay identifies Collectin-12 as a non-apoptotic microglial caspase-3 substrate.

Grabert K, Engskog-Vlachos P, Škandík M, ..., Joseph B, Cheray M

Cell Death Dis 14 (3) 192 [2023-03-11; online 2023-03-11]

Chemical Proteomics [Service]

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]

Melatonin Prescription in Children and Adolescents in Relation to Body Weight and Age.

Kimland EE, Dahlén E, Martikainen J, Célind J, Kindblom JM

Pharmaceuticals (Basel) 16 (3) - [2023-03-06; online 2023-03-06]

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]

Clinical Genomics Lund [Service]

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]

Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming.

Pateras IS, Williams C, Gianniou DD, ..., Gilthorpe JD, Frisan T

J Transl Med 21 (1) 169 [2023-03-03; online 2023-03-03]

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]

Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.

Pushparaj P, Nicoletto A, Dopico XC, ..., Corcoran M, Karlsson Hedestam GB

Front Virol 3 (-) 1128253 [2023-03-01; online 2023-04-13]

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]

Glycoproteomics [Collaborative]

Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.

Mühleip A, Flygaard RK, Baradaran R, ..., Sharma V, Amunts A

Nature 615 (7954) 934-938 [2023-03-00; online 2023-03-22]

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]

Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children.

Stratmann S, Vesterlund M, Umer HM, ..., Lehtiö J, Holmfeldt L

Leukemia 37 (3) 550-559 [2023-03-00; online 2022-12-26]

Global Proteomics and Proteogenomics [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]

Multidrug-resistant Neisseria gonorrhoeae isolate SE690: mosaic penA-60.001 gene causing ceftriaxone resistance internationally has spread to the more antimicrobial-susceptible genomic lineage, Sweden, September 2022.

Golparian D, Vestberg N, Södersten W, ..., Bhattarai KH, Unemo M

Euro Surveill. 28 (10) - [2023-03-00; online 2023-03-10]

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]

Glycoproteomics [Collaborative]

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]

Chitosan-Modified Polyethyleneimine Nanoparticles for Enhancing the Carboxylation Reaction and Plants' CO2 Uptake.

Routier C, Vallan L, Daguerre Y, ..., Pavlopoulou E, Stavrinidou E

ACS Nano 17 (4) 3430-3441 [2023-02-28; online 2023-02-16]

Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics

Jun SH, 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]

Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.

Sjödin KS, Sjödin A, Ruszczyński M, ..., Szajewska H, West CE

BMC Biol. 21 (1) 38 [2023-02-20; online 2023-02-20]

Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest.

Xu W, Sato H, Bente H, Santos-González J, Köhler C

Plant Cell 35 (2) 874-888 [2023-02-20; online 2022-11-26]

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

Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris.

Christensen S, Stenström O, Akke M, Bülow L

Int J Mol Sci 24 (4) - [2023-02-16; online 2023-02-16]

Boron-Mediated Regioselective Aromatic C-H Functionalization via an Aryl BF2 Complex.

Shinde GH, Sundén H

Chemistry 29 (10) e202203505 [2023-02-16; online 2022-12-23]

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]

Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows

Salas SM, Czarnewski P, Kuemmerle LB, ..., Ishaque N, Nilsson M

- - (-) - [2023-02-14; online 2023-02-14]

In Situ Sequencing (ISS) [Technology development]

Array-Based Multiplex and High-Throughput Serology Assays.

Olofsson J, Hellström C, Andersson E, ..., Nilsson P, Pin E

Methods Mol. Biol. 2628 (-) 535-553 [2023-02-14; online 2023-02-14]

Autoimmunity and Serology Profiling [Technology development]

Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students.

Olof S, Lorraine E, Berhane A I, ..., Paula M, Susanne J

Epidemiol. Infect. 151 (-) e25 [2023-02-13; online 2023-02-13]

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]

Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics.

Salvà-Serra F, Jaén-Luchoro D, Marathe NP, ..., Moore ERB, Karlsson R

Front Microbiol 13 (-) 1089140 [2023-02-09; online 2023-02-09]

Clinical Genomics Gothenburg [Service]

Primary Structure of Glycans by NMR Spectroscopy.

Fontana C, Widmalm G

Chem. Rev. 123 (3) 1040-1102 [2023-02-08; online 2023-01-09]

A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function.

Bahnan W, Happonen L, Khakzad H, ..., Malmström J, Nordenfelt P

EMBO Mol Med 15 (2) e16208 [2023-02-08; online 2022-12-12]

Microneedle Patch for Painless Intradermal Collection of Interstitial Fluid Enabling Multi-analyte Measurement of Small Molecules, SARS-CoV-2 Antibodies, and Protein Profiling.

Ribet F, Bendes A, Fredolini C, ..., Stemme G, Roxhed N

Adv Healthc Mater - (-) e2202564 [2023-02-07; online 2023-02-07]

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data.

Gustafsson J, Anton M, Roshanzamir F, ..., Robinson JL, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 120 (6) e2217868120 [2023-02-07; online 2023-01-31]

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

GAUT10 is required for Arabidopsis root cell differentiation and elongation

Dash L, Swaminathan S, Šimura J, ..., Zabotina OA, Kelley DR

- - (-) - [2023-02-07; online 2023-02-07]

Cohort profile: The Clinical and Multi-omic (CAMO) cohort, part of the Norwegian Women and Cancer (NOWAC) study.

Delgado AB, Tylden ES, Lukic M, ..., Lund E, Olsen KS

PLoS ONE 18 (2) e0281218 [2023-02-06; online 2023-02-06]

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

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 and Infrastructure [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]

Simultaneous membrane and RNA binding by tick-borne encephalitis virus capsid protein.

Pulkkinen LIA, Barrass SV, Lindgren M, ..., Lundmark R, Butcher SJ

PLoS Pathog. 19 (2) e1011125 [2023-02-00; online 2023-02-14]

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]

Clinical Genomics Lund [Service]

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]

Chemical composition and species identification of microalgal biomass grown at pilot-scale with municipal wastewater and CO2 from flue gases.

Lage S, Gentili FG

Chemosphere 313 (-) 137344 [2023-02-00; online 2022-11-26]

Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions

Maheshwari A, Jones CM, Tiemann M, Hallin S

Soil Biology and Biochemistry 177 (-) 108909 [2023-02-00; online 2023-02-00]

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] In Situ Sequencing (ISS) [Service] 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]

The motor system is exceptionally vulnerable to absence of the ubiquitously expressed superoxide dismutase-1.

Park JH, Nordström U, Tsiakas K, ..., Marklund SL, Andersen PM

Brain Commun 5 (1) fcad017 [2023-01-27; online 2023-01-27]

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]

Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.

Cotman AE, Durcik M, Benedetto Tiz D, ..., Sterk GJ, Kikelj D

J. Med. Chem. 66 (2) 1380-1425 [2023-01-26; online 2023-01-12]

Drug Discovery and Development (DDD) [Service]

Biocontrol Effect of Clonostachys rosea on Fusarium graminearum Infection and Mycotoxin Detoxification in Oat (Avena sativa).

Khairullina A, Micic N, Jørgensen HJL, ..., Collinge DB, Jensen B

Plants (Basel) 12 (3) - [2023-01-21; online 2023-01-21]

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

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]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Lund [Service]

Fluorogenic properties of 4-dimethylaminocinnamaldehyde (DMACA) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues.

Chowdhury J, Ferdous J, Lihavainen J, Albrectsen BR, Lundberg-Felten J

Front Plant Sci 13 (-) 1060804 [2023-01-16; online 2023-01-16]

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

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]

Clinical Genomics Stockholm [Service]

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 (-) 1079995 [2023-01-10; online 2023-01-10]

Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.

Pushparaj P, Nicoletto A, Sheward DJ, ..., Corcoran M, Karlsson Hedestam GB

Immunity 56 (1) 193-206.e7 [2023-01-10; online 2022-12-12]

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

Koptekin D, Yüncü E, Rodríguez-Varela R, ..., Götherström A, Somel M

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

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

Identification of novel autoantigens as potential biomarkers in juvenile idiopathic arthritis associated uveitis.

Arve-Butler S, Mossberg A, Kahn F, ..., Månsson B, Kahn R

Front Pediatr 10 (-) 1091308 [2023-01-09; online 2023-01-09]

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.

Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, ..., Helgason A, Götherström A

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.

Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL

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]

Cytokinin signaling regulates two-stage inflorescence arrest in Arabidopsis.

Walker CH, Ware A, Šimura J, ..., Wilson Z, Bennett T

Plant Physiol. 191 (1) 479-495 [2023-01-02; online 2022-11-05]

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]

Clinical Genomics Gothenburg [Service] Clinical Genomics Lund [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 145 (1) 13-28 [2023-01-00; online 2022-11-16]

Integrated Microscopy Technologies Umeå [Service]

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 43 (1) 136-150 [2023-01-00; online 2022-09-02]

Cellular Immunomonitoring [Collaborative] Clinical Genomics Stockholm [Service]

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]

NMR spectrum reconstruction as a pattern recognition problem.

Jahangiri A, Han X, Lesovoy D, ..., Achour A, Orekhov V

J Magn Reson 346 (-) 107342 [2023-01-00; online 2022-11-24]

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.

Gueto-Tettay C, Tang D, Happonen L, ..., Malmström J, Malmström L

PLoS Comput. Biol. 19 (1) e1010457 [2023-01-00; online 2023-01-20]

Structural Proteomics [Technology development]

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]

Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3

Behanova A, Avenel C, Andersson A, ..., Östman A, Wählby C

Biol. Imaging 3 (-) - [2023-00-00; online 2023-02-20]

BioImage Informatics [Technology development]

Influence of Divalent Cations on the Extraction of Organic Acids in Coffee Determined by Gc-Ms and Nmr

Bratthäll T, Figueira J, Nording ML

- - (-) - [2023-00-00; online 2023-00-00]