Publications 2022

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) - [2022-12-00; online 2022-06-13]

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, ..., None , None

Commun Biol 5 (1) - [2022-12-00; online 2022-06-13]

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

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]

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]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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 - (-) - [2022-09-07; online 2022-09-07]

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

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]

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. - (-) - [2022-09-04; online 2022-09-04]

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

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]

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]

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]

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]

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]

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

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]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

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] 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]

Cryo-EM [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]

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

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

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

Genome Res. - (-) - [2022-08-10; online 2022-08-10]

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

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

Ageing desexualizes the <i>Drosophila</i> brain transcriptome

Malacrinò A, Brengdahl MI, Kimber CM, ..., Mirabello C, Friberg U

Proc. R. Soc. B 289 (1980) - [2022-08-10; online 2022-08-10]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [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 - (-) - [2022-08-04; online 2022-08-04]

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

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]

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 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]

NGI Long read [Service] NGI Short read [Service] National Genomics Infrastructure [Service]

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 Single cell [Service] NGI Spatial omics [Service] National Genomics Infrastructure [Service]

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]

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]

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

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]

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]

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

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]

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 [Service]

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]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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 [2022-08-00; online 2022-08-00]

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

Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.

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

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

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

Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria.

Li P, Hendricks AL, Wang Y, ..., Wang K, Gourdon P

Nat Commun 13 (1) 4339 [2022-07-27; online 2022-07-27]

Cryo-EM

Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.

Rodríguez J, Andersson A, Björn E, ..., Skrobonja A, Rowe O

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

NGI Short read [Service] National Genomics Infrastructure [Service]

Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells.

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

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

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

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

Costa Svedman F, Das I, Tuominen R, ..., Höiom V, Egyhazi Brage S

Cancers (Basel) 14 (15) - [2022-07-22; online 2022-07-22]

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

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. - (-) - [2022-07-21; online 2022-07-21]

Cryo-EM

Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.

Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L

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

NGI Short read [Service] NGI Single cell [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 - (-) - [2022-07-19; online 2022-07-19]

NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]

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]

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.

Carreca AP, Gaetani M, Busà R, ..., Conaldi PG, Badami E

Viruses 14 (7) - [2022-07-14; online 2022-07-14]

Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.

Kuhl H, Du K, Schartl M, ..., Stöck M, Lamatsch DK

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

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

A Hitchhiker's guide through the bio-image analysis software universe.

Haase R, Fazeli E, Legland D, ..., Klemm A, Tischer C

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

BioImage Informatics [Collaborative]

Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.

Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR

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

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

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]

NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [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]

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] 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]

NGI Short read [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 - (-) - [2022-07-08; online 2022-07-08]

NGI Short read [Service] National Genomics Infrastructure [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) - (-) - [2022-07-08; online 2022-07-08]

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

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]

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] 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 (-) - [2022-07-05; online 2022-07-05]

Clinical Genomics Stockholm [Service]

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] 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]

NGI Short read [Service] National Genomics Infrastructure [Service]

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]

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]

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

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]

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]

NGI Short read [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]

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

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 Genome Engineering Zebrafish [Service]

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]

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] National Genomics Infrastructure [Service]

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 - (-) 2200008 [2022-06-14; online 2022-06-14]

Drug Discovery and Development (DDD) [Collaborative]

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. - (-) - [2022-06-13; online 2022-06-13]

BioImage Informatics [Technology development]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

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

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

Blood Adv - (-) - [2022-06-08; online 2022-06-08]

NGI Short read [Service] National Genomics Infrastructure [Service]

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]

NGI Short read [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]

NGI Short read [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]

NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]

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]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

<i>Scipion-ED</i>: 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 Cryst J Appl Crystallogr 55 (3) - [2022-06-01; online 2022-04-22]

Cryo-EM [Technology development]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

The immune cell atlas of human neuroblastoma

Verhoeven BM, Mei S, Olsen TK, ..., Johnsen JI, Baryawno N

Cell Reports Medicine - (-) 100657 [2022-06-00; online 2022-06-00]

Spatial Proteomics [Service]

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]

NGI Short read [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]

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

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]

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]

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

A new transgenic reporter line reveals expression of protocadherin 9 at a cellular level within the zebrafish central nervous system.

Habicher J, Manuel R, Pedroni A, ..., Ampatzis K, Boije H

Gene Expr Patterns 44 (-) 119246 [2022-06-00; online 2022-04-12]

Genome Engineering Zebrafish [Collaborative]

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

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

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

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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 (-) - [2022-05-26; online 2022-05-26]

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

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]

National Genomics Infrastructure

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

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] National Genomics Infrastructure [Service]

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]

Cryo-EM

Satellite DNA evolution in Corvoidea inferred from short and long reads

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

Mol Ecol - (-) - [2022-05-14; online 2022-05-14]

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

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. - (-) - [2022-05-12; online 2022-05-12]

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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]

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]

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

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

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

National Genomics Infrastructure

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]

NGI Short read [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] 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]

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

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]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

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]

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]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

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]

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 - (-) - [2022-04-28; online 2022-04-28]

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

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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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]

Auxilin is a novel susceptibility gene for congenital heart block which directly impacts fetal heart function.

Meisgen S, Hedlund M, Ambrosi A, ..., Sonesson SE, Wahren-Herlenius M

Ann. Rheum. Dis. - (-) - [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]

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

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]

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

Autoimmunity and Serology Profiling [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]

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]

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]

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]

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]

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]

NGI Short read [Service] National Genomics Infrastructure [Service]

Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.

Lewerentz J, Johansson AM, Larsson J, Stenberg P

BMC Genomics 23 (1) 276 [2022-04-07; online 2022-04-07]

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]

Microbial Single Cell Genomics NGI Single cell [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

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]

Glycoproteomics [Collaborative]

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]

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]

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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 [2022-04-00; online 2022-04-00]

Affinity Proteomics Stockholm [Service]

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]

Environmentally-induced DNA methylation is inherited across generations in an aquatic keystone species

Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T

iScience - (-) 104303 [2022-04-00; online 2022-04-00]

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

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

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]

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]

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]

NGI Short read [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

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

Spatial Proteomics

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]

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. - (-) - [2022-03-22; online 2022-03-22]

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

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]

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]

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]

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]

National Genomics Infrastructure [Service]

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 (-) - [2022-03-14; online 2022-03-14]

Integrated Microscopy Technologies Stockholm [Service]

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

- - (-) - [2022-03-09; online 2022-03-09]

Integrated Microscopy Technologies Stockholm [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 - (-) - [2022-03-08; online 2022-03-08]

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

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]

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)

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]

Cryo-EM

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]

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 [2022-03-01; online 2021-11-18]

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

Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.

Stenudd M, Sabelström H, Llorens-Bobadilla E, ..., Barnabé-Heider F, Frisén J

Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]

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GWAS in people of Middle Eastern descent reveals a locus protective of kidney function-a cross-sectional study.

Mohamed SA, Fernadez-Tajes J, Franks PW, Bennet L

BMC Med 20 (1) 76 [2022-03-01; online 2022-03-01]

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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern.

Ernst M, Jønsson KA, Ericson PGP, Blom MPK, Irestedt M

Heredity (Edinb) 128 (3) 159-168 [2022-03-00; online 2022-01-26]

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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]

Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?

Ljungström V, Mattisson J, Halvardson J, ..., Baliakas P, Forsberg LA

Leukemia 36 (3) 889-891 [2022-03-00; online 2021-11-01]

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Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.

Mueller JC, Botero-Delgadillo E, Espíndola-Hernández P, ..., Gruselius J, Kempenaers B

Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]

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Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris).

Kardum Hjort C, Paris JR, Olsson P, ..., Dudaniec RY, Smith HG

Evol Appl 15 (3) 365-382 [2022-03-00; online 2022-03-14]

NGI Short read [Service] National Genomics Infrastructure [Service]

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.

Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J

Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]

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Blood protein profiles related to preterm birth and retinopathy of prematurity.

Danielsson H, Tebani A, Zhong W, ..., Uhlén M, Hellström A

Pediatr. Res. 91 (4) 937-946 [2022-03-00; online 2021-04-24]

Affinity Proteomics Stockholm [Service]

Soil phosphorus forms show only minor changes across a 5000-year-old boreal wildfire chronosequence

Vincent AG, Schleucher J, Giesler R, Wardle DA

Biogeochemistry - (-) - [2022-02-27; online 2022-02-27]

Duration of SARS-CoV-2 Immune Responses Up to Six Months Following Homologous or Heterologous Primary Immunization with ChAdOx1 nCoV-19 and BNT162b2 mRNA Vaccines.

Marking U, Havervall S, Greilert-Norin N, ..., Åberg M, Thålin C

Vaccines (Basel) 10 (3) - [2022-02-24; online 2022-02-24]

Autoimmunity and Serology Profiling [Collaborative]

Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Luttens A, Gullberg H, Abdurakhmanov E, ..., Danielson UH, Carlsson J

J. Am. Chem. Soc. 144 (7) 2905-2920 [2022-02-23; online 2022-02-10]

Chemical Biology Consortium Sweden (CBCS) [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. - (-) - [2022-02-22; online 2022-02-22]

Clinical Genomics Stockholm [Technology development]

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 - (-) - [2022-02-19; online 2022-02-19]

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Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

Nguyen D, Peona V, Unneberg P, ..., Jern P, Johannesson H

Fungal Genetics Reports 66 (1) - [2022-02-18; online 2022-02-18]

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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.

Sturk-Andreaggi K, Ring JD, Ameur A, ..., Marshall C, Allen M

Int J Mol Sci 23 (4) - [2022-02-17; online 2022-02-17]

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Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.

André D, Zambrano JA, Zhang B, ..., Marcon A, Nilsson O

Front Plant Sci 13 (-) 823019 [2022-02-17; online 2022-02-17]

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Longitudinal Serum Metabolomics in Extremely Premature Infants: Relationships With Gestational Age, Nutrition, and Morbidities.

Nilsson AK, Tebani A, Malmodin D, ..., Uhlén M, Hellström A

Front. Neurosci. 16 (-) 830884 [2022-02-17; online 2022-02-17]

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 - (-) - [2022-02-15; online 2022-02-15]

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

Production of Exopolysaccharides by Cultivation of Halotolerant Bacillus atrophaeus BU4 in Glucose- and Xylose-Based Synthetic Media and in Hydrolysates of Quinoa Stalks

Chambi D, Lundqvist J, Nygren E, ..., Jönsson LJ, Martín C

Fermentation 8 (2) 79 [2022-02-14; online 2022-02-14]

Differences between Arterial and Venous Umbilical Cord Plasma Metabolome and Association with Parity.

Hartvigsson O, Barman M, Savolainen O, ..., Sandberg AS, Brunius C

Metabolites 12 (2) - [2022-02-13; online 2022-02-13]

Swedish Metabolomics Centre (SMC)

1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution.

Agback P, Lesovoy DM, Han X, ..., Achour A, Orekhov VY

Biomol NMR Assign - (-) - [2022-02-12; online 2022-02-12]

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.

Vickovic S, Schapiro D, Carlberg K, ..., Regev A, Ståhl PL

Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]

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The spatial transcriptomic landscape of the healing mouse intestine following damage.

Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ

Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]

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NMR Backbone Assignment of VIM-2 and Identification of the Active Enantiomer of a Potential Inhibitor

Wieske LHE, Bogaerts J, Leding AAM, ..., Bayer A, Erdélyi M

ACS Med Chem Lett 13 (2) 257-261 [2022-02-10; online 2022-01-28]

Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae.

Nadeem A, Berg A, Pace H, ..., Uhlin BE, Wai SN

Elife 11 (-) - [2022-02-08; online 2022-02-08]

Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service] Swedish NMR Centre (SNC) [Collaborative]

Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters.

Palica K, Vorácová M, Skagseth S, ..., Andersson H, Erdélyi M

ACS Omega 7 (5) 4550-4562 [2022-02-08; online 2022-01-25]

Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids.

Hou X, Zhang D, Powell D, ..., Andersson MN, Löfstedt C

BMC Biol. 20 (1) 34 [2022-02-07; online 2022-02-07]

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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.

Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A

Front Genet 12 (-) 803683 [2022-02-04; online 2022-02-04]

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Mutation analysis of disease causing genes in patients with early onset or familial forms of Alzheimer's disease and frontotemporal dementia.

Pagnon de la Vega M, Näslund C, Brundin R, ..., Ingelsson M, Giedraitis V

BMC Genomics 23 (1) 99 [2022-02-04; online 2022-02-04]

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

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 - (-) - [2022-02-04; online 2022-02-04]

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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.

Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T

Sci Adv 8 (5) eabl6496 [2022-02-04; online 2022-02-04]

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A Sparse Model-Inspired Deep Thresholding Network for Exponential Signal Reconstruction--Application in Fast Biological Spectroscopy.

Wang Z, Guo D, Tu Z, ..., Orekhov V, Qu X

IEEE Trans Neural Netw Learn Syst PP (-) - [2022-02-04; online 2022-02-04]

ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.

Widmark A, Sagredo EA, Karlström V, ..., Daniel C, Öhman M

J. Biol. Chem. 298 (3) 101682 [2022-02-03; online 2022-02-03]

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Urinary Metabolomic Changes Accompanying Albuminuria Remission following Gastric Bypass Surgery for Type 2 Diabetic Kidney Disease.

Martin WP, Malmodin D, Pedersen A, ..., le Roux CW, Docherty NG

Metabolites 12 (2) 139 [2022-02-02; online 2022-02-22]

Comprehensive Peak Characterization (CPC) in Untargeted LC-MS Analysis.

Pirttilä K, Balgoma D, Rainer J, ..., Hedeland M, Brunius C

Metabolites 12 (2) - [2022-02-02; online 2022-02-02]

Swedish Metabolomics Centre (SMC) [Technology development]

CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations.

Höijer I, Emmanouilidou A, Östlund R, ..., den Hoed M, Ameur A

Nat Commun 13 (1) 627 [2022-02-02; online 2022-02-02]

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

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides.

Rush JS, Parajuli P, Ruda A, ..., Widmalm G, Korotkova N

Nat Commun 13 (1) 590 [2022-02-01; online 2022-02-01]

ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal.

Jalalvand E, Alvelid J, Coceano G, ..., Grillner S, Testa I

Elife 11 (-) - [2022-02-01; online 2022-02-01]

Integrated Microscopy Technologies Stockholm [Service]

The antimicrobial drug pyrimethamine inhibits STAT3 transcriptional activity by targeting the enzyme dihydrofolate reductase.

Heppler LN, Attarha S, Persaud R, ..., Page BDG, Frank DA

J. Biol. Chem. 298 (2) 101531 [2022-02-00; online 2021-12-23] Open Access

Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.

Hernandez-Castro LE, Villacís AG, Jacobs A, ..., Llewellyn MS, Grijalva MJ

PLoS Genet. 18 (2) e1010019 [2022-02-00; online 2022-02-04]

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Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress.

Bonagas N, Gustafsson NMS, Henriksson M, ..., Homan EJ, Helleday T

Nat Cancer 3 (2) 156-172 [2022-02-00; online 2022-02-28]

Drug Discovery and Development (DDD) [Collaborative]

Links between boreal forest management, soil fungal communities and below‐ground carbon sequestration

Jörgensen K, Granath G, Strengbom J, Lindahl BD

Functional Ecology 36 (2) 392-405 [2022-02-00; online 2021-12-22]

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

Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding

Eshghi Sahraei S, Furneaux B, Kluting K, ..., Hytteborn H, Rosling A

Ecol Evol 12 (3) - [2022-02-00; online 2022-03-08]

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In situ 13 C solid-state polarization transfer NMR to follow starch transformations in food.

Nowacka-Perrin A, Steglich T, Topgaard D, Bernin D

Magn Reson Chem - (-) - [2022-01-30; online 2022-01-30]

Longitudinal analyses of development of the immune system during the first five years of life in relation to lifestyle.

Olin A, Acevedo N, Lakshmikanth T, ..., Scheynius A, Brodin P

Allergy - (-) - [2022-01-29; online 2022-01-29]

Cellular Immunomonitoring [Collaborative]

Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter.

Chaptal V, Zampieri V, Wiseman B, ..., Boumendjel A, Falson P

Sci Adv 8 (4) eabg9215 [2022-01-28; online 2022-01-26]

Cryo-EM [Service]

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 - (-) - [2022-01-28; online 2022-01-28]

Autoimmunity and Serology Profiling [Service]

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

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

Neuron - (-) - [2022-01-28; online 2022-01-28]

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Intramolecular carbon isotope signals reflect metabolite allocation in plants.

Wieloch T, Sharkey TD, Werner RA, Schleucher J

J. Exp. Bot. - (-) - [2022-01-27; online 2022-01-27]

Medications Activating Tubular Fatty Acid Oxidation Enhance the Protective Effects of Roux-en-Y Gastric Bypass Surgery in a Rat Model of Early Diabetic Kidney Disease.

Martin WP, Chuah YHD, Abdelaal M, ..., le Roux CW, Docherty NG

Front Endocrinol (Lausanne) 12 (-) 757228 [2022-01-26; online 2022-01-26]

Standards recommendations for the Earth BioGenome Project.

Lawniczak MKN, Durbin R, Flicek P, ..., Lewin HA, Richards S

Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-20]

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

Occasional paternal inheritance of the germline-restricted chromosome in songbirds.

Pei Y, Forstmeier W, Ruiz-Ruano FJ, ..., Suh A, Kempenaers B

Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]

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Massive genome inversion drives coexistence of divergent morphs in common quails.

Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, ..., Leonard JA, Vilà C

Curr. Biol. 32 (2) 462-469.e6 [2022-01-24; online 2021-11-29]

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Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.

Berggren H, Tibblin P, Yıldırım Y, ..., Lundin D, Forsman A

Front Microbiol 12 (-) 767770 [2022-01-21; online 2022-01-21]

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Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.

Nilsson E, Li K, Hoetzinger M, Holmfeldt K

Environ. Microbiol. - (-) - [2022-01-20; online 2022-01-20]

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An Image-Analysis-Based Method for the Prediction of Recombinant Protein Fiber Tensile Strength.

Bäcklund FG, Schmuck B, Miranda GHB, ..., Rydén J, Rising A

Materials (Basel) 15 (3) - [2022-01-18; online 2022-01-18]

BioImage Informatics [Collaborative]

Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt.

de Miranda JR, Brettell LE, Chejanovsky N, ..., Martin SJ, Ball BV

Virol J 19 (1) 12 [2022-01-15; online 2022-01-15]

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

Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.

Öhlund P, Delhomme N, Hayer J, Hesson JC, Blomström A

Int J Mol Sci 23 (2) - [2022-01-14; online 2022-01-14]

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Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.

Ghadamgahi F, Tarighi S, Taheri P, ..., Ortiz R, Vetukuri RR

Biology (Basel) 11 (1) - [2022-01-14; online 2022-01-14]

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

3D Microvascularized Tissue Models by Laser-Based Cavitation Molding of Collagen.

Enrico A, Voulgaris D, Östmans R, ..., Herland A, Stemme G

Adv Mater - (-) e2109823 [2022-01-14; online 2022-01-14]

Integrated Microscopy Technologies Stockholm [Service]

Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer.

Thomas CE, Dahl L, Byström S, ..., Schwenk JM, Gabrielson M

Transl Oncol 17 (-) 101339 [2022-01-13; online 2022-01-13]

Affinity Proteomics Stockholm [Service]

The formation of avian montane diversity across barriers and along elevational gradients.

Pujolar JM, Blom MPK, Reeve AH, ..., Irestedt M, Jønsson KA

Nat Commun 13 (1) 268 [2022-01-12; online 2022-01-12]

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

SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection.

Havervall S, Jernbom Falk A, Klingström J, ..., Nilsson P, Thålin C

PLoS ONE 17 (1) e0262169 [2022-01-12; online 2022-01-12]

Autoimmunity and Serology Profiling [Collaborative]

Anaplerotic flux into the Calvin-Benson cycle: hydrogen isotope evidence for in vivo occurrence in C3 metabolism.

Wieloch T, Augusti A, Schleucher J

New Phytol. - (-) - [2022-01-12; online 2022-01-12]

Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.

Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L

Blood Adv 6 (1) 152-164 [2022-01-11; online 2021-10-08]

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

Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.

Westmeijer G, Mehrshad M, Turner S, ..., Bertilsson S, Dopson M

Commun Biol 5 (1) 37 [2022-01-11; online 2022-01-11]

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Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.

Chachoua I, Tzelepis I, Dai H, ..., Mehmood R, Göndör A

Nat Commun 13 (1) 204 [2022-01-11; online 2022-01-11]

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

Fungal Perspective of Pine and Oak Colonization in Mediterranean Degraded Ecosystems

Adamo I, Dashevskaya S, Alday JG

Forests 13 (1) 88 [2022-01-08; online 2022-01-08]

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

Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.

Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T

Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]

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

MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome".

Das SK, Kuzin V, Cameron DP, ..., Levens D, Baranello L

Mol. Cell 82 (1) 140-158.e12 [2022-01-06; online 2021-12-09]

CRISPR Functional Genomics [Service]

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.

Romdhane S, Spor A, Banerjee S, ..., Saghai A, Philippot L

Environ Microbiome 17 (1) 1 [2022-01-06; online 2022-01-06]

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Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.

Mennuni M, Filograna R, Felser A, ..., Lytovchenko O, Larsson N

EMBO Rep. 23 (1) e53054 [2022-01-05; online 2021-11-15]

CRISPR Functional Genomics [Service] NGI Short read [Service] National Genomics Infrastructure [Service]

Backbone chemical shift assignment and dynamics of the N-terminal domain of ClpB from Francisella tularensis type VI secretion system.

Mushtaq AU, Ådén J, Alam A, Sjöstedt A, Gröbner G

Biomol NMR Assign - (-) - [2022-01-05; online 2022-01-05]

Risk of Revision After Arthroplasty Associated with Specific Gene Loci: A Genomewide Association Study of Single-Nucleotide Polymorphisms in 1,130 Twins Treated with Arthroplasty.

Brüggemann A, Eriksson N, Michaëlsson K, Hailer NP

J Bone Joint Surg Am - (-) - [2022-01-04; online 2022-01-04]

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

Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.

Skaftason A, Qu Y, Abdulla M, ..., Rosenquist R, Mansouri L

Genes Chromosomes Cancer 61 (1) 27-36 [2022-01-00; online 2021-10-23]

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

Sustained Response to Entrectinib in an Infant With a Germline ALKAL2 Variant and Refractory Metastatic Neuroblastoma With Chromosomal 2p Gain and Anaplastic Lymphoma Kinase and Tropomyosin Receptor Kinase Activation

Treis D, Umapathy G, Fransson S, ..., Martinsson T, Kogner P

JCO Precision Oncology - (6) - [2022-01-00; online 2022-01-00]

Clinical Genomics Stockholm [Service]

Super-Resolution Imaging of the Filtration Barrier Suggests a Role for Podocin R229Q in Genetic Predisposition to Glomerular Disease.

Butt L, Unnersjö-Jess D, Höhne M, ..., Schermer B, Benzing T

J. Am. Soc. Nephrol. 33 (1) 138-154 [2022-01-00; online 2021-12-01]

Integrated Microscopy Technologies Stockholm [Collaborative]

Salivary IgG to SARS-CoV-2 indicates seroconversion and correlates to serum neutralization in mRNA-vaccinated immunocompromised individuals

Healy K, Pin E, Chen P, ..., Aleman S, Chen MS

Med - (-) - [2022-01-00; online 2022-01-00]

Autoimmunity and Serology Profiling [Collaborative]

Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.

Benz C, Ali M, Krystkowiak I, ..., Davey NE, Ivarsson Y

Mol. Syst. Biol. 18 (1) e10584 [2022-01-00; online 2022-01-20]

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

Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells

Hühn D, Martí‐Rodrigo P, Mouron S, ..., Carreras‐Puigvert J, Fernandez‐Capetillo O

Mol Oncol 16 (1) 148-165 [2022-01-00; online 2021-08-29]

Chemical Biology Consortium Sweden (CBCS) [Service]

Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors.

Brem J, Panduwawala T, Hansen JU, ..., Walsh TR, Schofield CJ

Nat Chem 14 (1) 15-24 [2022-01-00; online 2021-12-13]

Drug Discovery and Development (DDD) [Service]

Fibroblast growth factor 23 is associated with risk of intracerebral hemorrhage.

Svensson EH, Söderholm M

Eur. J. Neurol. 29 (1) 114-120 [2022-01-00; online 2021-08-31]

Affinity Proteomics Uppsala [Service]

Exploiting low-grade waste heat to produce electricity through supercapacitor containing carbon electrodes and ionic liquid electrolytes

Haque M, Abdurrokhman I, Idström A, ..., Lundgren P, Enoksson P

Electrochimica Acta 403 (-) 139640 [2022-01-00; online 2022-01-00]

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity.

Fallerini C, Picchiotti N, Baldassarri M, ..., Renieri A, Furini S

Hum. Genet. 141 (1) 147-173 [2022-01-00; online 2021-12-10]

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

Amplification of ERBB2 (HER2) in embryonal rhabdomyosarcoma: A potential treatment target in rare cases?

Mitra S, Sydow S, Magnusson L, ..., Gisselsson D, Mertens F

Genes Chromosomes Cancer 61 (1) 5-9 [2022-01-00; online 2021-09-01]

Clinical Genomics Lund [Service]

Metabolomics analysis of cerebrospinal fluid suggests citric acid cycle aberrations in bipolar disorder

Smedler E, Salehi AM, Pelanis A, ..., Sparding T, Landén M

Neuroscience Applied 1 (-) 100108 [2022-00-00; online 2022-00-00]

Design of a green chemoenzymatic cascade for scalable synthesis of bio-based styrene alternatives

Petermeier P, Bittner JP, Müller S, Byström E, Kara S

Green Chem. - (-) - [2022-00-00; online 2022-00-00]

A complementary chemical probe approach towards customized studies of G-quadruplex DNA structures in live cells

Prasad B, Doimo M, Andréasson M, ..., Chorell E, Wanrooij S

Chem. Sci. 13 (8) 2347-2354 [2022-00-00; online 2022-00-00]