Publications 2022

<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]

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]

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]

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

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]

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]

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

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]

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]

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]

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 PL, Batista R, Andermann T, ..., Bacon CD, Antonelli A

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

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

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]

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]

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]

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 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]

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]

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

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

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]

Integrated Microscopy Technologies Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

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

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

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

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]

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

Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.

Stsiapanava A, Xu C, Nishio S, ..., Wu B, Jovine L

Nat. Struct. Mol. Biol. 29 (3) 190-193 [2022-03-00; online 2022-03-10]

Cryo-EM [Collaborative]

Pseudouridine-modified tRNA fragments repress aberrant protein synthesis and predict leukaemic progression in myelodysplastic syndrome.

Guzzi N, Muthukumar S, Cieśla M, ..., Dimitriou M, Bellodi C

Nat Cell Biol 24 (3) 299-306 [2022-03-00; online 2022-03-15]

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]

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

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]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [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]

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

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]

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

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]

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

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]

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

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]

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

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]

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]

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

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]

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

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 XQ, Zhang DD, Powell D, ..., Andersson MN, Löfstedt C

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

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

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]

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

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]

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

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]

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

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]

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

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]

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]

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]

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

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]

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

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]

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

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]

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

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]

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

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]

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

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]

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

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 AL

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

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

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 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 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]

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

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

Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.

Yekta SS, Elreedy A, Liu T, ..., Fujii M, Schnürer A

Sci. Total Environ. - (-) 152967 [2022-01-08; online 2022-01-08]

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]

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

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]