Publications

Inherent backbone dynamics fine-tune the functional plasticity of Tudor domains.

Kawale AA, Burmann BM

Structure 29 (11) 1253-1265.e4 [2021-11-04; online 2021-06-30]

A common polymorphism in the dopamine transporter gene predicts working memory performance and in vivo dopamine integrity in aging.

Karalija N, Köhncke Y, Düzel S, ..., Lindenberger U, Brandmaier AM

Neuroimage 245 (-) 118707 [2021-11-03; online 2021-11-03]

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

cGMP-PKG dependent transcriptome in normal and degenerating retinas: Novel insights into the retinitis pigmentosa pathology.

Zhou J, Rasmussen M, Ekström P

Exp. Eye Res. 212 (-) 108752 [2021-11-00; online 2021-08-31]

Systemic Inflammation in Preclinical Ulcerative Colitis.

Bergemalm D, Andersson E, Hultdin J, ..., Karling P, Halfvarson J

Gastroenterology 161 (5) 1526-1539.e9 [2021-11-00; online 2021-07-21]

Risk of SARS-CoV-2 exposure among hospital healthcare workers in relation to patient contact and type of care.

Klevebro S, Bahram F, Elfström KM, ..., Dillner J, Melén E

Scand J Public Health 49 (7) 707-712 [2021-11-00; online 2021-06-19]

Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms.

Lehtiö J, Arslan T, Siavelis I, ..., Staaf J, Orre LM

Nat Cancer 2 (11) 1224-1242 [2021-11-00; online 2021-11-22]

Global Proteomics and Proteogenomics [Technology development]

Multiplex protein screening of biomarkers associated with major bleeding in patients with atrial fibrillation treated with oral anticoagulation.

Siegbahn A, Lindbäck J, Hijazi Z, ..., Yusuf S, Wallentin L

J. Thromb. Haemost. 19 (11) 2726-2737 [2021-11-00; online 2021-08-24]

Affinity Proteomics Uppsala [Collaborative]

Longitudinal study of Staphylococcus aureus genotypes isolated from bovine clinical mastitis.

Leijon M, Atkins E, Persson Waller K, Artursson K

J Dairy Sci 104 (11) 11945-11954 [2021-11-00; online 2021-08-26]

Increased diagnostic sensitivity of palpation-guided thyroid nodule fine-needle aspiration cytology by BRAF V600E-mutation analysis.

Gimm O, Ivansson K, Beka E, ..., Garvin S, Söderkvist P

J Pathol Clin Res 7 (6) 556-564 [2021-11-00; online 2021-06-22]

Clinical Genomics Linköping [Collaborative]

Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.

Kawahara R, Chernykh A, Alagesan K, ..., Packer NH, Thaysen-Andersen M

Nat. Methods 18 (11) 1304-1316 [2021-11-00; online 2021-11-01]

Glycoproteomics [Technology development]

BMP2-induction of FN14 promotes protumorigenic signaling in gynecologic cancer cells.

Fukuda T, Fukuda R, Koinuma D, ..., Miyazono K, Heldin CH

Cell. Signal. 87 (-) 110146 [2021-11-00; online 2021-09-10]

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

Antibacterial activity of apramycin at acidic pH warrants wide therapeutic window in the treatment of complicated urinary tract infections and acute pyelonephritis.

Becker K, Cao S, Nilsson A, ..., Liepinsh E, Hobbie SN

EBioMedicine 73 (-) 103652 [2021-11-00; online 2021-11-02]

5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA.

Kugelberg U, Nätt D, Skog S, Kutter C, Öst A

RNA Biol 18 (11) 1588-1599 [2021-11-00; online 2020-12-31]

Utredning av den initiala smittspridningen av SARS-CoV-2 till och inom Sverige

Dyrdak R, Albert J

SOU 89 (-) - [2021-10-29]

Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line.

Öhlund P, Hayer J, Hesson JC, Blomström AL

Viruses 13 (11) - [2021-10-29; online 2021-10-29]

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

Microbial Plankton Community Structure and Function Responses to Vitamin B12 and B1 Amendments in an Upwelling System.

Joglar V, Pontiller B, Martínez-García S, ..., Fernández E, Teira E

Appl. Environ. Microbiol. 87 (22) e0152521 [2021-10-28; online 2021-09-08]

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

Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.

Wallander K, Thonberg H, Nilsson D, Tham E

Hered Cancer Clin Pract 19 (1) 46 [2021-10-28; online 2021-10-28]

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

The structure of neurofibromin isoform 2 reveals different functional states.

Naschberger A, Baradaran R, Rupp B, Carroni M

Nature - (-) - [2021-10-27; online 2021-10-27]

Monensin induces selective mast cell apoptosis through a secretory granule-mediated pathway.

Maccarana M, Liu J, Lampinen M, ..., Pejler G, Paivandy A

Allergy - (-) - [2021-10-27; online 2021-10-27]

Chemical Biology Consortium Sweden (CBCS) [Service]

Human AdV-20-42-42, a Promising Novel Adenoviral Vector for Gene Therapy and Vaccine Product Development.

Ballmann MZ, Raus S, Engelhart R, ..., Havenga M, Baker AH

J. Virol. 95 (22) e0038721 [2021-10-27; online 2021-09-01]

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

Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).

Rendón-Anaya M, Wilson J, Sveinsson S, ..., Street NR, Ingvarsson PK

Mol. Biol. Evol. 38 (11) 5034-5050 [2021-10-27; online 2021-07-31]

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

A missense mutation converts the Na+,K+-ATPase into an ion channel and causes therapy-resistant epilepsy.

Ygberg S, Akkuratov EE, Howard RJ, ..., Brismar H, Aperia A

J. Biol. Chem. - (-) 101355 [2021-10-27; online 2021-10-27]

Integrated Microscopy Technologies Stockholm [Service]

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.

Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L

Mol. Ecol. - (-) - [2021-10-26; online 2021-10-26]

Bioinformatics Compute and Storage [Service] 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]

Streptococcus pyogenes Forms Serotype- and Local Environment-Dependent Interspecies Protein Complexes.

Chowdhury S, Khakzad H, Bergdahl GE, ..., Happonen L, Malmström J

mSystems 6 (5) e0027121 [2021-10-26; online 2021-09-28]

Structural Proteomics [Collaborative]

Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort.

Carapito R, Li R, Helms J, ..., Chittenden TW, Bahram S

Sci Transl Med - (-) eabj7521 [2021-10-26; online 2021-10-26]

Carbon flux around leaf-cytosolic glyceraldehyde-3-phosphate dehydrogenase introduces a 13C signal in plant glucose.

Wieloch T, Werner RA, Schleucher J

J. Exp. Bot. 72 (20) 7136-7144 [2021-10-26; online 2021-07-06]

Unambiguous Tracking of Protein Phosphorylation by Fast High-Resolution FOSY NMR*.

Lesovoy DM, Georgoulia PS, Diercks T, ..., Bermel W, Orekhov VY

Angew. Chem. Int. Ed. Engl. 60 (44) 23540-23544 [2021-10-25; online 2021-07-13]

Tonsillar Cancer with High CD8+ T-Cell Infiltration Features Increased Levels of Dendritic Cells and Transcriptional Regulation Associated with an Inflamed Tumor Microenvironment.

Jimenez DG, Sobti A, Askmyr D, ..., Greiff L, Lindstedt M

Cancers (Basel) 13 (21) - [2021-10-25; online 2021-10-25]

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

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.

Brealey JC, Leitão HG, Hofstede T, Kalthoff DC, Guschanski K

Curr. Biol. 31 (20) 4650-4658.e6 [2021-10-25; online 2021-08-25]

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

The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle.

Omnus DJ, Fink MJ, Szwedo K, Jonas K

Elife 10 (-) - [2021-10-25; online 2021-10-25]

X-Linked TLR7 Deficiency Underlies Critical COVID-19 Pneumonia in a Male Patient with Ataxia-Telangiectasia.

Abolhassani H, Vosughimotlagh A, Asano T, ..., Hammarström L, Pan-Hammarström Q

J Clin Immunol - (-) - [2021-10-23; online 2021-10-23]

Milking system and premilking routines have strong effect on the microbial community in bulk tank milk.

Sun L, Lundh Å, Höjer A, ..., Saedén KH, Dicksved J

J Dairy Sci - (-) - [2021-10-22; online 2021-10-22]

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

Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8.

Paulsson JO, Rafati N, DiLorenzo S, ..., Zedenius J, Juhlin CC

J. Clin. Endocrinol. Metab. 106 (11) 3265-3282 [2021-10-21; online 2021-06-26]

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

Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.

Tang Q, Burri R, Liu Y, ..., Heckel G, Schweizer M

Mol. Ecol. - (-) - [2021-10-21; online 2021-10-21]

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

SLC4A2 Deficiency Causes a New Type of Osteopetrosis.

Xue JY, Grigelioniene G, Wang Z, ..., Ikegawa S, Guo L

J. Bone Miner. Res. - (-) - [2021-10-20; online 2021-10-20]

Symptoms and oxylipins in plasma before and after exposure to rooms in which individuals have both experienced and not experienced building-related symptoms - an exploratory study.

Claeson AS, Sommar J, Liljelind I

Int J Environ Health Res - (-) 1-11 [2021-10-19; online 2021-10-19]

Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani.

Brouwer SM, Brus-Szkalej M, Saripella GV, ..., Liljeroth E, Grenville-Briggs LJ

Plants (Basel) 10 (10) - [2021-10-18; online 2021-10-18]

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

Frailty and the risk of dementia: is the association explained by shared environmental and genetic factors?

Bai G, Wang Y, Kuja-Halkola R, ..., Hägg S, Jylhävä J

BMC Med 19 (1) 248 [2021-10-18; online 2021-10-18]

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

scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

Raine A, Lundmark A, Annett A, ..., Bergin C, Nordlund J

- - (-) - [2021-10-15; online 2021-10-15]

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

RNA sequencing reveals metabolic and regulatory changes leading to more robust fermentation performance during short-term adaptation of Saccharomyces cerevisiae to lignocellulosic inhibitors.

van Dijk M, Rugbjerg P, Nygård Y, Olsson L

Biotechnol Biofuels 14 (1) 201 [2021-10-15; online 2021-10-15]

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

Glioblastoma cytotoxicity conferred through dual disruption of endolysosomal homeostasis by Vacquinol-1.

Kwak D, Hammarström LGJ, Haraldsson M, Ernfors P

Neurooncol Adv 3 (1) vdab152 [2021-10-15; online 2021-10-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.

Andersson A, Larsson L, Stenbeck L, ..., Engblom C, Lundeberg J

Nat Commun 12 (1) 6012 [2021-10-14; online 2021-10-14]

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

Imatinib protects against human beta-cell death via inhibition of mitochondrial respiration and activation of AMPK.

Elksnis A, Schiffer TA, Palm F, ..., Welsh N, Wang X

Clin Sci (Lond) 135 (19) 2243-2263 [2021-10-14; online 2021-09-28]

Swedish Metabolomics Centre (SMC) [Collaborative]

Unraveling the Metabolic Derangements Occurring in Non-infarcted Areas of Pig Hearts With Chronic Heart Failure.

Correia C, Wang QD, Linhardt G, ..., Jennbacken K, Synnergren J

Front Cardiovasc Med 8 (-) 753470 [2021-10-13; online 2021-10-13]

Fine Tuning of Phosphorothioate Inclusion in 2'-O-Methyl Oligonucleotides Contributes to Specific Cell Targeting for Splice-Switching Modulation.

Aoki Y, Rocha CSJ, Lehto T, ..., Behlke MA, Andaloussi SE

Front Physiol 12 (-) 689179 [2021-10-13; online 2021-10-13]

Evolutionary history of the extinct Sardinian dhole.

Ciucani MM, Jensen JK, Sinding MS, ..., Gilbert MTP, Gopalakrishnan S

Curr. Biol. - (-) - [2021-10-13; online 2021-10-13]

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

Coordinated pyruvate kinase activity is crucial for metabolic adaptation and cell survival during mitochondrial dysfunction.

Zhou X, Mikaeloff F, Curbo S, ..., Neogi U, Karlsson A

Hum. Mol. Genet. 30 (21) 2012-2026 [2021-10-13; online 2021-06-26]

Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.

Li J, Lee MO, Chen J, ..., Chuong CM, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 118 (41) - [2021-10-12; online 2021-10-06]

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

Potassium transporter TRH1/KUP4 contributes to distinct auxin-mediated root system architecture responses.

Templalexis D, Tsitsekian D, Liu C, ..., Hatzopoulos P, Rigas S

Plant Physiol. - (-) - [2021-10-11; online 2021-10-11]

Philippine Ayta possess the highest level of Denisovan ancestry in the world.

Larena M, McKenna J, Sanchez-Quinto F, ..., Endicott P, Jakobsson M

Curr. Biol. 31 (19) 4219-4230.e10 [2021-10-11; online 2021-08-12]

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

HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes.

Chatzittofis A, Boström ADE, Ciuculete DM, ..., Schiöth HB, Jokinen J

Sci Rep 11 (1) 20134 [2021-10-11; online 2021-10-11]

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

Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14.

Martín-Hernández GC, Müller B, Chmielarz M, ..., Viehweger A, Passoth V

Genomics 113 (6) 4022-4027 [2021-10-11; online 2021-10-11]

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

Changes in serum and urinary metabolomic profile after a dietary intervention in patients with irritable bowel syndrome.

Nybacka S, Simrén M, Störsrud S, ..., Winkvist A, Lindqvist HM

PLoS ONE 16 (10) e0257331 [2021-10-11; online 2021-10-11]

A Glycoproteomic Approach to Identify Novel Proteoglycans.

Noborn F, Nikpour M, Persson A, ..., Nilsson J, Larson G

Methods Mol. Biol. 2303 (-) 71-85 [2021-10-10; online 2021-10-10]

Glycoproteomics [Technology development]

Comparison of sequencing data processing pipelines and application to underrepresented African human populations.

Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M

BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]

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

An atlas of the Norway spruce needle seasonal transcriptome.

Bag P, Lihavainen J, Delhomme N, ..., Robinson KM, Jansson S

Plant J. - (-) - [2021-10-08; online 2021-10-08]

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

Ultrafast and Selective Labeling of Endogenous Proteins Using Affinity-based Benzotriazole Chemistry

Xin X, Zhang Y, Gaetani M, ..., Corkery D, Wu Y

- - (-) - [2021-10-07; online 2021-10-07] Open Access

Chemical Proteomics [Collaborative]

A cell-free high throughput assay for assessment of SARS-CoV-2 neutralizing antibodies.

Mravinacova S, Jönsson M, Christ W, ..., Månberg A, Hober S

N Biotechnol 66 (-) 46-52 [2021-10-07; online 2021-10-07]

Autoimmunity and Serology Profiling [Technology development]

Proteomic and Metabolomic Characterization of Metabolically Healthy Obesity: A Descriptive Study from a Swedish Cohort.

Korduner J, Nilsson PM, Melander O, ..., Magnusson M, Ottosson F

J Obes 2021 (-) 6616983 [2021-10-06; online 2021-10-06]

Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound.

Giovannucci TA, Salomons FA, Haraldsson M, ..., Johnsen JI, Dantuma NP

Cell Death Dis 12 (10) 914 [2021-10-06; online 2021-10-06]

CRISPR Functional Genomics [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication.

Krishnan S, Nordqvist H, Ambikan AT, ..., Treutiger CJ, Neogi U

Mol. Cell Proteomics 20 (-) 100159 [2021-10-05; online 2021-10-05]

Phytophthora infestans Ago1-associated miRNA promotes potato late blight disease.

Hu X, Persson Hodén K, Liao Z, Åsman A, Dixelius C

New Phytol. - (-) - [2021-10-04; online 2021-10-04]

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

Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.

Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S

BMC Genomics 22 (1) 710 [2021-10-02; online 2021-10-02]

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

Automating classification of osteoarthritis according to Kellgren-Lawrence in the knee using deep learning in an unfiltered adult population.

Olsson S, Akbarian E, Lind A, Razavian AS, Gordon M

BMC Musculoskelet Disord 22 (1) 844 [2021-10-02; online 2021-10-02]

AIDA Data Hub [Service]

Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia.

Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T

Semin. Cancer Biol. - (-) - [2021-10-01; online 2021-10-01]

Predicting outcome in acute myocardial infarction: an analysis investigating 175 circulating biomarkers.

Eggers KM, Lindhagen L, Baron T, ..., Spaak J, Lindahl B

Eur Heart J Acute Cardiovasc Care 10 (7) 806-812 [2021-10-01; online 2021-06-09]

A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.

Johansson PA, Brattås PL, Douse CH, ..., Eichler EE, Jakobsson J

Cell Stem Cell - (-) - [2021-10-01; online 2021-10-01]

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

Urinary cytokines correlate with acute kidney injury in critically ill COVID-19 patients.

Gradin A, Andersson H, Luther T, ..., Frithiof R, Hultström M

Cytokine 146 (-) 155589 [2021-10-00; online 2021-05-24]

Affinity Proteomics Uppsala [Collaborative]

The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation.

Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J

Sci Adv 7 (40) eabh4390 [2021-10-00; online 2021-10-01]

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

The effect of sulfate half-ester groups on cellulose nanocrystal periodate oxidation

Llàcer Navarro S, Nakayama K, Idström A, ..., Ström A, Nypelö T

Cellulose 28 (15) 9633-9644 [2021-10-00; online 2021-08-17]

Sleep duration is associated with protein biomarkers for cardiometabolic health: A large-scale population study.

Theorell-Haglöw J, Hammar U, Lind L, ..., Lindberg E, Fall T

J Sleep Res 30 (5) e13284 [2021-10-00; online 2021-03-09]

Presenting artificial intelligence, deep learning, and machine learning studies to clinicians and healthcare stakeholders: an introductory reference with a guideline and a Clinical AI Research (CAIR) checklist proposal.

Olczak J, Pavlopoulos J, Prijs J, ..., Hedlund J, Gordon M

Acta Orthop 92 (5) 513-525 [2021-10-00; online 2021-05-14]

AIDA Data Hub [Collaborative]

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

Amiel Castro R, Kunovac Kallak T, Sundström Poromaa I, ..., Ehlert U, Skalkidou A

Psychoneuroendocrinology 132 (-) 105361 [2021-10-00; online 2021-07-17]

Population genomics of the critically endangered kākāpō

Dussex N, van der Valk T, Morales HE, ..., Robertson BC, Dalén L

Cell Genomics 1 (1) 100002 [2021-10-00; online 2021-10-00]

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

Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes.

Ilumäe AM, Post H, Flores R, ..., Rootsi S, Villems R

Eur. J. Hum. Genet. 29 (10) 1510-1519 [2021-10-00; online 2021-05-07]

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

Milligram scale expression, refolding, and purification of Bombyx mori cocoonase using a recombinant E. coli system.

Phoeurk C, Mushtaq AU, Rogne P, Wolf-Watz M

Protein Expression and Purification 186 (-) 105919 [2021-10-00; online 2021-05-24]

Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.

Juras A, Ehler E, Chyleński M, ..., Jakobsson M, Dabert M

Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]

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

Inflammatory proteins and miRNA-144-5p in patients with depression, anxiety, or stress- and adjustment disorders after psychological treatment.

Sundquist K, Memon AA, Palmér K, Sundquist J, Wang X

Cytokine 146 (-) 155646 [2021-10-00; online 2021-07-27]

Immune responses against oxidized LDL as possible targets for prevention of atherosclerosis in systemic lupus erythematosus.

Yao Mattisson I, Rattik S, Björkbacka H, ..., Nilsson J, Wigren M

Vascul Pharmacol 140 (-) 106863 [2021-10-00; online 2021-04-15]

Hyperglycaemia-associated Caspase-3 predicts diabetes and coronary artery disease events.

Sun J, Singh P, Österlund J, ..., Engström G, Edsfeldt A

J. Intern. Med. 290 (4) 855-865 [2021-10-00; online 2021-07-26]

High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.

Hammarsjö A, Pettersson M, Chitayat D, ..., Lindstrand A, Grigelioniene G

J. Hum. Genet. 66 (10) 995-1008 [2021-10-00; online 2021-04-20]

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

Genome-wide association study of liver enzyme elevation in rheumatoid arthritis patients starting methotrexate.

Sundbaum JK, Baecklund E, Eriksson N, ..., Wadelius M, Hallberg P

Pharmacogenomics 22 (15) 973-982 [2021-10-00; online 2021-09-15]

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

Ecologically coherent population structure of uncultivated bacterioplankton.

Sjöqvist C, Delgado LF, Alneberg J, Andersson AF

ISME J 15 (10) 3034-3049 [2021-10-00; online 2021-05-05]

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

DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha.

Lagercrantz U, Billhardt A, Rousku SN, ..., Reza SH, Eklund DM

New Phytol. 232 (2) 595-609 [2021-10-00; online 2021-08-19]

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

Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.

Zeybel M, Altay O, Arif M, ..., Borén J, Mardinoglu A

Mol. Syst. Biol. 17 (10) e10459 [2021-10-00; online 2021-10-26]

Affinity Proteomics Stockholm [Collaborative]

Carotid atherosclerosis, changes in tissue remodeling and repair in patients with aortic coarctation.

Hlebowicz J, Holm J, Lindstedt S, Goncalves I, Nilsson J

Atherosclerosis 335 (-) 47-52 [2021-10-00; online 2021-09-21]

Broadening the roles of UDP-glycosyltransferases in auxin homeostasis and plant development.

Mateo-Bonmatí E, Casanova-Sáez R, Šimura J, Ljung K

New Phytol. 232 (2) 642-654 [2021-10-00; online 2021-08-10]

A single sulfatase is required to access colonic mucin by a gut bacterium.

Luis AS, Jin C, Pereira GV, ..., Cartmell A, Martens EC

Nature 598 (7880) 332-337 [2021-10-00; online 2021-10-06]

ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression.

Naboulsi R, Larsson M, Andersson L, Younis S

Sci Rep 11 (1) 19484 [2021-09-30; online 2021-09-30]

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

Design and development of a photoswitchable DFG-out kinase inhibitor.

Xu Y, Gao C, Håversen L, ..., Andréasson J, Grøtli M

Chem. Commun. (Camb.) 57 (78) 10043-10046 [2021-09-30; online 2021-09-30]

Chemical Biology Consortium Sweden (CBCS) [Service]

An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses.

Mangsbo SM, Havervall S, Laurén I, ..., Klingström J, Thålin C

PLoS ONE 16 (9) e0258041 [2021-09-30; online 2021-09-30]

Autoimmunity and Serology Profiling [Technology development]

In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A

Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]

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

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.

Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C

Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]

Composition and Seasonality of Membrane Transporters in Marine Picoplankton.

Hagström Å, Zweifel UL, Sundh J, ..., Müller-Karulis B, Pinhassi J

Front Microbiol 12 (-) 714732 [2021-09-28; online 2021-09-28]

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

A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma.

Milon B, Shulman ED, So KS, ..., Elkon R, Hertzano R

Cell Rep 36 (13) 109758 [2021-09-28; online 2021-10-01]

Eukaryotic Single Cell Genomics (ESCG) [Service]

Saturation mutagenesis charts the functional landscape of Salmonella ProQ and reveals a gene regulatory function of its C-terminal domain.

Rizvanovic A, Kjellin J, Söderbom F, Holmqvist E

Nucleic Acids Res. 49 (17) 9992-10006 [2021-09-27; online 2021-08-28]

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

Covid-19 in patients with chronic lymphocytic leukemia: clinical outcome and B- and T-cell immunity during 13 months in consecutive patients.

Blixt L, Bogdanovic G, Buggert M, ..., Hansson L, Österborg A

Leukemia - (-) - [2021-09-25; online 2021-09-25]

Development of humoral and cellular immunological memory against SARS-CoV-2 despite B cell depleting treatment in multiple sclerosis.

Asplund Högelin K, Ruffin N, Pin E, ..., Piehl F, Al Nimer F

iScience 24 (9) 103078 [2021-09-24; online 2021-09-02]

Autoimmunity and Serology Profiling [Collaborative]

Glycemic Control and Metabolic Adaptation in Response to High-Fat versus High-Carbohydrate Diets-Data from a Randomized Cross-Over Study in Healthy Subjects.

Wallenius V, Elebring E, Casselbrant A, ..., Marschall HU, Fändriks L

Nutrients 13 (10) - [2021-09-23; online 2021-09-23]

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.

Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K

Sci Rep 11 (1) 18822 [2021-09-22; online 2021-09-22]

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

Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.

Arroyo Mühr LS, Dillner J, Ure AE, Sundström K, Hultin E

Sci Rep 11 (1) 18852 [2021-09-22; online 2021-09-22]

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

Sulfation of O-glycans on Mucin-type Proteins From Serous Ovarian Epithelial Tumors.

Thomsson KA, Vitiazeva V, Mateoiu C, ..., Sundfeldt K, Karlsson NG

Mol. Cell Proteomics 20 (-) 100150 [2021-09-21; online 2021-09-21]

Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.

Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B

Mol. Biol. Evol. - (-) - [2021-09-20; online 2021-09-20]

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

Long-Term Elevated Inflammatory Protein Levels in Asymptomatic SARS-CoV-2 Infected Individuals.

Tserel L, Jõgi P, Naaber P, ..., Lutsar I, Peterson P

Front Immunol 12 (-) 709759 [2021-09-17; online 2021-09-17]

Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.

Li D, Cheng S, Pei Y, ..., Deng Q, Xu Landén N

J. Invest. Dermatol. - (-) - [2021-09-16; online 2021-09-16]

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

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP

Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]

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

Nontypeable Haemophilus influenzae P5 Binds Human C4b-Binding Protein, Promoting Serum Resistance.

Thofte O, Bettoni S, Su Y, ..., Blom AM, Riesbeck K

J. Immunol. 207 (6) 1566-1577 [2021-09-15; online 2021-08-25]

Integrated Microscopy Technologies Umeå [Collaborative]

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.

Glaros V, Rauschmeier R, Artemov AV, ..., Busslinger M, Kreslavsky T

Immunity 54 (9) 2005-2023.e10 [2021-09-14; online 2021-09-16]

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

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.

Sandholt AKS, Wattrang E, Lilja T, ..., Svärd SG, Söderlund R

BMC Genomics 22 (1) 660 [2021-09-14; online 2021-09-14]

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

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.

Peona V, Palacios-Gimenez OM, Blommaert J, ..., Jern P, Suh A

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1833) 20200186 [2021-09-13; online 2021-07-26]

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

Autoantibody profiles associated with clinical features in psychotic disorders.

Jernbom Falk A, Galletly C, Just D, ..., Månberg A, Schubert KO

Transl Psychiatry 11 (1) 474 [2021-09-13; online 2021-09-13]

Autoimmunity and Serology Profiling [Collaborative]

PubMed

Increased antibody reactivity against insulin receptor-A and insulin like growth factor 1 receptor and their ligands in cerebrospinal fluid and serum of patients with schizophrenia or related psychosis.

Melkersson K, Bensing S

Neuro Endocrinol. Lett. 42 (5) 339-358 [2021-09-10; online 2021-09-10]

The liver-alpha-cell axis after a mixed meal and during weight loss in type 2 diabetes.

Otten J, Stomby A, Waling M, ..., Holst JJ, Olsson T

Endocr Connect 10 (9) 1101-1110 [2021-09-09; online 2021-09-09]

Proteoglycan profiling of human, rat and mouse insulin-secreting cells.

Nikpour M, Nilsson J, Persson A, ..., Vorontsov E, Larson G

Glycobiology 31 (8) 916-930 [2021-09-09; online 2021-05-18]

A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.

Powell D, Groβe-Wilde E, Krokene P, ..., Andersson MN, Schlyter F

Commun Biol 4 (1) 1059 [2021-09-09; online 2021-09-09]

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

Temporally balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring.

Durland E, De Wit P, Langdon C

Proc. Biol. Sci. 288 (1958) 20203223 [2021-09-08; online 2021-09-01]

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

Selection on accessible chromatin regions in Capsella grandiflora.

Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T

Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]

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

Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin.

Bäckdahl J, Franzén L, Massier L, ..., Ståhl PL, Mejhert N

Cell Metab. 33 (9) 1869-1882.e6 [2021-09-07; online 2021-08-10]

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

Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.

Bedoya-Reina OC, Li W, Arceo M, ..., Kogner P, Schlisio S

Nat Commun 12 (1) 5309 [2021-09-07; online 2021-09-07]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion.

Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P

Nat Commun 12 (1) 5277 [2021-09-06; online 2021-09-06]

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome.

Bacic L, Gaullier G, Sabantsev A, ..., Boulton SJ, Deindl S

Elife 10 (-) - [2021-09-06; online 2021-09-06]

Allogeneic Hematopoietic Stem Cell Transplantation for Chronic Myelomonocytic Leukemia: Clinical and Molecular Genetic Prognostic Factors in a Nordic Population.

Wedge E, Hansen JW, Dybedal I, ..., Ljungman P, Friis LS

Transplant Cell Ther - (-) - [2021-09-06; online 2021-09-06]

Clinical Genomics Uppsala [Service]

The genomics of heart failure: design and rationale of the HERMES consortium.

Lumbers RT, Shah S, Lin H, ..., Vasan RS, Smith JG

ESC Heart Failure - (-) - [2021-09-03; online 2021-09-03]

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

Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.

Zhao Y, Lindberg BG, Esfahani SS, ..., Piazza S, Engström Y

BMC Biol. 19 (1) 185 [2021-09-03; online 2021-09-03]

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

Neuropharmacokinetic visualization of regional and subregional unbound antipsychotic drug transport across the blood-brain barrier.

Luptáková D, Vallianatou T, Nilsson A, ..., Loryan I, Andrén PE

Mol. Psychiatry - (-) - [2021-09-03; online 2021-09-03]

Spatial Mass Spectrometry [Technology development]

Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma.

Cao X, Sandberg A, Araújo JE, ..., Eriksson LE, Pernemalm M

J. Proteome Res. 20 (9) 4610-4620 [2021-09-03; online 2021-07-28]

Global Proteomics and Proteogenomics [Technology development]

Immunoglobulin A Autoreactivity toward Brain Enriched and Apoptosis-Regulating Proteins in Saliva of Athletes after Acute Concussion and Subconcussive Impacts.

Pin E, Petricoin EF, Cortes N, ..., Nilsson P, Caswell SV

J. Neurotrauma 38 (17) 2373-2383 [2021-09-01; online 2021-05-24]

Autoimmunity and Serology Profiling [Collaborative]

Genetic Variant Score and Arrhythmogenic Right Ventricular Cardiomyopathy Phenotype in Plakophilin-2 Mutation Carriers.

Svensson A, Platonov PG, Haugaa KH, ..., Svendsen JH, Gunnarsson C

Cardiology 146 (6) 763-771 [2021-09-01; online 2021-09-01]

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.

Xiao W, Ren L, Chen Z, ..., Wang C, Shi L

Nat. Biotechnol. 39 (9) 1141-1150 [2021-09-00; online 2021-09-09]

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

The microRNA response associated with methyl jasmonate-induced resistance in Norway spruce bark

Wilkinson SW, Vivian-Smith A, Krokene P, Mageroy MH

Plant Gene 27 (-) 100301 [2021-09-00; online 2021-09-00]

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

The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels.

Axelsson E, Ljungvall I, Bhoumik P, ..., Häggström J, Lindblad-Toh K

PLoS Genet. 17 (9) e1009726 [2021-09-00; online 2021-09-02]

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

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Matalonga L, Hernández-Ferrer C, Piscia D, ..., Beltran S, Solve-RD Consortia

Eur. J. Hum. Genet. 29 (9) 1337-1347 [2021-09-00; online 2021-06-01]

Soil physico-chemical properties have a greater effect on soil fungi than host species in Mediterranean pure and mixed pine forests

Adamo I, Castaño C, Bonet JA, ..., Martínez de Aragón J, Alday JG

Soil Biology and Biochemistry 160 (-) 108320 [2021-09-00; online 2021-09-00]

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

Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage.

Ylänne H, Madsen RL, Castaño C, Metcalfe DB, Clemmensen KE

Glob Chang Biol 27 (18) 4254-4268 [2021-09-00; online 2021-06-14]

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

Regulatory T cells reduce endothelial neutral sphingomyelinase 2 to prevent T-cell migration into tumors.

Akeus P, Szeponik L, Langenes V, ..., Slusher BS, Quiding-Järbrink M

Eur. J. Immunol. 51 (9) 2317-2329 [2021-09-00; online 2021-07-29]

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

Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.

Chase MA, Ellegren H, Mugal CF

Evolution 75 (9) 2179-2196 [2021-09-00; online 2021-05-03]

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

Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change.

Chattopadhyay B, Forcina G, Garg KM, ..., Barbanera F, Rheindt FE

Genomics 113 (5) 3430-3438 [2021-09-00; online 2021-08-13]

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

Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus.

Reid S, Hagberg N, Sandling JK, ..., Rönnblom L, Leonard D

Ann. Rheum. Dis. 80 (9) 1183-1189 [2021-09-00; online 2021-03-25]

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

Impact of Different Synthesis Methods on the Low-Temperature Deactivation of Cu/SAPO-34 for NH3-SCR Reaction

Woo J, Wang A, Bernin D, ..., Zammit M, Olsson L

Emiss. Control Sci. Technol. 7 (3) 198-209 [2021-09-00; online 2021-08-03]

Genomic and transcriptomic characterization of desmoplastic small round cell tumors.

Sydow S, Versleijen-Jonkers YMH, Hansson M, ..., Flucke UE, Mertens F

Genes Chromosomes Cancer 60 (9) 595-603 [2021-09-00; online 2021-05-17]

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

Evaluation of 92 cardiovascular proteins in dried blood spots collected under field-conditions: Off-the-shelf affinity-based multiplexed assays work well, allowing for simplified sample collection.

Broberg K, Svensson J, Grahn K, ..., Selander J, Enroth S

Bioessays 43 (9) e2000299 [2021-09-00; online 2021-02-15]

Affinity Proteomics Uppsala [Collaborative]

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Fang LT, Zhu B, Zhao Y, ..., Xiao W, Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium

Nat. Biotechnol. 39 (9) 1151-1160 [2021-09-00; online 2021-09-09]

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

Efficacy of EBL-1003 (apramycin) against Acinetobacter baumannii lung infections in mice.

Becker K, Aranzana-Climent V, Cao S, ..., Hobbie SN, ENABLE consortium

Clin. Microbiol. Infect. 27 (9) 1315-1321 [2021-09-00; online 2020-12-11]

Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient

Leizeaga A, Hicks LC, Manoharan L, Hawkes CV, Rousk J

J Ecol 109 (9) 3195-3210 [2021-09-00; online 2020-11-26]

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

Distinct plasma biomarkers confirm the diagnosis of mastocytosis and identify increased risk of anaphylaxis.

Gülen T, Teufelberger A, Ekoff M, ..., Dahlén B, Nilsson G

J. Allergy Clin. Immunol. 148 (3) 889-894 [2021-09-00; online 2021-03-02]

Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19.

Altay O, Arif M, Li X, ..., Uhlén M, Mardinoglu A

Adv Sci (Weinh) 8 (17) e2101222 [2021-09-00; online 2021-06-28]

Affinity Proteomics Stockholm [Service]

Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak.

Faticov M, Abdelfattah A, Roslin T, ..., Lindahl BD, Tack AJM

New Phytol. 231 (5) 1770-1783 [2021-09-00; online 2021-06-18]

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

Calcium and pH interaction limits bloom formation and expansion of a nuisance microalga

Gollnisch R, Alling T, Stockenreiter M, ..., Grabowska M, Rengefors K

Limnol Oceanogr 66 (9) 3523-3534 [2021-09-00; online 2021-07-30]

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

Branched-chain amino acid metabolism is regulated by ERRα in primary human myotubes and is further impaired by glucose loading in type 2 diabetes.

Sjögren RJO, Rizo-Roca D, Chibalin AV, ..., Näslund E, Zierath JR

Diabetologia 64 (9) 2077-2091 [2021-09-00; online 2021-06-16]

A roadmap for the Human Developmental Cell Atlas.

Haniffa M, Taylor D, Linnarsson S, ..., Webb S, Human Cell Atlas Developmental Biological Network

Nature 597 (7875) 196-205 [2021-09-00; online 2021-09-08]

In Situ Sequencing (ISS) [Collaborative] Spatial Proteomics

A novel silver(I) di-iso-butyldithiocarbamate: Unusually complicated 1-D polymeric structure, multiple ligand-supported Ag–Ag interactions and its capability to bind gold(III). Preparation, structural organisation and (13C, 15N) CP-MAS NMR of [Ag6(S2CNiBu2)6] and [Au(S2CNiBu2)2][AgCl2]

Korneeva EV, Smolentsev AI, Antzutkin ON, Ivanov AV

Inorganica Chimica Acta 525 (-) 120383 [2021-09-00; online 2021-09-00]

A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.

Wightman DP, Jansen IE, Savage JE, ..., Andreassen OA, Posthuma D

Nat. Genet. 53 (9) 1276-1282 [2021-09-00; online 2021-09-07]

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

A genome-wide association study of the frailty index highlights brain pathways in ageing.

Atkins JL, Jylhävä J, Pedersen NL, ..., Williams DM, Pilling LC

Aging Cell 20 (9) e13459 [2021-09-00; online 2021-08-25]

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

A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis.

de Boer E, Ockeloen CW, Matalonga L, ..., Verloes A, Vissers LELM

Eur. J. Hum. Genet. 29 (9) 1359-1368 [2021-09-00; online 2021-06-01]

Robust humoral and cellular immune responses and low risk for reinfection at least 8 months following asymptomatic to mild COVID-19.

Havervall S, Ng H, Jernbom Falk A, ..., Hober S, Thålin C

J. Intern. Med. - (-) - [2021-08-30; online 2021-08-30]

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

Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures.

Deiana M, Mosser M, Le Bahers T, ..., Monnereau C, Guy L

Nanoscale 13 (32) 13795-13808 [2021-08-28; online 2021-08-04]

Novel Microdialysis Technique Reveals a Dramatic Shift in Metabolite Secretion during the Early Stages of the Interaction between the Ectomycorrhizal Fungus Pisolithus microcarpus and Its Host Eucalyptus grandis.

Plett KL, Buckley S, Plett JM, ..., Lundberg-Felten J, Jämtgård S

Microorganisms 9 (9) - [2021-08-26; online 2021-08-26]

Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.

Martin F, Halvarsson P, Delhomme N, Höglund J, Tydén E

International Journal for Parasitology: Drugs and Drug Resistance 17 (-) 84-91 [2021-08-26; online 2021-08-26]

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

Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia.

Kolijn PM, Muggen AF, Ljungström V, ..., Rosenquist R, Langerak AW

Front Oncol 11 (-) 740083 [2021-08-26; online 2021-08-26]

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

Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.

Grochowski CM, Krepischi ACV, Eisfeldt J, ..., Lindstrand A, Carvalho CMB

Front Genet 12 (-) 708348 [2021-08-26; online 2021-08-26]

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

Amnion signals are essential for mesoderm formation in primates.

Yang R, Goedel A, Kang Y, ..., Niu Y, Chien KR

Nat Commun 12 (1) 5126 [2021-08-26; online 2021-08-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes.

Lepzien R, Nie M, Czarnewski P, ..., Grunewald J, Smed-Sörensen A

J Leukoc Biol - (-) - [2021-08-25; online 2021-08-25]

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

Interleukin 6 and Cardiovascular Outcomes in Patients With Chronic Kidney Disease and Chronic Coronary Syndrome.

Batra G, Ghukasyan Lakic T, Lindbäck J, ..., Wallentin L, STABILITY Investigators

JAMA Cardiol - (-) - [2021-08-25; online 2021-08-25]

The Amot/integrin protein complex transmits mechanical forces required for vascular expansion.

Zhang Y, Zhang Y, Kameishi S, ..., Cavallo F, Holmgren L

Cell Rep 36 (8) 109616 [2021-08-24; online 2021-08-26]

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.

Mahboubi A, Delhomme N, Häggström S, Hanson J

Plant Methods 17 (1) 92 [2021-08-24; online 2021-08-24]

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

Genomic Epidemiology of Azithromycin-Nonsusceptible Neisseria gonorrhoeae, Argentina, 2005-2019.

Gianecini RA, Poklepovich T, Golparian D, ..., Galarza P, Gonococcal Antimicrobial Susceptibility Surveillance Programme—Argentina1

Emerg. Infect. Dis. 27 (9) 2369-2378 [2021-08-24; online 2021-08-24]

Comprehensive in situ mapping of human cortical transcriptomic cell types.

Langseth CM, Gyllborg D, Miller JA, ..., Hilscher MM, Nilsson M

Commun Biol 4 (1) 998 [2021-08-24; online 2021-08-24]

In Situ Sequencing (ISS) [Technology development]

Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.

Westbury MV, Le Duc D, Duchêne DA, ..., Schöneberg T, Hofreiter M

Mol. Biol. Evol. 38 (9) 3884-3897 [2021-08-23; online 2021-08-25]

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

RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system.

Takada H, Crowe-McAuliffe C, Polte C, ..., Wilson DN, Hauryliuk V

Nucleic Acids Res. 49 (14) 8355-8369 [2021-08-20; online 2021-07-14]

A Minimalistic Coumarin Turn-On Probe for Selective Recognition of Parallel G-Quadruplex DNA Structures.

Deiana M, Obi I, Andreasson M, ..., Chorell E, Sabouri N

ACS Chem. Biol. 16 (8) 1365-1376 [2021-08-20; online 2021-07-30]

The broad role of Nkx3.2 in the development of the zebrafish axial skeleton.

Waldmann L, Leyhr J, Zhang H, ..., Allalou A, Haitina T

PLoS ONE 16 (8) e0255953 [2021-08-19; online 2021-08-19]

BioImage Informatics [Collaborative] Genome Engineering Zebrafish [Service]

Community composition of aquatic fungi across the thawing Arctic.

Kluge M, Wurzbacher C, Wauthy M, ..., Stenlid J, Peura S

Sci Data 8 (1) 221 [2021-08-19; online 2021-08-19]

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

A simple pressure-assisted method for MicroED specimen preparation.

Zhao J, Xu H, Lebrette H, ..., Högbom M, Zou X

Nat Commun 12 (1) 5036 [2021-08-19; online 2021-08-19]

(p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains.

Roghanian M, Van Nerom K, Takada H, ..., Garcia-Pino A, Hauryliuk V

Mol. Cell 81 (16) 3310-3322.e6 [2021-08-19; online 2021-08-21]

Structural Proteomics [Collaborative]

Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.

Houtman M, Hesselberg E, Rönnblom L, ..., Malmström V, Padyukov L

Front Immunol 12 (-) 707217 [2021-08-17; online 2021-08-17]

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

Association of Variants Near the Bradykinin Receptor B2 Gene With Angioedema in Patients Taking ACE Inhibitors.

Ghouse J, Ahlberg G, Andreasen L, ..., Bundgaard H, Olesen MS

J. Am. Coll. Cardiol. 78 (7) 696-709 [2021-08-17; online 2021-08-14]

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

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community.

Singh A, Moestedt J, Berg A, Schnürer A

Front Microbiol 12 (-) 700256 [2021-08-16; online 2021-08-16]

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

Metabolomics profiling predicts outcome of tocilizumab in rheumatoid arthritis: an exploratory study.

Murillo-Saich JD, Diaz-Torne C, Ortiz MA, ..., Vidal S, Guma M

Metabolomics 17 (9) 74 [2021-08-16; online 2021-08-16]

Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey.

Rahimi Y, Ingvarsson PK, Bihamta MR, ..., Taleei A, Khoshnoodi Jabar Abadi S

Front Plant Sci 12 (-) 710867 [2021-08-16; online 2021-08-16]

NGI Uppsala (SNP&SEQ Technology Platform) [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 - (-) - [2021-08-15; online 2021-08-15]

Chemical Biology Consortium Sweden (CBCS) [Service]

Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods.

Freire RVM, Pillco-Valencia Y, da Hora GCA, ..., Soares TA, Salentinig S

Journal of Colloid and Interface Science 596 (-) 352-363 [2021-08-15; online 2021-03-16]

Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.

Lindholm Carlström E, Niazi A, Etemadikhah M, ..., Nilsson B, Feuk L

Genes 12 (8) - [2021-08-13; online 2021-08-13]

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

Site-Dependent Relationships Between Fungal Community Composition, Plant Genotypic Diversity and Environmental Drivers in a Salix Biomass System

Hoeber S, Baum C, Weih M, Manzoni S, Fransson P

Front. Fungal Biol. 2 (-) - [2021-08-13; online 2021-08-13]

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

Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.

Ma J, Tibbitt CA, Georén SK, ..., Bachert C, Coquet JM

Sci Immunol 6 (62) - [2021-08-13; online 2021-08-15]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Expanding the Chondroitin Sulfate Glycoproteome - But How Far?

Noborn F, Nikpour M, Persson A, Nilsson J, Larson G

Front Cell Dev Biol 9 (-) 695970 [2021-08-13; online 2021-08-13]

Glycoproteomics [Service]

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.

Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S

Front Microbiol 12 (-) 669937 [2021-08-12; online 2021-08-12]

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

Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.

Bellenberg S, Salas B, Ganji S, ..., Dopson M, Vera M

Sci Rep 11 (1) 16275 [2021-08-11; online 2021-08-11]

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

Sensitive Measurement of Drug-Target Engagement by a Cellular Thermal Shift Assay with Multiplex Proximity Extension Readout.

Al-Amin RA, Gallant CJ, Muthelo PM, Landegren U

Anal. Chem. 93 (31) 10999-11009 [2021-08-10; online 2021-07-28]

Genomic profile - a possible diagnostic and prognostic marker in upper tract urothelial carcinoma.

Grahn A, Eisfeldt J, Malm C, ..., Tham E, Brehmer M

BJU Int. - (-) - [2021-08-10; online 2021-08-10]

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

A Super-Resolved View of the Alzheimer's Disease-Related Amyloidogenic Pathway in Hippocampal Neurons.

Yu Y, Gao Y, Winblad B, Tjernberg LO, Schedin-Weiss S

J. Alzheimers Dis. 83 (2) 833-852 [2021-08-10; online 2021-08-10]

Integrated Microscopy Technologies Stockholm [Service]

Genome assemblies of three closely related leaf beetle species (Galerucella spp.).

Yang X, Slotte T, Dainat J, Hambäck PA

G3 (Bethesda) 11 (8) - [2021-08-07; online 2021-12-02]

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

Using multimarker screening to identify biomarkers associated with cardiovascular death in patients with atrial fibrillation.

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

Cardiovasc. Res. - (-) - [2021-08-06; online 2021-08-06]

O-145 Green Tea catechins EGCG and pro-drug of EGCG (Pro-EGCG) inhibit endometriosis through targeting molecules regulating macrophages and B cells

Hung SW, Gaetani M, Tan ZYR, ..., Zubarev RA, Wang CC

Hum. Reprod. 36 (Supplement_1) - [2021-08-06; online 2021-08-06]

Chemical Proteomics [Collaborative]

Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.

Sayyab S, Lundmark A, Larsson M, ..., Nordlund J, Syvänen A

Sci Rep 11 (1) 15988 [2021-08-06; online 2021-08-06]

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

High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins.

Niksirat H, Siino V, Steinbach C, Levander F

J. Proteome Res. 20 (8) 4075-4088 [2021-08-06; online 2021-06-29]

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

Shifts in gene expression variability in the blood-stage of Plasmodium relictum.

Kalbskopf V, Ahrén D, Valkiūnas G, Palinauskas V, Hellgren O

Gene 792 (-) 145723 [2021-08-05; online 2021-05-18]

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

Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae.

Tellgren-Roth C, Thorell K, Galperin MY, ..., Sjöling Å, Martín-Rodríguez AJ

Microbiol Resour Announc 10 (31) e0055921 [2021-08-05; online 2021-08-05]

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

Cerebrospinal fluid proteomics targeted for central nervous system processes in bipolar disorder.

Göteson A, Isgren A, Jonsson L, ..., Holmén-Larsson J, Landén M

Mol. Psychiatry - (-) - [2021-08-04; online 2021-08-04]

Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.

Natarajan K, Eisfeldt J, Hammond M, ..., Öijerstedt L, Graff C

Acta Neuropathol Commun 9 (1) 132 [2021-08-03; online 2021-08-03]

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

PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.

Seyfferth C, Wessels BA, Vahala J, ..., Tuominen H, Lundberg-Felten J

Cells 10 (8) 1971 [2021-08-03; online 2021-08-03]

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

Persisting Salivary IgG Against SARS-CoV-2 at 9 Months After Mild COVID-19: A Complementary Approach to Population Surveys.

Alkharaan H, Bayati S, Hellström C, ..., Pin E, Sällberg Chen M

J. Infect. Dis. 224 (3) 407-414 [2021-08-02; online 2021-05-13]

Autoimmunity and Serology Profiling [Collaborative]

Three weeks of interrupting sitting lowers fasting glucose and glycemic variability, but not glucose tolerance, in free-living women and men with obesity.

Smith JAB, Savikj M, Sethi P, ..., Zierath JR, Näslund E

Am J Physiol Endocrinol Metab 321 (2) E203-E216 [2021-08-01; online 2021-06-21]

Single-cell atlas reveals meningeal leukocyte heterogeneity in the developing mouse brain.

Zelco A, Börjesson V, de Kanter JK, ..., Holstege FCP, Wang X

Genes Dev. 35 (15-16) 1190-1207 [2021-08-01; online 2021-07-22]

Clinical Genomics Gothenburg [Service]

Genome-wide estrogen receptor β chromatin binding in human colon cancer cells reveals its tumor suppressor activity.

Indukuri R, Jafferali MH, Song D, ..., Archer A, Williams C

Int. J. Cancer 149 (3) 692-706 [2021-08-01; online 2021-04-05]

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

Transcriptional study reveals a potential leptin-dependent gene regulatory network in zebrafish brain.

Ahi EP, Tsakoumis E, Brunel M, Schmitz M

Fish Physiol Biochem 47 (4) 1283-1298 [2021-08-00; online 2021-07-08]

Genome Engineering Zebrafish [Service]

The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.

Kanellis DC, Espinoza JA, Zisi A, ..., Lindström MS, Bartek J

Sci Adv 7 (32) - [2021-08-00; online 2021-08-04]

Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The effects of chemical and structural factors on the enzymatic saccharification of Eucalyptus sp. samples pre-treated by various technologies

Thoresen M, Malgas S, Gandla ML, ..., Sithole B, Pletschke BI

Industrial Crops and Products 166 (-) 113449 [2021-08-00; online 2021-08-00]

Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).

Figueroa D, Capo E, Lindh MV, ..., Pinhassi J, Andersson A

Environ. Microbiol. 23 (8) 4200-4213 [2021-08-00; online 2021-06-01]

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

Strong Associations Between Early Tubular Damage and Urinary Cytokine, Chemokine, and Growth Factor Levels in Elderly Males and Females.

Fellström B, Helmersson-Karlqvist J, Lind L, ..., Kultima K, Larsson A

Journal of Interferon & Cytokine Research 41 (8) 283-290 [2021-08-00; online 2021-08-20]

Serum profiling of anorexia nervosa: A 1H NMR-based metabolomics study.

Salehi M A, Nilsson IA, Figueira J, ..., Bulik CM, Landén M

Eur Neuropsychopharmacol 49 (-) 1-10 [2021-08-00; online 2021-03-18]

SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.

Guo M, Goudarzi KM, Abedi S, ..., Nistér M, Hägerstrand D

Oncogene 40 (32) 5066-5080 [2021-08-00; online 2021-05-21]

Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

SARS-CoV-2 infections amongst personnel providing home care services for older persons in Stockholm, Sweden.

Hassan SS, Seigerud Å, Abdirahman R, ..., Conneryd Lundgren K, Dillner J

J. Intern. Med. 290 (2) 430-436 [2021-08-00; online 2021-04-12]

Plasma proteome alterations by MAPK inhibitors in BRAFV600-mutated metastatic cutaneous melanoma.

Babačić H, Eriksson H, Pernemalm M

Neoplasia 23 (8) 783-791 [2021-08-00; online 2021-07-08]

Optimization of droplet digital PCR assays for the type-specific detection and quantification of five HPV genotypes, including additional data on viral loads of nine different HPV genotypes in cervical carcinomas.

Malin K, Louise BM, Gisela H, Mats KG, Gabriella L

J Virol Methods 294 (-) 114193 [2021-08-00; online 2021-05-19]

Molecular architecture of the developing mouse brain.

La Manno G, Siletti K, Furlan A, ..., Lönnerberg P, Linnarsson S

Nature 596 (7870) 92-96 [2021-08-00; online 2021-07-28]

In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.

Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M

Mol Ecol Resour 21 (6) 1833-1849 [2021-08-00; online 2021-05-06]

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

Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).

Nadachowska-Brzyska K, Dutoit L, Smeds L, ..., Gustafsson L, Ellegren H

Mol. Ecol. 30 (16) 3965-3973 [2021-08-00; online 2021-07-01]

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

Genetic insights into biological mechanisms governing human ovarian ageing.

Ruth KS, Day FR, Hussain J, ..., Roig I, Perry JRB

Nature 596 (7872) 393-397 [2021-08-00; online 2021-08-04]

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

Electrochemical N2 reduction at ambient condition – Overcoming the selectivity issue via control of reactants’ availabilities

Kwong WL, Wågberg T, Messinger J

International Journal of Hydrogen Energy 46 (59) 30366-30372 [2021-08-00; online 2021-08-00]

Dynamics of Baltic Sea phages driven by environmental changes.

Hoetzinger M, Nilsson E, Arabi R, ..., Middelboe M, Holmfeldt K

Environ. Microbiol. 23 (8) 4576-4594 [2021-08-00; online 2021-07-07]

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

Decidual stromal cells support tolerance at the human foetal-maternal interface by inducing regulatory M2 macrophages and regulatory T-cells.

Lindau R, Vondra S, Spreckels J, ..., Jenmalm MC, Ernerudh J

J Reprod Immunol 146 (-) 103330 [2021-08-00; online 2021-05-12]

Comparison of RNA- and DNA-based methods for measurable residual disease analysis in NPM1-mutated acute myeloid leukemia.

Pettersson L, Johansson Alm S, Almstedt A, ..., Fogelstrand L, Ehinger M

Int J Lab Hematol 43 (4) 664-674 [2021-08-00; online 2021-05-30]

Clinical Genomics Gothenburg [Collaborative]

Co-mutation pattern, clonal hierarchy, and clone size concur to determine disease phenotype of SRSF2P95-mutated neoplasms.

Todisco G, Creignou M, Gallì A, ..., Cazzola M, Malcovati L

Leukemia 35 (8) 2371-2381 [2021-08-00; online 2020-12-21]

Clinical Genomics Uppsala [Service]

Antibody responses after a single dose of ChAdOx1 nCoV-19 vaccine in healthcare workers previously infected with SARS-CoV-2.

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

EBioMedicine 70 (-) 103523 [2021-08-00; online 2021-08-12]

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

Anti-tumor effects of rigosertib in high-risk neuroblastoma.

Radke K, Hansson K, Sjölund J, ..., Gisselsson D, Bexell D

Transl Oncol 14 (8) 101149 [2021-08-00; online 2021-06-09]

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.

Marco Salas S, Gyllborg D, Mattsson Langseth C, Nilsson M

BMC Bioinformatics 22 (1) 391 [2021-07-31; online 2021-07-31]

In Situ Sequencing (ISS) [Technology development]

High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.

Graça AT, Hall M, Persson K, Schröder WP

Sci Rep 11 (1) 15534 [2021-07-30; online 2021-07-30]

Genetic association study of childhood aggression across raters, instruments, and age.

Ip HF, van der Laan CM, Krapohl EML, ..., Nivard MG, Boomsma DI

Transl Psychiatry 11 (1) 413 [2021-07-30; online 2021-07-30]

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

Bacterial Composition and Metabolomics of Dental Plaque From Adolescents.

Havsed K, Stensson M, Jansson H, ..., Svensäter G, Mira A

Front. Cell. Infect. Microbiol. 11 (-) 716493 [2021-07-30; online 2021-07-30]

Neuroinflammation and Alzheimer's Disease: A Machine Learning Approach to CSF Proteomics.

Gaetani L, Bellomo G, Parnetti L, ..., Zetterberg H, Di Filippo M

Cells 10 (8) - [2021-07-29; online 2021-07-29]

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.

Christmas MJ, Jones JC, Olsson A, ..., Geib JC, Webster MT

Mol. Biol. Evol. 38 (8) 3126-3143 [2021-07-29; online 2021-04-07]

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

Complex population structure of the Atlantic puffin revealed by whole genome analyses.

Kersten O, Star B, Leigh DM, ..., Jakobsen KS, Boessenkool S

Commun Biol 4 (1) 922 [2021-07-29; online 2021-07-29]

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

Unraveling negative biotic interactions determining soil microbial community assembly and functioning.

Romdhane S, Spor A, Aubert J, ..., Tsiknia M, Philippot L

ISME J - (-) - [2021-07-28; online 2021-07-28]

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

Strong Associations between Plasma Osteopontin and Several Inflammatory Chemokines, Cytokines, and Growth Factors.

Larsson A, Helmersson-Karlqvist J, Lind L, Ärnlöv J, Feldreich TR

Biomedicines 9 (8) - [2021-07-28; online 2021-07-28]

Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.

Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC

Elife 10 (-) - [2021-07-28; online 2021-07-28]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] Microbial Single Cell Genomics NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Metabolomics analysis for diagnosis and biomarker discovery of transthyretin amyloidosis.

Olsson M, Hellman U, Wixner J, Anan I

Amyloid - (-) 1-9 [2021-07-28; online 2021-07-28]

Super-resolution microscopy reveals that Na+/K+-ATPase signaling protects against glucose-induced apoptosis by deactivating Bad.

Bernhem K, Fontana JM, Svensson D, ..., Brismar H, Aperia A

Cell Death Dis 12 (8) 739 [2021-07-27; online 2021-07-27]

Integrated Microscopy Technologies Stockholm [Technology development]

Genome-scale metabolic network reconstruction of model animals as a platform for translational research.

Wang H, Robinson JL, Kocabas P, ..., Zetterberg H, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 118 (30) e2102344118 [2021-07-27; online 2021-07-21]

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

Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy.

Hasan M, Banerjee I, Rozman Grinberg I, Sjöberg BM, Logan DT

Front Mol Biosci 8 (-) 713608 [2021-07-26; online 2021-07-26]

Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.

Mattisson J, Danielsson M, Hammond M, ..., Halvardson J, Forsberg LA

Sci Rep 11 (1) 15160 [2021-07-26; online 2021-07-26]

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

Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.

Svensson E, Günther T, Hoischen A, ..., Netea MG, Jakobsson M

Curr. Biol. 31 (14) 2973-2983.e9 [2021-07-26; online 2021-05-18]

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

Association between Cardiorespiratory Fitness and Circulating Proteins in 50-Year-Old Swedish Men and Women: a Cross-Sectional Study.

Enarsson M, Feldreich T, Byberg L, ..., Lind L, Ärnlöv J

Sports Med Open 7 (1) 52 [2021-07-26; online 2021-07-26]

The enigmatic RNase MRP of kinetoplastids.

Alm Rosenblad M, López MD, Samuelsson T

RNA Biol - (-) 1-9 [2021-07-25; online 2021-07-25]

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

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis.

Costa ZP, Varani AM, Cauz-Santos LA, ..., Monteiro-Vitorello CB, Carneiro Vieira ML

Plant Genome - (-) e20117 [2021-07-23; online 2021-07-23]

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

Bifidobacteria-mediated immune system imprinting early in life.

Henrick BM, Rodriguez L, Lakshmikanth T, ..., Frese SA, Brodin P

Cell 184 (15) 3884-3898.e11 [2021-07-22; online 2021-06-17]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cellular Immunomonitoring [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Promotor and Poison Effects of the Inorganic Elements of Kraft Lignin during Hydrotreatment over NiMoS Catalyst

Sebastian J, Cheah YW, Bernin D, Creaser D, Olsson L

Catalysts 11 (8) 874 [2021-07-21; online 2021-07-21]

Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.

Ojeda-May P, Mushtaq AU, Rogne P, ..., Wolf-Watz M, Nam K

Biochemistry 60 (28) 2246-2258 [2021-07-20; online 2021-07-12]

A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients.

Wendt C, Muranen TA, Mielikäinen L, ..., Borg Å, Lindblom A

Sci Rep 11 (1) 14763 [2021-07-20; online 2021-07-20]

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

Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.

Hober S, Hellström C, Olofsson J, ..., Hedhammar M, Nilsson P

Clin Transl Immunology 10 (7) e1312 [2021-07-19; online 2021-07-19]

Autoimmunity and Serology Profiling [Technology development]

DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome.

Imgenberg-Kreuz J, Sandling JK, Norheim KB, ..., Eloranta ML, Nordmark G

Front Immunol 12 (-) 702037 [2021-07-16; online 2021-07-16]

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

Large-scale serum analysis identifies unique systemic biomarkers in psoriasis and hidradenitis suppurativa.

Navrazhina K, Renert-Yuval Y, Frew JW, ..., Garcet S, Krueger JG

Br J Dermatol - (-) - [2021-07-13; online 2021-07-13]

Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis.

Grankvist A, Jaén-Luchoro D, Wass L, Sikora P, Wennerås C

Microorganisms 9 (7) - [2021-07-13; online 2021-07-13]

Clinical Genomics Gothenburg [Collaborative]

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Nat Commun 12 (1) 4253 [2021-07-12; online 2021-07-12]

Bioinformatics Compute and Storage [Service] 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]

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

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Dev. Dyn. - (-) - [2021-07-09; online 2021-07-09]

BioImage Informatics [Collaborative] Genome Engineering Zebrafish [Service]

Wide-Ranging Effects on the Brain Proteome in a Transgenic Mouse Model of Alzheimer's Disease Following Treatment with a Brain-Targeting Somatostatin Peptide.

Rofo F, Sandbaumhüter FA, Chourlia A, ..., Jansson ET, Hultqvist G

ACS Chem Neurosci 12 (13) 2529-2541 [2021-07-07; online 2021-06-25]

Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy.

Peltonen K, Feola S, Umer HM, ..., Lehtiö J, Cerullo V

Cancers (Basel) 13 (14) - [2021-07-07; online 2021-07-07]

Global Proteomics and Proteogenomics [Technology development]

Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations.

Kerzeli IK, Lord M, Doroszko M, ..., Segersten U, Mangsbo SM

PLoS ONE 16 (7) e0253178 [2021-07-07; online 2021-07-07]

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

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.

Calleja-Rodriguez A, Chen Z, Suontama M, Pan J, Wu HX

Front Plant Sci 12 (-) 666820 [2021-07-07; online 2021-07-07]

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

Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.

Kundu S, Ali MA, Handin N, ..., Globisch D, Sjöblom T

J. Exp. Clin. Cancer Res. 40 (1) 225 [2021-07-07; online 2021-07-07]

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

Pharmacological activation of p53 triggers viral mimicry response thereby abolishing tumor immune evasion and promoting anti-tumor immunity.

Zhou X, Singh M, Sanz Santos G, ..., Johnsen JI, Selivanova G

Cancer Discov - (-) - [2021-07-06; online 2021-07-06]

Cellular Immunomonitoring [Service]

High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.

Zhang L, Steward RA, Wheat CW, Reed RD

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-07-21]

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

Chick fetal organ spheroids as a model to study development and disease.

Dakhel S, Davies WIL, Joseph JV, ..., Remeseiro S, Gunhaga L

BMC Mol Cell Biol 22 (1) 37 [2021-07-05; online 2021-07-05]

Integrated Microscopy Technologies Umeå [Service]

Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.

Haas JC, Vergara A, Serrano AR, ..., Hurry V, Street NR

Tree Physiol 41 (7) 1230-1246 [2021-07-05; online 2021-01-09]

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

Metabolic Profiling of Plasma in Patients with Irritable Bowel Syndrome after a 4-Week Starch- and Sucrose-Reduced Diet.

Stenlund H, Nilholm C, Chorell E, ..., D'Amato M, Ohlsson B

Metabolites 11 (7) - [2021-07-04; online 2021-07-04]

Swedish Metabolomics Centre (SMC) [Collaborative]

Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires.

Elfstrand M, Chen J, Cleary M, ..., Stadler M, Durling MB

BMC Genomics 22 (1) 503 [2021-07-04; online 2021-07-04]

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

Real-world effectiveness of vedolizumab in inflammatory bowel disease: week 52 results from the Swedish prospective multicentre SVEAH study.

Eriksson C, Rundquist S, Lykiardopoulos V, ..., Halfvarson J, SWIBREG SVEAH Study Group

Therap Adv Gastroenterol 14 (-) 17562848211023386 [2021-07-03; online 2021-07-03]

Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer.

Qvick A, Stenmark B, Carlsson J, ..., Karlsson C, Helenius G

Mol. Med. 27 (1) 68 [2021-07-03; online 2021-07-03]

Clinical Genomics Örebro [Technology development]

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.

Éliás S, Schmidt A, Gomez-Cabrero D, Tegnér J

J Immunol Res 2021 (-) 8880585 [2021-07-03; online 2021-07-03]

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

High Amounts of SARS-CoV-2 Precede Sickness Among Asymptomatic Health Care Workers.

Dillner J, Elfström KM, Blomqvist J, ..., Arroyo Mühr LS, Lundgren KC

J. Infect. Dis. 224 (1) 14-20 [2021-07-02; online 2021-02-14]

TAAR1-Dependent and -Independent Actions of Tyramine in Interaction With Glutamate Underlie Central Effects of Monoamine Oxidase Inhibition.

Mantas I, Vallianatou T, Yang Y, ..., Andrén PE, Svenningsson P

Biol. Psychiatry 90 (1) 16-27 [2021-07-01; online 2020-12-19]

Structural determinants of multimerization and dissociation in 2-Cys peroxiredoxin chaperone function.

Troussicot L, Burmann BM, Molin M

Structure 29 (7) 640-654 [2021-07-01; online 2021-05-03]

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.

Jensen A, Lillie M, Bergström K, Larsson P, Höglund J

Heredity (Edinb) 127 (1) 79-91 [2021-07-00; online 2021-05-07]

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

Variants in BANK1 are associated with lupus nephritis of European ancestry.

Bolin K, Imgenberg-Kreuz J, Leonard D, ..., Rönnblom L, Nordmark G

Genes Immun. 22 (3) 194-202 [2021-07-00; online 2021-06-14]

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

Thermal proteome profiling identifies PIP4K2A and ZADH2 as off-targets of Polo-like kinase 1 inhibitor volasertib.

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The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.

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Mol. Ecol. 30 (14) 3530-3547 [2021-07-00; online 2021-06-08]

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

Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death.

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Forensic Sci Int Genet 53 (-) 102522 [2021-07-00; online 2021-04-26]

Clinical Genomics Örebro [Technology development]

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Nat Protoc 16 (7) 3298-3321 [2021-07-00; online 2021-06-02]

Spatial Mass Spectrometry [Technology development]

Single-cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs.

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Genes Chromosomes Cancer 60 (7) 504-524 [2021-07-00; online 2021-03-15]

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.

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Nat. Biotechnol. 39 (7) 825-835 [2021-07-00; online 2021-04-12]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

STED and parallelized RESOLFT optical nanoscopy of the tubular endoplasmic reticulum and its mitochondrial contacts in neuronal cells.

Damenti M, Coceano G, Pennacchietti F, Bodén A, Testa I

Neurobiol. Dis. 155 (-) 105361 [2021-07-00; online 2021-04-12]

Integrated Microscopy Technologies Stockholm [Service]

Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.

Izabel-Shen D, Albert S, Winder M, Farnelid H, Nascimento FJA

Mol. Ecol. 30 (14) 3515-3529 [2021-07-00; online 2021-06-11]

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

Plasma S1P (Sphingosine-1-Phosphate) Links to Hypertension and Biomarkers of Inflammation and Cardiovascular Disease: Findings From a Translational Investigation.

Jujic A, Matthes F, Vanherle L, ..., Magnusson M, Meissner A

Hypertension 78 (1) 195-209 [2021-07-00; online 2021-05-17]

On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).

Bachmann JA, Tedder A, Fracassetti M, ..., Köhler C, Slotte T

Heredity (Edinb) 127 (1) 124-134 [2021-07-00; online 2021-04-19]

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

Non-uniform sampling for NOESY? A case study on spiramycin.

Wieske LHE, Erdélyi M

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Nicotinamide provides neuroprotection in glaucoma by protecting against mitochondrial and metabolic dysfunction.

Tribble JR, Otmani A, Sun S, ..., Votruba M, Williams PA

Redox Biol 43 (-) 101988 [2021-07-00; online 2021-04-24]

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Eur. Respir. J. 58 (1) 2003468 [2021-07-00; online 2021-07-22]

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

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J Extracell Vesicles 10 (9) e12128 [2021-07-00; online 2021-07-22]

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

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Trends Genet. 37 (7) 682-683 [2021-07-00; online 2021-05-11]

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

Lack of diagnostic-escape mutants of group B streptococcus in Slovenia.

Perme T, Golparian D, Unemo M, Jeverica S

Clin. Microbiol. Infect. 27 (7) 1054-1055 [2021-07-00; online 2021-02-02]

Insights into the multitrophic interactions between the biocontrol agent Bacillus subtilis MBI 600, the pathogen Botrytis cinerea and their plant host.

Samaras A, Karaoglanidis GS, Tzelepis G

Microbiol Res 248 (-) 126752 [2021-07-00; online 2021-04-02]

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

Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease.

Wijk SC, Prabhala P, Michaliková B, ..., Westergren-Thorsson G, Magnusson M

Am J Respir Cell Mol Biol 65 (1) 103-113 [2021-07-00; online 2021-04-01]

High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.

Broman E, Bonaglia S, Norkko A, Creer S, Nascimento FJA

Mol. Ecol. 30 (13) 3023-3039 [2021-07-00; online 2020-08-19]

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

HIV-Infected Individuals on ART With Impaired Immune Recovery Have Altered Plasma Metabolite Profiles.

Nyström S, Govender M, Yap SH, ..., Rajasuriar R, Larsson M

Open Forum Infect Dis 8 (7) ofab288 [2021-07-00; online 2021-06-02]

Genomic signatures of rapid adaptive divergence in a tropical montane species.

Ericson PGP, Irestedt M, She H, Qu Y

Biol. Lett. 17 (7) 20210089 [2021-07-00; online 2021-07-28]

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

Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector.

Sekar V, Rivero A, Pigeault R, ..., Ahren D, Hellgren O

Genomics 113 (4) 2327-2337 [2021-07-00; online 2021-05-21]

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

FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response.

Bogatyrova O, Mattsson JSM, Ross EM, ..., Esdar C, Micke P

Eur. J. Cancer 151 (-) 136-149 [2021-07-00; online 2021-05-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish.

Sandkam BA, Almeida P, Darolti I, ..., Breden F, Mank JE

Nat Ecol Evol 5 (7) 939-948 [2021-07-00; online 2021-05-06]

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

Exercise training improves mitochondrial respiration and is associated with an altered intramuscular phospholipid signature in women with obesity.

Mendham AE, Goedecke JH, Zeng Y, ..., Olsson T, Chorell E

Diabetologia 64 (7) 1642-1659 [2021-07-00; online 2021-03-26]

A single-cell type transcriptomics map of human tissues.

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Sci Adv 7 (31) eabh2169 [2021-07-00; online 2021-07-28]

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A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest.

Lindahl BD, Kyaschenko J, Varenius K, ..., Karltun E, Stendahl J

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

Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.

Bellenberg S, Turner S, Seidel L, ..., Leiviskä T, Dopson M

Front Microbiol 12 (-) 693615 [2021-06-30; online 2021-06-30]

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

DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.

Novotny A, Zamora-Terol S, Winder M

Proc. Biol. Sci. 288 (1953) 20210908 [2021-06-30; online 2021-06-16]

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

Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells.

Huoman J, Martínez-Enguita D, Olsson E, ..., Gustafsson M, Jenmalm MC

Clin Epigenetics 13 (1) 135 [2021-06-30; online 2021-06-30]

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

Proteomic Profiling of Tissue Exosomes Indicates Continuous Release of Malignant Exosomes in Urinary Bladder Cancer Patients, Even with Pathologically Undetectable Tumour.

Eldh M, Mints M, Hiltbrunner S, ..., Sherif A, Gabrielsson S

Cancers (Basel) 13 (13) - [2021-06-29; online 2021-06-29]

Inhibition of iduronic acid biosynthesis by ebselen reduces GAG accumulation in MPS-I fibroblasts.

Maccarana M, Tykesson E, Pera EM, ..., Ghiselli G, Li J

Glycobiology - (-) - [2021-06-29; online 2021-06-29]

Chemical Biology Consortium Sweden (CBCS) [Service]

Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis.

Khademi SMH, Gabrielaite M, Paulsson M, ..., Marvig RL, Påhlman LI

mSystems - (-) e0052321 [2021-06-29; online 2021-06-29]

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

Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging.

McCartney DL, Min JL, Richmond RC, ..., Horvath S, Marioni RE

Genome Biol. 22 (1) 194 [2021-06-29; online 2021-06-29]

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

A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids.

Jhun M, Mendelson M, Wilson R, ..., Irvin MR, Assimes TL

Nat Commun 12 (1) 3987 [2021-06-28; online 2021-06-28]

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

Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.

Bai X, Narayanan A, Nowak P, ..., Neogi U, Sönnerborg A

Front Microbiol 12 (-) 667718 [2021-06-25; online 2021-06-25]

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

Structure and transport mechanism of P5B-ATPases.

Li P, Wang K, Salustros N, Grønberg C, Gourdon P

Nat Commun 12 (1) 3973 [2021-06-25; online 2021-06-25]

Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.

Dainat J, Pontarotti P

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

Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.

Chen J, Bi H, Pettersson ME, ..., Scheerer P, Andersson L

Commun Biol 4 (1) 795 [2021-06-25; online 2021-06-25]

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

Toll-like receptor 4 methylation grade is linked to depressive symptom severity.

Rasmusson AJ, Gallwitz M, Soltanabadi B, ..., Schiöth HB, Cunningham JL

Transl Psychiatry 11 (1) 371 [2021-06-24; online 2021-06-24]

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

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.

Singh A, Müller B, Schnürer A

Sci Rep 11 (1) 13298 [2021-06-24; online 2021-06-24]

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

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.

Simonetti M, Zhang N, Harbers L, ..., Ghisetti V, Crosetto N

Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]

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

The γ-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.

Corvaisier M, Zhou J, Malycheva D, ..., Lindström L, Alvarado-Kristensson M

Commun Biol 4 (1) 767 [2021-06-22; online 2021-06-22]

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

Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells.

Mathew NR, Jayanthan JK, Smirnov IV, ..., Bemark M, Angeletti D

Cell Rep 35 (12) 109286 [2021-06-22; online 2021-06-24]

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

Characterization of Individual Projections Reveal That Neuromasts of the Zebrafish Lateral Line are Innervated by Multiple Inhibitory Efferent Cells.

Manuel R, Iglesias Gonzalez AB, Habicher J, Koning HK, Boije H

Front Neuroanat 15 (-) 666109 [2021-06-21; online 2021-06-21]

Genome Engineering Zebrafish

A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism.

Melo GA, Abreu IN, de Oliveira MB, ..., Pimenta MAS, Moritz T

Sci Rep 11 (1) 12933 [2021-06-21; online 2021-06-21]

Swedish Metabolomics Centre (SMC) [Collaborative]

Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion.

Sork H, Conceicao M, Corso G, ..., El Andaloussi S, Mäger I

Cells 10 (6) 1543 [2021-06-18; online 2021-06-18]

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

Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici.

Samils B, Andersson B, Edin E, ..., Hellin P, Kildea S

Front Microbiol 12 (-) 692845 [2021-06-18; online 2021-06-18]

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

Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.

Roxhed N, Bendes A, Dale M, ..., Fredolini C, Schwenk JM

Nat Commun 12 (1) 3695 [2021-06-17; online 2021-06-17]

Affinity Proteomics Stockholm [Technology development]

Cooperativity of α-Synuclein Binding to Lipid Membranes.

Makasewicz K, Wennmalm S, Stenqvist B, ..., Linse S, Sparr E

ACS Chem Neurosci 12 (12) 2099-2109 [2021-06-16; online 2021-06-02]

Integrated Microscopy Technologies Stockholm [Collaborative]

Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury.

Abu Hamdeh S, Ciuculete DM, Sarkisyan D, ..., Schiöth HB, Marklund N

J. Neurotrauma 38 (12) 1679-1688 [2021-06-15; online 2021-01-08]

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

Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data.

Khakzad H, Happonen L, Malmström J, Malmström L

Bioinformatics - (-) - [2021-06-15; online 2021-06-15]

Structural Proteomics [Technology development]

Guve, Ygle och Rane DNA-analyser löser frågan om släktskap

Arcini C, Hedvall R

Arkeologi i Östergötland - (1) 46-47 [2021-06-14]

Ancient DNA [Service]

Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.

Morris ERA, Boyle AG, Riihimäki M, ..., Pringle J, Cohen ND

PLoS ONE 16 (6) e0252804 [2021-06-14; online 2021-06-14]

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

Cyclotide host-defense tailored for species and environments in violets from the Canary Islands.

Slazak B, Kaltenböck K, Steffen K, ..., Andrén PE, Göransson U

Sci Rep 11 (1) 12452 [2021-06-14; online 2021-06-14]

Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.

Chen ZQ, Zan Y, Milesi P, ..., Lascoux M, Wu HX

Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]

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

Bead-Based Assays for Validating Proteomic Profiles in Body Fluids.

Bendes A, Dale M, Mattsson C, ..., Schwenk JM, Fredolini C

Methods Mol. Biol. 2344 (-) 65-78 [2021-06-12; online 2021-06-12]

Affinity Proteomics Stockholm [Technology development]

Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.

Crowe-McAuliffe C, Murina V, Turnbull KJ, ..., Hauryliuk V, Wilson DN

Nat Commun 12 (1) 3577 [2021-06-11; online 2021-06-11]

DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).

Krali O, Palle J, Bäcklin CL, ..., Zeller B, Nordlund J

Genes 12 (6) 895 [2021-06-10; online 2021-06-10]

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

Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies.

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ACS Med Chem Lett 12 (6) 983-990 [2021-06-10; online 2021-05-18]

Silica Particles Trigger the Exopolysaccharide Production of Harsh Environment Isolates of Growth-Promoting Rhizobacteria and Increase Their Ability to Enhance Wheat Biomass in Drought-Stressed Soils.

Fetsiukh A, Conrad J, Bergquist J, Timmusk S

Int J Mol Sci 22 (12) 6201 [2021-06-08; online 2021-06-08]

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.

Gustafsson J, Robinson J, Nielsen J, Pachter L

Genome Biol. 22 (1) 174 [2021-06-08; online 2021-06-08]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

Yaka R, Mapelli I, Kaptan D, ..., Özer F, Somel M

Curr. Biol. 31 (11) 2455-2468.e18 [2021-06-07; online 2021-04-14]

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

Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation.

Karampelias C, Rezanejad H, Rosko M, ..., Korbutt GS, Andersson O

Nat Commun 12 (1) 3362 [2021-06-07; online 2021-06-07]

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

Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.

de Rojas I, Moreno-Grau S, Tesi N, ..., van der Lee SJ, Ruiz A

Nat Commun 12 (1) 3417 [2021-06-07; online 2021-06-07]

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

Osteoprotegerin predicts cardiovascular events in patients treated with hemodialysis.

Wu PH, Glerup RI, Svensson MHS, ..., Ljunggren Ö, Fellström B

Nephrol Dial Transplant - (-) - [2021-06-04; online 2021-06-04]

Machine learning for cell classification and neighborhood analysis in glioma tissue.

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Cytometry A - (-) - [2021-06-04; online 2021-06-04]

Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing.

Walcher L, Kistenmacher AK, Sommer C, ..., Dünkel A, Fricke S

Front Immunol 12 (-) 684052 [2021-06-04; online 2021-06-04]

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

CryoEM reveals BIN1 (isoform 8) does not bind to single actin filaments in vitro.

Wang Z, Mim C

MicroPubl Biol 2021 (-) - [2021-06-04; online 2021-06-04]

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172.

Tõlgo M, Hüttner S, Rugbjerg P, ..., Larsbrink J, Olsson L

Biotechnol Biofuels 14 (1) 131 [2021-06-03; online 2021-06-03]

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

EBF1 and PAX5 control pro-B cell expansion via opposing regulation of the Myc gene.

Somasundaram R, Jensen CT, Tingvall-Gustafsson J, ..., Ungerbäck J, Sigvardsson M

Blood 137 (22) 3037-3049 [2021-06-03; online 2021-02-24]

Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.

Friess L, Cheray M, Keane L, Grabert K, Joseph B

Mol Brain 14 (1) 87 [2021-06-03; online 2021-06-03]

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

RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.

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Nat Commun 12 (1) 3282 [2021-06-02; online 2021-06-02]

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

Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).

Eriksson JS, Bacon CD, Bennett DJ, ..., Oxelman B, Antonelli A

BMC Ecol Evol 21 (1) 107 [2021-06-02; online 2021-06-02]

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

B Lymphocyte Specification Is Preceded by Extensive Epigenetic Priming in Multipotent Progenitors.

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

The trans-ancestral genomic architecture of glycemic traits.

Chen J, Spracklen CN, Marenne G, ..., Barroso I, Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC)

Nat. Genet. 53 (6) 840-860 [2021-06-00; online 2021-05-31]

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

The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases.

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Chemical Biology Consortium Sweden (CBCS) [Service] Swedish Metabolomics Centre (SMC) [Service]

RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children.

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Cancer Med 10 (12) 3997-4003 [2021-06-00; online 2021-05-13]

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

Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.

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

Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress.

Mishra LS, Kim SY, Caddell DF, Coleman-Derr D, Funk C

Physiol Plantarum 172 (2) 1045-1058 [2021-06-00; online 2020-12-16]

Large-scale identification of protein histidine methylation in human cells.

Kapell S, Jakobsson ME

NAR Genom Bioinform 3 (2) lqab045 [2021-06-00; online 2021-05-22]

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

Genomic and fitness consequences of inbreeding in an endangered carnivore.

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Mol. Ecol. 30 (12) 2790-2799 [2021-06-00; online 2021-05-20]

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

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.

Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A

Mar Biotechnol (NY) 23 (3) 402-416 [2021-06-00; online 2021-05-01]

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

Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.

de Las Fuentes L, Sung YJ, Noordam R, ..., Rao DC, Fornage M

Mol. Psychiatry 26 (6) 2111-2125 [2021-06-00; online 2020-05-05]

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

ENABLE: an engine for European antibacterial drug discovery and development.

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Nat Rev Drug Discov 20 (6) 407-408 [2021-06-00; online 2021-05-06]

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DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan.

van Dongen J, Hagenbeek FA, Suderman M, ..., Bartels M, Boomsma DI

Mol. Psychiatry 26 (6) 2148-2162 [2021-06-00; online 2021-01-08]

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

Cancer diagnostics based on plasma protein biomarkers: hard times but great expectations.

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Mol Oncol 15 (6) 1715-1726 [2021-06-00; online 2020-11-17]

CO2 fertilization of Sphagnum peat mosses is modulated by water table level and other environmental factors.

Serk H, Nilsson MB, Figueira J, Wieloch T, Schleucher J

Plant Cell Environ. 44 (6) 1756-1768 [2021-06-00; online 2021-03-29]

Klevebro S, Björkander S, Ekström S, ..., Bergström A, Melén E

Sci Rep 11 (1) 11391 [2021-05-31; online 2021-05-31]

NK cells integrate signals over large areas when building immune synapses but require local stimuli for degranulation.

Verron Q, Forslund E, Brandt L, ..., Olofsson PE, Önfelt B

Sci Signal 14 (684) eabe2740 [2021-05-25; online 2021-05-25]

Integrated Microscopy Technologies Stockholm [Service]

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.

Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F

Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]

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

Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.

Mold JE, Modolo L, Hård J, ..., Michaëlsson J, Frisén J

Cell Rep 35 (8) 109174 [2021-05-25; online 2021-05-27]

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

A combined approach for single-cell mRNA and intracellular protein expression analysis.

Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ

Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]

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

Trailblazing precision medicine in Europe: A joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany.

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Clinical Genomics Lund [Service] Clinical Genomics Stockholm [Collaborative] Clinical Genomics Uppsala [Collaborative]

Crystal structure of a homotrimeric verrucomicrobial exo-β-1,4-mannosidase active in the hindgut of the wood-feeding termite Reticulitermes flavipes.

Kalyani DC, Reichenbach T, Keskitalo MM, ..., Aspeborg H, Divne C

Journal of Structural Biology: X 5 (-) 100048 [2021-05-24; online 2021-05-24]

Adsorption of bio-organic eco-corona molecules reduces the toxic response to metallic nanoparticles in Daphnia magna.

Ekvall MT, Hedberg J, Odnevall Wallinder I, ..., Hansson LA, Cedervall T

Sci Rep 11 (1) 10784 [2021-05-24; online 2021-05-24]

Stromal Heterogeneity in the Human Proliferative Endometrium-A Single-Cell RNA Sequencing Study.

Queckbörner S, von Grothusen C, Boggavarapu NR, ..., Davies LC, Gemzell-Danielsson K

J Pers Med 11 (6) - [2021-05-22; online 2021-05-22]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]

Pharmacodynamic Evaluation of Dosing, Bacterial Kill, and Resistance Suppression for Zoliflodacin Against Neisseria gonorrhoeae in a Dynamic Hollow Fiber Infection Model.

Jacobsson S, Golparian D, Oxelbark J, ..., Drusano G, Unemo M

Front Pharmacol 12 (-) 682135 [2021-05-21; online 2021-05-21]

Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry.

de Miranda JR, Granberg F, Low M, ..., Jansson A, Berggren Å

Front Vet Sci 8 (-) 642085 [2021-05-20; online 2021-05-20]

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

Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe.

Salmón P, Jacobs A, Ahrén D, ..., Visser ME, Isaksson C

Nat Commun 12 (1) 2983 [2021-05-20; online 2021-05-20]

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

Complement-Opsonized HIV Modulates Pathways Involved in Infection of Cervical Mucosal Tissues: A Transcriptomic and Proteomic Study.

Svanberg C, Ellegård R, Crisci E, ..., Shankar EM, Larsson M

Front Immunol 12 (-) 625649 [2021-05-20; online 2021-05-20]

Which image-based phenotypes are most promising for using AI to understand cellular functions and why?

Lundberg E, Funke J, Uhlmann V, ..., Carpenter A, Coehlo LP

Cell Syst 12 (5) 384-387 [2021-05-19; online 2021-05-21]

Spatial Proteomics [Technology development]

Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex.

Hartmann FE, Ament-Velásquez SL, Vogan AA, ..., Silar P, Giraud T

Mol. Biol. Evol. 38 (6) 2475-2492 [2021-05-19; online 2021-02-09]

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

Integration of Mass Spectrometry Imaging and Machine Learning Visualizes Region-Specific Age-Induced and Drug-Target Metabolic Perturbations in the Brain.

Vallianatou T, Shariatgorji R, Nilsson A, ..., Svenningsson P, Andrén PE

ACS Chem Neurosci 12 (10) 1811-1823 [2021-05-19; online 2021-05-03]

Spatial Mass Spectrometry [Technology development]

X-chromosome variants are associated with aldosterone producing adenomas.

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Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18]

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

Symptoms and Functional Impairment Assessed 8 Months After Mild COVID-19 Among Health Care Workers.

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JAMA 325 (19) 2015-2016 [2021-05-18; online 2021-04-08]

Autoimmunity and Serology Profiling [Collaborative]

Factors Affecting Detoxification of Softwood Enzymatic Hydrolysates Using Sodium Dithionite

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Processes 9 (5) 887 [2021-05-18; online 2021-05-18]

Phage Biocontrol of Pseudomonas aeruginosa in Water.

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Viruses 13 (5) 928 [2021-05-17; online 2021-05-17]

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

Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.

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Rheumatology (Oxford) - (-) - [2021-05-16; online 2021-05-16]

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

A plasma lipid signature predicts incident coronary artery disease.

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

Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.

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Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]

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

Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.

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Clin Epigenetics 13 (1) 107 [2021-05-12; online 2021-05-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy.

Hellberg S, Raffetseder J, Rundquist O, ..., Ernerudh J, Gustafsson M

Front Immunol 12 (-) 672168 [2021-05-12; online 2021-05-12]

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

Dynamics of Auxin and Cytokinin Metabolism during Early Root and Hypocotyl Growth in Theobroma cacao.

Mboene Noah A, Casanova-Sáez R, Makondy Ango RE, ..., Niemenak N, Ljung K

Plants (Basel) 10 (5) - [2021-05-12; online 2021-05-12]

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.

Garcia SL, Mehrshad M, Buck M, ..., Greening C, Peura S

mSystems 6 (3) - [2021-05-11; online 2021-05-11]

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

PubMed

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NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP.

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BMC Biol. 19 (1) 98 [2021-05-10; online 2021-05-10]

African and Asian leopards are highly differentiated at the genomic level.

Paijmans JLA, Barlow A, Becker MS, ..., Manica A, Hofreiter M

Curr. Biol. 31 (9) 1872-1882.e5 [2021-05-10; online 2021-04-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan.

Hollfelder N, Babiker H, Granehäll L, Schlebusch CM, Jakobsson M

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]

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

The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.

Boman J, Mugal CF, Backström N

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]

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

Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.

Morgell A, Reisz JA, Ateeb Z, ..., Chen MS, D'Alessandro A

J. Proteome Res. 20 (5) 2725-2738 [2021-05-07; online 2021-03-15]

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

INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.

Yadav VK, Santos-González J, Köhler C

Nucleic Acids Res. 49 (8) 4371-4385 [2021-05-07; online 2021-03-22]

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

Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality.

Schunk SJ, Kleber ME, März W, ..., eQTLGen consortium , BIOS consortium

Eur. Heart J. 42 (18) 1742-1756 [2021-05-07; online 2021-03-23]

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

Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).

Celorio-Mancera MP, Rastas P, Steward RA, Nylin S, Wheat CW

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-23]

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

Serine Protease HTRA1 as a Novel Target Antigen in Primary Membranous Nephropathy.

Al-Rabadi LF, Caza T, Trivin-Avillach C, ..., Larsen C, Beck LH

J. Am. Soc. Nephrol. 32 (7) 1666-1681 [2021-05-05; online 2021-05-05]

Plasma Protein Profile of Carotid Artery Atherosclerosis and Atherosclerotic Outcomes: Meta-Analyses and Mendelian Randomization Analyses.

Lind L, Gigante B, Borné Y, ..., Engström G, Mälarstig A

Arterioscler. Thromb. Vasc. Biol. 41 (5) 1777-1788 [2021-05-05; online 2021-03-04]

The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns.

Seeger C, Dyrhage K, Mahajan M, ..., Lind SB, Andersson SGE

Front Microbiol 12 (-) 643045 [2021-05-04; online 2021-05-04]

Integrated Microscopy Technologies Umeå [Service]

How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent.

Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ

Mol. Biol. Evol. 38 (5) 1715-1730 [2021-05-04; online 2020-11-11]

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

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.

Talibov VO, Fabini E, FitzGerald EA, ..., Del Rio A, Danielson UH

ChemBioChem 22 (9) 1597-1608 [2021-05-04; online 2021-02-11]

Drug Discovery and Development (DDD) [Service]

False Positive Results in SARS-CoV-2 Serological Tests for Samples From Patients With Chronic Inflammatory Diseases.

Kharlamova N, Dunn N, Bedri SK, ..., Fink K, Fogdell-Hahn A

Front Immunol 12 (-) 666114 [2021-05-03; online 2021-05-03]

Activation of endogenous retroviruses during brain development causes an inflammatory response.

Jönsson ME, Garza R, Sharma Y, ..., Jern P, Jakobsson J

EMBO J. 40 (9) e106423 [2021-05-03; online 2021-03-01]

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

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.

Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J

Cell Res 31 (5) 554-568 [2021-05-00; online 2021-01-08]

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

The association between genetically determined ABO blood types and major depressive disorder.

Garvert L, Baune BT, Berger K, ..., Grabe HJ, Van der Auwera S

Psychiatry Res 299 (-) 113837 [2021-05-00; online 2021-02-24]

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

The Enterprise, a massive transposon carrying Spok meiotic drive genes.

Vogan AA, Ament-Velásquez SL, Bastiaans E, ..., Suh A, Johannesson H

Genome Res. 31 (5) 789-798 [2021-05-00; online 2021-04-19]

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

Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals.

Lihavainen J, Edlund E, Björkén L, ..., Robinson KM, Jansson S

Physiol Plantarum 172 (1) 201-217 [2021-05-00; online 2021-01-07]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.

Kameneva P, Artemov AV, Kastriti ME, ..., Kharchenko PV, Adameyko I

Nat. Genet. 53 (5) 694-706 [2021-05-00; online 2021-04-08]

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

Serum metabolomic profiling correlated with ISS and clinical outcome for multiple myeloma patients treated with high-dose melphalan and autologous stem cell transplantation.

Veskovski L, Andersson PO, Turesson I, ..., Pedersen A, Mellqvist UH

Exp Hematol 97 (-) 79-88.e8 [2021-05-00; online 2021-02-18]

Self-generation of low ash carbon microspheres from the hydrothermal supernatant of anaerobic digestate: Formation insights and supercapacitor performance

Latham KG, Kozyatnyk I, Figueira J, ..., Rosenbaum E, Jansson S

Chemical Engineering Journal Advances 6 (-) 100097 [2021-05-00; online 2021-05-00]

Prediction of complex phenotypes using the Drosophila melanogaster metabolome.

Rohde PD, Kristensen TN, Sarup P, Muñoz J, Malmendal A

Heredity (Edinb) 126 (5) 717-732 [2021-05-00; online 2021-01-28]

Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.

Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S

J. Med. Genet. 58 (5) 351-356 [2021-05-00; online 2020-06-26]

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

In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.

Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O

Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]

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

ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.

Dobson ETA, Cimini B, Klemm AH, ..., Carpenter AE, Eliceiri KW

Curr Protoc 1 (5) e89 [2021-05-00; online 2021-05-27]

Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.

Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A

Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]

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

Histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes.

Granlund L, Hedin A, Wahlhütter M, ..., Skog O, Lundberg M

BMJ Open Diabetes Res Care 9 (1) - [2021-05-00; online 2021-05-26]

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

Genetic basis of lacunar stroke: a pooled analysis of individual patient data and genome-wide association studies.

Traylor M, Persyn E, Tomppo L, ..., UK DNA Lacunar Stroke Study Investigators , International Stroke Genetics Consortium

Lancet Neurol 20 (5) 351-361 [2021-05-00; online 2021-03-25]

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

Examination of how variations in lignin properties from Kraft and organosolv extraction influence the physicochemical characteristics of hydrothermal carbon

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

Journal of Analytical and Applied Pyrolysis 155 (-) 105095 [2021-05-00; online 2021-05-00]

Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.

Sandholt AKS, Xu F, Söderlund R, ..., Svärd SG, Wattrang E

Parasitology 148 (6) 712-725 [2021-05-00; online 2021-02-04]

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

Dissolution of wood components during hot water extraction of birch

Wojtasz-Mucha J, Hasani M, Theliander H

Wood Sci Technol 55 (3) 811-835 [2021-05-00; online 2021-04-05]

Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.

Olsson Lindvall M, Angerfors A, Andersson B, ..., Stanne TM, Jern C

Thromb. Haemost. 121 (5) 573-583 [2021-05-00; online 2020-11-17]

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

Binding of the human antioxidation protein α1-microglobulin (A1M) to heparin and heparan sulfate. Mapping of binding site, molecular and functional characterization, and co-localization in vivo and in vitro.

Bergwik J, Kristiansson A, Larsson J, ..., Åkerström B, Allhorn M

Redox Biol 41 (-) 101892 [2021-05-00; online 2021-02-10]

Structural Proteomics [Collaborative]

Association between inflammasome-related polymorphisms and psoriatic arthritis.

Juneblad K, Kastbom A, Johansson L, ..., Söderkvist P, Alenius G

Scand. J. Rheumatol. 50 (3) 206-212 [2021-05-00; online 2020-12-10]

A chemical screen for modulators of mRNA translation identifies a distinct mechanism of toxicity for sphingosine kinase inhibitors.

Corman A, Kanellis DC, Michalska P, ..., Carreras-Puigvert J, Fernandez-Capetillo O

PLoS Biol. 19 (5) e3001263 [2021-05-00; online 2021-05-25]

Chemical Biology Consortium Sweden (CBCS) [Service]

Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists.

Martins GG, Cordelières FP, Colombelli J, ..., Tinevez JY, Miura K

F1000Res 10 (-) 334 [2021-04-30; online 2021-04-30]

Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden.

Saxenborn P, Baxter J, Tilevik A, ..., Enroth H, Tilevik D

Front Microbiol 12 (-) 640408 [2021-04-30; online 2021-04-30]

Clinical Genomics Stockholm

Spatial Proteomics [Technology development]

Subcellular proteomics.

Christopher JA, Stadler C, Martin CE, ..., Emili A, Lilley KS

Nat Rev Methods Primers 1 (1) - [2021-04-29; online 2021-04-29]

Complete Genome Sequence of an Antimicrobial-Producing Bacillus velezensis Sam8H1 Isolate from the Makgadikgadi Saltpans of Botswana.

Modikwe G, Manoharan L, Mabutho G, ..., Lebogang L, Zhou N

Microbiol Resour Announc 10 (17) - [2021-04-29; online 2021-04-29]

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

Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain.

Säll O, Stenmark B, Jacobsson S, ..., Sundqvist M, Mölling P

Epidemiol. Infect. 149 (-) e126 [2021-04-29; online 2021-04-29]

How Does Liquid-Liquid Phase Separation in Model Membranes Reflect Cell Membrane Heterogeneity?

Sych T, Gurdap CO, Wedemann L, Sezgin E

Membranes 11 (5) 323 [2021-04-28; online 2021-04-28]

Integrated Microscopy Technologies Stockholm [Service]

Cyanophage Diversity and Community Structure in Dead Zone Sediments.

Broman E, Holmfeldt K, Bonaglia S, Hall POJ, Nascimento FJA

mSphere 6 (2) - [2021-04-28; online 2021-04-28]

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

Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.

Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]

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

Neutron reflectometry and NMR spectroscopy of full-length Bcl-2 protein reveal its membrane localization and conformation.

Mushtaq AU, Ådén J, Clifton LA, ..., Sparrman T, Gröbner G

Commun Biol 4 (1) 507 [2021-04-27; online 2021-04-27]

An introgressed gene causes meiotic drive in Neurospora sitophila.

Svedberg J, Vogan AA, Rhoades NA, ..., Hammond TM, Johannesson H

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2026605118 [2021-04-27; online 2021-04-21]

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

Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.

Barlow A, Paijmans JLA, Alberti F, ..., Baryshnikov G, Hofreiter M

Curr. Biol. 31 (8) 1771-1779.e7 [2021-04-26; online 2021-02-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Live Cell FRET Imaging Reveals Amyloid β-Peptide Oligomerization in Hippocampal Neurons.

Gao Y, Wennmalm S, Winblad B, Schedin-Weiss S, Tjernberg LO

Int J Mol Sci 22 (9) 4530 [2021-04-26; online 2021-04-26]

Integrated Microscopy Technologies Stockholm [Service]

Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.

von Seth J, Dussex N, Díez-Del-Molino D, ..., Götherström A, Dalén L

Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]

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

Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C.

Wallerstein J, Ekberg V, Ignjatović MM, ..., Ryde U, Akke M

JACS Au 1 (4) 484-500 [2021-04-26; online 2021-04-01]

Bioimage analysis workflows: community resources to navigate through a complex ecosystem.

Paul-Gilloteaux P, Tosi S, Hériché JK, ..., Miura K, Colombelli J

F1000Res 10 (-) 320 [2021-04-26; online 2021-04-26]

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

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

Pediatr. Res. - (-) - [2021-04-24; online 2021-04-24]

Affinity Proteomics Stockholm [Service]

Divergent airway microbiomes in lung transplant recipients with or without pulmonary infection.

Påhlman LI, Manoharan L, Aspelund AS

Respir. Res. 22 (1) 118 [2021-04-23; online 2021-04-23]

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

Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.

Mattsson L, Sörenson E, Capo E, ..., Lindehoff E, Legrand C

Front Bioeng Biotechnol 9 (-) 651895 [2021-04-22; online 2021-04-22]

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

Epigenome-wide association study of level and change in cognitive abilities from midlife through late life.

Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Pedersen NL

Clin Epigenetics 13 (1) 85 [2021-04-21; online 2021-04-21]

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

Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture.

Wahlgren WY, Golonka D, Westenhoff S, Möglich A

Front Plant Sci 12 (-) 663751 [2021-04-21; online 2021-04-21]

smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites.

Persson Hodén K, Hu X, Martinez G, Dixelius C

Int J Mol Sci 22 (8) 4267 [2021-04-20; online 2021-04-20]

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

Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders.

Gillentine MA, Wang T, Hoekzema K, ..., Bernier RA, Eichler EE

Genome Med 13 (1) 63 [2021-04-19; online 2021-04-19]

A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.

Sánchez-Busó L, Yeats CA, Taylor B, ..., Unemo M, Aanensen DM

Genome Med 13 (1) 61 [2021-04-19; online 2021-04-19]

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

Gong B, Li D, Kusko R, ..., Jones W, Xu J

Genome Biol. 22 (1) 109 [2021-04-16; online 2021-04-16]

Clinical Genomics Stockholm [Collaborative]

Metabolomic profiling reveals plasma GlycA and GlycB as a potential biomarkers for treatment efficiency in rheumatoid arthritis.

Dudka I, Chachaj A, Sebastian A, ..., Gröbner G, Szuba A

Journal of Pharmaceutical and Biomedical Analysis 197 (-) 113971 [2021-04-15; online 2021-02-17]

Swedish Metabolomics Centre (SMC) [Service] Swedish NMR Centre (SNC) [Collaborative]

Active DNRA and denitrification in oxic hypereutrophic waters.

Broman E, Zilius M, Samuiloviene A, ..., Nascimento FJA, Bonaglia S

Water Res. 194 (-) 116954 [2021-04-15; online 2021-02-21]

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

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.

Rosengren MK, Sigurðardóttir H, Eriksson S, ..., Solé M, Lindgren G

BMC Genomics 22 (1) 267 [2021-04-14; online 2021-04-14]

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

A Combined Theoretical and Experimental Study of the Polymer Matrix-Mediated Stress Transfer in a Cellulose Nanocomposite

Peterson A, Mehandzhiyski AY, Svenningsson L, ..., Zozoulenko I, Müller C

Macromolecules 54 (7) 3507-3516 [2021-04-13; online 2021-03-19]

DNA methylation in cord blood in association with prenatal depressive symptoms.

Kallak TK, Bränn E, Fransson E, ..., Lyle R, Skalkidou A

Clin Epigenetics 13 (1) 78 [2021-04-12; online 2021-04-12]

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

Sex-differences in circulating biomarkers during acute myocardial infarction: An analysis from the SWEDEHEART registry.

Eggers KM, Lindhagen L, Baron T, ..., Spaak J, Lindahl B

PLoS ONE 16 (4) e0249830 [2021-04-08; online 2021-04-08]

CA10 regulates neurexin heparan sulfate addition via a direct binding in the secretory pathway.

Montoliu-Gaya L, Tietze D, Kaminski D, ..., Tietze AA, Sterky FH

EMBO Rep. 22 (4) e51349 [2021-04-07; online 2021-02-15]

Glycoproteomics [Collaborative] Swedish NMR Centre (SNC) [Service]

A spinal organ of proprioception for integrated motor action feedback.

Picton LD, Bertuzzi M, Pallucchi I, ..., Shearing PR, El Manira A

Neuron 109 (7) 1188-1201.e7 [2021-04-07; online 2021-02-11]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Serum proteins associated with periodontitis relapse post-surgery: A pilot study.

Esberg A, Isehed C, Holmlund A, Lindquist S, Lundberg P

J Periodontol - (-) - [2021-04-04; online 2021-04-04]

Using RELION software within the Scipion framework.

Sharov G, Morado DR, Carroni M, de la Rosa-Trevín JM

Acta Crystallogr D Struct Biol 77 (4) 403-410 [2021-04-01; online 2021-03-30]

Cryo-EM [Technology development]

Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.

Fatima A, Hoeber J, Schuster J, ..., Klar J, Dahl N

Am. J. Hum. Genet. 108 (4) 739-748 [2021-04-01; online 2021-03-11]

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

Chemical Biology Consortium Sweden; Experiences in academic and industry partnerships – forging a path to translational drug discovery. - Book chapter

Gustavsson A, Chorell E

Burger's Medicinal Chemistry, Drug Discovery and Development, Volumes 1 - 8 Volume 3 (chapter 2) - [2021-04-01]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Artificial intelligence for the classification of fractures around the knee in adults according to the 2018 AO/OTA classification system.

Lind A, Akbarian E, Olsson S, ..., Razavian AS, Gordon M

PLoS ONE 16 (4) e0248809 [2021-04-01; online 2021-04-01]

AIDA Data Hub [Service]

Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size.

Tyson Y, Hillman C, Majenburg N, ..., Mohaddes M, Hailer NP

Acta Orthop 92 (2) 143-150 [2021-04-00; online 2020-11-12]

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

The heart microbiome of insectivorous bats from Central and South Eastern Europe.

Corduneanu A, Mihalca AD, Sándor AD, ..., Viso NP, Bongcam-Rudloff E

Comp Immunol Microbiol Infect Dis 75 (-) 101605 [2021-04-00; online 2021-01-07]

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

The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation.

Thörn F, Rödin-Mörch P, Cortazar-Chinarro M, ..., Laurila A, Höglund J

Heredity (Edinb) 126 (4) 656-667 [2021-04-00; online 2021-02-09]

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

Severe congenital lactic acidosis and hypertrophic cardiomyopathy caused by an intronic variant in NDUFB7.

Correia SP, Moedas MF, Naess K, ..., Wedell A, Wredenberg A

Hum. Mutat. 42 (4) 378-384 [2021-04-00; online 2021-02-04]

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

PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS.

Abdulla M, Alexsson A, Sundström C, ..., Hollander P, Amini R

Acta Oncol 60 (4) 531-538 [2021-04-00; online 2021-02-12]

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

Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.

Bruhn H, Samuelsson K, Schober FA, ..., Wedell A, Wredenberg A

Neurol Genet 7 (2) e566 [2021-04-00; online 2021-03-15]

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

Modulation of Arabidopsis root growth by specialized triterpenes.

Bai Y, Fernández-Calvo P, Ritter A, ..., Goossens A, Pollier J

New Phytol. 230 (1) 228-243 [2021-04-00; online 2021-01-19]

Swedish Metabolomics Centre (SMC)

Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline.

Gorski M, Jung B, Li Y, ..., Pattaro C, Heid IM

Kidney Int. 99 (4) 926-939 [2021-04-00; online 2020-10-31]

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

Machine learning-based investigation of the cancer protein secretory pathway.

Saghaleyni R, Sheikh Muhammad A, Bangalore P, Nielsen J, Robinson JL

PLoS Comput. Biol. 17 (4) e1008898 [2021-04-00; online 2021-04-05]

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

Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.

Lind L, Sundström J, Ärnlöv J, ..., Lumbers RT, Lampa E

Circ Genom Precis Med 14 (2) e002963 [2021-04-00; online 2021-02-26]

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

Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.

Coutinho A, Malmström H, Edlund H, ..., Schlebusch CM, Jakobsson M

Am. J. Phys. Anthropol. 174 (4) 701-713 [2021-04-00; online 2021-02-04]

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

Integrating omics to characterize eco-physiological adaptations: How moose diet and metabolism differ across biogeographic zones.

Fohringer C, Dudka I, Spitzer R, ..., Ericsson G, Singh NJ

Ecol Evol 11 (7) 3159-3183 [2021-04-00; online 2021-03-04]

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.

Dumanski JP, Halvardson J, Davies H, ..., Ryś J, Forsberg LA

Cell. Mol. Life Sci. 78 (8) 4019-4033 [2021-04-00; online 2021-04-10]

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

Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics.

Gnann C, Cesnik AJ, Lundberg E

Trends Cancer 7 (4) 278-282 [2021-04-00; online 2021-01-10]

Spatial Proteomics [Technology development]

Function of the pseudo phosphotransfer proteins has diverged between rice and Arabidopsis.

Vaughan-Hirsch J, Tallerday EJ, Burr CA, ..., Bishopp A, Kieber JJ

Plant J. 106 (1) 159-173 [2021-04-00; online 2021-02-08]

Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root.

Abdelfattah A, Wisniewski M, Schena L, Tack AJM

Environ. Microbiol. 23 (4) 2199-2214 [2021-04-00; online 2021-01-21]

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

Direct observation of hyperpolarization breaking through the spin diffusion barrier.

Stern Q, Cousin SF, Mentink-Vigier F, ..., Cala O, Jannin S

Sci Adv 7 (18) - [2021-04-00; online 2021-04-30]

Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.

Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX

Mol Ecol Resour 21 (3) 880-896 [2021-04-00; online 2020-12-02]

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

A modified protein marker panel to identify four consensus molecular subtypes in colorectal cancer using immunohistochemistry.

Li X, Larsson P, Ljuslinder I, ..., Edin S, Palmqvist R

Pathol Res Pract 220 (-) 153379 [2021-04-00; online 2021-03-05]

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

A fast and simple clearing and swelling protocol for 3D in-situ imaging of the kidney across scales.

Unnersjö-Jess D, Butt L, Höhne M, ..., Brismar H, Blom H

Kidney Int. 99 (4) 1010-1020 [2021-04-00; online 2020-12-05]

Integrated Microscopy Technologies Stockholm [Technology development]

Deletions on Chromosome Y and Downregulation of the SRY Gene in Tumor Tissue Are Associated with Worse Survival of Glioblastoma Patients.

Łysiak M, Smits A, Roodakker KR, ..., Söderkvist P, Malmström A

Cancers (Basel) 13 (7) - [2021-03-31; online 2021-03-31]

The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.

Qu Y, Chen C, Chen X, ..., Zhang YE, Lei F

Proc. Natl. Acad. Sci. U.S.A. 118 (13) e2012398118 [2021-03-30; online 2021-03-24]

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

The associations between red cell distribution width and plasma proteins in a general population.

Pan J, Borné Y, Orho-Melander M, ..., Melander O, Engström G

Clin Proteomics 18 (1) 12 [2021-03-30; online 2021-03-30]

Multiple migrations to the Philippines during the last 50,000 years.

Larena M, Sanchez-Quinto F, Sjödin P, ..., Endicott P, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 118 (13) - [2021-03-30; online 2021-03-24]

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

Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.

Indukuri R, Hases L, Archer A, Williams C

Front Endocrinol (Lausanne) 12 (-) 650625 [2021-03-30; online 2021-03-30]

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

High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer.

Ku A, Fredsøe J, Sørensen KD, ..., Lilja H, Ceder Y

Front Oncol 11 (-) 631021 [2021-03-25; online 2021-03-25]

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

Case Report: A Novel Mutation in the Mitochondrial MT-ND5 Gene Is Associated With Leber Hereditary Optic Neuropathy (LHON).

Engvall M, Kawasaki A, Carelli V, ..., Wedell A, Träisk F

Front Neurol 12 (-) 652590 [2021-03-25; online 2021-03-25]

Methodological considerations for identifying multiple plasma proteins associated with all-cause mortality in a population-based prospective cohort.

Drake I, Hindy G, Almgren P, ..., Melander O, Orho-Melander M

Sci Rep 11 (1) 6734 [2021-03-24; online 2021-03-24]

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus).

Pappas F, Palaiokostas C

Animals (Basel) 11 (3) - [2021-03-21; online 2021-03-21]

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

Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans.

Persson A, Nikpour M, Vorontsov E, Nilsson J, Larson G

Mol. Cell Proteomics 20 (-) 100074 [2021-03-20; online 2021-03-20]