Publications 2020

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Fatima N, Petri A, Gyllensten U, Feuk L, Ameur A

Genes 11 (12) 1444 [2020-11-30; online 2020-11-30]

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

CRISPR and Long-Read Sequencing: A Perfect Match

Ameur A

The CRISPR Journal - (-) - [2020-11-30; online 2020-11-30]

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

TrackMate: My favorite image analysis tool, by Neubias members

Klemm A

Wiley Analytical Science https://analyticalscience.wiley.com/do/10.1002/was.000400044 (-) - [2020-11-30; online 2020-05-26]

BioImage Informatics [Service]

Single nucleus transcriptomics data integration recapitulates the major cell types in human liver

Diamanti K, Inda Díaz JS, Raine A, ..., Wadelius C, Cavalli M

Hepatol Res 51 (2) 233-238 [2020-11-28; online 2020-11-28]

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

New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth

Manoharan L, Brundin M, Rakhimova O, Chávez de Paz L, Romani Vestman N

J Clin Med 9 (12) 3877 [2020-11-28; online 2020-11-28]

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

Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions.

Sousa JAB, Bolgár A, Christel S, ..., Stams AJM, Plugge CM

pii: S0048-9697(20)34546-0

Sci. Total Environ. 745 (-) 141017 [2020-11-25; online 2020-07-22]

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

Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.

Liao Z, Hodén KP, Singh RK, Dixelius C

pii: 10.1038/s41598-020-77593-y pmc: PMC7689493

Sci Rep 10 (1) 20577 [2020-11-25; online 2020-11-25]

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

High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood.

Petkov S, Bekele Y, Lakshmikanth T, ..., Brodin P, Chiodi F

pii: 10.1038/s41598-020-77433-z pmc: PMC7686502

Sci Rep 10 (1) 20425 [2020-11-24; online 2020-11-24]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

CUBIC-f: An optimized clearing method for cell tracing and evaluation of neurite density in the salamander brain

Tiago Pinheiro IMSEAJCGKMKAS

Journal of Neuroscience Methods - (-) - [2020-11-24; online 2020-11-17]

Advanced Light Microscopy (ALM) [Technology development]

Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.

Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B

pii: 2012265117

Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-11-23; online 2020-11-23]

Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]

Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress

Liu S, Jonge J, Trejo‐Arellano MS, ..., Köhler C, Hennig L

New Phytol - (-) - [2020-11-22; online 2020-11-22]

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

Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.

Näsvall K, Wiklund C, Mrazek V, ..., Vila R, Backström N

Mol. Ecol. 30 (2) 499-516 [2020-11-20; online 2020-11-20]

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

In Situ Assembly of Choline Acetyltransferase Ligands by a Hydrothiolation Reaction Reveals Key Determinants for Inhibitor Design

Wiktelius D, Allgardsson A, Bergström T, ..., Linusson A, Ekström F

Angew. Chem. Int. Ed. 60 (2) 813-819 [2020-11-20; online 2020-11-20]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.

Khandagale A, Holmlund T, Entesarian M, ..., Nordenskjöld M, Fadeel B

Br. J. Haematol. - (-) - [2020-11-18; online 2020-11-18]

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

A complex DICER1 syndrome phenotype associated with a germline pathogenic variant affecting the RNase IIIa domain of DICER1.

Pontén E, Frisk S, Taylan F, ..., Lagerstedt-Robinson K, Nordgren A

pii: jmedgenet-2020-107385

J. Med. Genet. - (-) - [2020-11-18; online 2020-11-18]

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. - (-) - [2020-11-17; online 2020-11-17]

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

Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury.

Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G

pii: 10.1038/s41467-020-19453-x pmc: PMC7673029

Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]

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

Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities

Coll C, Bier R, Li Z, ..., Gorokhova E, Sobek A

Environ. Sci. Technol. 54 (22) 14380-14392 [2020-11-17; online 2020-10-26]

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

Cryo‐EM structure of native human uromodulin, a zona pellucida module polymer

Stsiapanava A, Xu C, Brunati M, ..., Wu B, Jovine L

EMBO J - (-) e106807 [2020-11-16; online 2020-11-16]

Cryo-EM [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 H, Marklund N

J. Neurotrauma - (-) - [2020-11-15; online 2020-11-15]

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

One-Pot, Metal-Free Synthesis of Dimethyl Carbonate from CO2 at Room Temperature

Khokarale SG, Bui TQ, Mikkola JP

Sustainable Chemistry 1 (3) 298-314 [2020-11-13; online 2020-11-13]

Identification of Pre-Diagnostic Metabolic Patterns for Glioma Using Subset Analysis of Matched Repeated Time Points

Jonsson P, Antti H, Späth F, Melin B, Björkblom B

Cancers (Basel) 12 (11) 3349 [2020-11-12; online 2020-11-12]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [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 - (-) 1-8 [2020-11-12; online 2020-11-12]

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

Development of a highly efficient 50K SNP genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome re-sequencing and its transferability to other spruce species.

Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX

Mol Ecol Resour - (-) - [2020-11-11; online 2020-11-11]

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

Metabolomics of Interstitial Fluid, Plasma and Urine in Patients with Arterial Hypertension: New Insights into the Underlying Mechanisms

Chachaj A, Matkowski R, Gröbner G, Szuba A, Dudka I

Diagnostics 10 (11) 936 [2020-11-11; online 2020-11-11]

A novel heterozygous variant in FGF9 associated with previously unreported features of multiple synostosis syndrome 3.

Thuresson AC, Croft B, Hailer YD, ..., Harley VR, Stattin EL

Clin. Genet. - (-) - [2020-11-11; online 2020-11-11]

Clinical Genomics Uppsala [Collaborative]

Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis

Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M

mSystems 5 (6) - [2020-11-10; online 2020-11-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [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. - (-) - [2020-11-10; online 2020-11-10]

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

Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.

Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K

pii: 10.1038/s41398-020-01056-1 pmc: PMC7652854

Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]

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]

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

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

J Ecol - (-) - [2020-11-05; online 2020-11-05]

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

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish ( Silurus glanis) Using Linked-Read Sequencing.

Ozerov MY, Flajšhans M, Noreikiene K, Vasemägi A, Gross R

pii: g3.120.401711 pmc: PMC7642921

G3 (Bethesda) 10 (11) 3897-3906 [2020-11-05; online 2020-11-05]

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

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M

- 48 (19) e112-e112 [2020-11-04; online 2020-09-29]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Technology development]

MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.

Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R

pii: 5922798 pmc: PMC7641766

Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]

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

Evolution from adherent to suspension: systems biology of HEK293 cell line development.

Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J

pii: 10.1038/s41598-020-76137-8 pmc: PMC7642379

Sci Rep 10 (1) 18996 [2020-11-04; online 2020-11-04]

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

Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the "PI-POC" Trial.

Gaudenzi G, Kumbakumba E, Rasti R, ..., Mwanga-Amumpaire J, Alfvén T

pii: v9i11e21430 pmc: PMC7690656 ClinicalTrials.gov: NCT03900091

JMIR Res Protoc 9 (11) e21430 [2020-11-04; online 2020-11-04]

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, ..., Sällberg Chen M, D'Alessandro A

pmc: PMC7654893

medRxiv - (-) - [2020-11-04; online 2020-11-04]

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

Cross-validated Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Quantitation Protocol for a Pharmaceutical Drug and Its Drug-Target Effects in the Brain Using Time-of-Flight and Fourier Transform Ion Cyclotron Resonance Analyzers.

Källback P, Vallianatou T, Nilsson A, ..., Svenningsson P, Andrén PE

pmc: PMC7660593

Anal. Chem. 92 (21) 14676-14684 [2020-11-03; online 2020-10-21]

National Resource for Mass Spectrometry Imaging [Technology development]

From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.

Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F

pii: 5912529 pmc: PMC7674688

Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]

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

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.

Pértille F, Ibelli AMG, Sharif ME, ..., Guerrero-Bosagna C, Coutinho LL

pmc: PMC7667380

Front Genet 11 (-) 508809 [2020-11-02; online 2020-11-02]

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

Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16.

Golparian D, Bazzo ML, Golfetto L, ..., Unemo M, Brazilian-GASP Network

pii: 5891806

J. Antimicrob. Chemother. 75 (11) 3163-3172 [2020-11-01; online 2020-08-14]

Dense sampling of bird diversity increases power of comparative genomics.

Feng S, Stiller J, Deng Y, ..., Paten B, Zhang G

pii: 10.1038/s41586-020-2873-9

Nature 587 (7833) 252-257 [2020-11-00; online 2020-11-11]

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

Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP

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

Molecular Cell - (-) - [2020-11-00; online 2020-11-00]

Leaf shape in Populus tremula is a complex, omnigenic trait.

Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR

pii: ECE36691 pmc: PMC7663049 Dryad: 10.5061/dryad.3n5tb2rdt

Ecol Evol 10 (21) 11922-11940 [2020-11-00; online 2020-10-13]

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

Crown‐fire severity is more important than ground‐fire severity in determining soil fungal community development in the boreal forest

Pérez‐Izquierdo L, Clemmensen KE, Strengbom J, ..., Nilsson M, Lindahl BD

J Ecol - (-) - [2020-11-00; online 2020-11-00]

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

Divergent above- and below-ground responses of fungal functional groups to forest thinning

Collado E, Castaño C, Bonet JA, ..., Martínez de Aragón J, de-Miguel S

Soil Biology and Biochemistry 150 (-) 108010 [2020-11-00; online 2020-11-00]

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

Cytogenetically visible inversions are formed by multiple molecular mechanisms.

Pettersson M, Grochowski CM, Wincent J, ..., Carvalho CMB, Lindstrand A

Hum. Mutat. 41 (11) 1979-1998 [2020-11-00; online 2020-10-01]

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

Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis

He Q, Li X, He L, ..., Betsholtz C, Welsh M

Int. J. Cancer 147 (9) 2634-2644 [2020-11-00; online 2020-05-30]

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

Sahelian pastoralism from the perspective of variants associated with lactase persistence

Priehodová E, Austerlitz F, Čížková M, ..., Schlebusch CM, Černý V

Am J Phys Anthropol 173 (3) 423-436 [2020-11-00; online 2020-08-19]

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

Disassociated molecular orientation distributions of a composite cellulose–lignin carbon fiber precursor: A study by rotor synchronized NMR spectroscopy and X-ray scattering

Svenningsson L, Bengtsson J, Jedvert K, ..., Theliander H, Evenäs L

Carbohydr Polym - (-) 117293 [2020-11-00; online 2020-11-00]

Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer.

Mehmeti-Ajradini M, Bergenfelz C, Larsson AM, ..., Bexell D, Leandersson K

pii: 3/11/e202000893

Life Sci. Alliance 3 (11) - [2020-11-00; online 2020-09-21]

Mass Cytometry [Service]

Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline.

Gorski M, Jung B, Li Y, ..., Pattaro C, Heid IM

pii: S0085-2538(20)31239-4

Kidney Int. 99 (4) 926-939 [2020-10-30; online 2020-10-30]

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

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome

Ehrenbolger K, Jespersen N, Sharma H, ..., Vossbrinck CR, Barandun J

PLoS Biol. 18 (10) e3000958 [2020-10-30; online 2020-10-30]

Root trait–microbial relationships across tundra plant species

Spitzer CM, Lindahl B, Wardle DA, ..., Fanin N, Kardol P

New Phytol - (-) - [2020-10-30; online 2020-10-30]

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

Origins and genetic legacy of prehistoric dogs.

Bergström A, Frantz L, Schmidt R, ..., Larson G, Skoglund P

pii: 370/6516/557 pmc: PMC7116352 mid: EMS103415

Science 370 (6516) 557-564 [2020-10-30; online 2020-10-29]

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

Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9

Winkelmann I, Matsuoka R, Meier PF, ..., Beckstein O, Drew D

EMBO J - (-) - [2020-10-29; online 2020-10-29]

Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.

Liang D, Andersen CB, Vetukuri RR, Dou D, Grenville-Briggs LJ

pmc: PMC7720654

Front Microbiol 11 (-) 581698 [2020-10-29; online 2020-10-29]

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

Activation of RAS Signalling is Associated with Altered Cell Adhesion in Phaeochromocytoma.

Rossitti HM, Dutta RK, Larsson C, ..., Söderkvist P, Gimm O

pii: ijms21218072 pmc: PMC7663737

Int J Mol Sci 21 (21) 8072 [2020-10-29; online 2020-10-29]

Bioinformatics Compute and Storage [Service] Clinical Genomics Linköping

DNA methylation in canine brains is related to domestication and dog-breed formation

Sundman AS, Pértille F, Lehmann Coutinho L, ..., Guerrero-Bosagna C, Jensen P

PLoS ONE 15 (10) e0240787 [2020-10-29; online 2020-10-29]

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

Intra-Individual Behavioural Variability: A Trait under Genetic Control

Henriksen R, Höglund A, Fogelholm J, ..., Dingemanse NJ, Wright D

Int J Mol Sci 21 (21) 8069 [2020-10-29; online 2020-10-29]

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

Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility

Sjöberg S, Stairs CW, Allard B, ..., Ettema TJG, Dupraz C

FEMS Microbiol. Ecol. 96 (11) - [2020-10-28; online 2020-08-20]

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

Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.

Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L

pii: 10.1038/s41598-020-75315-y pmc: PMC7591532

Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]

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

Coupling stabilizers open KV1-type potassium channels

Silverå Ejneby M, Wallner B, Elinder F

Proc Natl Acad Sci USA 117 (43) 27016-27021 [2020-10-27; online 2020-10-13]

Chemical Biology Consortium Sweden (CBCS) [Service]

Vibrio cholerae cytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy

Corkery DP, Nadeem A, Aung KM, ..., Wai SN, Wu YW

J Cell Sci - (-) jcs.252015 [2020-10-26; online 2020-10-26]

Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.

Lundtoft C, Pucholt P, Imgenberg-Kreuz J, ..., Rönnblom L, Hagberg N

pii: PGENETICS-D-20-01001

PLoS Genet. 16 (10) e1009199 [2020-10-26; online 2020-10-26]

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

Autoantibodies against type I IFNs in patients with life-threatening COVID-19.

Bastard P, Rosen LB, Zhang Q, ..., Su HC, Casanova JL

pii: science.abd4585

Science 370 (6515) - [2020-10-23; online 2020-09-24]

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.

Zhang Q, Bastard P, Liu Z, ..., Su HC, Casanova JL

pii: science.abd4570 Dryad: 10.5061/dryad.8pk0p2nkk

Science 370 (6515) - [2020-10-23; online 2020-09-24]

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.

Flygaard RK, Mühleip A, Tobiasson V, Amunts A

pii: 10.1038/s41467-020-18993-6

Nat Commun 11 (1) 5342 [2020-10-22; online 2020-10-22]

Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce.

Nakamura M, Batista RA, Köhler C, Hennig L

pii: 5902563 pmc: PMC7586741

J. Exp. Bot. 71 (20) 6366-6378 [2020-10-22; online 2020-09-08]

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

Epigenetic alterations in skin homing CD4 +CLA+ T cells of atopic dermatitis patients.

Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A

pii: 10.1038/s41598-020-74798-z pmc: PMC7582180

Sci Rep 10 (1) 18020 [2020-10-22; online 2020-10-22]

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

Genetic Variants Associated with Non-Alcoholic Fatty Liver Disease Do Not Associate with Measures of Sub-Clinical Atherosclerosis: Results from the IMPROVE Study.

Castaldo L, Laguzzi F, Strawbridge RJ, ..., Mälarstig A, Gigante B

pii: genes11111243

Genes 11 (11) - [2020-10-22; online 2020-10-22]

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

Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO 2

Walker AP, De Kauwe MG, Bastos A, ..., Whelan ME, Zuidema PA

New Phytol - (-) - [2020-10-21; online 2020-10-21]

Automated identification of the mouse brain's spatial compartments from in situ sequencing data.

Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C

pii: 10.1186/s12915-020-00874-5 pmc: PMC7574211

BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]

BioImage Informatics Bioinformatics Compute and Storage [Service]

A high-stringency blueprint of the human proteome.

Adhikari S, Nice EC, Deutsch EW, ..., Aebersold R, Baker MS

pii: 10.1038/s41467-020-19045-9 pmc: PMC7568584

Nat Commun 11 (1) 5301 [2020-10-16; online 2020-10-16]

The Structure of Riparian Vegetation in Agricultural Landscapes Influences Spider Communities and Aquatic-Terrestrial Linkages

Ramberg E, Burdon FJ, Sargac J, ..., Johnson RK, McKie BG

Water 12 (10) 2855 [2020-10-14; online 2020-10-14]

Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome.

Zhang C, Mazzeu JF, Eisfeldt J, ..., Sutton VR, Carvalho CMB

Am. J. Med. Genet. A - (-) - [2020-10-13; online 2020-10-13]

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

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A

Mol Ecol Resour 21 (1) 263-286 [2020-10-10; online 2020-10-10]

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

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.

Barnett R, Westbury MV, Sandoval-Velasco M, ..., Yamaguchi N, Gilbert MTP

pii: S0960-9822(20)31421-4

Curr. Biol. - (-) - [2020-10-09; online 2020-10-09]

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

Optotracing for selective fluorescence-based detection, visualization and quantification of live S. aureus in real-time.

Butina K, Tomac A, Choong FX, ..., Löffler S, Richter-Dahlfors A

pii: 10.1038/s41522-020-00150-y

NPJ Biofilms Microbiomes 6 (1) 35 [2020-10-09; online 2020-10-09]

Advanced Light Microscopy (ALM) [Service]

Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing

Sandling JK, Pucholt P, Hultin Rosenberg L, ..., Rönnblom L, None

Ann Rheum Dis 80 (1) annrheumdis-2020-218636 [2020-10-09; online 2020-10-09]

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

Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases.

Preger C, Wigren E, Ossipova E, ..., Gräslund S, Persson H

pii: RA120.012893 pmc: PMC7549041

J. Biol. Chem. 295 (41) 13981-13993 [2020-10-09; online 2020-08-14]

Drug Discovery and Development (DDD) [Collaborative]

SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden.

Rudberg AS, Havervall S, Månberg A, ..., Hober S, Thålin C

pii: 10.1038/s41467-020-18848-0

Nat Commun 11 (1) 5064 [2020-10-08; online 2020-10-08]

Autoimmunity and Serology Profiling [Collaborative]

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.

Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D

pii: 10.1186/s12859-020-03784-z pmc: PMC7542881

BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]

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

Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.

Arroyo Mühr LS, Lagheden C, Lei J, ..., Sundström K, Dillner J

pii: 10.1038/s41416-020-01111-0

Br. J. Cancer - (-) - [2020-10-06; online 2020-10-06]

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

Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.

Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M

pii: 10.1186/s12870-020-02656-1 pmc: PMC7541206

BMC Plant Biol. 20 (1) 455 [2020-10-06; online 2020-10-06]

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

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

Almeida P, Sandkam BA, Morris J, ..., Breden F, Mank JE

Mol. Biol. Evol. - (-) - [2020-10-06; online 2020-10-06]

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

A latent lineage potential in resident neural stem cells enables spinal cord repair.

Llorens-Bobadilla E, Chell JM, Le Merre P, ..., Carlén M, Frisén J

pii: 370/6512/eabb8795

Science 370 (6512) eabb8795 [2020-10-02; online 2020-10-03]

Advanced Light Microscopy (ALM) [Service] Eukaryotic Single Cell Genomics (ESCG)

Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens

Schlebusch CM, Sjödin P, Breton G, ..., Soodyall H, Jakobsson M

Mol. Biol. Evol. 37 (10) 2944-2954 [2020-10-01; online 2020-07-22]

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

Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians

Sjöstrand AE, Sjödin P, Hegay T, ..., Heyer E, Jakobsson M

Eur J Hum Genet - (-) - [2020-10-01; online 2020-10-01]

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

Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.

Phoon YP, Chivukula IV, Tsoi YL, ..., Kuiper R, Lendahl U

pii: S0014-4827(20)30403-1

Exp. Cell Res. 395 (1) 112156 [2020-10-01; online 2020-07-22]

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

Development of a chemical probe against NUDT15

Zhang SM, Desroses M, Hagenkort A, ..., Stenmark P, Helleday T

PDB: 6T5J

Nat Chem Biol 16 (10) 1120-1128 [2020-10-00; online 2020-07-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes.

Bernard E, Nannya Y, Hasserjian RP, ..., Ogawa S, Papaemmanuil E

pii: 10.1038/s41591-020-1008-z

Nat. Med. 26 (10) 1549-1556 [2020-10-00; online 2020-08-03]

Whole genome sequencing of apparently mutation-negative MEN1 patients

Backman S, Bajic D, Crona J, ..., Skogseid B, Stålberg P

Eur. J. Endocrinol. 182 (1) 35-45 [2020-10-00; online 2019-10-00]

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]

Metagenomic analysis of bacteria in stallion semen

Al-Kass Z, Guo Y, Vinnere Pettersson O, Niazi A, Morrell JM

Animal Reproduction Science 221 (-) 106568 [2020-10-00; online 2020-10-00]

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

Clonal hematopoiesis in patients with high‐grade B‐cell lymphoma is associated with inferior outcome

Amini R, Ljungström V, Abdulla M, ..., Enblad G, Baliakas P

Am J Hematol 95 (10) - [2020-10-00; online 2020-08-12]

Clinical Genomics Uppsala [Collaborative]

Geographically widespread invasive meningococcal disease caused by a ciprofloxacin resistant non-groupable strain of the ST-175 clonal complex.

Willerton L, Lucidarme J, Campbell H, ..., Vogel U, Borrow R

pii: S0163-4453(20)30570-3

J Infect 81 (4) 575-584 [2020-10-00; online 2020-08-25]

Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.

Hong M, Dodig-Crnković T, Chen X, ..., Magnusson PK, Schwenk JM

pii: 3/10/e202000817

Life Sci. Alliance 3 (10) e202000817 [2020-10-00; online 2020-07-31]

Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Collaborative]

Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals

Folkersen L, Gustafsson S, Wang Q, ..., Ingelsson E, Mälarstig A

Nat Metab 2 (10) 1135-1148 [2020-10-00; online 2020-10-16]

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

Discovery of USP7 small-molecule allosteric inhibitors

Engström O, Belda O, Kullman-Magnusson M, ..., Parkes KEB, Zhao H

Bioorganic & Medicinal Chemistry Letters 30 (20) 127471 [2020-10-00; online 2020-10-00]

HEARTBREAK Controls Post-translational Modification of INDEHISCENT to Regulate Fruit Morphology in Capsella

Dong Y, Majda M, Šimura J, ..., Smith RS, Østergaard L

Current Biology 30 (19) 3880-3888.e5 [2020-10-00; online 2020-10-00]

Swedish Metabolomics Centre (SMC)

Exploring the bacterial nano-universe

Söderholm N, Singh B, Uhlin BE, Sandblad L

Current Opinion in Structural Biology 64 (-) 166-173 [2020-10-00; online 2020-10-00]

Cryo-EM [Collaborative]

High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.

Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C

pii: 10.1038/s41598-020-73166-1 pmc: PMC7527340

Sci Rep 10 (1) 16160 [2020-09-30; online 2020-09-30]

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

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts

Mondav R, Bertilsson S, Buck M, ..., Lindström ES, Garcia SL

mSystems 5 (5) - [2020-09-29; online 2020-09-29]

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

Toll-like receptors revisited; a possible role for TLR1 in lupus nephritis

Yavuz S, Bianchi M, Kozyrev S, ..., Lindblad-Toh K, Rönnblom L

Ann Rheum Dis - (-) annrheumdis-2020-218373 [2020-09-29; online 2020-09-29]

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

Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3

Rogne P, Dulko-Smith B, Goodman J, ..., Sauer-Eriksson AE, Wolf-Watz M

Biochemistry 59 (38) 3570-3581 [2020-09-29; online 2020-08-21]

MAIT cell activation and dynamics associated with COVID-19 disease severity.

Parrot T, Gorin JB, Ponzetta A, ..., Strålin K, Sandberg JK

pii: 5/51/eabe1670

Sci Immunol 5 (51) - [2020-09-28; online 2020-09-30]

Translational Plasma Profiling [Service]

A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.

Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U

Mol. Microbiol. - (-) - [2020-09-28; online 2020-09-28]

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

Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation

Wallentin L, Lindbäck J, Eriksson N, ..., Oldgren J, Siegbahn A

- - (-) - [2020-09-27; online 2020-09-27]

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

Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.

Pontiller B, Martínez-García S, Lundin D, Pinhassi J

pmc: PMC7546218

Front Microbiol 11 (-) 588778 [2020-09-25; online 2020-09-25]

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

Epilepsy syndromes, etiologies, and the use of next-generation sequencing in epilepsy presenting in the first 2 years of life: A population-based study.

Stödberg T, Tomson T, Barbaro M, ..., Åmark P, Wedell A

Epilepsia - (-) - [2020-09-23; online 2020-09-23]

Small-scale population divergence is driven by local larval environment in a temperate amphibian

Rödin-Mörch P, Palejowski H, Cortazar-Chinarro M, ..., Höglund J, Laurila A

Heredity - (-) - [2020-09-21; online 2020-09-21]

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

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Bailey MH, Meyerson WU, Dursi LJ, ..., Ding L, PCAWG Consortium

pii: 10.1038/s41467-020-18151-y pmc: PMC7505971

Nat Commun 11 (1) 4748 [2020-09-21; online 2020-09-21]

Sources of variation in cell-type RNA-Seq profiles.

Gustafsson J, Held F, Robinson JL, ..., Jörnsten R, Nielsen J

pii: PONE-D-20-18758 pmc: PMC7505444

PLoS ONE 15 (9) e0239495 [2020-09-21; online 2020-09-21]

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

The methylation landscape and its role in domestication and gene regulation in the chicken

Höglund A, Henriksen R, Fogelholm J, ..., Jensen P, Wright D

Nat Ecol Evol 4 (12) 1713-1724 [2020-09-21; online 2020-09-21]

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

Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.

Ignatov D, Vaitkevicius K, Johansson J

pii: S2666-1667(20)30033-2 pmc: PMC7580233

STAR Protoc 1 (2) 100046 [2020-09-18; online 2020-06-06]

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

Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells.

Niklasson CU, Fredlund E, Monni E, ..., Bronner ME, Mohlin S

Dev. Dyn. - (-) - [2020-09-17; online 2020-09-17]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L

pii: 2009925117

Proc. Natl. Acad. Sci. U.S.A. 117 (39) 24359-24368 [2020-09-16; online 2020-09-16]

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

High-resolution imaging of tumour spheroids and organoids enabled by expansion microscopy

Edwards S, Carannante V, Kuhnigk K, ..., Önfelt B, Brismar H

Front. Mol. Biosci. - (-) - [2020-09-16; online 2020-07-29]

Advanced Light Microscopy (ALM) [Technology development]

Transcriptome analysis of EPO and GFP HEK293 Cell-lines Reveal Shifts in Energy and ER Capacity Support Improved Erythropoietin Production in HEK293F Cells

Saghaleyni R, Malm M, Zrimec J, ..., Robinson JL, Rockberg J

- - (-) - [2020-09-16; online 2020-09-16]

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

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.

Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S

pii: 10.1038/s41598-020-71939-2 pmc: PMC7486370

Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]

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

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne

Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E

Microorganisms 8 (9) 1394 [2020-09-11; online 2020-09-11]

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

Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity

Yaghootkar H, Zhang Y, Spracklen CN, ..., Loos RJ, Kilpeläinen TO

Diabetes - (-) db200070 [2020-09-11; online 2020-09-11]

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

A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences

Svensson D, Rentoft M, Dahlin AM, ..., Trygg J, Johansson E

PLoS ONE 15 (9) e0237721 [2020-09-11; online 2020-09-11]

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

Complete Genome Sequence of Francisella halioticida Type Strain DSM 23729 (FSC1005)

Uneklint I, Öhrman C, Karlsson L, ..., Forsman M, Sjödin A

Microbiol Resour Announc 9 (37) - [2020-09-10; online 2020-09-10]

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

A genome‐wide association study revealed five SNPs affecting 8‐month weight in sheep

Pasandideh M, Gholizadeh M, Rahimi‐Mianji G

Anim Genet - (-) - [2020-09-10; online 2020-09-10]

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

Integration of molecular profiles in a longitudinal wellness profiling cohort.

Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L

pii: 10.1038/s41467-020-18148-7

Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]

Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Mass Cytometry [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative] Translational Plasma Profiling [Collaborative]

Profiling of Inflammatory Proteins in Plasma of HIV-1-Infected Children Receiving Antiretroviral Therapy.

Lemma M, Petkov S, Bekele Y, ..., Howe R, Chiodi F

pii: proteomes8030024 pmc: PMC7563605

Proteomes 8 (3) - [2020-09-07; online 2020-09-07]

Translational Plasma Profiling [Service]

Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns

Ugalde‐Morales E, Grassmann F, Humphreys K, ..., Hall P, Czene K

Int. J. Cancer - (-) - [2020-09-05; online 2020-09-05]

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

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.

Hanke L, Vidakovics Perez L, Sheward DJ, ..., Murrell B, McInerney GM

pii: 10.1038/s41467-020-18174-5 PDB: 6ZXN

Nat Commun 11 (1) 4420 [2020-09-04; online 2020-09-04]

Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]

Genome sequence of segmented filamentous bacteria present in the human intestine.

Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF

pii: 10.1038/s42003-020-01214-7 pmc: PMC7474095

Commun Biol 3 (1) 485 [2020-09-04; online 2020-09-04]

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

A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site

Martínez-Carranza M, Jonna VR, Lundin D, ..., Stenmark P, Hofer A

PDB: 6ZJK

J. Biol. Chem. 295 (46) jbc.RA120.014895 [2020-09-03; online 2020-09-03]

Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]

Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum

Mahajan M, Seeger C, Yee B, Andersson SGE

Genome Biol Evol 12 (9) 1528-1548 [2020-09-01; online 2020-08-06]

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

Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken

Li J, Lee M, Davis BW, ..., Siegel PB, Andersson* L

- 37 (9) 2477-2486 [2020-09-01; online 2020-04-28]

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

River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs

Freixa A, Perujo N, Langenheder S, Romaní AM

FEMS Microbiol. Ecol. 96 (9) - [2020-09-01; online 2020-08-07]

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

Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.

Svedberg A, Björn N, Sigurgeirsson B, ..., Lundeberg J, Gréen H

pii: S0169-5002(20)30516-X

Lung Cancer 147 (-) 106-114 [2020-09-00; online 2020-07-12]

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

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.

Dias JM, Alekseenko Z, Jeggari A, ..., Iber D, Ericson J

pii: 6/38/eaba8196 pmc: PMC7494341

Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]

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

Hemolytic uremic syndrome caused by Shiga toxin-producing Escherichia coli in children: incidence, risk factors, and clinical outcome.

Ylinen E, Salmenlinna S, Halkilahti J, ..., Jalanko H, Saxén H

pii: 10.1007/s00467-020-04560-0 pmc: PMC7385025

Pediatr Nephrol 35 (9) 1749-1759 [2020-09-00; online 2020-04-22]

A dynamic mutational landscape associated with an inter‐regionally diverse immune response in malignant rhabdoid tumour

Yasui H, Valind A, Karlsson J, ..., Backman T, Gisselsson D

J. Pathol 252 (1) 22-28 [2020-09-00; online 2020-07-22]

Clinical Genomics Lund

The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19

Consiglio CR, Cotugno N, Sardh F, ..., Palma P, Brodin P

Cell 183 (4) 968-981.e7 [2020-09-00; online 2020-09-00]

Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]

DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.

Guerrero-Bosagna C, Pértille F, Gomez Y, ..., Voelkl B, Toscano MJ

pii: S1744-117X(20)30047-2

Comp Biochem Physiol Part D Genomics Proteomics 35 (-) 100700 [2020-09-00; online 2020-06-02]

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

Reconstructing marine plankton food web interactions using DNA metabarcoding.

Zamora-Terol S, Novotny A, Winder M

Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]

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

The impact of damage-associated molecular patterns on the neurotransmitter release and gene expression in the ex vivo rat carotid body.

Mkrtchian S, Kåhlin J, Gómez-Galán M, ..., Erlandsson Harris H, Eriksson LI

Exp. Physiol. 105 (9) 1634-1647 [2020-09-00; online 2020-07-24]

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

NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2

Zhou S, Pettersson P, Huang J, ..., Mäler L, Ädelroth P

Structure - (-) - [2020-09-00; online 2020-09-00]

Swedish NMR Centre (SNC)

Prenylated Flavonoids from the Roots of Tephrosia rhodesica

Atilaw Y, Muiva-Mutisya L, Bogaerts J, ..., Erdélyi M, Yenesew A

J. Nat. Prod. 83 (8) 2390-2398 [2020-08-28; online 2020-08-13]

Sex differences in oncogenic mutational processes.

Li CH, Prokopec SD, Sun RX, ..., Boutros PC, PCAWG Consortium

pii: 10.1038/s41467-020-17359-2 pmc: PMC7455744

Nat Commun 11 (1) 4330 [2020-08-28; online 2020-08-28]

Genetics meets proteomics: perspectives for large population-based studies.

Suhre K, McCarthy MI, Schwenk JM

pii: 10.1038/s41576-020-0268-2

Nat. Rev. Genet. - (-) - [2020-08-28; online 2020-08-28]

Fulvestrant-mediated attenuation of the innate immune response decreases ER+ breast cancer growth in vivo more effectively than tamoxifen.

Abrahamsson A, Vazquez Rodriguez G, Dabrosin C

pii: 0008-5472.CAN-20-1705

Cancer Res. - (-) - [2020-08-27; online 2020-08-27]

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

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B

Front Microbiol 11 (-) - [2020-08-27; online 2020-08-27]

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

Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.

Soratto TAT, Darban H, Bjerkner A, ..., Allander T, Andersson B

pii: 9/35/e00934-20 pmc: PMC7453295

Microbiol Resour Announc 9 (35) - [2020-08-27; online 2020-08-27]

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

µ Opioid Receptor Agonism for L-DOPA-Induced Dyskinesia in Parkinson's Disease.

Bezard E, Li Q, Hulme H, ..., Andren PE, Crossman AR

pii: JNEUROSCI.0610-20.2020 pmc: PMC7455220

J. Neurosci. 40 (35) 6812-6819 [2020-08-26; online 2020-07-20]

National Resource for Mass Spectrometry Imaging [Service]

Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity.

Lytrivi M, Ghaddar K, Lopes M, ..., Eizirik DL, Cnop M

pii: 10.1186/s12864-020-07003-0 pmc: PMC7448506

BMC Genomics 21 (1) 590 [2020-08-26; online 2020-08-26]

Proteogenomics [Collaborative]

Brain transcriptomics of wild and domestic rabbits suggests that changes in dopamine signalling and ciliary function contributed to evolution of tameness

Sato DX, Rafati N, Ring H, ..., Carneiro M, Andersson L

Genome Biol Evol 12 (10) 1918-1928 [2020-08-24; online 2020-08-24]

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

Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.

Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H

pii: 10.1038/s41540-020-00146-6 pmc: PMC7445166

npj Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]

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

Unraveling the Immune Response in Severe COVID-19

Rodriguez L, Brodin P

J Clin Immunol 40 (7) 958-959 [2020-08-22; online 2020-08-22]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

Natural killer cell immunotypes related to COVID-19 disease severity.

Maucourant C, Filipovic I, Ponzetta A, ..., Björkström NK, Karolinska COVID-19 Study Group

pii: 5/50/eabd6832 pmc: PMC7665314

Sci Immunol 5 (50) eabd6832 [2020-08-21; online 2020-08-23]

Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Service]

13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking.

Yang M, Safavi S, Woodward EL, ..., Nord KH, Paulsson K

pii: 454973 pmc: PMC7498303

Blood 136 (8) 946-956 [2020-08-20; online 2020-05-10]

Clinical Genomics Lund

Structural basis of mitochondrial translation

Aibara S, Singh V, Modelska A, Amunts A

Elife 9 (-) 1-17 [2020-08-19; online 2020-08-19]

Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.

Nascimento Lemos L, Manoharan L, William Mendes L, ..., Satler Pylro V, Tsai SM

Environ Microbiol Rep 12 (6) 651-655 [2020-08-19; online 2020-08-19]

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

Clinical Presentation, Genetic Etiology, and Coenzyme Q10 Levels in 55 Children with Combined Enzyme Deficiencies of the Mitochondrial Respiratory Chain.

Naess K, Bruhn H, Stranneheim H, ..., Wedell A, von Döbeln U

pii: S0022-3476(20)31007-6

J Pediatr - (-) - [2020-08-19; online 2020-08-19]

Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".

Woods R, Turvey ST, Brace S, ..., Brown MJF, Barnes I

pii: 10.1186/s12862-020-01668-7 pmc: PMC7437022

BMC Evol. Biol. 20 (1) 106 [2020-08-18; online 2020-08-18]

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

High Cysteine Membrane Proteins (HCMPs) Are Up-Regulated During Giardia-Host Cell Interactions.

Peirasmaki D, Ma'ayeh SY, Xu F, ..., Liu J, Svärd SG

pmc: PMC7461913

Front Genet 11 (-) 913 [2020-08-18; online 2020-08-18]

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

Designing custom CRISPR libraries for hypothesis-driven drug target discovery.

Iyer VS, Jiang L, Shen Y, ..., Schmierer B, Wermeling F

pii: S2001-0370(20)30362-7 pmc: PMC7479249

Computational and Structural Biotechnology Journal 18 (-) 2237-2246 [2020-08-18; online 2020-08-18]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative]

Association of Established Blood Pressure Loci With 10-Year Change in Blood Pressure and Their Ability to Predict Incident Hypertension.

Poveda A, Atabaki-Pasdar N, Ahmad S, ..., Renström F, Franks PW

J Am Heart Assoc 9 (16) e014513 [2020-08-18; online 2020-08-04]

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

Platelet-Specific PDGFB Ablation Impairs Tumor Vessel Integrity and Promotes Metastasis

Zhang Y, Cedervall J, Hamidi A, ..., Dimberg A, Olsson AK

Cancer Res 80 (16) 3345-3358 [2020-08-15; online 2020-06-25]

PLA and Single Cell Proteomics [Service]

Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target.

Škerlová J, Unterlass J, Göttmann M, ..., Jemth AS, Stenmark P

PDB: 6YB8 PDB: 6YB9

J. Biol. Chem. 295 (33) 11656-11668 [2020-08-14; online 2020-06-22]

Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.

Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F

pii: 10.1038/s41467-020-17871-5 pmc: PMC7426940

Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]

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

Variations in Plasma Membrane Topography Can Explain Heterogenous Diffusion Coefficients Obtained by Fluorescence Correlation Spectroscopy

Gesper A, Wennmalm S, Hagemann P, ..., Happel P, Parmryd I

Front. Cell Dev. Biol. 8 (-) 767 [2020-08-11]

Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.

Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K

pii: 10.1038/s41598-020-70412-4 pmc: PMC7419513

Sci Rep 10 (1) 13513 [2020-08-11; online 2020-08-11]

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

Regular use of depot medroxyprogesterone acetate causes thinning of the superficial lining and apical distribution of HIV target cells in the human ectocervix.

Edfeldt G, Lajoie J, Röhl M, ..., Broliden K, Tjernlund A

pii: 5891260

J. Infect. Dis. - (-) - [2020-08-11; online 2020-08-11]

BioImage Informatics

Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy.

Mikus M, Zandian A, Sjöberg R, ..., van Hage M, Ohlin M

pii: S0091-6749(20)31108-8

J. Allergy Clin. Immunol. - (-) - [2020-08-10; online 2020-08-10]

Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Compute and Storage [Service]

Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

Tedersoo L, Anslan S, Bahram M, Kõljalg U, Abarenkov K

Fungal Diversity - (-) - [2020-08-08; online 2020-08-08]

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

Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder

Ramos J, Proven M, Halvardson J, ..., Thuresson AC, Fu D

RNA 26 (11) rna.076380.120 [2020-08-06; online 2020-08-06]

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

Mebendazole is unique among tubulin-active drugs in activating the MEK-ERK pathway.

Andersson CR, Selvin T, Blom K, ..., Nygren P, Larsson R

pii: 10.1038/s41598-020-68986-0 pmc: PMC7403428

Sci Rep 10 (1) 13124 [2020-08-04; online 2020-08-04]

Drug Discovery and Development (DDD) [Service]

Heterogeneous somatostatin-expressing neuron population in mouse ventral tegmental area

Nagaeva E, Zubarev I, Bengtsson Gonzales C, ..., Augustine GJ, Korpi ER

Elife 9 (-) - [2020-08-04; online 2020-08-04]

Eukaryotic Single Cell Genomics (ESCG)

zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.

Zhang H, Waldmann L, Manuel R, ..., Haitina T, Allalou A

pii: 393519 pmc: PMC7449731

Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]

BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.

Ljunggren M, Theorell-Haglöw J, Freyhult E, ..., Janson C, Lindberg E

J Sleep Res 29 (4) e13041 [2020-08-00; online 2020-04-08]

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

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly

Juottonen H, Fontaine L, Wurzbacher C, ..., Peura S, Eiler A

Environ Microbiol 22 (8) 3158-3171 [2020-08-00; online 2020-06-03]

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

Management of an outbreak of postpartum Streptococcus pyogenes emm75 infections.

Trell K, Jörgensen J, Rasmussen M, Senneby E

pii: S0195-6701(20)30280-2

J. Hosp. Infect. 105 (4) 752-756 [2020-08-00; online 2020-06-01]

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

Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Peart CR, Tusso S, Pophaly SD, ..., Shafer ABA, Wolf JBW

Nat Ecol Evol 4 (8) 1095-1104 [2020-08-00; online 2020-06-08]

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

Lysophosphatidic Acid-Mediated GPR35 Signaling in CX3CR1+ Macrophages Regulates Intestinal Homeostasis

Kaya B, Doñas C, Wuggenig P, ..., Villablanca EJ, Niess JH

Cell Rep 32 (5) 107979 [2020-08-00; online 2020-08-00]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Preclinical safety studies of human embryonic stem cell‐derived retinal pigment epithelial cells for the treatment of age‐related macular degeneration

Petrus‐Reurer S, Kumar P, Padrell Sánchez S, ..., Kvanta A, Lanner F

STEM CELLS Transl Med 9 (8) 936-953 [2020-08-00; online 2020-04-22]

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

A 3D Cell Culture Model Identifies Wnt/ β-Catenin Mediated Inhibition of p53 as a Critical Step during Human Hepatocyte Regeneration.

Oliva-Vilarnau N, Vorrink SU, Ingelman-Sundberg M, Lauschke VM

pii: ADVS1906 pmc: PMC7404138

Adv Sci (Weinh) 7 (15) 2000248 [2020-08-00; online 2020-06-23]

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

The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders

Coutinho A, Günther T, Munters AR, ..., Malmström H, Jakobsson M

Am J Phys Anthropol 172 (4) 638-649 [2020-08-00; online 2020-06-04]

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

Higher host plant specialization of root‐associated endophytes than mycorrhizal fungi along an arctic elevational gradient

Abrego N, Huotari T, Tack AJM, ..., Ovaskainen O, Roslin T

Ecol Evol 10 (16) 8989-9002 [2020-08-00; online 2020-08-06]

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

Systems-level immunomonitoring from acute to recovery phase of severe COVID-19

Rodriguez L, Pekkarinen PT, Lakshmikanth T, ..., Kekäläinen E, Brodin P

Cell Reports Medicine 1 (5) 100078 [2020-08-00; online 2020-08-00]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]

SLC12A2 mutations cause NKCC1 deficiency with encephalopathy and impaired secretory epithelia.

Stödberg T, Magnusson M, Lesko N, ..., Stranneheim H, Wedell A

pii: NG2020013649 pmc: PMC7357422

Neurol Genet 6 (4) e478 [2020-08-00; online 2020-07-02]

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.

Xu F, Jiménez-González A, Einarsson E, ..., Svärd SG, Jerlström-Hultqvist J

pmc: PMC7641422

Microb Genom 6 (8) - [2020-08-00; online 2020-07-03]

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

A novel recombinant expression and purification approach for the full-length anti-apoptotic membrane protein Bcl-2

Ådén J, Mushtaq AU, Dingeldein A, Wallgren M, Gröbner G

Protein Expression and Purification 172 (-) 105628 [2020-08-00; online 2020-08-00]

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros

Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L

Current Biology 30 (19) 3871-3879.e7 [2020-08-00; online 2020-08-00]

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 influence of forest surroundings on the soil fungal community of black truffle (Tuber melanosporum) plantations

Oliach D, Colinas C, Castaño C, ..., Bonet JA, Oliva J

Forest Ecology and Management 469 (-) 118199 [2020-08-00; online 2020-08-00]

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

Editorial overview: Evolutionary and systems immunology – methods to understand human immune system variation

Brodin P, Quintana-Murci L

Current Opinion in Immunology 65 (-) iv [2020-08-00; online 2020-08-00]

The importance of the ZBED6‐IGF2 axis for metabolic regulation in mouse myoblast cells

Younis S, Naboulsi R, Wang X, ..., Welsh N, Andersson L

The FASEB Journal 34 (8) 10250-10266 [2020-08-00; online 2020-06-19]

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

Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.

Ottenburghs J, Honka J, Müskens GJDM, Ellegren H

pii: 10.1038/s41437-020-0322-z pmc: PMC7413267

Heredity (Edinb) 125 (1-2) 73-84 [2020-08-00; online 2020-05-26]

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

Technologies for assessing vaccine responses in the very young

Brodin P

Current Opinion in Immunology 65 (-) 28-31 [2020-08-00; online 2020-08-00]

Mass Cytometry [Technology development]

Immunocyte single cell analysis of vaccine‐induced narcolepsy

Lind A, Salami F, Landtblom A, ..., Adolfsson J, Elding Larsson H

Eur. J. Immunol. - (-) - [2020-07-30; online 2020-07-30]

Mass Cytometry [Service]

Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.

Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Kular L

Mult. Scler. - (-) 1352458520943768 [2020-07-30; online 2020-07-30]

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

Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics.

Engvall M, Cahill N, Jonsson BI, ..., Hallböök H, Cavelier L

pii: 10.1186/s12920-020-00739-4 pmc: PMC7388219

BMC Med Genomics 13 (1) 106 [2020-07-29; online 2020-07-29]

Clinical Genomics Uppsala [Technology development]

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.

Höglund A, Strempfl K, Fogelholm J, Wright D, Henriksen R

pii: 10.1186/s12864-020-06908-0

BMC Genomics 21 (1) 518 [2020-07-29; online 2020-07-29]

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

A repertory of rearrangements and the loss of an inverted repeat region in Passiflora chloroplast genomes

Cauz-Santos LA, da Costa ZP, Callot C, ..., van den Berg C, Vieira MLC

Genome Biol Evol - (-) - [2020-07-28; online 2020-07-28]

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

Prototypical pacemaker neurons interact with the resident microbiota.

Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG

pii: 1920469117 pmc: PMC7395494

Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]

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

Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.

Stanton DWG, Alberti F, Plotnikov V, ..., Skoglund P, Dalén L

pii: 10.1038/s41598-020-69474-1 pmc: PMC7387438

Sci Rep 10 (1) 12621 [2020-07-28; online 2020-07-28]

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

A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation.

Reynolds CA, Tan Q, Munoz E, ..., Hägg S, Pedersen NL

Aging Cell 19 (8) e13197 [2020-07-24; online 2020-07-24]

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

A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold.

Gandini R, Reichenbach T, Spadiut O, ..., Kalyani DC, Divne C

pii: S0022-2836(20)30412-5 PDB: 6YV8 PDB: 6YB7 PDB: 6YV9

J. Mol. Biol. 432 (16) 4658-4672 [2020-07-24; online 2020-06-19]

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. - (-) - [2020-07-24; online 2020-07-24]

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

A framework to assess the quality and impact of bioinformatics training across ELIXIR

Gurwitz KT, Singh Gaur P, Bellis LJ, ..., Morgan SL, Rustici G

PLoS Comput. Biol. 16 (7) e1007976 [2020-07-23; online 2020-07-23]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Descriptive Proteome Analysis to Investigate Context-Dependent Treatment Responses to OXPHOS Inhibition in Colon Carcinoma Cells Grown as Monolayer and Multicellular Tumor Spheroids.

Steinmetz J, Senkowski W, Lengqvist J, ..., Fryknäs M, Kultima K

pmc: PMC7376893

ACS Omega 5 (28) 17242-17254 [2020-07-21; online 2020-07-06]

Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]

Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?

Ebrahimi P, Luthman H, McGuigan FE, Akesson KE

Epigenetics - (-) 1-14 [2020-07-21; online 2020-07-21]

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

Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression.

Hagenaars SP, Coleman JRI, Choi SW, ..., Breen G, Lewis CM

Am. J. Med. Genet. B Neuropsychiatr. Genet. - (-) - [2020-07-18; online 2020-07-18]

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

Optimized metabarcoding with Pacific biosciences enables semi‐quantitative analysis of fungal communities

Castaño C, Berlin A, Brandström Durling M, ..., Clemmensen KE, Olson Å

New Phytol 228 (3) - [2020-07-17; online 2020-07-17]

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

Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by 19F NMR

Liebau J, Tersa M, Trastoy B, ..., Guerin ME, Mäler L

J. Biol. Chem. 295 (29) 9868-9878 [2020-07-17; online 2020-05-20]

Structural basis of DegP-protease temperature-dependent activation

Šulskis D, Thoma J, Burmann BM

- - (-) - [2020-07-15; online 2020-07-15]

Adding seemingly uninformative labels helps in low data regimes

Matsoukas C, Hernandez A, Liu Y, ..., Strand F, Smith K

International Conference on Machine Learning (ICML) - (-) - [2020-07-15]

BioImage Informatics [Collaborative]

Seamless integration of image and molecular analysis for spatial transcriptomics workflows.

Bergenstråhle J, Larsson L, Lundeberg J

pii: 10.1186/s12864-020-06832-3 pmc: PMC7386244

BMC Genomics 21 (1) 482 [2020-07-14; online 2020-07-14]

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

A Patient-Derived Cell Atlas Informs Precision Targeting of Glioblastoma.

Johansson P, Krona C, Kundu S, ..., Marino S, Nelander S

pii: S2211-1247(20)30878-0

Cell Rep 32 (2) 107897 [2020-07-14; online 2020-07-16]

Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]

Association of Factor V Leiden with Subsequent Atherothrombotic Events: A GENIUS-CHD Study of Individual Participant Data.

Mahmoodi BK, Tragante V, Kleber ME, ..., Asselbergs FW, Patel R

Circulation - (-) - [2020-07-13; online 2020-07-13]

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

Single-cell analysis of mosquito hemocytes identifies signatures of immune cell sub-types and cell differentiation

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

- - (-) - [2020-07-11; online 2020-07-11]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative]

Ouabain Modulates the Functional Interaction Between Na,K-ATPase and NMDA Receptor

Akkuratov EE, Westin L, Vazquez-Juarez E, ..., Brismar H, Aperia A

Mol Neurobiol - (-) - [2020-07-10; online 2020-07-10]

Advanced Light Microscopy (ALM) [Technology development]

SF3B1-mutant MDS as a distinct disease subtype: a proposal from the International Working Group for the Prognosis of MDS.

Malcovati L, Stevenson K, Papaemmanuil E, ..., Hellstrom-Lindberg E, Cazzola M

pii: 454668 pmc: PMC7362582

Blood 136 (2) 157-170 [2020-07-09; online 2020-04-30]

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.

Broman E, Sun X, Stranne C, ..., Humborg C, Nascimento FJA

pmc: PMC7362727

Front Microbiol 11 (-) 1536 [2020-07-07; online 2020-07-07]

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

Systems biology of acidophile biofilms for efficient metal extraction.

Buetti-Dinh A, Herold M, Christel S, ..., Pivkin IV, Dopson M

pii: 10.1038/s41597-020-0519-2 pmc: PMC7340779

Sci Data 7 (1) 215 [2020-07-07; online 2020-07-07]

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

VEGF‐B signaling impairs endothelial glucose transcytosis by decreasing membrane cholesterol content

Moessinger C, Nilsson I, Muhl L, ..., Skogsberg J, Eriksson U

EMBO rep 21 (7) - [2020-07-03; online 2020-05-24]

meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes.

Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB

pii: 10.1186/s13148-020-00884-8 pmc: PMC7333393

Clin Epigenetics 12 (1) 99 [2020-07-02; online 2020-07-02]

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

Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

Naidoo T, Xu J, Vicente M, ..., Jakobsson M, Schlebusch CM

Genome Biol Evol 12 (7) 1031-1039 [2020-07-01; online 2020-07-22]

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

Loqusdb: added value of an observations database of local genomic variation.

Magnusson M, Eisfeldt J, Nilsson D, ..., Wedell A, Stranneheim H

pii: 10.1186/s12859-020-03609-z pmc: PMC7329469

BMC Bioinformatics 21 (1) 273 [2020-07-01; online 2020-07-01]

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

Serum Metabolites in Hand-Arm Vibration Exposed Workers

Vihlborg P, Graff P, Hagenbjörk A, ..., Bryngelsson IL, Eriksson K

- 62 (7) 460-465 [2020-07-00; online 2020-04-06]

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling.

Dodig-Crnković T, Hong M, Thomas CE, ..., Uhlén M, Schwenk JM

pii: S2352-3964(20)30229-2 pmc: PMC7334812

EBioMedicine 57 (-) 102854 [2020-07-00; online 2020-07-03]

Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA.

Baronti L, Guzzetti I, Ebrahimi P, ..., Chen AA, Petzold K

pii: 10.1038/s41586-020-2336-3

Nature 583 (7814) 139-144 [2020-07-00; online 2020-05-27]

DNA demethylation regulates gene expression in IgE-activated mouse mast cells.

Paivandy A, Grujic M, Rafati N, Pejler G

Allergy 75 (7) 1776-1780 [2020-07-00; online 2020-02-12]

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

Growth-Inhibitory Activity of Bone Morphogenetic Protein 4 in Human Glioblastoma Cell Lines Is Heterogeneous and Dependent on Reduced SOX2 Expression

Dalmo E, Johansson P, Niklasson M, ..., Nelander S, Westermark B

Mol Cancer Res 18 (7) 981-991 [2020-07-00; online 2020-03-31]

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

Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.

Gonzalez F, Borrero-Echeverry F, Jósvai JK, ..., Bengtsson M, Walker WB

pii: ECE36458 pmc: PMC7391548

Ecol Evol 10 (14) 7334-7348 [2020-07-00; online 2020-06-30]

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

Tissue‐specific isolation of Arabidopsis/plant mitochondria – IMTACT (isolation of mitochondria tagged in specific cell types)

Boussardon C, Przybyla‐Toscano J, Carrie C, Keech O

Plant J 103 (1) 459-473 [2020-07-00; online 2020-03-13]

Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.

Ndegwa N, Ploner A, Andersson AF, ..., Agreus L, Ye W

pii: 01720094-202007000-00013 pmc: PMC7431247

Clin Transl Gastroenterol 11 (7) e00191 [2020-07-00; online 2020-08-09]

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

Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.

Zhong X, Lundberg M, Råberg L

pii: ECE36377 pmc: PMC7381583 Dryad: 10.5061/dryad.t1g1jwt02

Ecol Evol 10 (13) 6421-6434 [2020-07-00; online 2020-05-25]

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

Human Immune System Variation during 1 Year

Lakshmikanth T, Muhammad SA, Olin A, ..., Uhlen M, Brodin P

Cell Rep 32 (3) 107923 [2020-07-00; online 2020-07-00]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]

Female-biased gene flow between two species of Darwin’s finches

Lamichhaney S, Han F, Webster MT, ..., Grant PR, Andersson L

Nat Ecol Evol 4 (7) 979-986 [2020-07-00; online 2020-05-04]

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

Deactivation mechanism of Cu active sites in Cu/SSZ-13 — Phosphorus poisoning and the effect of hydrothermal aging

Wang A, Xie K, Bernin D, ..., Kamasamudram K, Olsson L

Applied Catalysis B: Environmental 269 (-) 118781 [2020-07-00; online 2020-07-00]

Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor

Köhler C, Carlström G, Gunnarsson A, ..., Edman K, Akke M

Sci Adv 6 (29) eabb5277 [2020-07-00; online 2020-07-17]

Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin

Tengvall K, Bergvall K, Olsson M, ..., Lindblad-Toh K, Andersson G

Immunogenetics 72 (5) 315-323 [2020-07-00; online 2020-06-18]

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

Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.

Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J

pii: 10.1038/s41591-020-0969-2

Nat. Med. 26 (7) 992-994 [2020-07-00; online 2020-07-08]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Collaborative] Proteogenomics [Technology development]

Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.

Bonaglia S, Hedberg J, Marzocchi U, ..., Glud RN, Nascimento FJA

pii: S0141-1136(19)30836-0 pmc: PMC7369627

Mar Environ Res 159 (-) 104968 [2020-07-00; online 2020-03-29]

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

Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities

Abrego N, Roslin T, Huotari T, ..., Schmidt NM, Ovaskainen O

Mol Ecol 29 (14) 2736-2746 [2020-07-00; online 2020-07-04]

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

Genomic epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates from Ukraine, 2013-2018.

Boiko I, Golparian D, Jacobsson S, ..., Shevchenko T, Unemo M

APMIS 128 (7) 465-475 [2020-07-00; online 2020-05-23]

Probing the retention mechanism of small hydrophilic molecules in hydrophilic interaction chromatography using saturation transfer difference nuclear magnetic resonance spectroscopy

Shamshir A, Dinh NP, Jonsson T, Sparrman T, Irgum K

Journal of Chromatography A 1623 (-) 461130 [2020-07-00; online 2020-07-00]

Association of serum anti-centromere protein F antibodies with clinical response to infliximab in patients with rheumatoid arthritis: A prospective study.

Lourido L, Ruiz-Romero C, Picchi F, ..., Nilsson P, Blanco FJ

pii: S0049-0172(20)30190-6

Semin. Arthritis Rheum. 50 (5) 1101-1108 [2020-06-30; online 2020-06-30]

Autoimmunity and Serology Profiling [Collaborative]

Age-of-onset information helps identify 76 genetic variants associated with allergic disease

Ferreira MAR, Vonk JM, Baurecht H, ..., None , None

PLoS Genet. 16 (6) e1008725 [2020-06-30; online 2020-06-30]

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

High content drug screening for Fanconi anemia therapeutics.

Montanuy H, Camps-Fajol C, Carreras-Puigvert J, ..., Minguillón J, Surrallés J

pii: 10.1186/s13023-020-01437-1 pmc: PMC7325660

Orphanet J Rare Dis 15 (1) 170 [2020-06-30; online 2020-06-30]

Drug Discovery and Development (DDD)

Evolutionary History of the Marchantia polymorpha Complex

Linde AM, Sawangproh W, Cronberg N, Szövényi P, Lagercrantz U

Front Plant Sci 11 (-) - [2020-06-26; online 2020-06-26]

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

Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.

Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S

pii: jmedgenet-2020-106929

J. Med. Genet. - (-) jmedgenet-2020-106929 [2020-06-26; online 2020-06-26]

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

Serum choline in extremely preterm infants declines with increasing parenteral nutrition

Nilsson AK, Pedersen A, Malmodin D, ..., Pupp IH, Hellström A

Eur J Nutr - (-) - [2020-06-25; online 2020-06-25]

Interspecific gene flow and the evolution of specialisation in black and white rhinoceros.

Moodley Y, Westbury MV, Russo IM, ..., Dalén L, Bruford MW

pii: 5862640

Mol. Biol. Evol. - (-) - [2020-06-25; online 2020-06-25]

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

RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.

Nilsson LM, Castresana-Aguirre M, Scott L, Brismar H

pii: 10.1038/s41598-020-67361-3 pmc: PMC7316724

Sci Rep 10 (1) 10390 [2020-06-25; online 2020-06-25]

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

Lysine-specific demethylase 1A (LSD1) restricts ex vivo propagation of human HSCs and is a target of UM171

Subramaniam A, Žemaitis K, Safaee Talkhoncheh M, ..., Zubarev RA, Larsson J

Blood 136 (19) 2151-2161 [2020-06-24; online 2020-06-24]

Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]

Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.

Zhong W, Gummesson A, Tebani A, ..., Fagerberg L, Uhlén M

pii: 10.1186/s13073-020-00755-0 pmc: PMC7310558

Genome Med 12 (1) 53 [2020-06-23; online 2020-06-23]

Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Collaborative]

Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.

Chapman MA, Arif M, Emanuelsson EB, ..., Mardinoglu A, Sundberg CJ

pii: S2211-1247(20)30789-0

Cell Rep 31 (12) 107808 [2020-06-23; online 2020-06-25]

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

Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.

Watanabe A, Miyake K, Nordlund J, ..., Sugita K, Inukai T

pii: 461098

Blood 136 (20) 2319-2333 [2020-06-23; online 2020-06-23]

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

Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.

Remnestål J, Öijerstedt L, Ullgren A, ..., Graff C, Nilsson P

pii: 10.1186/s40035-020-00198-y pmc: PMC7310563

Transl Neurodegener 9 (1) 27 [2020-06-23; online 2020-06-23]

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

A sample preparation protocol for high throughput immunofluorescence of suspension cells

Backstrom A, Kugel L, Gnann C, ..., Lundberg E, Stadler C

J. Histochem. Cytochem. 68 (7) 473-489 [2020-06-20; online 2020-01-20]

Bioinformatics Compute and Storage [Service] Cell Profiling [Technology development]

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.

Ji AL, Rubin AJ, Thrane K, ..., Lundeberg J, Khavari PA

pii: S0092-8674(20)30672-3

Cell - (-) - [2020-06-19; online 2020-06-19]

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

A family‐based genome‐wide association study of recurrent aphthous stomatitis

Bankvall M, Östman S, Jontell M, Torinsson Naluai Å

Oral Dis - (-) - [2020-06-18; online 2020-06-18]

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

Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation

Tobiasson V, Amunts A

Elife 9 (-) 1-15 [2020-06-18; online 2020-06-18]

Chanjo: Clincal grade sequence coverage analysis

Andeer R, Magnusson M, Wedell A, Stranneheim H

F1000Res 9 (-) 615 [2020-06-16; online 2020-06-16]

Clinical Genomics Stockholm [Technology development]

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.

Kralemann LEM, Liu S, Trejo-Arellano MS, ..., Köhler C, Hennig L

pii: 10.1186/s13059-020-02062-8 pmc: PMC7296913

Genome Biol. 21 (1) 144 [2020-06-16; online 2020-06-16]

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

Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting.

Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ

Hum. Mutat. - (-) - [2020-06-09; online 2020-06-09]

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

CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.

Hagey DW, Topcic D, Kee N, ..., Perlmann T, Muhr J

pii: 10.1038/s41467-020-16597-8 pmc: PMC7283355

Nat Commun 11 (1) 2898 [2020-06-09; online 2020-06-09]

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

Sales of antibiotics and occurrence of resistance in Sweden

Swedres-Svarm 19088 (-) 1-128 [2020-06-09; online 2020-06-09]

High genomic-based predicted strain coverage among invasive meningococcal isolates when combining Bexsero and Trumenba vaccines.

Säll O, Olofsson E, Jacobsson S

pii: S0264-410X(20)30591-0

Vaccine 38 (28) 4374-4378 [2020-06-09; online 2020-05-12]

LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.

Jhamat N, Niazi A, Guo Y, ..., Andersson G, Humblot P

pii: 10.1186/s12864-020-06777-7

BMC Genomics 21 (1) 385 [2020-06-03; online 2020-06-03]

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

Vegetation type determines spore deposition within a forest–agricultural mosaic landscape

Redondo MA, Berlin A, Boberg J, Oliva J

- 96 (6) - [2020-06-01; online 2020-05-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16.

Lan PT, Golparian D, Ringlander J, ..., Van Thuong N, Unemo M

pii: 5740025 pmc: PMC7382555

J. Antimicrob. Chemother. 75 (6) 1432-1438 [2020-06-01; online 2020-02-19]

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.

Zhu Y, Orre LM, Zhou Tran Y, ..., Anders S, Lehtiö J

pii: TIR119.001646 pmc: PMC7261819

Mol. Cell Proteomics 19 (6) 1047-1057 [2020-06-00; online 2020-03-23]

Proteogenomics [Technology development]

Normal Testosterone but Higher Luteinizing Hormone Plasma Levels in Men With Hypersexual Disorder.

Chatzittofis A, Boström AE, Öberg KG, ..., Arver S, Jokinen J

pii: S2050-1161(20)30028-3 pmc: PMC7261685

Sex Med 8 (2) 243-250 [2020-06-00; online 2020-03-12]

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

Size-Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe-by-Design.

Rodrigues AF, Newman L, Jasim D, ..., Kostarelos K, Bussy C

pii: ADVS1753 pmc: PMC7312279

Adv Sci (Weinh) 7 (12) 1903200 [2020-06-00; online 2020-05-07]

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

Radiation Triggers a Dynamic Sequence of Transient Microglial Alterations in Juvenile Brain

Osman AM, Sun Y, Burns TC, ..., Kele J, Blomgren K

Cell Rep 31 (9) 107699 [2020-06-00; online 2020-06-00]

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

Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations

Juras A, Makarowicz P, Chyleński M, ..., Jakobsson M, Dabert M

Am J Phys Anthropol 172 (2) 176-188 [2020-06-00; online 2020-04-15]

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

Illuminating Genetic Mysteries of the Dead Sea Scrolls

Anava S, Neuhof M, Gingold H, ..., Jakobsson M, Rechavi O

Cell 181 (6) 1218-1231.e27 [2020-06-00; online 2020-06-00]

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

Mending Fences: Na,K-ATPase signaling via Ca2+ in the maintenance of epithelium integrity

Aperia A, Brismar H, Uhlén P

Cell Calcium 88 (-) 102210 [2020-06-00; online 2020-06-00]

Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors.

Xu J, Zhou C, Foo KS, ..., Sahara M, Chien KR

Stem Cells 38 (6) 741-755 [2020-06-00; online 2020-03-10]

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

The mating type system of the rare polypore Hapalopilus croceus

Redr D, Dahlberg A, Stenlid J, ..., Vasaitis R, Menkis A

Fungal Ecology 45 (-) 100941 [2020-06-00; online 2020-06-00]

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

Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.

Bonaglia S, Broman E, Brindefalk B, ..., Udekwu K, Gunnarsson JS

pii: S0045-6535(20)30216-2

Chemosphere 248 (-) 126023 [2020-06-00; online 2020-01-24]

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

Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts.

Atabaki-Pasdar N, Ohlsson M, Viñuela A, ..., Pavo I, Franks PW

pii: PMEDICINE-D-20-00136 pmc: PMC7304567 ClinicalTrials.gov: NCT03814915

PLoS Med. 17 (6) e1003149 [2020-06-00; online 2020-06-19]

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.

Mereu E, Lafzi A, Moutinho C, ..., Stegle O, Heyn H

pii: 10.1038/s41587-020-0469-4

Nat. Biotechnol. 38 (6) 747-755 [2020-06-00; online 2020-04-06]

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

An immune gene expression signature distinguishes central nervous system metastases from primary tumours in non-small-cell lung cancer.

Tsakonas G, Lewensohn R, Botling J, ..., Hydbring P, Ekman S

pii: S0959-8049(20)30155-6

Eur. J. Cancer 132 (-) 24-34 [2020-06-00; online 2020-04-20]

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

Auxin export from proximal fruits drives arrest in temporally competent inflorescences

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

NPLANTS 6 (6) 699-707 [2020-06-00; online 2020-05-25]

In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization

Michel M, Homan EJ, Wiita E, ..., Helleday T, Warpman Berglund U

Front. Chem. 8 (-) - [2020-05-29; online 2020-05-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Staphylococcus argenteus as an etiological agent of prosthetic hip joint infection: a case presentation.

Söderquist B, Wildeman P, Stenmark B, Stegger M

pii: jbjiv05p0172 pmc: PMC7358968

J Bone Jt Infect 5 (4) 172-175 [2020-05-25; online 2020-05-25]

GPSeq reveals the radial organization of chromatin in the cell nucleus

Girelli G, Custodio J, Kallas T, ..., Crosetto N, Bienko M

Nat Biotechnol - (-) - [2020-05-25; online 2020-05-25]

Advanced Light Microscopy (ALM) [Service]

Linked-read sequencing enables haplotype-resolved resequencing at population scale.

Lutgen D, Ritter R, Olsen R, ..., Suh A, Burri R

Mol Ecol Resour 20 (5) 1311-1322 [2020-05-18; online 2020-05-18]

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

Extended-Spectrum β-Lactamase- and plasmid AmpC- producing Escherichia coli causing community-onset bloodstream infection: the association of bacterial clones and virulence genes with septic shock, source of infection and recurrencies.

Fröding I, Hasan B, Sylvin I, ..., Nauclér P, Giske CG

pii: AAC.02351-19

Antimicrob. Agents Chemother. - (-) - [2020-05-18; online 2020-05-18]

Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.

Ericson PGP, Irestedt M, Nylander JAA, ..., Joseph L, Qu Y

pii: 5838197

Syst. Biol. 69 (5) 820-829 [2020-05-16; online 2020-05-16]

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

Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.

Grankvist R, Chireh A, Sandell M, ..., Daub CO, Holmin S

pii: 10.1038/s41598-020-64900-w pmc: PMC7229024

Sci Rep 10 (1) 8029 [2020-05-15; online 2020-05-15]

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

Validating STAT Protein-inhibitor Interactions using Biochemical and Cellular Thermal Shift Assays

Attarha S, Reithmeier A, Busker S, Desroses M, Page BDG

ACS Chem. Biol. - (-) - [2020-05-15; online 2020-05-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Altered Thermal and Mechanical Properties of Spruce Galactoglucomannan Films Modified with an Etherification Reaction

Härdelin L, Bernin D, Börjesson M, Ström A, Larsson A

Biomacromolecules 21 (5) 1832-1840 [2020-05-11; online 2020-02-18]

A chemical screen identifies a link between lipid metabolism and mRNA translation

Corman A, Kanellis DC, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O

- - (-) - [2020-05-11; online 2020-05-11]

Chemical Biology Consortium Sweden (CBCS) [Service]

Interphase Design of Cellulose Nanocrystals/Poly(hydroxybutyrate-ran-valerate) Bionanocomposites for Mechanical and Thermal Properties Tuning

Magnani C, Idström A, Nordstierna L, ..., Raquez JM, Lo Re G

Biomacromolecules 21 (5) 1892-1901 [2020-05-11; online 2020-02-20]

Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.

Floudas D, Bentzer J, Ahrén D, ..., Persson P, Tunlid A

pii: 10.1038/s41396-020-0667-6

ISME J - (-) - [2020-05-07; online 2020-05-07]

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

Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.

Lundberg M, Zhong X, Konrad A, Olsen R, Råberg L

Mol. Ecol. 29 (11) 1990-2003 [2020-05-06; online 2020-05-06]

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

Srebf1 Controls Midbrain Dopaminergic Neurogenesis.

Toledo EM, Yang S, Gyllborg D, ..., Linnarsson S, Arenas E

pii: S2211-1247(20)30550-7

Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]

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

High-Resolution In Situ NMR Spectroscopy of Bacterial Envelope Proteins in Outer Membrane Vesicles

Thoma J, Burmann BM

Biochemistry 59 (17) 1656-1660 [2020-05-05; online 2020-04-01]

Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci

de las Fuentes L, None , Sung YJ, ..., Rao DC, Fornage M

Mol. Psychiatry - (-) - [2020-05-05; online 2020-05-05]

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

Lipid accumulation controls the balance between surface connection and scission of caveolae

Hubert M, Larsson E, Vegesna NVG, ..., Moodie LW, Lundmark R

Elife 9 (-) - [2020-05-04; online 2020-05-04]

Swedish Metabolomics Centre (SMC) [Collaborative]

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

Hagemann-Jensen M, Ziegenhain C, Chen P, ..., Faridani OR, Sandberg R

Nat Biotechnol - (-) - [2020-05-04; online 2020-05-04]

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

Joint impact of common risk factors on incident dementia: A cohort study of the Swedish Twin Registry.

Tomata Y, Li X, Karlsson IK, ..., Pedersen NL, Hägg S

J. Intern. Med. 288 (2) 234-247 [2020-05-03; online 2020-05-03]

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

Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.

Yang X, Fors L, Slotte T, ..., Wheat CW, Hambäck PA

pii: 5819554 pmc: PMC7211424

Genome Biol Evol 12 (5) 522-534 [2020-05-01; online 2020-04-14]

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

Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report.

Bieder A, Einarsdottir E, Matsson H, ..., Kere J, Tapia-Páez I

pii: 10.1186/s12881-020-01020-2 pmc: PMC7193346

BMC Med. Genet. 21 (1) 87 [2020-05-01; online 2020-05-01]

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

Behavioural characterization of dmrt3a mutant zebrafish reveals crucial aspects of vertebrate locomotion through phenotypes related to acceleration

del Pozo Cano A, Manuel R, Iglesias Gonzalez AB, ..., Kullander K, Boije H

eNeuro 7 (3) ENEURO.0047-20.2020 [2020-05-01; online 2020-05-01]

BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin.

Saei AA, Gullberg H, Sabatier P, ..., Arnér ESJ, Zubarev RA

pii: S2213-2317(20)30243-3 pmc: PMC7082630

Redox Biol 32 (-) 101491 [2020-05-00; online 2020-03-03]

Drug Discovery and Development (DDD)

Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.

Chen Y, Hesla AC, Lin Y, ..., Larsson O, Haglund F

pmc: PMC7191197

Mol Oncol 14 (5) 1101-1117 [2020-05-00; online 2020-03-13]

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

Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.

Plesser Duvdevani M, Pettersson M, Eisfeldt J, ..., Lindstrand A, Harel T

Am. J. Med. Genet. A 182 (5) 1143-1151 [2020-05-00; online 2020-03-03]

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

Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma

Mitra S, Lauss M, Cabrita R, ..., Brown KM, Jönsson G

Mol Oncol 14 (5) 933-950 [2020-05-00; online 2020-03-21]

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

Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma

Puls F, Agaimy A, Flucke U, ..., Arbajian E, Mertens F

Am. J. Surg. Pathol. 44 (5) 594-606 [2020-05-00; online 2020-05-00]

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

Next-Generation Sequencing Reveals Differential Responses to Acute versus Long-Term Exposures to Graphene Oxide in Human Lung Cells.

Mukherjee SP, Gupta G, Klöditz K, ..., Kostarelos K, Fadeel B

Small 16 (21) e1907686 [2020-05-00; online 2020-03-29]

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

A molecular mechanism explaining albuminuria in kidney disease

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

Nat Metab 2 (5) 461-474 [2020-05-00; online 2020-05-11]

Whole-genome sequencing of human remains to enable genealogy DNA database searches – A case report

Tillmar A, Sjölund P, Lundqvist B, ..., Älgenäs C, Green H

Forensic Sci Int Genet 46 (-) 102233 [2020-05-00; online 2020-05-00]

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

A global effort to define the human genetics of protective immunity to SARS-CoV-2 infection

Casanova JL, Su HC

Cell - (-) - [2020-05-00; online 2020-05-00]

Interactions of the Lysosomotropic Detergent O-Methyl-Serine Dodecylamide Hydrochloride (MSDH) with Lipid Bilayer Membranes—Implications for Cell Toxicity

Villamil Giraldo AM, Eriksson I, Wennmalm S, ..., Ederth T, Öllinger K

Int J Mol Sci 21 (9) 3136 [2020-04-29; online 2020-04-29]

Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Lazarević J, Menkis A

Diversity 12 (5) 172 [2020-04-28; online 2020-04-28]

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

Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.

Bryois J, Skene NG, Hansen TF, ..., Hjerling-Leffler J, Sullivan PF

pii: 10.1038/s41588-020-0610-9

Nat. Genet. 52 (5) 482-493 [2020-04-27; online 2020-04-27]

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

Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.

Atherton S, Jondelius U

pii: 51813 pmc: PMC7198628

Biodivers Data J 8 (-) e51813 [2020-04-27; online 2020-04-27]

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

Dramatic changes in blood protein levels during the first week of life in extremely preterm infants

Zhong W, Danielsson H, Tebani A, ..., Fagerberg L, Uhlén M

Pediatr Res - (-) - [2020-04-24; online 2020-04-24]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]

Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.

Petrus-Reurer S, Kumar P, Padrell Sánchez S, ..., Kvanta A, Lanner F

Stem Cells Transl Med - (-) - [2020-04-22; online 2020-04-22]

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

Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs

Danelius E, Poongavanam V, Peintner S, ..., Erdélyi M, Kihlberg J

Chem. Eur. J. 26 (23) 5231-5244 [2020-04-21; online 2020-04-06]

Studies of Emission Processes of Polymer Additives into Water Using Quartz Crystal Microbalance—A Case Study on Organophosphate Esters

Xiao L, Zheng Z, Irgum K, Andersson PL

Environ. Sci. Technol. 54 (8) 4876-4885 [2020-04-21; online 2020-03-18]

Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis.

Chen HY, Jolly C, Bublys K, Marcu D, Immler S

pii: 1918205117 pmc: PMC7183174

Proc. Natl. Acad. Sci. U.S.A. 117 (16) 8973-8979 [2020-04-21; online 2020-04-03]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Molecular profiling of driver events in metastatic uveal melanoma.

Karlsson J, Nilsson LM, Mitra S, ..., Olofsson Bagge R, Nilsson JA

pii: 10.1038/s41467-020-15606-0 pmc: PMC7171146

Nat Commun 11 (1) 1894 [2020-04-20; online 2020-04-20]

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

Effect of Cobalt, Nickel, and Selenium/Tungsten Deficiency on Mesophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Šafarič L, Yekta SS, Svensson BH, ..., Bastviken D, Björn A

Microorganisms 8 (4) 598 [2020-04-20; online 2020-04-20]

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

Fungi and Oomycetes in the Irrigation Water of Forest Nurseries

Marčiulynas A, Marčiulynienė D, Lynikienė J, ..., Vaičiukynė M, Menkis A

Forests 11 (4) 459 [2020-04-18; online 2020-04-18]

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

Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.

Larsson I, Uhlén M, Zhang C, Mardinoglu A

pmc: PMC7181968

Front Genet 11 (-) 381 [2020-04-17; online 2020-04-17]

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

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.

Bianchi M, Rafati N, Karlsson Å, ..., Lindblad-Toh K, Rosengren Pielberg G

pii: 10.1186/s12864-020-6700-3 pmc: PMC7160888

BMC Genomics 21 (1) 307 [2020-04-16; online 2020-04-16]

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

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.

Berglund E, Saarenpää S, Jemt A, ..., Lundeberg J, Giacomello S

pii: 10.1186/s12864-020-6631-z pmc: PMC7158132

BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]

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

Difference in virulence between Neisseria meningitidis serogroups W and Y in transgenic mice.

Eriksson L, Stenmark B, Deghmane AE, ..., Mölling P, Taha MK

pii: 10.1186/s12866-020-01760-4 pmc: PMC7160935

BMC Microbiol. 20 (1) 92 [2020-04-15; online 2020-04-15]

Why is COVID‐19 so mild in children?

Brodin P

Acta Paediatr - (-) - [2020-04-15; online 2020-04-15]

Mass Cytometry [Technology development]

Genetic Associations Between Childhood Psychopathology and Adult Depression and Associated Traits in 42 998 Individuals: A Meta-Analysis.

Akingbuwa WA, Hammerschlag AR, Jami ES, ..., Middeldorp CM, and the Bipolar Disorder and Major Depressive Disorder Working Groups of the Psychiatric Genomics Consortium

pii: 2763801 pmc: PMC7160753

JAMA Psychiatry - (-) - [2020-04-15; online 2020-04-15]

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

Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.

Petrus-Reurer S, Winblad N, Kumar P, ..., Kvanta A, Lanner F

pii: S2213-6711(20)30062-X pmc: PMC7160308

Stem Cell Reports 14 (4) 648-662 [2020-04-14; online 2020-03-19]

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

Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study.

Sutton L, Ljungström V, Enjuanes A, ..., Rosenquist R, European Research Initiative on CLL (ERIC)

pii: haematol.2019.234716

Haematologica - (-) - [2020-04-09; online 2020-04-09]

Optimization of Tetrahydroindazoles as Inhibitors of Human Dihydroorotate Dehydrogenase and Evaluation of Their Activity and In Vitro Metabolic Stability

Popova G, Ladds MJGW, Johansson L, ..., Yngve U, Lain S

J. Med. Chem. 63 (8) 3915-3934 [2020-04-08; online 2020-04-08]

Drug Discovery and Development (DDD) [Service]

Hybrid Aspen Expressing a Carbohydrate Esterase Family 5 Acetyl Xylan Esterase Under Control of a Wood-Specific Promoter Shows Improved Saccharification

Wang Z, Pawar PMA, Derba-Maceluch M, ..., Jönsson LJ, Mellerowicz EJ

Front Plant Sci 11 (-) - [2020-04-08; online 2020-04-08]

Building blocks are synthesized on demand during the yeast cell cycle

Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J

Proc Natl Acad Sci USA 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]

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

The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.

Yañez O, Chávez-Galarza J, Tellgren-Roth C, ..., Neumann P, de Miranda JR

pii: 10.1038/s41598-020-62673-w pmc: PMC7136270

Sci Rep 10 (1) 5956 [2020-04-06; online 2020-04-06]

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

Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.

Shafeeq S, Wang X, Lünsdorf H, Brauner A, Römling U

pii: microorganisms8040522

Microorganisms 8 (4) 522 [2020-04-05; online 2020-04-05]

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]

Guidelines for curriculum and course development in higher education and training

Tractenberg RE, Lindvall JM, Attwood T, Via A

- - (-) - [2020-04-03; online 2020-04-03]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus.

Wildeman P, Tevell S, Eriksson C, ..., Söderquist B, Stenmark B

pii: 10.1038/s41598-020-62751-z pmc: PMC7125104

Sci Rep 10 (1) 5938 [2020-04-03; online 2020-04-03]

Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.

Eriksen AK, Brunius C, Mazidi M, ..., Dicksved J, Landberg R

pii: 5758012 ClinicalTrials.gov: NCT02987595

Am. J. Clin. Nutr. 111 (4) 864-876 [2020-04-01; online 2020-02-26]

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

Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.

Mahajan M, Yee B, Hägglund E, ..., Fuerst JA, Andersson SGE

pii: 5663460

Mol. Biol. Evol. 37 (4) 1020-1040 [2020-04-01; online 2019-12-07]

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

Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.

Andersson N, Bakker B, Karlsson J, ..., Foijer F, Gisselsson D

pii: 0008-5472.CAN-19-3468

Cancer Res. 80 (7) 1512-1523 [2020-04-01; online 2020-02-10]

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

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

José Miguel de la Rosa-Trevín PAHVJOaEL

Acta Crystallographica Section D (v. 76 pp. 350–356) - (-) - [2020-04-01]

Cryo-EM [Technology development]

Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment‐based lead discovery

Opassi G, Nordström H, Lundin A, ..., Klebe G, Danielson UH

Protein Science 29 (4) 977-989 [2020-04-00; online 2020-02-07]

Drug Discovery and Development (DDD)

Polymerase IV Plays a Crucial Role in Pollen Development in Capsella

Wang Z, Butel N, Santos-González J, ..., Martinez G, Köhler C

Plant Cell 32 (4) 950-966 [2020-04-00; online 2020-01-27]

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

A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver.

Cavalli M, Diamanti K, Pan G, ..., Komorowski J, Wadelius C

pmc: PMC7185313

OMICS 24 (4) 180-194 [2020-04-00; online 2020-03-16]

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

Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome.

Rutgersson C, Ebmeyer S, Lassen SB, ..., Flach CF, Larsson DGJ

pii: S0160-4120(19)31788-X

Environ Int 137 (-) 105339 [2020-04-00; online 2020-02-06]

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

ABCB1 single-nucleotide variants and survival in patients with glioblastoma treated with radiotherapy concomitant with temozolomide.

Malmström A, Łysiak M, Åkesson L, ..., Green H, Söderkvist P

pii: 10.1038/s41397-019-0107-z

Pharmacogenomics J. 20 (2) 213-219 [2020-04-00; online 2019-10-17]

Bioinformatics Compute and Storage [Service] Clinical Genomics Linköping

Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics.

Herr P, Boström J, Rullman E, ..., Maddalo G, Altun M

pii: RA120.001938 pmc: PMC7124475

Mol. Cell Proteomics 19 (4) 608-623 [2020-04-00; online 2020-02-12]

Proteogenomics [Collaborative]

Substantial intrinsic variability in chemoradiosensitivity of newly established anaplastic thyroid cancer cell-lines.

Gretarsson S, Nygren A, Rosendahl AH, ..., Wennerberg J, Ekblad L

Acta Otolaryngol. 140 (4) 337-343 [2020-04-00; online 2020-01-10]

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

The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.

Zhang C, Bjornson E, Arif M, ..., Borén J, Mardinoglu A

pmc: PMC7184219

Mol. Syst. Biol. 16 (4) e9495 [2020-04-00; online 2020-04-28]

Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Service]

Transcriptome Profiling and Toxicity Following Long-Term, Low Dose Exposure of Human Lung Cells to Ni and NiO Nanoparticles-Comparison with NiCl 2.

Gliga AR, Di Bucchianico S, Åkerlund E, Karlsson HL

pii: nano10040649 pmc: PMC7221965

Nanomaterials (Basel) 10 (4) - [2020-03-31; online 2020-03-31]

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

Comparative analysis of genome-wide DNA methylation in Neurospora

Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H

Epigenetics 15 (9) 1-16 [2020-03-31; online 2020-03-31]

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

Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.

Andersson K, Malmgren B, Åström E, ..., Taylan F, Dahllöf G

pii: 10.1186/s13023-020-01361-4 pmc: PMC7110904

Orphanet J Rare Dis 15 (1) 80 [2020-03-31; online 2020-03-31]

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

Deficits in Motor Performance, Neurotransmitters and Synaptic Plasticity in Elderly and Experimental Parkinsonian Mice Lacking GPR37.

Zhang X, Mantas I, Fridjonsdottir E, ..., Chergui K, Svenningsson P

pmc: PMC7120535

Front Aging Neurosci 12 (-) 84 [2020-03-27; online 2020-03-27]

National Resource for Mass Spectrometry Imaging [Service]

An atlas of human metabolism.

Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J

pii: 13/624/eaaz1482 pmc: PMC7331181 mid: NIHMS1590510

Sci Signal 13 (624) - [2020-03-24; online 2020-03-24]

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

An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.

Ignatov D, Vaitkevicius K, Durand S, ..., Condon C, Johansson J

pii: S2211-1247(20)30304-1

Cell Rep 30 (12) 4027-4040.e7 [2020-03-24; online 2020-03-27]

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

Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia

Ivanov Öfverholm I, Zachariadis V, Taylan F, ..., Nordlund J, Barbany G

Leukemia & Lymphoma 61 (3) 1-10 [2020-03-22; online 2019-10-22]

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

Molecular Profiling for Predictors of Radiosensitivity in Patients with Breast or Head-and-Neck Cancer.

Drobin K, Marczyk M, Halle M, ..., Schwenk JM, Haghdoost S

pii: cancers12030753 pmc: PMC7140105

Cancers (Basel) 12 (3) - [2020-03-22; online 2020-03-22]

Non-dopaminergic Alterations in Depression-Like FSL Rats in Experimental Parkinsonism and L-DOPA Responses.

Schintu N, Zhang X, Stroth N, ..., Andrén PE, Svenningsson P

pmc: PMC7099513

Front Pharmacol 11 (-) 304 [2020-03-20; online 2020-03-20]

National Resource for Mass Spectrometry Imaging [Service]

The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines their Interactions with G-Quadruplex DNA

Prasad B, Das RN, Jamroskovic J, ..., Sabouri N, Chorell E

Chem. Eur. J. - (-) - [2020-03-18; online 2020-03-18]

Newborn Screening for Presymptomatic Diagnosis of Complement and Phagocyte Deficiencies.

Dezfouli M, Bergström S, Skattum L, ..., Nilsson P, Hammarström L

pmc: PMC7090021

Front Immunol 11 (-) 455 [2020-03-17; online 2020-03-17]

Effects of acute sleep loss on diurnal plasma dynamics of CNS health biomarkers in young men

Benedict C, Blennow K, Zetterberg H, Cedernaes J

Neurology 94 (11) e1181-e1189 [2020-03-17; online 2020-01-08]

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

Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.

Rantapero T, Wahlfors T, Kähler A, ..., Schleutker J, Wiklund F

pii: genes11030314 pmc: PMC7140841

Genes 11 (3) 314 [2020-03-14; online 2020-03-14]

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

Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike ( Esox lucius) and a Synthesis of Previous Studies.

Sunde J, Yıldırım Y, Tibblin P, Forsman A

pmc: PMC7082332

Front Genet 11 (-) 218 [2020-03-13; online 2020-03-13]

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

Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.

Alneberg J, Bennke C, Beier S, ..., Pinhassi J, Andersson AF

pii: 10.1038/s42003-020-0856-x pmc: PMC7070063

Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]

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

Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly

Chen M, Perez-Boerema A, Zhang L, ..., Li S, Amunts A

NPLANTS 6 (3) 314-320 [2020-03-09; online 2020-03-09]

Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.

Forsberg A, Huoman J, Söderholm S, ..., Gustafsson M, Jenmalm MC

Pediatr Allergy Immunol 31 (5) 544-553 [2020-03-09; online 2020-03-09]

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

Ribonucleotide reductase inhibitors suppress SAMHD 1 ara‐ CTP ase activity enhancing cytarabine efficacy

Rudd SG, Tsesmetzis N, Sanjiv K, ..., Helleday T, Herold N

EMBO Mol Med 12 (3) - [2020-03-06; online 2020-01-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Uncovering diversity and metabolic spectrum of animals in dead zone sediments.

Broman E, Bonaglia S, Holovachov O, ..., Hall POJ, Nascimento FJA

pii: 10.1038/s42003-020-0822-7 pmc: PMC7060179

Commun Biol 3 (1) 106 [2020-03-06; online 2020-03-06]

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

An atlas of the protein-coding genes in the human, pig, and mouse brain.

Sjöstedt E, Zhong W, Fagerberg L, ..., Uhlén M, Mulder J

pii: 367/6482/eaay5947

Science 367 (6482) eaay5947 [2020-03-06; online 2020-03-07]

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

MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool.

Scaletti ER, Vallin KS, Bräutigam L, ..., Stenmark P, Jemth AS

pii: RA120.012636 PDB: 6QVO

J. Biol. Chem. - (-) - [2020-03-06; online 2020-03-06]

Transcriptomic resources for evolutionary studies in flat periwinkles and related species.

Marques JP, Sotelo G, Galindo J, ..., Hollander J, Faria R

pii: 10.1038/s41597-020-0408-8

Sci Data 7 (1) 73 [2020-03-03; online 2020-03-03]

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

Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.

Esberg A, Haworth S, Hasslöf P, Lif Holgerson P, Johansson I

pii: nu12030681

Nutrients 12 (3) - [2020-03-03; online 2020-03-03]

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

Structure of a minimal photosystem I from the green alga Dunaliella salina

Perez-Boerema A, Klaiman D, Caspy I, ..., Amunts A, Nelson N

NPLANTS 6 (3) 321-327 [2020-03-02; online 2020-03-02]

High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.

Reid S, Alexsson A, Frodlund M, ..., Rönnblom L, Leonard D

pii: annrheumdis-2019-216227

Ann. Rheum. Dis. 79 (3) 363-369 [2020-03-01; online 2019-12-11]

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

Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals.

Danielsson M, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA

pii: 10.1038/s41431-019-0533-z

Eur. J. Hum. Genet. 28 (3) 349-357 [2020-03-01; online 2019-10-25]

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

A link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying bla SHV-12 from horses in Sweden.

Börjesson S, Greko C, Myrenås M, ..., Nilsson O, Pedersen K

pii: S2213-7165(19)30205-X

J Glob Antimicrob Resist 20 (-) 285-289 [2020-03-00; online 2019-09-05]

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

Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro‐Oxindole Dihydroquinazolinones as IRAP Inhibitors

Engen K, Vanga SR, Lundbäck T, ..., Larhed M, Rosenström U

ChemistryOpen 9 (3) 325-337 [2020-03-00; online 2020-03-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The nf-core framework for community-curated bioinformatics pipelines

Ewels PA, Peltzer A, Fillinger S, ..., Di Tommaso P, Nahnsen S

Nat Biotechnol 38 (3) 276-278 [2020-03-00; online 2020-02-13]

NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]

Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity

Fenton TM, Jørgensen PB, Niss K, ..., Johansson-Lindbom B, Agace WW

Immunity 52 (3) 557-570.e6 [2020-03-00; online 2020-03-00]

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

Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.

Marisca R, Hoche T, Agirre E, ..., Castelo-Branco G, Czopka T

pii: 10.1038/s41593-019-0581-2 pmc: PMC7292734 mid: EMS85307

Nat. Neurosci. 23 (3) 363-374 [2020-03-00; online 2020-02-17]

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

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.

Westbury MV, Hartmann S, Barlow A, ..., Heller R, Hofreiter M

pii: aay0456 pmc: PMC7069707

Sci Adv 6 (11) eaay0456 [2020-03-00; online 2020-03-13]

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

Irreversible TrxR1 inhibitors block STAT3 activity and induce cancer cell death

Busker S, Qian W, Haraldsson M, ..., Tamm KP, Page BDG

Sci Adv 6 (12) eaax7945 [2020-03-00; online 2020-03-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Heritability of Caries Scores, Trajectories, and Disease Subtypes

Haworth S, Esberg A, Lif Holgerson P, ..., Franks PW, Johansson I

J Dent Res 99 (3) 264-270 [2020-03-00; online 2020-01-06]

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

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

Dharamshi JE, Tamarit D, Eme L, ..., Spang A, Ettema TJG

Current Biology 30 (6) 1032-1048.e7 [2020-03-00; online 2020-03-00]

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

Stressful Beginnings with Long-Term Consequences

Consiglio CR, Brodin P

Cell 180 (5) 820-821 [2020-03-00; online 2020-03-00]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

In Situ Encapsulation of Nile Red or Doxorubicin during RAFT‐Mediated Emulsion Polymerization via Polymerization‐Induced Self‐Assembly for Biomedical Applications

Engström J, Asem H, Brismar H, ..., Malkoch M, Malmström E

Macromol. Chem. Phys. 221 (5) 1900443 [2020-03-00; online 2020-02-10]

Advanced Light Microscopy (ALM) [Service]

Tumor localized agonistic anti-CD40 therapy and beyond.

Eltahir M, Persson H, Mangsbo S

Expert Opin Biol Ther 20 (3) 215-217 [2020-03-00; online 2020-01-10]

Drug Discovery and Development (DDD) [Collaborative]

Metabolomics analyses in non-diabetic middle-aged individuals reveal metabolites impacting early glucose disturbances and insulin sensitivity

Bos MM, Noordam R, Bennett K, ..., Surowiec I, van Heemst D

Metabolomics 16 (3) - [2020-03-00; online 2020-03-02]

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.

Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK

GENBANK: PRJNA576115

Mol. Ecol. 29 (6) 1120-1136 [2020-03-00; online 2020-03-09]

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

Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs

Wille M, Wensman JJ, Larsson S, ..., Hayer J, Malmberg M

Infection, Genetics and Evolution 82 (-) 104290 [2020-03-00; online 2020-03-00]

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

Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.

Stenmark B, Harrison OB, Eriksson L, ..., Maiden MCJ, Mölling P

pii: 10.1038/s41598-020-59509-y pmc: PMC7046676

Sci Rep 10 (1) 3644 [2020-02-27; online 2020-02-27]

The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia.

Richards AL, Pardiñas AF, Frizzati A, ..., O'Donovan MC, Walters JTR

pii: 5519548

Schizophr Bull 46 (2) 336-344 [2020-02-26; online 2019-06-18]

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

Streptococcus pneumoniae Nasopharyngeal Carriage among PCV-10-Vaccinated HIV-1-Infected Children with Maintained Serological Memory in Ethiopia.

Lemma M, Bekele Y, Petkov S, ..., Howe R, Chiodi F

pii: pathogens9030159 pmc: PMC7157605

Pathogens 9 (3) - [2020-02-25; online 2020-02-25]

Clinical Genomics Stockholm

Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles

Nunez JCB, Flight PA, Neil KB, ..., Blomberg A, Rand DM

Proc Natl Acad Sci USA 117 (10) 201918232 [2020-02-25; online 2020-02-25]

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

Patterns of African and Asian admixture in the Afrikaner population of South Africa.

Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM

pii: 10.1186/s12915-020-0746-1

BMC Biol. 18 (1) 16 [2020-02-24; online 2020-02-24]

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

Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment.

Rasmussen ER, Hallberg P, Baranova EV, ..., Palmer CNA, Wadelius M

pii: 10.1038/s41397-020-0165-2

Pharmacogenomics J. 20 (6) 770-783 [2020-02-21; online 2020-02-21]

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

Backbone Cyclization and Dimerization of LL-37-Derived Peptides Enhance Antimicrobial Activity and Proteolytic Stability

Gunasekera S, Muhammad T, Strömstedt AA, Rosengren KJ, Göransson U

Front Microbiol 11 (-) - [2020-02-21; online 2020-02-21]

Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass.

Dussex N, Stanton DWG, Sigeman H, ..., Hansson B, Dalén L

pii: 10.1038/s42003-020-0806-7 pmc: PMC7035339

Commun Biol 3 (1) 84 [2020-02-21; online 2020-02-21]

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

Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans.

Tzelepis G, Hodén KP, Fogelqvist J, ..., Vetukuri RR, Dixelius C

pmc: PMC7046690

Front Microbiol 11 (-) 252 [2020-02-21; online 2020-02-21]

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

Achieving symptom relief in patients with Myalgic encephalomyelitis by targeting the neuro-immune interface and inducing disease tolerance

Rodriguez LST, Pou C, Lakshmikanth T, ..., Julin P, Brodin P

- - (-) - [2020-02-21; online 2020-02-21]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

Short-Range Order and Transport Properties in Mixtures of the Protic Ionic Liquid [C2HIm][TFSI] with Water or Imidazole

Hasani M, Varela LM, Martinelli A

J. Phys. Chem. B - (-) - [2020-02-20; online 2020-02-20]

Genome-Wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.

Li C, Stoma S, Lotta LA, ..., Langenberg C, Codd V

pii: S0002-9297(20)30048-3

Am. J. Hum. Genet. - (-) - [2020-02-20; online 2020-02-20]

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

Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes

Kumar R, Chand K, Bhowmik S, ..., Hedenström M, Chorell E

Nucleic Acids Res 48 (3) 1108-1119 [2020-02-20; online 2020-01-08]

Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry.

Engqvist H, Parris TZ, Kovács A, ..., Karlsson P, Helou K

pmc: PMC7040170

Front Oncol 10 (-) 162 [2020-02-18; online 2020-02-18]

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

Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies.

Munn-Chernoff MA, Johnson EC, Chou YL, ..., Bulik CM, Agrawal A

Addict Biol - (-) e12880 [2020-02-16; online 2020-02-16]

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

Managed and Unmanaged Pinus sylvestris Forest Stands Harbour Similar Diversity and Composition of the Phyllosphere and Soil Fungi.

Lynikienė J, Marčiulynienė D, Marčiulynas A, ..., Vaičiukynė M, Menkis A

pii: microorganisms8020259

Microorganisms 8 (2) - [2020-02-15; online 2020-02-15]

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

The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.

Scaletti E, Claesson M, Helleday T, Jemth AS, Stenmark P

PDB: 6SQW PDB: 6SQY PDB: 6SQZ

J. Mol. Biol. 432 (4) 1126-1142 [2020-02-14; online 2020-01-15]

Screening for autoantibody targets in post-vaccination narcolepsy using proteome arrays.

Lind A, Eriksson D, Akel O, ..., Elding Larsson H, Landegren N

Scand. J. Immunol. 91 (4) e12864 [2020-02-13; online 2020-02-13]

Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service]

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing.

Nordlund J, Marincevic-Zuniga Y, Cavelier L, ..., Lönnerholm G, Syvänen AC

pii: 10.1038/s41598-020-59214-w pmc: PMC7018692

Sci Rep 10 (1) 2512 [2020-02-13; online 2020-02-13]

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

Longitudinal trajectories, correlations and mortality associations of nine biological ages across 20-years follow-up.

Li X, Ploner A, Wang Y, ..., Jylhävä J, Hägg S

pii: 51507 pmc: PMC7012595

Elife 9 (-) - [2020-02-11; online 2020-02-11]

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

Urine Metabolite Profiles and Nutrient Intake Based on 4-Day Weighed Food Diary in Habitual Vegans, Vegetarians, and Omnivores

Lindqvist HM, Rådjursöga M, Torstensson T, ..., Ellegård L, Winkvist A

J. Nutr. - (-) - [2020-02-11; online 2020-02-11]

Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.

Dahl S, Pettersson M, Eisfeldt J, ..., Anderlid BM, Lindstrand A

pii: PONE-D-19-12114 pmc: PMC7010252

PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]

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

New approaches to the study of immune responses in humans

Brodin P

Hum Genet - (-) - [2020-02-10; online 2020-02-10]

Mass Cytometry [Technology development]

Low concentrations of the benzodiazepine drug oxazepam induce anxiolytic effects in wild-caught but not in laboratory zebrafish.

Vossen LE, Červený D, Sen Sarma O, ..., Brodin T, Winberg S

pii: S0048-9697(19)34692-3

Sci. Total Environ. 703 (-) 134701 [2020-02-10; online 2019-11-01]

Genome Engineering Zebrafish [Service]

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia.

Grönroos T, Mäkinen A, Laukkanen S, ..., Heinäniemi M, Lohi O

pii: 10.1038/s41598-020-58970-z pmc: PMC7005266

Sci Rep 10 (1) 2043 [2020-02-06; online 2020-02-06]

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

Capsid Structure of a Marine Algal Virus of the Order Picornavirales

Munke A, Kimura K, Tomaru Y, Okamoto K

J Virol 94 (9) - [2020-02-05; online 2020-04-16]

Thermal proteome profiling identifies oxidative-dependent inhibition of the transcription of major oncogenes as a new therapeutic mechanism for select anticancer compounds

Peuget S, Zhu J, Sanz G, ..., Zubarev R, Selivanova G

Cancer Res - (-) canres.2069.2019 [2020-02-04; online 2020-02-04]

Chemical Proteomics [Collaborative]

A chromosome-scale reference genome for Giardia intestinalis WB.

Xu F, Jex A, Svärd SG

pii: 10.1038/s41597-020-0377-y

Sci Data 7 (1) 38 [2020-02-04; online 2020-02-04]

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

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses

Phad GE, Pushparaj P, Tran K, ..., Wyatt RT, Karlsson Hedestam GB

J. Exp. Med. 217 (2) - [2020-02-03; online 2019-11-08]

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

Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).

Wang X, Bernhardsson C, Ingvarsson PK

pii: 5709816 pmc: PMC7046165

Genome Biol Evol 12 (2) 3803-3817 [2020-02-01; online 2020-01-21]

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

Glycogenin is Dispensable for Glycogen Synthesis in Human Muscle, and Glycogenin Deficiency Causes Polyglucosan Storage.

Visuttijai K, Hedberg-Oldfors C, Thomsen C, ..., Roach P, Oldfors A

pii: 5599738

J. Clin. Endocrinol. Metab. 105 (2) - [2020-02-01; online 2019-10-20]

Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss

Lewis WH, Lind AE, Sendra KM, ..., Ettema TJG, Embley TM

Mol. Biol. Evol. 37 (2) 524-539 [2020-02-01; online 2019-10-24]

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

Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon

Sanz-Carbonell A, Marques MC, Martinez G, Gomez G

RNA Biol 17 (2) 292-308 [2020-02-01; online 2019-12-10]

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

rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression

Pan G, Cavalli M, Carlsson B, ..., Kumar C, Wadelius C

iScience 23 (2) 100808 [2020-02-00; online 2020-02-00]

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

Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development

Köster J, Arbajian E, Viklund B, ..., Mandahl N, Mertens F

Cancer Genet 241 (-) 34-41 [2020-02-00; online 2020-02-00]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.

Ström P, Kartasalo K, Olsson H, ..., Egevad L, Eklund M

pii: S1470-2045(19)30738-7

Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]

BioImage Informatics Bioinformatics Compute and Storage [Service]

The Molecular Anatomy of Mouse Skin during Hair Growth and Rest

Joost S, Annusver K, Jacob T, ..., Sandberg R, Kasper M

Cell Stem Cell 26 (3) 441-457.e7 [2020-02-00; online 2020-02-00]

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]

Exosomes influence the behavior of human mesenchymal stem cells on titanium surfaces.

Wang X, Shah FA, Vazirisani F, ..., Ekström K, Thomsen P

pii: S0142-9612(19)30670-2

Biomaterials 230 (-) 119571 [2020-02-00; online 2019-10-24]

Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.

Nilsson E, Bayfield OW, Lundin D, Antson AA, Holmfeldt K

pii: v12020158 pmc: PMC7077304

Viruses 12 (2) 158 [2020-01-30; online 2020-01-30]

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

Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.

Ekhteraei-Tousi S, Lewerentz J, Larsson J

pii: cells9020323 pmc: PMC7072490

Cells 9 (2) 323 [2020-01-30; online 2020-01-30]

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

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B

F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization

Jamroskovic J, Doimo M, Chand K, ..., Chorell E, Sabouri N

J. Am. Chem. Soc. - (-) - [2020-01-28; online 2020-01-28]

Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin.

Roemhild R, Linkevicius M, Andersson DI

pii: PBIOLOGY-D-19-02723

PLoS Biol. 18 (1) e3000612 [2020-01-27; online 2020-01-27]

Extracellular Vesicles Released From the Skin Commensal Yeast Malassezia sympodialis Activate Human Primary Keratinocytes

Vallhov H, Johansson C, Veerman RE, Scheynius A

Front. Cell. Infect. Microbiol. 10 (-) - [2020-01-24; online 2020-01-24]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service]

Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR

pii: 10.1038/s41467-019-13869-w pmc: PMC6981202

Nat Commun 11 (1) 470 [2020-01-24; online 2020-01-24]

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

CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.

Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D

pii: 10.1038/s41598-020-57710-7 pmc: PMC6981141

Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]

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

Image-Based Morphological Profiling Identifies a Lysosomotropic, Iron-Sequestering Autophagy Inhibitor

Laraia L, Garivet G, Foley DJ, ..., Rodriguez R, Waldmann H

Angew. Chem. Int. Ed. - (-) - [2020-01-24; online 2020-01-24]

Biochemical Imaging Centre Umeå [Service]

The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly.

Pinese M, Lacaze P, Rath EM, ..., Dinger ME, Thomas DM

pii: 10.1038/s41467-019-14079-0 pmc: PMC6978518

Nat Commun 11 (1) 435 [2020-01-23; online 2020-01-23]

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

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.

Buetti-Dinh A, Herold M, Christel S, ..., Friedman R, Dopson M

pii: 10.1186/s12859-019-3337-9 pmc: PMC6975020

BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]

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

Loss of centromere function drives karyotype evolution in closely related Malassezia species.

Sankaranarayanan SR, Ianiri G, Coelho MA, ..., Heitman J, Sanyal K

pii: 53944

Elife 9 (-) - [2020-01-20; online 2020-01-20]

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

Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica

Redl S, Poehlein A, Esser C, ..., Dürre P, Nielsen AT

Front Microbiol 10 (-) - [2020-01-17; online 2020-01-17]

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

SWEDEGENE-a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions.

Hallberg P, Yue QY, Eliasson E, ..., Ås J, Wadelius M

pii: 10.1038/s41397-020-0148-3

Pharmacogenomics J. 20 (4) 579-585 [2020-01-17; online 2020-01-17]

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

Evolution of a new function by fusion between phage DNA and a bacterial gene.

Warsi O, Knopp M, Surkov S, Hultqvist JJ, Andersson DI

pii: 5707441

Mol. Biol. Evol. - (-) - [2020-01-16; online 2020-01-16]

Proteomic analysis of follicular fluid during human ovulation.

Zakerkish F, Brännström M, Carlsohn E, ..., van der Post S, Thoroddsen A

Acta Obstet Gynecol Scand - (-) - [2020-01-16; online 2020-01-16]

Discovery of species-unique peptide biomarkers of bacterial pathogens by tandem mass spectrometry-based proteotyping.

Karlsson R, Thorsell A, Gomila M, ..., Kristiansson E, Moore E

pii: RA119.001667

Mol. Cell Proteomics - (-) - [2020-01-15; online 2020-01-15]

Glycoproteomics [Collaborative]

Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study.

Bonomi A, Veglia F, Baldassarre D, ..., Gigante B, on behalf of the IMPROVE study group

pii: 10.1038/s41435-019-0090-z

Genes Immun. - (-) - [2020-01-14; online 2020-01-14]

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

Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.

Rugiu L, Panova M, Pereyra RT, Jormalainen V

pii: 10.1186/s12864-020-6470-y pmc: PMC6958763

BMC Genomics 21 (1) 42 [2020-01-13; online 2020-01-13]

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

Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines.

Lethin J, Shakil SSM, Hassan S, ..., Olsson O, Aronsson H

pii: 10.1186/s12870-019-2137-8 pmc: PMC6958588

BMC Plant Biol. 20 (1) 18 [2020-01-13; online 2020-01-13]

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

A regulatory role for CHD2 in myelopoiesis.

Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A

Epigenetics 15 (6-7) 1-13 [2020-01-10; online 2020-01-10]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.

Nunes L, Aasebø K, Mathot L, ..., Sjöblom T, Glimelius B

Acta Oncol 59 (4) 1-10 [2020-01-10; online 2020-01-10]

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

Simultaneous mass spectrometry imaging of multiple neuropeptides in the brain and alterations induced by experimental parkinsonism and L-DOPA therapy.

Hulme H, Fridjonsdottir E, Gunnarsdottir H, ..., Svenningsson P, Andrén PE

pii: S0969-9961(20)30013-9

Neurobiol. Dis. 137 (-) 104738 [2020-01-09; online 2020-01-09]

National Resource for Mass Spectrometry Imaging [Collaborative]

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure.

Shah S, Henry A, Roselli C, ..., Swerdlow DI, Lumbers RT

pii: 10.1038/s41467-019-13690-5

Nat Commun 11 (1) 163 [2020-01-09; online 2020-01-09]

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

DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes.

Sen I, Zhou X, Chernobrovkin A, ..., Zubarev RA, Riedel CG

pii: 10.1038/s41467-019-13931-7 pmc: PMC6952425

Nat Commun 11 (1) 138 [2020-01-09; online 2020-01-09]

Bioinformatics Compute and Storage [Service] Chemical Proteomics [Service]

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.

Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N

pii: 10.1186/s13148-019-0803-1 pmc: PMC6950999

Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]

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

A Light-up Logic Platform for Selective Recognition of Parallel G-Quadruplex Structures via Disaggregation-Induced Emission

Deiana M, Chand K, Jamroskovic J, ..., Chorell E, Sabouri N

Angew. Chem. Int. Ed. 59 (2) 896-902 [2020-01-07; online 2019-11-22]

Biochemical Imaging Centre Umeå [Service]

Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.

Gelabert P, Sandoval-Velasco M, Serres A, ..., Gilbert MTP, Lalueza-Fox C

pii: S0960-9822(19)31438-1

Curr. Biol. 30 (1) 108-114.e5 [2020-01-06; online 2019-12-12]

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

Integrative discovery of treatments for high-risk neuroblastoma.

Almstedt E, Elgendy R, Hekmati N, ..., Krona C, Nelander S

pii: 10.1038/s41467-019-13817-8 pmc: PMC6941971

Nat Commun 11 (1) 71 [2020-01-03; online 2020-01-03]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum

Khoomrung S, Nookaew I, Sen P, ..., Harandi AM, Nielsen J

J. Proteome Res. 19 (1) 269-278 [2020-01-03; online 2019-10-18]

PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.

Rykaczewska U, Suur BE, Röhl S, ..., Hedin U, Matic L

Circ. Res. 126 (5) 571-585 [2020-01-02; online 2020-01-02]

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

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

Sullivan AR, Eldfjell Y, Schiffthaler B, ..., Street NR, Wang XR

Genome Biol Evol 12 (1) 3586-3598 [2020-01-01; online 2019-11-27]

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

A dual-action peptide-containing hydrogel targets wound infection and inflammation

Puthia M, Butrym M, Petrlova J, ..., Kjellström S, Schmidtchen A

Sci. Transl. Med. 12 (524) eaax6601 [2020-01-01; online 2020-01-01]

Targeted and Structural Proteomics [Collaborative]

The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets

van der Valk T, Gonda CM, Silegowa H, ..., Detwiler KM, Guschanski K

Mol. Biol. Evol. 37 (1) 183-194 [2020-01-01; online 2019-09-16]

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

Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds.

Elfstrand M, Zhou L, Baison J, ..., Stenlid J, García-Gil MR

Mol. Ecol. 29 (1) 199-213 [2020-01-00; online 2019-12-09]

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

Hepatitis E virus genotype 3 strains and a plethora of other viruses detected in raw and still in tap water

Wang H, Kjellberg I, Sikora P, ..., Bergstedt O, Norder H

Water Research 168 (-) 115141 [2020-01-00; online 2020-01-00]

Clinical Genomics Gothenburg [Collaborative]

Genome-wide signatures of environmental adaptation in European aspen ( Populus tremula) under current and future climate conditions.

Ingvarsson PK, Bernhardsson C

pii: EVA12792 pmc: PMC6935590

Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]

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

Screening for bioactive secondary metabolites in Sri Lankan medicinal plants by microfractionation and targeted isolation of antimicrobial flavonoids from Derris scandens

Mohotti S, Rajendran S, Muhammad T, ..., Hettiarachchi CM, Gunasekera S

Journal of Ethnopharmacology 246 (-) 112158 [2020-01-00; online 2020-01-00]

Circadian regulation of phosphodiesterase 6 genes in zebrafish differs between cones and rods: Implications for photopic and scotopic vision.

Abalo XM, Lagman D, Heras G, ..., Eggert J, Larhammar D

pii: S0042-6989(19)30195-6

Vision Res. 166 (-) 43-51 [2020-01-00; online 2019-12-16]

Genome Engineering Zebrafish [Service]

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

Millard PS, Bugge K, Marabini R, ..., Burow M, Kragelund BB

Protein Science 29 (1) 169-183 [2020-01-00; online 2019-11-11]

Identification of novel diagnostic and prognostic biomarkers for abdominal aortic aneurysm

Memon AA, Zarrouk M, Ågren-Witteschus S, ..., Gottsäter A, Sundquist K

Eur J Prev Cardiolog 27 (2) 132-142 [2020-01-00; online 2019-08-29]

Clinical Biomarkers [Service]

Developmental exposure to a human relevant mixture of endocrine disruptors alters metabolism and adipogenesis in zebrafish (Danio rerio)

Mentor A, Brunström B, Mattsson A, Jönsson M

Chemosphere 238 (-) 124584 [2020-01-00; online 2020-01-00]

Genome Engineering Zebrafish [Service]

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.

Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S

pii: RA119.001737

Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]

Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]

Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome

Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, ..., Nordmark G, Wahren-Herlenius M

RMD Open 6 (1) e000995 [2020-01-00; online 2020-01-07]

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

Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.

Myers L, Blyth M, Moradkhani K, ..., Anderlid BM, Tammimies K

pmc: PMC6978403

Mol Genet Genomic Med 8 (1) e1013 [2020-01-00; online 2019-11-15]

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

Association of genetic variants related to plasma fatty acids with type 2 diabetes mellitus and glycaemic traits: a Mendelian randomisation study.

Yuan S, Larsson SC

pii: 10.1007/s00125-019-05019-0 pmc: PMC6890658

Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]

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

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods.

De Leoz MLA, Duewer DL, Fung A, ..., Yuan H, Stein SE

pii: RA119.001677 pmc: PMC6944243

Mol. Cell Proteomics 19 (1) 11-30 [2020-01-00; online 2019-10-07]

Glycoproteomics [Collaborative]

Effect of sample preparation techniques upon single cell chemical imaging: A practical comparison between synchrotron radiation based X-ray fluorescence (SR-XRF) and Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS)

De Samber B, De Rycke R, De Bruyne M, ..., Polerecky L, Vincze L

Analytica Chimica Acta 1106 (-) 22-32 [2020-01-00; online 2020-01-00]

Cryo-EM [Collaborative]

Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma-associated antigens via human scFv antibodies.

Mehdipour T, Tohidkia MR, Ata Saei A, ..., Zubarev RA, Nouri M

pmc: PMC6904653

Immunology 159 (1) 96-108 [2020-01-00; online 2019-11-08]

Chemical Proteomics [Service]

NMR Spectroscopic Analysis to Evaluate the Quality of Insulin: Concentration, Variability, and Excipient Content

Malmodin D, Pedersen A, Karlsson BG, Forsander G

J Diabetes Sci Technol 14 (1) 180-184 [2020-01-00; online 2019-02-19]

Regulation of α-synuclein by chaperones in mammalian cells

Burmann BM, Gerez JA, Matečko-Burmann I, ..., Riek R, Hiller S

Nature 577 (7788) 127-132 [2020-01-00; online 2019-12-04]

Do we really know who has an MGMT methylated glioma? Results of an international survey regarding use of MGMT analyses for glioma.

Malmström A, Łysiak M, Kristensen BW, ..., Henriksson R, Söderkvist P

pii: npz039 pmc: PMC6993038

Neurooncol Pract 7 (1) 68-76 [2020-01-00; online 2019-09-24]

Clinical Genomics Linköping

Metabolic response patterns in brain microdialysis fluids and serum during interstitial cisplatin treatment of high-grade glioma

Björkblom B, Jonsson P, Tabatabaei P, ..., Bergenheim AT, Antti H

Br J Cancer 122 (2) 221-232 [2020-01-00; online 2019-12-10]

Probabilistic cell typing enables fine mapping of closely related cell types in situ

Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M

Nat Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Service]

A site-specific self-assembled light-up rotor probe for selective recognition and stabilization of c-MYC G-quadruplex DNA

Deiana M, Chand K, Jamroskovic J, ..., Chorell E, Sabouri N

Nanoscale 12 (24) 12950-12957 [2020-00-00; online 2020-00-00]

An integrative toolbox to unlock the structure and dynamics of protein–surfactant complexes

Sanchez-Fernandez A, Diehl C, Houston JE, ..., Sjögren H, Wahlgren M

Nanoscale Adv. 2 (9) 4011-4023 [2020-00-00; online 2020-00-00]

In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections

Hilscher MM, Gyllborg D, Yokota C, Nilsson M

Methods Mol. Biol. - (-) 313-329 [2020-00-00; online 2020-05-12]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative]

In-plate toxicometabolomics of single zebrafish embryos

Ribbenstedt A, Posselt M, Brunius C, Benskin JP

Mol Omics 16 (3) 185-194 [2020-00-00; online 2020-00-00]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Macrocyclization of bis-indole quinolines for selective stabilization of G-quadruplex DNA structures

Das RN, Andréasson M, Kumar R, Chorell E

Chem. Sci. 11 (38) 10529-10537 [2020-00-00; online 2020-00-00]

Recording In-Cell NMR-Spectra in Living Mammalian Cells

Matečko-Burmann I, Burmann BM

Methods Mol. Biol. - (-) 857-871 [2020-00-00; online 2020-07-22]

Regeneration of water-deactivated Cu/SAPO-34(MO) with acids

Woo J, Bernin D, Ahari H, ..., Zammit M, Olsson L

Catal. Sci. Technol. 10 (5) 1539-1550 [2020-00-00; online 2020-00-00]

Swedish NMR Centre (SNC)

Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy

Isaksson L, Pedersen A

Methods Mol. Biol. - (-) 233-245 [2020-00-00; online 2020-07-22]

Resolution enhancement in NMR spectra by deconvolution with compressed sensing reconstruction

Kazimierczuk K, Kasprzak P, Georgoulia PS, ..., Westenhoff S, Orekhov VY

Chem. Commun. 56 (93) 14585-14588 [2020-00-00; online 2020-00-00]