Publications

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Publications

2020 (16)

2019 (602)

2018 (560)

2017 (613)

2016 (635)

2015 (424)

2014 (373)

2013 (319)

2012 (243)

2011 (164)

2010 (139)

All (4088)


Facilities

Journals

4088 publications

PubMed DOI Crossref
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
Genes Immun. - (-) - [2020-01-14; online 2020-01-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
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
Nat Commun 11 (1) 163 [2020-01-09; online 2020-01-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
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
pmc
Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
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
Curr. Biol. 30 (1) 108-114.e5 [2020-01-06; online 2019-12-12]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative]
DOI Crossref
A sample preparation protocol for high throughput immunofluorescence of suspension cells
Backstrom A, Kugel L, Gnann C, ..., Lundberg E, Stadler C
- - (-) - [2020-01-06; online 2020-01-06]
Cell Profiling [Technology development]
PubMed DOI Crossref
Integrative discovery of treatments for high-risk neuroblastoma.
Almstedt E, Elgendy R, Hekmati N, ..., Krona C, Nelander S
pmc
Nat Commun 11 (1) 71 [2020-01-03; online 2020-01-03]
Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
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. - (-) - [2020-01-02; online 2020-01-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
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]
In Situ Sequencing (ISS) [Service]
DOI Crossref
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]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
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]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
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
pmc
Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
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
Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]
Chemical Proteomics & Proteogenomics [Collaborative]
DOI Crossref
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]
DOI Crossref
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]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
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]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Genome-wide signatures of environmental adaptation in European aspen ( Populus tremula) under current and future climate conditions.
Ingvarsson PK, Bernhardsson C
pmc
Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver
Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C
Thromb. Haemost. - (-) - [2019-12-30; online 2019-12-30]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling.
Ahi EP, Brunel M, Tsakoumis E, Schmitz M
pmc
Sci Rep 9 (1) 20166 [2019-12-27; online 2019-12-27]
Genome Engineering Zebrafish [Service]
DOI Crossref
Dynamic Chirality in the Mechanism of Action of Allosteric CD36 Modulators of Macrophage-Driven Inflammation
Danelius E, Ohm RG, Ahsanullah , ..., Erdelyi M, Lubell WD
J. Med. Chem. 62 (24) 11071-11079 [2019-12-26; online 2019-11-27]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.
Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N
Ann. Bot. - (-) - [2019-12-24; online 2019-12-24]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox
Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L
Phil. Trans. R. Soc. B 374 (1788) 20190212 [2019-12-23; online 2019-11-04]
Bioinformatics Long-term Support WABI [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Estimating Detection Limits of Potentiometric DNA Sensors Using Surface Plasmon Resonance Analyses
Xu X, Makaraviciute A, Abdurakhmanov E, ..., Nyholm L, Zhang Z
ACS Sens. - (-) - [2019-12-23; online 2019-12-23]
Drug Discovery and Development (DDD) [Technology development]
DOI Crossref
Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste
Moestedt J, Westerholm M, Isaksson S, Schnürer A
Bioengineering 7 (1) 3 [2019-12-23; online 2019-12-23]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Gene Expression Alterations during Development of Castration-Resistant Prostate Cancer Are Detected in Circulating Tumor Cells.
Josefsson A, Larsson K, Freyhult E, Damber J, Welén K
Cancers (Basel) 12 (1) - [2019-12-21; online 2019-12-21]
Bioinformatics Support and Infrastructure [Collaborative]
PubMed DOI Crossref
Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers.
Arroyo Mühr LS, Lagheden C, Eklund C, ..., Sundström K, Dillner J
J. Gen. Virol. - (-) - [2019-12-20; online 2019-12-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.
Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P
Science 366 (6472) - [2019-12-20; online 2019-12-21]
Mass Cytometry [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.
Smedfors G, Liesecke F, Ran C, ..., Karlsson TE, Carmine Belin A
Brain Sci 10 (1) - [2019-12-20; online 2019-12-20]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression.
Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB
Epigenetics - (-) 1-18 [2019-12-19; online 2019-12-19]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Levels of caspase-3 and histidine-rich glycoprotein in the embryo secretome as biomarkers of good-quality day-2 embryos and high-quality blastocysts
Kaihola H, Yaldir FG, Bohlin T, ..., Hreinsson J, Åkerud H
PLoS ONE 14 (12) e0226419 [2019-12-19; online 2019-12-19]
PLA and Single Cell Proteomics [Service]
DOI Crossref
Comparison of a Deep Learning Risk Score and Standard Mammographic Density Score for Breast Cancer Risk Prediction
Dembrower K, Liu Y, Azizpour H, ..., Lindholm P, Strand F
Radiology - (-) 190872 [2019-12-17; online 2019-12-17]
PubMed DOI Crossref
A transposable element insertion is associated with an alternative life history strategy.
Woronik A, Tunström K, Perry MW, ..., Käkelä R, Wheat CW
pmc
Nat Commun 10 (1) 5757 [2019-12-17; online 2019-12-17]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.
Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S
pmc
Arthritis Res. Ther. 21 (1) 288 [2019-12-16; online 2019-12-16]
Plasma Profiling [Service]
PubMed DOI Crossref
NGS targeted screening of 100 Scandinavian patients with coronal synostosis.
Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L
Am. J. Med. Genet. A - (-) - [2019-12-14; online 2019-12-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.
Ueberschär M, Wang H, Zhang C, ..., Wen J, Dai Q
pmc
Nat Commun 10 (1) 5700 [2019-12-13; online 2019-12-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
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
Ann. Rheum. Dis. - (-) - [2019-12-11; online 2019-12-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion
van der Woude LC, Perrella G, Snoek BL, ..., Kaiserli E, van Zanten M
Proc Natl Acad Sci USA 116 (50) 25343-25354 [2019-12-10; online 2019-11-25]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.
Rivera NV, Patasova K, Kullberg S, ..., Grunewald J, Padyukov L
Sci Rep 9 (1) 18633 [2019-12-09; online 2019-12-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Comprehensive longitudinal study of epigenetic mutations in aging.
Wang Y, Karlsson R, Jylhävä J, ..., Almgren M, Hägg S
Clin Epigenetics 11 (1) 187 [2019-12-09; online 2019-12-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Plasma Lipidome and Prediction of Type 2 Diabetes in the Population-Based Malmö Diet and Cancer Cohort
Fernandez C, Surma MA, Klose C, ..., Simons K, Melander O
Dia Care - (-) dc191199 [2019-12-08; online 2019-12-08]
Bioinformatics Long-term Support WABI [Collaborative]
PubMed DOI Crossref
Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.
Ignjatovic V, Geyer PE, Palaniappan KK, ..., Deutsch EW, Schwenk JM
pmc mid
J. Proteome Res. 18 (12) 4085-4097 [2019-12-06; online 2019-10-11]
Plasma Profiling [Collaborative]
DOI Crossref
Depression, GABA, and Age Correlate with Plasma Levels of Inflammatory Markers
Bhandage AK, Cunningham JL, Jin Z, ..., Ekselius L, Birnir B
Int J Mol Sci 20 (24) 6172 [2019-12-06; online 2019-12-06]
PLA and Single Cell Proteomics [Collaborative]
PubMed DOI Crossref
Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group.
Jia T, Chu C, Liu Y, ..., Schumann G, Desrivières S
Mol. Psychiatry - (-) - [2019-12-06; online 2019-12-06]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.
Pineau C, Hikmet F, Zhang C, ..., Uhlén M, Lindskog C
J. Proteome Res. 18 (12) 4215-4230 [2019-12-06; online 2019-08-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
GLUL Ablation Can Confer Drug Resistance to Cancer Cells via a Malate-Aspartate Shuttle-Mediated Mechanism
Muthu M, Kumar R, Syed Khaja AS, ..., Persson JL, Nordström A
Cancers (Basel) 11 (12) 1945 [2019-12-05; online 2019-12-05]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.
Nicholls TJ, Spåhr H, Jiang S, ..., Larsson NG, Gustafsson CM
Mol. Cell 76 (5) 784-796.e6 [2019-12-05; online 2019-10-03]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Replicating associations between DNA methylation and body mass index in a longitudinal sample of older twins.
Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Dahl Aslan AK
Int J Obes (Lond) - (-) - [2019-12-04; online 2019-12-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.
Ameen C, Feuerborn TR, Brown SK, ..., Darwent CM, Evin A
Proc. Biol. Sci. 286 (1916) 20191929 [2019-12-04; online 2019-11-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy.
Tsagiopoulou M, Papakonstantinou N, Moysiadis T, ..., Rosenquist R, Stamatopoulos K
Clin Epigenetics 11 (1) 177 [2019-12-02; online 2019-12-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
High throughput barcoding method for genome-scale phasing.
Redin D, Frick T, Aghelpasand H, ..., Olsen RA, Ahmadian A
pmc
Sci Rep 9 (1) 18116 [2019-12-02; online 2019-12-02]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative]
PubMed DOI Crossref
Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.
Günaydın G, Edfeldt G, Garber DA, ..., Tjernlund A, Broliden K
Sci Rep 9 (1) 18120 [2019-12-02; online 2019-12-02]
BioImage Informatics [Service]
DOI Crossref
The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Batista RA, Moreno-Romero J, Qiu Y, ..., Figueiredo DD, Köhler C
Elife 8 (-) - [2019-12-02; online 2019-12-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.
Vicente M, Priehodová E, Diallo I, ..., Černý V, Schlebusch CM
BMC Genomics 20 (1) 915 [2019-12-02; online 2019-12-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats
Dong Y, Sanford RA, Inskeep WP, ..., Fried GA, Fouke BW
Astrobiology 19 (12) 1442-1458 [2019-12-01; online 2019-12-01]
Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
Arteria: An automation system for a sequencing core facility
Dahlberg J, Hermansson J, Sturlaugsson S, ..., Hofmann O, Larsson P
Gigascience 8 (12) - [2019-12-01; online 2019-12-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Technology development]
PubMed DOI Crossref
From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability
Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D
Genome Med 11 (1) - [2019-12-00; online 2019-11-07]
Bioinformatics Long-term Support WABI [Collaborative] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS
Zhu S, Wuolikainen A, Wu J, ..., Forsgren L, Trupp M
J Mol Neurosci 69 (4) 643-657 [2019-12-00; online 2019-11-12]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development
Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T
GEO
Nat Commun 10 (1) - [2019-12-00; online 2019-02-04]
Bioinformatics Long-term Support WABI [Collaborative] In Situ Sequencing (ISS) [Service]
PubMed DOI Crossref
PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding
Kloth KJ, Abreu IN, Delhomme N, ..., Moritz T, Albrectsen BR
Plant Physiol. 181 (4) 1704-1720 [2019-12-00; online 2019-09-24]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Towards a standardized bioinformatics infrastructure for N- and O-glycomics
Rojas-Macias MA, Mariethoz J, Andersson P, ..., Lisacek F, Karlsson NG
Nat Commun 10 (1) - [2019-12-00; online 2019-07-22]
Bioinformatics Support and Infrastructure [Technology development]
PubMed DOI Crossref
Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.
Morales HE, Faria R, Johannesson K, ..., Westram AM, Butlin RK
pmc
Sci Adv 5 (12) eaav9963 [2019-12-00; online 2019-12-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice.
Ross JM, Coppotelli G, Branca RM, ..., Sinclair DA, Olson L
pmc
Aging Cell 18 (6) e13029 [2019-12-00; online 2019-09-06]
Chemical Proteomics & Proteogenomics [Collaborative]
PubMed DOI Crossref
Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J
Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Breast cancer quantitative proteome and proteogenomic landscape
Johansson HJ, None , Socciarelli F, ..., Børresen-Dale AL, Lehtiö J
Nat Commun 10 (1) - [2019-12-00; online 2019-04-08]
Advanced Light Microscopy (ALM) [Service] Bioinformatics Long-term Support WABI [Collaborative] Chemical Proteomics & Proteogenomics [Technology development]
DOI Crossref
Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes
Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C
Sci Rep 9 (1) - [2019-12-00; online 2019-06-03]
Systems Biology [Collaborative]
DOI Crossref
Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads
Shakeri Yekta S, Liu T, Axelsson Bjerg M, ..., Björn A, Schnürer A
Biotechnol Biofuels 12 (1) - [2019-12-00; online 2019-11-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
The genomic footprint of sexual conflict.
Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G
Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Meckel syndrome: Clinical and mutation profile in six fetuses.
Radhakrishnan P, Nayak SS, Shukla A, Lindstrand A, Girisha KM
Clin. Genet. 96 (6) 560-565 [2019-12-00; online 2019-08-21]
Clinical Genomics Stockholm [Service]
DOI Crossref
The genomics of major psychiatric disorders in a large pedigree from Northern Sweden
Szatkiewicz J, Crowley JJ, Adolfsson AN, ..., Adolfsson R, Sullivan PF
Transl Psychiatry 9 (1) - [2019-12-00; online 2019-02-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida
Stairs CW, Kokla A, Ástvaldsson Á, ..., Svärd S, Ettema TJG
BMC Biol. 17 (1) - [2019-12-00; online 2019-03-01]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide
Wu M, Farkas D, Eriksson LA, Strid Å
Sci Rep 9 (1) - [2019-12-00; online 2019-01-28]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
The potential of magnetisation transfer NMR to monitor the dissolution process of cellulose in cold alkali
Gunnarsson M, Hasani M, Bernin D
Cellulose 26 (18) 9403-9412 [2019-12-00; online 2019-09-12]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
The 1H NMR serum metabolomics response to a two meal challenge: a cross-over dietary intervention study in healthy human volunteers
Rådjursöga M, Lindqvist HM, Pedersen A, ..., Ellegård L, Winkvist A
Nutr J 18 (1) - [2019-12-00; online 2019-04-08]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma
Carow B, Hauling T, Qian X, ..., Nilsson M, Rottenberg ME
Nat Commun 10 (1) - [2019-12-00; online 2019-04-23]
In Situ Sequencing (ISS) [Service]
DOI Crossref
Mercury methylating microbial communities of boreal forest soils
Xu J, Buck M, Eklöf K, ..., Bertilsson S, Bravo AG
Sci Rep 9 (1) - [2019-12-00; online 2019-01-24]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family
Lindholm Carlström E, Halvardson J, Etemadikhah M, ..., Gustavson KH, Feuk L
BMC Med Genomics 12 (1) - [2019-12-00; online 2019-11-06]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations
Filppula AM, Parvizi R, Mateus A, Baranczewski P, Artursson P
Sci Rep 9 (1) - [2019-12-00; online 2019-04-10]
Drug Discovery and Development (DDD) [Technology development]
PubMed DOI Crossref
An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition.
Wessels B, Seyfferth C, Escamez S, ..., Felten J, Tuominen H
New Phytol. 224 (4) 1585-1599 [2019-12-00; online 2019-07-02]
Cryo-EM [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm
Moreno-Romero J, Del Toro-De León G, Yadav VK, Santos-González J, Köhler C
Genome Biol. 20 (1) - [2019-12-00; online 2019-02-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type
Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M
Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å
Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]
Bioinformatics Long-term Support WABI [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C
GEO
Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Systems Biology [Collaborative]
DOI Crossref
Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes
Diamanti K, Cavalli M, Pan G, ..., Komorowski J, Wadelius C
Sci Rep 9 (1) - [2019-12-00; online 2019-07-04]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile
Hofvander J, Puls F, Pillay N, ..., Nilsson J, Mertens F
J. Pathol 249 (4) 425-434 [2019-12-00; online 2019-08-27]
Clinical Genomics Lund [Service]
DOI Crossref
Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases
Cavalli M, Baltzer N, Pan G, ..., Komorowski J, Wadelius C
Hum Genomics 13 (1) - [2019-12-00; online 2019-04-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity
Hajheidari M, Wang Y, Bhatia N, ..., Gan X, Tsiantis M
Current Biology 29 (24) 4183-4192.e6 [2019-12-00; online 2019-12-00]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation
Baião GC, Schneider DI, Miller WJ, Klasson L
BMC Genomics 20 (1) - [2019-12-00; online 2019-06-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry
Rende U, Niittylä T, Moritz T
Plant Methods 15 (1) - [2019-12-00; online 2019-11-07]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery
Saei AA, Beusch CM, Chernobrovkin A, ..., Végvári Á, Zubarev RA
Nat Commun 10 (1) - [2019-12-00; online 2019-12-16]
Chemical Proteomics & Proteogenomics [Technology development]
DOI Crossref
Morphological analysis of Apolipoprotein E binding to Aβ Amyloid using a combination of Surface Plasmon Resonance, Immunogold Labeling and Scanning Electron Microscopy
Islam T, Gharibyan AL, Lee CC, Olofsson A
BMC Biotechnol. 19 (1) - [2019-12-00; online 2019-12-11]
Cryo-EM [Collaborative]
DOI Crossref
Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data
Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A
Sci Rep 9 (1) - [2019-12-00; online 2019-02-20]
Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
A microfluidic platform towards automated multiplexed in situ sequencing
Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M
Sci Rep 9 (1) - [2019-12-00; online 2019-03-05]
In Situ Sequencing (ISS) [Service]
DOI Crossref
Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder
Tammimies K, Li D, Rabkina I, ..., Choque-Olsson N, Bölte S
Sci Rep 9 (1) - [2019-12-00; online 2019-07-08]
Bioinformatics Long-term Support WABI [Service]
PubMed DOI Crossref
Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes
Marathe NP, Berglund F, Razavi M, ..., Kristiansson E, Larsson DGJ
Microbiome 7 (1) - [2019-12-00; online 2019-06-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Publisher Correction: Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial
He X, Parenti M, Grip T, ..., Timby N, Slupsky CM
Sci Rep 9 (1) - [2019-12-00; online 2019-08-22]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Polymer gels with tunable ionic Seebeck coefficient for ultra-sensitive printed thermopiles
Zhao D, Martinelli A, Willfahrt A, ..., Fabiano S, Crispin X
Nat Commun 10 (1) - [2019-12-00; online 2019-03-06]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members
Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA
Sci Rep 9 (1) - [2019-12-00; online 2019-12-17]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas
Backman S, Åkerström T, Maharjan R, ..., Hellman P, Björklund P
Sci Rep 9 (1) - [2019-12-00; online 2019-04-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Coro2b, a podocyte protein downregulated in human diabetic nephropathy, is involved in the development of protamine sulphate-induced foot process effacement
Schwarz A, Möller-Hackbarth K, Ebarasi L, ..., Lal M, Patrakka J
Sci Rep 9 (1) - [2019-12-00; online 2019-06-20]
Advanced Light Microscopy (ALM) [Collaborative]
DOI Crossref
A bacterial assay for rapid screening of IAA catabolic enzymes
Brunoni F, Collani S, Šimura J, ..., Bellini C, Ljung K
Plant Methods 15 (1) - [2019-12-00; online 2019-11-04]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Genomic regions of speciation and adaptation among three species of grouse
Kozma R, Rödin-Mörch P, Höglund J
Sci Rep 9 (1) - [2019-12-00; online 2019-01-28]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA
Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA
BMC Evol. Biol. 19 (1) - [2019-12-00; online 2019-06-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Genetic Prediction of Serum 25-Hydroxyvitamin D, Calcium, and Parathyroid Hormone Levels in Relation to Development of Type 2 Diabetes: A Mendelian Randomization Study.
Yuan S, Jiang X, Michaëlsson K, Larsson SC
Diabetes Care 42 (12) 2197-2203 [2019-12-00; online 2019-09-23]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae
Bergman A, Hellgren J, Moritz T, ..., Nielsen J, Chen Y
Microb. Cell Fact. 18 (1) - [2019-12-00; online 2019-02-01]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
Gelali E, Girelli G, Matsumoto M, ..., Crosetto N, Bienko M
Nat Commun 10 (1) - [2019-12-00; online 2019-04-09]
Bioinformatics Support and Infrastructure [Service]
DOI Crossref
Genetic variation in CADM2 as a link between psychological traits and obesity
Morris J, Bailey MES, Baldassarre D, ..., Smith DJ, Strawbridge RJ
Sci Rep 9 (1) - [2019-12-00; online 2019-05-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Angioimmunoblastic T-cell lymphoma and myelodysplastic syndrome with mutations in TET2, DNMT3 and CUX1 - azacitidine induces only lymphoma remission.
Tobiasson M, Pandzic T, Cavelier L, Sander B, Wahlin BE
Leuk. Lymphoma 60 (13) 3316-3319 [2019-12-00; online 2019-06-17]
Clinical Genomics Uppsala [Collaborative]
DOI Crossref
Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce
Nakamura M, Köhler C, Hennig L
BMC Genomics 20 (1) - [2019-12-00; online 2019-12-19]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model
Velie BD, Lillie M, Fegraeus KJ, ..., Strand E, Lindgren G
BMC Genomics 20 (1) - [2019-12-00; online 2019-02-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows
Svensson D, Sjögren R, Sundell D, Sjödin A, Trygg J
BMC Bioinformatics 20 (1) - [2019-12-00; online 2019-10-15]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson ML
Sci Rep 9 (1) - [2019-12-00; online 2019-07-24]
BioImage Informatics [Collaborative] Bioinformatics Support and Infrastructure [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
A Spatiomolecular Map of the Striatum
Märtin A, Calvigioni D, Tzortzi O, ..., Wärnberg E, Meletis K
Cell Rep 29 (13) 4320-4333.e5 [2019-12-00; online 2019-12-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
A Cell-Free Approach Based on Phospholipid Characterization for Determination of the Cell Specific Unbound Drug Fraction (fu,cell)
Treyer A, Walday S, Boriss H, Matsson P, Artursson P
Pharm Res 36 (12) - [2019-12-00; online 2019-11-07]
Drug Discovery and Development (DDD) [Technology development]
DOI Crossref
Growth performance and nutrient removal of a Chlorella vulgaris-Rhizobium sp. co-culture during mixotrophic feed-batch cultivation in synthetic wastewater
Ferro L, Gojkovic Z, Muñoz R, Funk C
Algal Research 44 (-) 101690 [2019-12-00; online 2019-12-00]
Cryo-EM [Service]
DOI Crossref
Influence of urea on methyl $$\upbeta$$β-D-glucopyranoside in alkali at different temperatures
Gunnarsson M, Hasani M, Bernin D
Cellulose 26 (18) 9413-9422 [2019-12-00; online 2019-09-14]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Mycobacterium tuberculosis virulence inhibitors discovered by Mycobacterium marinum high-throughput screening
Tükenmez H, Edström I, Ummanni R, ..., Elofsson M, Larsson C
Sci Rep 9 (1) - [2019-12-00; online 2019-01-10]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-00; online 2019-12-00]
In Situ Sequencing (ISS) [Service]
DOI Crossref
Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 – tracking phylogenetic trajectories with Bayesian inference
Ny S, Sandegren L, Salemi M, Giske CG
Sci Rep 9 (1) - [2019-12-00; online 2019-07-16]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection
Zhao H, Chen M, Valdés A, Lind SB, Pettersson U
BMC Microbiol. 19 (1) - [2019-12-00; online 2019-01-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Inhibition of translation termination by small molecules targeting ribosomal release factors
Ge X, Oliveira A, Hjort K, ..., Sanyal S, Åqvist J
Sci Rep 9 (1) - [2019-12-00; online 2019-10-28]
Drug Discovery and Development (DDD) [Service]
PubMed DOI Crossref
A cell fitness selection model for neuronal survival during development
Wang Y, Wu H, Fontanet P, ..., Hadjab S, Lallemend F
Nat Commun 10 (1) - [2019-12-00; online 2019-09-12]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach
Zan Y, Payen T, Lillie M, ..., Siegel PB, Carlborg Ö
Genet. Sel. Evol. 51 (1) - [2019-12-00; online 2019-08-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment
Schuster J, Laan L, Klar J, ..., Birnir B, Dahl N
Neurobiology of Disease 132 (-) 104583 [2019-12-00; online 2019-12-00]
Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia
Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K
Nat Commun 10 (1) - [2019-12-00; online 2019-04-03]
Chemical Proteomics & Proteogenomics [Technology development] Clinical Genomics Lund [Service]
PubMed DOI Crossref
A Mitochondrial LYR Protein Is Required for Complex I Assembly.
Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW
pmc
Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]
Chemical Proteomics & Proteogenomics [Collaborative]
DOI Crossref
Amyloid fibrils prepared using an acetylated and methyl amidated peptide model of the α-Synuclein NAC 71–82 amino acid stretch contain an additional cross-β structure also found in prion proteins
Näsström T, Andersson PO, Lejon C, Karlsson BCG
Sci Rep 9 (1) - [2019-12-00; online 2019-11-04]
Cryo-EM [Service]
PubMed DOI Crossref
Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden
Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G
Sci Rep 9 (1) - [2019-12-00; online 2019-03-20]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC
Nirwan N, Itoh Y, Singh P, ..., Amunts A, Saikrishnan K
Nat Commun 10 (1) - [2019-12-00; online 2019-07-11]
Cryo-EM [Service]
DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-00; online 2019-12-00]
Bioinformatics Long-term Support WABI [Collaborative]
DOI Crossref
Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm
Moreno-Romero J, Del Toro-De León G, Yadav VK, Santos-González J, Köhler C
Genome Biol. 20 (1) - [2019-12-00; online 2019-02-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model
Kampfraath AA, Klasson L, Anvar SY, ..., Kraaijeveld K, Ellers J
BMC Genomics 20 (1) - [2019-12-00; online 2019-02-06]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden
Bai X, Zhang J, Ambikan A, ..., Xiong Y, Matussek A
Sci Rep 9 (1) - [2019-12-00; online 2019-04-04]
Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Programmed DNA elimination of germline development genes in songbirds.
Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, ..., Forstmeier W, Suh A
pmc
Nat Commun 10 (1) 5468 [2019-11-29; online 2019-11-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells
Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M
Front Immunol 10 (-) - [2019-11-26; online 2019-11-26]
Bioinformatics Support and Infrastructure [Service] Cell Profiling [Collaborative] Chemical Proteomics & Proteogenomics [Technology development]
DOI Crossref
Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media
Raethong N, Wang H, Nielsen J, Vongsangnak W
Computational and Structural Biotechnology Journal 18 (-) 1-8 [2019-11-26]
Systems Biology [Collaborative]
PubMed DOI Crossref
The human secretome
Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å
Sci. Signal. 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]
Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Plasma Profiling [Collaborative]
PubMed DOI Crossref
The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.
Tractenberg RE, Lindvall JM, Attwood TK, Via A
pmc
PLoS ONE 14 (11) e0225256 [2019-11-26; online 2019-11-26]
Bioinformatics Support and Infrastructure [Technology development]
PubMed DOI Crossref
MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M
pmc
iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]
Chemical Proteomics & Proteogenomics [Collaborative]
PubMed DOI Crossref
Evidence that genes involved in hedgehog signaling are associated with both bipolar disorder and high BMI.
Pisanu C, Williams MJ, Ciuculete DM, ..., Squassina A, Schiöth HB
Transl Psychiatry 9 (1) 315 [2019-11-21; online 2019-11-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells.
Čančer M, Drews LF, Bengtsson J, ..., Weishaupt H, Swartling FJ
Cell Death Dis 10 (12) 881 [2019-11-21; online 2019-11-21]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
The Swedish Twin Registry: Content and Management as a Research Infrastructure.
Zagai U, Lichtenstein P, Pedersen NL, Magnusson PKE
Twin Res Hum Genet - (-) 1-9 [2019-11-21; online 2019-11-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.
Stiller C, Aghelpasand H, Frick T, ..., Ahmadian A, Karlström AE
Bioconjug. Chem. 30 (11) 2790-2798 [2019-11-20; online 2019-10-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Interaction between Copper Chaperone Atox1 and Parkinson’s Disease Protein α-Synuclein Includes Metal-Binding Sites and Occurs in Living Cells
Horvath I, Blockhuys S, Šulskis D, ..., Burmann BM, Wittung-Stafshede P
ACS Chem Neurosci 10 (11) 4659-4668 [2019-11-20; online 2019-10-10]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Genetic predisposition to mosaic Y chromosome loss in blood
Thompson DJ, None , Genovese G, ..., None , None
Nature 575 (7784) 652-657 [2019-11-20; online 2019-11-20]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).
Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK
G3 (Bethesda) - (-) - [2019-11-19; online 2019-11-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.
Panula S, Kurek M, Kumar P, ..., Lanner F, Stukenborg JB
Hum. Reprod. - (-) - [2019-11-19; online 2019-11-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.
Meng W, Sjöholm LK, Kononenko O, ..., Rüegg J, Liu Y
Mol. Psychiatry - (-) - [2019-11-19; online 2019-11-19]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors
Xu X, Makaraviciute A, Kumar S, ..., Nyholm L, Zhang Z
Anal. Chem. 91 (22) 14697-14704 [2019-11-19; online 2019-10-25]
Drug Discovery and Development (DDD) [Technology development]
PubMed DOI Crossref
Boldness in Male and Female Zebrafish ( Danio rerio) Is Dependent on Strain and Test.
Mustafa A, Roman E, Winberg S
pmc
Front. Behav. Neurosci. 13 (-) 248 [2019-11-19; online 2019-11-19]
Genome Engineering Zebrafish [Service]
DOI Crossref
A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1–12): Synthesis and NMR Ensemble Analysis of Nisin(1–12) and Analogues
Dickman R, Danelius E, Mitchell SA, ..., Erdélyi M, Tabor AB
Chem. Eur. J. 25 (64) 14572-14582 [2019-11-18; online 2019-10-10]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
The genomic footprint of sexual conflict
Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G
Nat Ecol Evol - (-) - [2019-11-18; online 2019-11-18]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
DOI Crossref
Structure of a mitochondrial ATP synthase with bound native cardiolipin
Mühleip A, McComas SE, Amunts A
Elife 8 (-) - [2019-11-18; online 2019-11-18]
Chemical Proteomics & Proteogenomics [Service] Cryo-EM [Service]
PubMed DOI Crossref
Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions.
Al-Farsi HM, Al-Adwani S, Ahmed S, ..., Giske CG, Bergman P
pmc
Front Microbiol 10 (-) 2632 [2019-11-14; online 2019-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Daytime melatonin levels in saliva are associated with inflammatory markers and anxiety disorders.
Sundberg I, Rasmusson AJ, Ramklint M, ..., Ekselius L, Cunningham JL
Psychoneuroendocrinology - (-) 104514 [2019-11-14; online 2019-11-14]
Bioinformatics Support and Infrastructure [Service]
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Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.
Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K
Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]
Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension
Morikawa M, Mitani Y, Holmborn K, ..., Heldin CH, Miyazono K
Sci. Signal. 12 (607) eaay4430 [2019-11-12; online 2019-11-12]
Genome Engineering Zebrafish [Collaborative]
DOI Crossref
A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels
Van Moerkercke A, Duncan O, Zander M, ..., Millar AH, Van Aken O
Proc Natl Acad Sci USA 116 (46) 23345-23356 [2019-11-12; online 2019-10-29]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
On-demand virtual research environments using microservices
Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O
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Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
PIRIN2 suppresses S‐type lignin accumulation in a noncell‐autonomous manner in Arabidopsis xylem elements
Zhang B, Sztojka B, Escamez S, ..., Boerjan W, Tuominen H
New Phytol - (-) - [2019-11-11; online 2019-11-11]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
Jamy M, Foster R, Barbera P, ..., Bass D, Burki F
Mol Ecol Resour - (-) - [2019-11-09; online 2019-11-09]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Rapid biophysical characterization and NMR structural analysis of small proteins from bacteria and archaea
Kubatova N, Pyper DJ, Jonker HRA, ..., Schmitz-Streit R, Schwalbe H
ChemBioChem - (-) - [2019-11-09; online 2019-11-09]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Carnivores, competition and genetic connectivity in the Anthropocene.
Creel S, Spong G, Becker M, ..., Schiffthaler B, Chifunte C
pmc
Sci Rep 9 (1) 16339 [2019-11-08; online 2019-11-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Cell‐of‐origin determined by both gene expression profiling and immunohistochemistry is the strongest predictor of survival in patients with diffuse large B‐cell lymphoma
Abdulla M, Hollander P, Pandzic T, ..., Rosenquist R, Amini R
Am J Hematol - (-) - [2019-11-07; online 2019-11-07]
Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.
Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M
pmc
Front Microbiol 10 (-) 2579 [2019-11-07; online 2019-11-07]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.
Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL
Viruses 11 (11) - [2019-11-05; online 2019-11-05]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Myc‐dependent endothelial proliferation is controlled by phosphotyrosine 1212 in VEGF  receptor‐2
Testini C, Smith RO, Jin Y, ..., Hellström M, Claesson‐Welsh L
EMBO rep 20 (11) - [2019-11-05; online 2019-09-23]
Chemical Proteomics & Proteogenomics [Service]
An empirical study of the relation between network architecture and complexity
Konuk E, Smith K
ICCV - (-) - [2019-11-05; online 2019-11-05]
PubMed DOI Crossref
Genetic regulation of gene expression and splicing during a 10-year period of human aging.
Balliu B, Durrant M, Goede O, ..., Ingelsson E, Montgomery SB
pmc
Genome Biol. 20 (1) 230 [2019-11-04; online 2019-11-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia
Kosalai ST, Morsy MHA, Papakonstantinou N, ..., Rosenquist R, Kanduri M
Epigenetics 14 (11) 1125-1140 [2019-11-02; online 2019-06-26]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.
Gaetani M, Sabatier P, Saei AA, ..., Lundström SL, Zubarev RA
J. Proteome Res. 18 (11) 4027-4037 [2019-11-01; online 2019-10-14]
Chemical Proteomics & Proteogenomics [Technology development]
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Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.
Melhus H, Michaëlsson K, Larsson SC
J. Clin. Endocrinol. Metab. 104 (11) 5595-5600 [2019-11-01; online 2019-07-17]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
A genomic inference of the White Plymouth Rock genealogy
Guo Y, Lillie M, Zan Y, ..., Siegel PB, Carlborg Ö
Poult. Sci. 98 (11) 5272-5280 [2019-11-01; online 2019-07-15]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.
Marquina D, Esparza-Salas R, Roslin T, Ronquist F
pmc
Mol Ecol Resour 19 (6) 1516-1530 [2019-11-00; online 2019-09-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Diagnostic pitfalls in vitamin B6-dependent epilepsy caused by mutations in the PLPBP gene.
Jensen KV, Frid M, Stödberg T, ..., Darin N, Grønborg S
pmc
JIMD Rep 50 (1) 1-8 [2019-11-00; online 2019-09-30]
Clinical Genomics Stockholm [Service]
DOI Crossref
A revised solid-state NMR method to assess the crystallinity of cellulose
Sparrman T, Svenningsson L, Sahlin-Sjövold K, ..., Westman G, Bernin D
Cellulose 26 (17) 8993-9003 [2019-11-00; online 2019-09-03]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
PIN-driven auxin transport emerged early in streptophyte evolution
Skokan R, Medvecká E, Viaene T, ..., Petrášek J, Friml J
NPLANTS 5 (11) 1114-1119 [2019-11-00; online 2019-11-11]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Influence of blue mussel (Mytilus edulis) intake on fatty acid composition in erythrocytes and plasma phospholipids and serum metabolites in women with rheumatoid arthritis
Lindqvist HM, Gjertsson I, Andersson S, Calder PC, Bärebring L
Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 150 (-) 7-15 [2019-11-00; online 2019-11-00]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Leveraging European infrastructures to access 1 million human genomes by 2022.
Saunders G, Baudis M, Becker R, ..., Blomberg N, Scollen S
Nat. Rev. Genet. 20 (11) 693-701 [2019-11-00; online 2019-08-27]
Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area
Nilsson LKJ, de Oliveira MR, Marinotti O, ..., de Souza AQL, Terenius O
Microb Ecol 78 (4) 781-791 [2019-11-00; online 2019-04-15]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching
Gustavsson E, Isaksson L, Persson C, ..., Orekhov V, Westenhoff S
Biophysical Journal - (-) - [2019-11-00; online 2019-11-00]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Mass transport during coagulation of cellulose-ionic liquid solutions in different non-solvents
Hedlund A, Theliander H, Köhnke T
Cellulose 26 (16) 8525-8541 [2019-11-00; online 2019-08-19]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.
Papoutsoglou G, Lagani V, Schmidt A, ..., Tegnér J, Tsamardinos I
Cytometry A 95 (11) 1178-1190 [2019-11-00; online 2019-11-06]
Mass Cytometry [Service]
DOI Crossref
Electrochemical Evaluation of a Napthalene Diimide Derivative for Potential Application in Aqueous Organic Redox Flow Batteries
Wiberg C, Owusu F, Wang E, Ahlberg E
Energy Technol. 7 (11) 1900843 [2019-11-00; online 2019-08-23]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning
Ossinger A, Bajic A, Pan S, ..., Hailer NP, Schizas N
Journal of Neuroscience Methods - (-) 108522 [2019-11-00; online 2019-11-00]
BioImage Informatics [Service]
DOI Crossref
Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Dobie R, Wilson-Kanamori JR, Henderson BEP, ..., Marioni JC, Henderson NC
Cell Rep 29 (7) 1832-1847.e8 [2019-11-00; online 2019-11-00]
Eukaryotic Single Cell Genomics (ESCG) [Service]
DOI Crossref
Genetic differentiation between and within ecotypes of pike ( Esox lucius ) in the Baltic Sea
Nordahl O, Koch‐Schmidt P, Sunde J, ..., Forsman A, Larsson P
Aquatic Conserv: Mar Freshw Ecosyst 29 (11) 1923-1935 [2019-11-00; online 2019-08-16]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy
Čančer M, Hutter S, Holmberg KO, ..., Weishaupt H, Swartling FJ
Cell Stem Cell - (-) - [2019-11-00; online 2019-11-00]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
A revised solid-state NMR method to assess the crystallinity of cellulose
Sparrman T, Svenningsson L, Sahlin-Sjövold K, ..., Westman G, Bernin D
Cellulose 26 (17) 8993-9003 [2019-11-00; online 2019-09-03]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Tuning drug release from polyoxazoline-drug conjugates
Harris JM, Bentley MD, Moreadith RW, ..., Dizman B, Nordstierna L
European Polymer Journal 120 (-) 109241 [2019-11-00; online 2019-11-00]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.
Stjelja S, Fogelqvist J, Tellgren-Roth C, Dixelius C
pmc
Sci Rep 9 (1) 15753 [2019-10-31; online 2019-10-31]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Associations of autozygosity with a broad range of human phenotypes.
Clark DW, Okada Y, Moore KHS, ..., Kubo M, Wilson JF
pmc
Nat Commun 10 (1) 4957 [2019-10-31; online 2019-10-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Perspective on CETSA Literature: Toward More Quantitative Data Interpretation
Seashore-Ludlow B, Axelsson H, Lundbäck T
SLAS DISCOVERY: Advancing Life Sciences R&D - (-) 247255521988452 [2019-10-30; online 2019-10-30]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation.
Cook NL, Pjanic M, Emmerich AG, ..., Castillejo-López C, Ingelsson E
pmc
BMC Endocr Disord 19 (1) 115 [2019-10-29; online 2019-10-29]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
High-grade progression confers poor survival in pancreatic neuroendocrine tumors.
Botling J, Lamarca A, Bajic D, ..., Skogseid B, Crona J
Neuroendocrinology - (-) - [2019-10-29; online 2019-10-29]
Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540.
Tiukova IA, Jiang H, Dainat J, ..., Gu Z, Passoth V
Microorganisms 7 (11) - [2019-10-26; online 2019-10-26]
Bioinformatics Support and Infrastructure [Service]
PubMed DOI Crossref
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
Eur. J. Hum. Genet. - (-) - [2019-10-25; online 2019-10-25]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
Pettersson ME, Rochus CM, Han F, ..., Folkvord A, Andersson L
Genome Res. - (-) - [2019-10-24; online 2019-10-24]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Mining the Proteome Associated with Rheumatic and Autoimmune Diseases.
Ruiz-Romero C, Lam MPY, Nilsson P, ..., Watt FE, Blanco FJ
J. Proteome Res. - (-) - [2019-10-23; online 2019-10-23]
Autoimmunity Profiling [Technology development]
DOI Crossref
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 - (-) 1-10 [2019-10-22; online 2019-10-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative]
DOI Crossref
Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity
Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR
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Bioinformatics Support and Infrastructure [Service]
DOI Crossref
Genetic architecture of subcortical brain structures in 38,851 individuals
Satizabal CL, Adams HHH, Hibar DP, ..., Seshadri S, Ikram MA
Nat Genet - (-) - [2019-10-21; online 2019-10-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.
Saremi NF, Supple MA, Byrne A, ..., Wilmers CC, Shapiro B
pmc
Nat Commun 10 (1) 4769 [2019-10-18; online 2019-10-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State
Diab J, Hansen T, Goll R, ..., Florholmen J, Forsdahl G
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Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
The SH3 domains of the protein kinases ITK and LCK compete for adjacent sites on T cell–specific adapter protein
Andersen TCB, Kristiansen PE, Huszenicza Z, ..., Andreotti AH, Spurkland A
J. Biol. Chem. 294 (42) 15480-15494 [2019-10-18; online 2019-09-04]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Considerations and Implications in the Purification of Extracellular Vesicles – A Cautionary Tale
Lee YXF, Johansson H, Wood MJA, El Andaloussi S
Front. Neurosci. 13 (-) - [2019-10-18; online 2019-10-18]
Chemical Proteomics & Proteogenomics [Service]
DOI Crossref
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
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Bioinformatics Support and Infrastructure [Collaborative]
PubMed DOI Crossref
Whole‐genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation
Paulsson JO, Backman S, Wang N, ..., Zedenius J, Juhlin CC
J. Pathol - (-) - [2019-10-17; online 2019-10-17]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Microbe-host interplay in atopic dermatitis and psoriasis.
Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H
pmc
Nat Commun 10 (1) 4703 [2019-10-16; online 2019-10-16]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Root distribution in intercropping systems – a comparison of DNA based methods and visual distinction of roots
Hassan A, Dresbøll DB, Rasmussen CR, ..., Lund OS, Thorup-Kristensen K
Archives of Agronomy and Soil Science - (-) 1-14 [2019-10-16; online 2019-10-16]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.
Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, ..., Engblom S, Dopson M
pmc
Sci Data 6 (1) 207 [2019-10-16; online 2019-10-16]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.
Björn N, Sigurgeirsson B, Svedberg A, ..., Lundeberg J, Gréen H
Pharmacogenomics J. - (-) - [2019-10-15; online 2019-10-15]
Bioinformatics Support and Infrastructure [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
CSF levels of apolipoprotein C1 and autotaxin found to associate with neuropathic pain and fibromyalgia.
Lind AL, Just D, Mikus M, ..., Gordh T, Månberg A
pmc
J Pain Res 12 (-) 2875-2889 [2019-10-15; online 2019-10-15]
Plasma Profiling [Collaborative]
PubMed DOI Crossref
Associations Between Attention-Deficit/Hyperactivity Disorder and Various Eating Disorders: A Swedish Nationwide Population Study Using Multiple Genetically Informative Approaches.
Yao S, Kuja-Halkola R, Martin J, ..., Bulik CM, Larsson H
Biol. Psychiatry 86 (8) 577-586 [2019-10-15; online 2019-05-15]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Monitoring of Protein Biomarkers of Inflammation in Human Traumatic Brain Injury Using Microdialysis and Proximity Extension Assay Technology in Neurointensive Care.
Dyhrfort P, Shen Q, Clausen F, ..., Lewén A, Hillered L
pmc
J. Neurotrauma 36 (20) 2872-2885 [2019-10-15; online 2019-06-17]
PLA and Single Cell Proteomics [Technology development]
DOI Crossref
Dynamic Nanocellulose Networks for Thermoset-like yet Recyclable Plastics with a High Melt Stiffness and Creep Resistance
Peterson A, Östergren I, Lotsari A, ..., Boldizar A, Müller C
Biomacromolecules 20 (10) 3924-3932 [2019-10-14; online 2019-09-17]
Cryo-EM [Service]
DOI Crossref
N-Trifluoromethylthiolated Sulfonimidamides and Sulfoximines: Anti-microbial, Anti-mycobacterial, and Cytotoxic Activity
Thota N, Makam P, Rajbongshi KK, ..., Naicker T, Arvidsson PI
ACS Med Chem Lett 10 (10) 1457-1461 [2019-10-10; online 2019-09-11]
Drug Discovery and Development (DDD) [Technology development]
DOI Crossref
Apolipoprotein E impairs amyloid‐β fibril elongation and maturation
Islam T, Gharibyan AL, Golchin SA, ..., Olofsson L, Olofsson A
FEBS J - (-) - [2019-10-09; online 2019-10-09]
Cryo-EM [Service]
DOI Crossref
SynQuant: an automatic tool to quantify synapses from microscopy images
Wang Y, Wang C, Ranefall P, ..., Tian L, Yu G
- - (-) - [2019-10-09; online 2019-10-09]
BioImage Informatics [Collaborative]
DOI Crossref
The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon
Malmström H, Günther T, Svensson EM, ..., Storå J, Jakobsson M
Proc. R. Soc. B 286 (1912) 20191528 [2019-10-09; online 2019-10-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Intracrystalline Transport Barriers Affecting the Self-Diffusion of CH4 in Zeolites |Na12|-A and |Na12–xKx|-A
Hedin N, Rzepka P, Jasso-Salcedo AB, Church TL, Bernin D
Langmuir 35 (40) 12971-12978 [2019-10-08; online 2019-09-11]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Along the Indian Ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion.
Semo A, Gayà-Vidal M, Fortes-Lima C, ..., Schlebusch C, Rocha J
Mol. Biol. Evol. - (-) - [2019-10-08; online 2019-10-08]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Reduced sialyl-Lewis x on salivary MUC7 from patients with burning mouth syndrome.
Acharya S, Jin C, Bylund J, ..., Carlén A, Karlsson NG
Mol Omics 15 (5) 331-339 [2019-10-07; online 2019-08-16]
PLA and Single Cell Proteomics [Collaborative]
PubMed DOI Crossref
Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.
Nascimento FJA, Dahl M, Deyanova D, ..., Creer S, Gullström M
pmc
Commun Biol 2 (-) 362 [2019-10-04; online 2019-10-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.
Tin A, Marten J, Halperin Kuhns VL, ..., Vitart V, Köttgen A
Nat. Genet. - (-) - [2019-10-02; online 2019-10-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee.
Jones JC, Wallberg A, Christmas MJ, Kapheim KM, Webster MT
Mol. Biol. Evol. 36 (10) 2277-2291 [2019-10-01; online 2019-05-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.
Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N
pmc
Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]
Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Interoperable and scalable data analysis with microservices: applications in metabolomics
Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O
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Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates
Debiais-Thibaud M, Simion P, Ventéo S, ..., Mazan S, Haitina T
- 36 (10) 2265-2276 [2019-10-01; online 2019-07-04]
Genome Engineering Zebrafish [Service]
DOI Crossref
Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities
Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N
Water Research 162 (-) 437-445 [2019-10-00; online 2019-10-00]
Systems Biology [Collaborative]
DOI Crossref
Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation
Castillejo-Lopez C, Pjanic M, Pirona AC, ..., Arner E, Ingelsson E
iScience 20 (-) 42-59 [2019-10-00; online 2019-10-00]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Genetic basis and timing of a major mating system shift in Capsella
Bachmann JA, Tedder A, Laenen B, ..., Castric V, Slotte T
New Phytol 224 (1) 505-517 [2019-10-00; online 2019-08-00]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra)
Papazian S, Girdwood T, Wessels BA, ..., Moritz T, Albrectsen BR
Metabolomics 15 (10) - [2019-10-00; online 2019-09-28]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Real time MRI to elucidate the functionality of coating films intended for modified release
Bernin D, Marucci M, Boissier C, ..., Olsson U, Abrahmsén-Alami S
Journal of Controlled Release 311-312 (-) 117-124 [2019-10-00; online 2019-10-00]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Molecular characterization of particulate organic matter in full scale anaerobic digesters: An NMR spectroscopy study
Shakeri Yekta S, Hedenström M, Svensson BH, ..., Hertkorn N, Björn A
Science of The Total Environment 685 (-) 1107-1115 [2019-10-00; online 2019-10-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Cell generation dynamics underlying naive T-cell homeostasis in adult humans.
Mold JE, Réu P, Olin A, ..., Brodin P, Frisén J
PLoS Biol. 17 (10) e3000383 [2019-10-00; online 2019-10-29]
Mass Cytometry [Collaborative]
PubMed DOI Crossref
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.
Cappellini E, Welker F, Pandolfi L, ..., Lordkipanidze D, Willerslev E
Nature 574 (7776) 103-107 [2019-10-00; online 2019-09-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species
Kurland S, Wheat CW, Paz Celorio Mancera M, ..., Ryman N, Laikre L
Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]
Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Whole genome sequencing of apparently mutation-negative MEN1 patients
Backman S, Bajic D, Crona J, ..., Skogseid B, Stålberg P
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Bioinformatics Support and Infrastructure [Service]
DOI Crossref
Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality
Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A
Experimental Cell Research 383 (1) 111469 [2019-10-00; online 2019-10-00]
Bioinformatics Long-term Support WABI [Service]
DOI Crossref
Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A
Wehrli PM, Uzelac I, Olsson T, ..., Tietze D, Gottfries J
Bioorganic & Medicinal Chemistry 27 (19) 115043 [2019-10-00; online 2019-10-00]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A
Wehrli PM, Uzelac I, Olsson T, ..., Tietze D, Gottfries J
Bioorganic & Medicinal Chemistry 27 (19) 115043 [2019-10-00; online 2019-10-00]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
DOI Crossref
Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus
Odqvist L, Jevnikar Z, Riise R, ..., Collins B, Vaarala O
Ann Rheum Dis 78 (10) 1363-1370 [2019-10-00; online 2019-07-12]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer
Svedlund J, Strell C, Qian X, ..., Sieuwerts AM, Nilsson M
EBioMedicine 48 (-) 212-223 [2019-10-00; online 2019-10-00]
In Situ Sequencing (ISS) [Service]
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Endocytic pathway of vascular cell adhesion molecule 1 in human umbilical vein endothelial cell identified in vitro by using functionalized nontoxic fluorescent quantum dots
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Sensors and Actuators B: Chemical 297 (-) 126702 [2019-10-00; online 2019-10-00]
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Distribution of bacteria between different milk fractions, investigated using culture‐dependent methods and molecular‐based and fluorescent microscopy approaches
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J Appl Microbiol 127 (4) 1028-1037 [2019-10-00; online 2019-07-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL
pmc mid
Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.
Schweizer M, Warmuth VM, Alaei Kakhki N, ..., Suh A, Burri R
Mol. Phylogenet. Evol. 139 (-) 106568 [2019-10-00; online 2019-07-23]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service]
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A clonal expression biomarker associates with lung cancer mortality.
Biswas D, Birkbak NJ, Rosenthal R, ..., Swanton C, TRACERx Consortium
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Clinical Genomics Uppsala [Collaborative]
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Fam83F induces p53 stabilisation and promotes its activity.
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Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.
Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C
Cancer Med - (-) - [2019-09-30; online 2019-09-30]
Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Prognostic Impact of BRAF and KRAS Mutation in Patients with Colorectal and Appendiceal Peritoneal Metastases Scheduled for CRS and HIPEC.
Graf W, Cashin PH, Ghanipour L, ..., Terman A, Birgisson H
Ann. Surg. Oncol. - (-) - [2019-09-30; online 2019-09-30]
Clinical Genomics Uppsala [Collaborative]
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Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole.
Rodriguez-Furlan C, Domozych D, Qian W, ..., Raikhel NV, Hicks GR
Proc. Natl. Acad. Sci. U.S.A. - (-) - [2019-09-30; online 2019-09-30]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.
Dussex N, von Seth J, Knapp M, ..., Robertson BC, Dalén L
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Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]
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Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression.
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Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.
Seyfferth C, Wessels BA, Gorzsás A, ..., Sundberg B, Felten J
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Front Plant Sci 10 (-) 1101 [2019-09-26; online 2019-09-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.
Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C
pmc GEO
Elife 8 (-) - [2019-09-25; online 2019-09-25]
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Discovery of Novel Sequences in 1,000 Swedish Genomes.
Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A
Mol. Biol. Evol. - (-) - [2019-09-24; online 2019-09-24]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.
Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A
Blood Adv 3 (18) 2722-2731 [2019-09-24; online 2019-09-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186.
Kvarnung M, Shahsavani M, Taylan F, ..., Lindstrand A, Falk A
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Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186
Kvarnung M, Shahsavani M, Taylan F, ..., Lindstrand A, Falk A
Front Genet 10 (-) - [2019-09-24; online 2019-09-24]
NGI Uppsala (Uppsala Genome Center) [Service]
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Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development
Johansson MM, Pottmeier P, Suciu P, ..., Peuckert C, Jazin E
Front Genet 10 (-) - [2019-09-24; online 2019-09-24]
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IGEMS: The Consortium on Interplay of Genes and Environment Across Multiple Studies - An Update.
Pedersen NL, Gatz M, Finch BK, ..., Sachdev P, Whitfield KE
Twin Res Hum Genet - (-) 1-8 [2019-09-23; online 2019-09-23]
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Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes.
Boström AE, Chatzittofis A, Ciuculete DM, ..., Schiöth HB, Jokinen J
Epigenetics - (-) 1-16 [2019-09-22; online 2019-09-22]
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Microwave Synthesis of Alkali-Free Hexaniobate, Decaniobate, and Hexatantalate Polyoxometalate Ions
Rambaran MA, Pascual-Borràs M, Ohlin CA
Eur. J. Inorg. Chem. 2019 (35) 3913-3918 [2019-09-22; online 2019-09-05]
Swedish NMR Centre (SNC) [Service]
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The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity.
Papoutsoglou P, Tsubakihara Y, Caja L, ..., Heldin CH, Moustakas A
Cell Rep 28 (12) 3182-3198.e11 [2019-09-17; online 2019-09-19]
NGI Uppsala (Uppsala Genome Center) [Service]
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Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method
Rajan SK, Lindqvist M, Brummer RJ, Schoultz I, Repsilber D
PLoS ONE 14 (9) e0222171 [2019-09-17; online 2019-09-17]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341.
Nilsson E, Li K, Fridlund J, ..., Pinhassi J, Holmfeldt K
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Appl. Environ. Microbiol. 85 (18) - [2019-09-15; online 2019-08-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Anticancer effect of deuterium depleted water - redox disbalance leads to oxidative stress.
Zhang X, Gaetani M, Chernobrovkin A, Zubarev RA
Mol. Cell Proteomics - (-) - [2019-09-13; online 2019-09-13]
Chemical Proteomics & Proteogenomics [Collaborative]
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A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection.
Poux C, Dondalska A, Bergenstråhle J, ..., Tregoning JS, Spetz AL
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Front Immunol 10 (-) 2161 [2019-09-12; online 2019-09-12]
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Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture
Reddy HK, Carroni M, Hajdu J, Svenda M
Elife 8 (-) - [2019-09-12; online 2019-09-12]
Cryo-EM [Service]
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Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.
Teumer A, Li Y, Ghasemi S, ..., Pattaro C, Köttgen A
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Nat Commun 10 (1) 4130 [2019-09-11; online 2019-09-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota
Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C
MBio 10 (5) - [2019-09-10; online 2019-09-10]
Bioinformatics Support and Infrastructure [Collaborative]
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Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin
Hill J, Enbody ED, Pettersson ME, ..., Scheerer P, Andersson L
Proc Natl Acad Sci USA 116 (37) 18473-18478 [2019-09-10; online 2019-08-26]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
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Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease.
Stahel P, Nahmias A, Sud SK, ..., Batterham RL, Dash S
Diabetes - (-) - [2019-09-10; online 2019-09-10]
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Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status.
Das I, Wilhelm M, Höiom V, ..., Tuominen R, Egyhàzi Brage S
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Cell Death Dis 10 (9) 663 [2019-09-10; online 2019-09-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome
Milon N, Chantry-Darmon C, Satge C, ..., Bergès H, Bancaud A
Nucleic Acids Res 47 (15) 8050-8060 [2019-09-05; online 2019-07-25]
NGI Uppsala (Uppsala Genome Center) [Service]
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Chemical screening pipeline for identification of specific plant autophagy modulators
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Plant Physiol. - (-) pp.00647.2019 [2019-09-05; online 2019-09-05]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.
Pederson ERA, Warshan D, Rasmussen U
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G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]
Bioinformatics Support and Infrastructure [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Associations of Smoking and Alcohol and Coffee Intake with Fracture and Bone Mineral Density: A Mendelian Randomization Study.
Yuan S, Michaëlsson K, Wan Z, Larsson SC
Calcif. Tissue Int. - (-) - [2019-09-04; online 2019-09-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Association of Use of the Neonatal Early-Onset Sepsis Calculator With Reduction in Antibiotic Therapy and Safety: A Systematic Review and Meta-analysis.
Achten NB, Klingenberg C, Benitz WE, ..., van Rossum AMC, Plötz FB
JAMA Pediatr - (-) - [2019-09-03; online 2019-09-03]
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Genetic variance of metabolomic features and their relationship with body weight and body weight gain in Holstein cattle
Aliakbari A, Ehsani A, Vaez Torshizi R, ..., Jensen J, Sarup P
J. Anim. Sci. 97 (9) 3832-3844 [2019-09-03; online 2019-07-05]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.
Happel EM, Markussen T, Teikari JE, ..., Kisand V, Riemann L
FEMS Microbiol. Ecol. 95 (9) - [2019-09-01; online 2019-08-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
The autoantibody response to cyclic citrullinated collagen type II peptides in rheumatoid arthritis.
Liang B, Ge C, Lönnblom E, ..., Zhao M, Holmdahl R
Rheumatology (Oxford) 58 (9) 1623-1633 [2019-09-01; online 2019-03-21]
Autoimmunity Profiling [Service]
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Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.
Höök L, Leal L, Talla V, Backström N
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Genome Biol Evol 11 (9) 2633-2652 [2019-09-01; online 2019-08-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.
Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, ..., Jeffares DC, Wolf JBW
pmc
Mol. Biol. Evol. 36 (9) 1975-1989 [2019-09-01; online 2019-06-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Targeted ultra-deep sequencing of a South African Bantu-speaking cohort to comprehensively map and characterize common and novel variants in 65 pharmacologically-related genes.
Tshabalala S, Choudhury A, Beeton-Kempen N, ..., Ramsay M, Mancama D
pmc mid
Pharmacogenet. Genomics 29 (7) 167-178 [2019-09-00; online 2019-06-05]
NGI Uppsala (Uppsala Genome Center) [Service]
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A simultaneous assessment of organic matter and trace elements bio-accessibility in substrate and digestate from an anaerobic digestion plant
Laera A, Shakeri Yekta S, Hedenström M, ..., Esposito G, van Hullebusch ED
Bioresource Technology 288 (-) 121587 [2019-09-00; online 2019-09-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.
Karlsson CMG, Cerro-Gálvez E, Lundin D, ..., Vila-Costa M, Pinhassi J
pmc GENBANK
Microb Biotechnol 12 (5) 892-906 [2019-09-00; online 2019-07-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Multiplexed analysis of the secretin-like GPCR-RAMP interactome.
Lorenzen E, Dodig-Crnković T, Kotliar IB, ..., Schwenk JM, Sakmar TP
pmc
Sci Adv 5 (9) eaaw2778 [2019-09-00; online 2019-09-18]
Plasma Profiling [Collaborative]
DOI Crossref
A link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying blaSHV-12 from horses in Sweden
Börjesson S, Greko C, Myrenås M, ..., Nilsson O, Pedersen K
Journal of Global Antimicrobial Resistance - (-) - [2019-09-00; online 2019-09-00]
Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Whole exome sequencing identifies novel variant underlying hereditary spastic paraplegia in consanguineous Pakistani families.
Zulfiqar S, Tariq M, Ali Z, ..., Dahl N, Baig SM
J Clin Neurosci 67 (-) 19-23 [2019-09-00; online 2019-07-04]
NGI Uppsala (Uppsala Genome Center) [Service]
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Impact of demography on linked selection in two outcrossing Brassicaceae species
Mattila TM, Laenen B, Horvath R, ..., Savolainen O, Slotte T
Ecol Evol 9 (17) 9532-9545 [2019-09-00; online 2019-08-13]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
FLT3N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis
Hyrenius-Wittsten A, Pilheden M, Falqués-Costa A, ..., Järås M, Hagström-Andersson AK
Leukemia 33 (9) 2310-2314 [2019-09-00; online 2019-04-05]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.
Morais EB, Schönenberger J, Conti E, Antonelli A, Szövényi P
pmc
Appl Plant Sci 7 (9) e11290 [2019-09-00; online 2019-09-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Fast time-resolved NMR with non-uniform sampling
Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K
Progress in Nuclear Magnetic Resonance Spectroscopy - (-) - [2019-09-00; online 2019-09-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Copy number variation and neuropsychiatric problems in females and males in the general population.
Martin J, Tammimies K, Karlsson R, ..., Lichtenstein P, Magnusson PKE
Am. J. Med. Genet. B Neuropsychiatr. Genet. 180 (6) 341-350 [2019-09-00; online 2018-10-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Dimerization of 9,10-anthraquinone-2,7-Disulfonic acid (AQDS)
Wiberg C, Carney TJ, Brushett F, Ahlberg E, Wang E
Electrochimica Acta 317 (-) 478-485 [2019-09-00; online 2019-09-00]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.
Ganna A, Verweij KJH, Nivard MG, ..., Neale BM, Zietsch BP
Science 365 (6456) - [2019-08-30; online 2019-08-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
MiDRM pol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors.
Aralaguppe SG, Ambikan AT, Ashokkumar M, ..., Sönnerborg A, Neogi U
pmc
Viruses 11 (9) - [2019-08-30; online 2019-08-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Neuroticism as a predictor of frailty in old age: a genetically informative approach.
Danielsdottir HB, Jylhävä J, Hägg S, ..., Mosing MA, Lehto K
Psychosom Med - (-) - [2019-08-28; online 2019-08-28]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC
Reimegård J, Danielsson M, Tarbier M, ..., Friedländer MR, Gallant CJ
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PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology.
Lázaro-Ibáñez E, Lässer C, Shelke GV, ..., García-Rodríguez A, Lötvall J
pmc
J Extracell Vesicles 8 (1) 1656993 [2019-08-27; online 2019-08-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Profiling surface proteins on individual exosomes using a proximity barcoding assay.
Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M
pmc
Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]
PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.
Marquardt N, Kekäläinen E, Chen P, ..., Ljunggren HG, Michaëlsson J
pmc
Nat Commun 10 (1) 3841 [2019-08-26; online 2019-08-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
In search of causal pathways in diabetes: a study using proteomics and genotyping data from a cross-sectional study.
Beijer K, Nowak C, Sundström J, ..., Fall T, Lind L
Diabetologia - (-) - [2019-08-24; online 2019-08-24]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF.
Pin E, Sjöberg R, Andersson E, ..., Nilsson P, Månberg A
Methods Mol. Biol. 2044 (-) 303-318 [2019-08-23; online 2019-08-23]
Autoimmunity Profiling [Technology development]
PubMed DOI Crossref
Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk.
Tengvall K, Huang J, Hellström C, ..., Olsson T, Kockum I
pmc
Proc. Natl. Acad. Sci. U.S.A. 116 (34) 16955-16960 [2019-08-20; online 2019-08-02]
Autoimmunity Profiling [Collaborative]
PubMed DOI Crossref
Genome-wide systematic identification of methyltransferase recognition and modification patterns.
Jensen TØ, Tellgren-Roth C, Redl S, ..., Pedersen LE, Nielsen AT
pmc
Nat Commun 10 (1) 3311 [2019-08-19; online 2019-08-19]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.
Fernandes SJ, Morikawa H, Ewing E, ..., Tegnér J, Gomez-Cabrero D
pmc
Sci Rep 9 (1) 11996 [2019-08-19; online 2019-08-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Complete Genome Sequence of Hydrocarbon-Degrading Halotolerant Acinetobacter radioresistens DD78, Isolated from the Aconcagua River Mouth in Central Chile.
Macaya CC, Méndez V, Durán RE, ..., Moore ERB, Seeger M
Microbiol Resour Announc 8 (33) - [2019-08-15; online 2019-08-15]
NGI Uppsala (Uppsala Genome Center) [Service]
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Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.
Lopez-Fernandez M, Broman E, Simone D, Bertilsson S, Dopson M
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MBio 10 (4) - [2019-08-13; online 2019-08-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Nucleation of an Activating Conformational Change by a Cation−π Interaction
Rogne P, Andersson D, Grundström C, ..., Linusson A, Wolf-Watz M
Biochemistry 58 (32) 3408-3412 [2019-08-13; online 2019-07-24]
Swedish NMR Centre (SNC) [Service]
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Functional Identification of Target by Expression Proteomics (FITExP)
Gaetani M, Zubarev RA
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Chemical Proteomics & Proteogenomics [Technology development]
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The bio.tools registry of software tools and data resources for the life sciences.
Ison J, Ienasescu H, Chmura P, ..., Løngreen P, Brunak S
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Genome Biol. 20 (1) 164 [2019-08-12; online 2019-08-12]
Bioinformatics Support and Infrastructure [Collaborative]
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PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.
Costa TDF, Zhuang T, Lorent J, ..., Defilippi P, Strömblad S
pmc
Nat Commun 10 (1) 3589 [2019-08-09; online 2019-08-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species
Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N
Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Selective Enrichment of Phosphorylated Peptides by Monolithic Polymers Surface Imprinted with bis-Imidazolium Moieties by UV-Initiated Cryopolymerization
Liu M, Torsetnes SB, Wierzbicka C, ..., Sellergren B, Irgum K
Anal. Chem. 91 (15) 10188-10196 [2019-08-06; online 2019-06-25]
Swedish NMR Centre (SNC) [Service]
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Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.
Glanville KP, Coleman JRI, Hanscombe KB, ..., O'Reilly PF, Lewis CM
Biol. Psychiatry - (-) - [2019-08-05; online 2019-08-05]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Gene Flow in the Müllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves).
Garg KM, Sam K, Chattopadhyay B, ..., Ericson PGP, Rheindt FE
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Genome Biol Evol 11 (8) 2332-2343 [2019-08-01; online 2019-08-17]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells.
Amaral PP, Engström PG, Robson SC, ..., Kouzarides T, Castelo-Branco G
Exp. Cell Res. 381 (1) 129-138 [2019-08-01; online 2019-05-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
The Critical Role of Dysregulated RhoB Signaling Pathway in Radioresistance of Colorectal Cancer.
Liu N, Cui W, Jiang X, ..., Wang X, Sun XF
Int. J. Radiat. Oncol. Biol. Phys. 104 (5) 1153-1164 [2019-08-01; online 2019-04-27]
Mass Cytometry [Service]
PubMed DOI Crossref
Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.
Herlemann DPR, Markert S, Meeske C, ..., Jürgens K, Schweder T
pmc
Appl. Environ. Microbiol. 85 (15) - [2019-08-01; online 2019-07-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells
Li H, Lim HC, Zacharaki D, ..., Hansson J, Scheding S
Haematologica - (-) haematol.2019.216648 [2019-08-01; online 2019-08-01]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.
Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Ekström TJ
pmc
EBioMedicine 46 (-) 290-304 [2019-08-00; online 2019-07-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Viral mimetic priming enhances α-synuclein-induced degeneration: Implications for Parkinson’s disease
Olsen LK, Cairns AG, Ådén J, ..., Dowd E, McKernan DP
Brain, Behavior, and Immunity 80 (-) 525-535 [2019-08-00; online 2019-08-00]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.
von Holst S, Jiao X, Liu W, ..., Bryant P, Lindblom A
Eur. J. Hum. Genet. 27 (8) 1286-1295 [2019-08-00; online 2019-04-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.
Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA
pmc GENBANK
Mol. Ecol. 28 (16) 3813-3829 [2019-08-00; online 2019-09-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.
Kawakami T, Wallberg A, Olsson A, ..., Rundlöf M, Webster MT
pmc
Genetics 212 (4) 1101-1119 [2019-08-00; online 2019-05-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.
Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M
Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
In-hospital metabolite changes in infective endocarditis—a longitudinal 1H NMR-based study
Klein CF, Holle SLK, Andersen MH, ..., Iversen KK, Malmendal A
Eur J Clin Microbiol Infect Dis 38 (8) 1553-1560 [2019-08-00; online 2019-05-22]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
A role for the auxin precursor anthranilic acid in root gravitropism via regulation of PIN ‐ FORMED protein polarity and relocalisation in Arabidopsis
Doyle SM, Rigal A, Grones P, ..., Novák O, Robert S
New Phytol 223 (3) 1420-1432 [2019-08-00; online 2019-06-07]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Molecular insights into hypomineralized enamel
Malmberg P, Norén JG, Bernin D
Eur J Oral Sci 127 (4) 340-346 [2019-08-00; online 2019-04-29]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Reply to "CRISPR screens are feasible in TP53 wild-type cells".
Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J
pmc
Mol. Syst. Biol. 15 (8) e9059 [2019-08-00; online 2019-08-30]
High-throughput Genome Engineering (HTGE) [Collaborative]
PubMed DOI Crossref
Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades
Hiltunen M, Grudzinska-Sterno M, Wallerman O, Ryberg M, Johannesson H
Current Biology 29 (16) 2758-2765.e6 [2019-08-00; online 2019-08-00]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma.
Mohlin S, Hansson K, Radke K, ..., von Stedingk K, Bexell D
pmc GEO
EMBO Mol Med 11 (8) e10058 [2019-08-00; online 2019-07-16]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Early activating somatic PIK3CA mutations promote ectopic muscle development and upper limb overgrowth.
Frisk S, Taylan F, Blaszczyk I, ..., Laurell T, Nordgren A
pmc
Clin. Genet. 96 (2) 118-125 [2019-08-00; online 2019-05-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
31° South: The physiology of adaptation to arid conditions in a passerine bird.
Ribeiro ÂM, Puetz L, Pattinson NB, ..., Smit B, Gilbert MTP
GENBANK
Mol. Ecol. 28 (16) 3709-3721 [2019-08-00; online 2019-08-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures
Segura JH, Nilsson MB, Schleucher J, ..., Bertilsson S, Öquist MG
Soil Biology and Biochemistry 135 (-) 438-448 [2019-08-00; online 2019-08-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Goodbye reference, hello genome graphs.
Ameur A
Nat. Biotechnol. 37 (8) 866-868 [2019-08-00; online 2019-08-04]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Systematic Development of Sandwich Immunoassays for the Plasma Secretome.
Häussler RS, Bendes A, Iglesias M, ..., Qundos U, Schwenk JM
Proteomics 19 (15) e1900008 [2019-08-00; online 2019-07-22]
Plasma Profiling [Technology development]
DOI Crossref
Joint Image Deconvolution and Separation Using Mixed Dictionaries
Siadat M, Aghazadeh N, Akbarifard F, Brismar H, Oktem O
IEEE Trans. on Image Process. 28 (8) 3936-3945 [2019-08-00; online 2019-08-00]
Advanced Light Microscopy (ALM) [Service]
DOI Crossref
Boreal tree species affect soil organic matter composition and saprotrophic mineralization rates
Segura JH, Nilsson MB, Sparrman T, ..., Tolu J, Öquist MG
Plant Soil 441 (1-2) 173-190 [2019-08-00; online 2019-05-24]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Computational and Experimental Druggability Assessment of Human DNA Glycosylases
Michel M, Visnes T, Homan EJ, ..., Warpman Berglund U, Helleday T
ACS Omega 4 (7) 11642-11656 [2019-07-31; online 2019-07-05]
Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.
Imgenberg-Kreuz J, Almlöf JC, Leonard D, ..., Sandling JK, Nordmark G
pmc
Front Immunol 10 (-) 1686 [2019-07-30; online 2019-07-30]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts.
Saini A, Björkhem-Bergman L, Boström J, ..., Rullman E, Gustafsson T
pmc
Endocr Connect 8 (7) 1070-1081 [2019-07-29; online 2019-07-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Multiplex plasma protein profiling identifies novel markers to discriminate patients with adenocarcinoma of the lung.
Djureinovic D, Pontén V, Landelius P, ..., Micke P, Ståhle E
pmc
BMC Cancer 19 (1) 741 [2019-07-29; online 2019-07-29]
PLA and Single Cell Proteomics [Collaborative]
PubMed DOI Crossref
Combinations of Spok genes create multiple meiotic drivers in Podospora.
Vogan AA, Ament-Velásquez SL, Granger-Farbos A, ..., Saupe SJ, Johannesson H
pmc Dryad
Elife 8 (-) - [2019-07-26; online 2019-07-26]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Estrogen deprivation triggers an immunosuppressive phenotype in breast cancer cells
Hühn D, Martí-Rodrigo P, Mouron S, ..., Carreras-Puigvert J, Fernandez-Capetillo O
- - (-) - [2019-07-25; online 2019-07-25]
Chemical Biology Consortium Sweden (CBCS) [Service]
DOI Crossref
Analysis of the behaviour of confined molecules using 2H T1 nuclear magnetic relaxation dispersion
Shamshir A, Sparrman T, Westlund PO
Molecular Physics - (-) 1-10 [2019-07-24; online 2019-07-24]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.
Ericson PGP, Qu Y, Rasmussen PC, ..., Rheindt FE, Irestedt M
pmc
BMC Evol. Biol. 19 (1) 151 [2019-07-24; online 2019-07-24]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.
Wallander K, Liu W, von Holst S, ..., Lindblom A, Lagerstedt-Robinson K
Genes Chromosomes Cancer - (-) - [2019-07-23; online 2019-07-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Evolved for success in novel environments: The round goby genome
Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S
- - (-) - [2019-07-19; online 2019-07-19]
Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
Anti‐tumor effects of PIM / PI 3K/ mTOR triple kinase inhibitor IBL ‐302 in neuroblastoma
Mohlin S, Hansson K, Radke K, ..., Stedingk K, Bexell D
EMBO Mol Med - (-) - [2019-07-16; online 2019-07-16]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation.
Miller DSJ, Schmierer B, Hill CS
pmc
J. Cell. Sci. 132 (14) - [2019-07-15; online 2019-07-15]
High-throughput Genome Engineering (HTGE) [Collaborative]
DOI Crossref
Post‐metaphase correction of aberrant kinetochore‐microtubule attachments in mammalian eggs
Kouznetsova A, Kitajima TS, Brismar H, Höög C
EMBO rep - (-) - [2019-07-10; online 2019-07-10]
Advanced Light Microscopy (ALM) [Collaborative]
PubMed DOI Crossref
Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations.
Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM
Mol. Biol. Evol. - (-) - [2019-07-09; online 2019-07-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak
Bikkarolla SK, Nordberg V, Rajer F, ..., Sandegren L, Westerlund F
MBio 10 (4) - [2019-07-09; online 2019-07-09]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Systems-level immunomonitoring using self-sampled capillary blood
Josyula VS, Lakshmikanth T, Mikes J, Chen Y, Brodin P
- - (-) - [2019-07-08; online 2019-07-08]
Mass Cytometry [Technology development]
PubMed DOI Crossref
The antimalarial drug amodiaquine stabilizes p53 through ribosome biogenesis stress, independently of its autophagy-inhibitory activity
Espinoza JA, Zisi A, Kanellis DC, ..., Lindström MS, Bartek J
Cell Death Differ - (-) - [2019-07-08; online 2019-07-08]
Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files
Wik E, Olin H, Haughey C, Klasson L, Dainat J
JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]
Bioinformatics Support and Infrastructure [Collaborative]
PubMed DOI Crossref
Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.
Ranade SS, Delhomme N, García-Gil MR
pmc
PLoS ONE 14 (7) e0219272 [2019-07-05; online 2019-07-05]
Cryo-EM [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.
Edfors F, Forsström B, Vunk H, ..., Schwenk JM, Uhlen M
J. Proteome Res. 18 (7) 2706-2718 [2019-07-05; online 2019-06-07]
Plasma Profiling [Technology development]
PubMed DOI Crossref
Seeking the ultimate challenge.
Brodin P
Nat Med - (-) - [2019-07-03; online 2019-07-03]
PubMed DOI Crossref
Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.
Christel S, Yu C, Wu X, ..., Åström ME, Dopson M
Res. Microbiol. 170 (6-7) 288-295 [2019-07-03; online 2019-07-03]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification
Pértille F, Da Silva VH, Johansson AM, ..., Jensen P, Guerrero-Bosagna C
Epigenetics 14 (7) 685-707 [2019-07-03; online 2019-05-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection.
Kalyandurg PB, Tahmasebi A, Vetukuri RR, ..., Grenville-Briggs LJ, Savenkov EI
Virology 535 (-) 111-121 [2019-07-01; online 2019-07-01]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Serum metabolite profiles of habitual diet: evaluation by 1H-nuclear magnetic resonance analysis
Lindqvist HM, Rådjursöga M, Malmodin D, Winkvist A, Ellegård L
Am J Clin Nutr 110 (1) 53-62 [2019-07-01; online 2019-05-25]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Androgen Receptor Burden and Poor Response to Abiraterone or Enzalutamide in TP53 Wild-Type Metastatic Castration-Resistant Prostate Cancer.
De Laere B, Rajan P, Grönberg H, ..., Lindberg J, CORE-ARV-CTC and ProBIO Investigators
pmc
JAMA Oncol 5 (7) 1060-1062 [2019-07-01; online 2019-05-03]
Clinical Genomics Stockholm [Service]
DOI Crossref
Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.
Sen BC, Wasserstrom S, Findlay K, ..., von Wachenfeldt C, Flärdh K
Mol Microbiol 112 (1) 184-198 [2019-07-00; online 2019-05-17]
Cryo-EM [Collaborative]
PubMed DOI Crossref
Epigenome-wide association study of lung function level and its change.
Imboden M, Wielscher M, Rezwan FI, ..., Jarvis D, Probst-Hensch NM
pmc
Eur. Respir. J. 54 (1) - [2019-07-00; online 2019-07-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
1H NMR profiling of the 6-OHDA parkinsonian rat brain reveals metabolic alterations and signs of recovery after N-acetylcysteine treatment
Virel A, Dudka I, Laterveer R, af Bjerkén S
Molecular and Cellular Neuroscience 98 (-) 131-139 [2019-07-00; online 2019-07-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon.
Martijn J, Lind AE, Schön ME, ..., Pettersson OV, Ettema TJG
Environ. Microbiol. 21 (7) 2485-2498 [2019-07-00; online 2019-05-07]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
PubMed DOI Crossref
Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.
Andersson A, Remnestål J, Nellgård B, ..., Nilsson P, Fredolini C
Clin. Chim. Acta 494 (-) 79-93 [2019-07-00; online 2019-03-09]
Plasma Profiling [Technology development]
PubMed DOI Crossref
Expanding the phenotypic spectrum of osteogenesis imperfecta type V including heterotopic ossification of muscle origins and attachments.
Clewemar P, Hailer NP, Hailer Y, ..., Ljunggren Ö, Stattin EL
pmc
Mol Genet Genomic Med 7 (7) e00723 [2019-07-00; online 2019-05-16]
Clinical Genomics Uppsala [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.
Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM
Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Systems Biology [Collaborative]
DOI Crossref
OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis
Wang W, Zhang X, Niittylä T
Plant Cell 31 (7) 1446-1465 [2019-07-00; online 2019-04-25]
Cryo-EM [Service]
DOI Crossref
Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain
Bigalke JM, Aibara S, Roth R, ..., Amunts A, Sandmark J
Sci Adv 5 (7) eaau4202 [2019-07-00; online 2019-07-31]
Cryo-EM [Service]
PubMed DOI Crossref
Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS G13D mutation.
Charitou T, Srihari S, Lynn MA, ..., Kolch W, Lynn DJ
pmc
Br. J. Cancer 121 (1) 37-50 [2019-07-00; online 2019-05-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.
Torabi Moghadam B, Etemadikhah M, Rajkowska G, ..., Feuk L, Carlström EL
J Psychiatr Res 114 (-) 41-47 [2019-07-00; online 2019-04-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality
Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A
Experimental Cell Research - (-) 111469 [2019-07-00; online 2019-07-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Transcriptome analysis of shade avoidance and shade tolerance in conifers.
Ranade SS, Delhomme N, García-Gil MR
Planta 250 (1) 299-318 [2019-07-00; online 2019-04-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
TRAF6 function as a novel co-regulator of Wnt3a target genes in prostate cancer
Aripaka K, Gudey SK, Zang G, ..., von Hofsten J, Landström M
EBioMedicine 45 (-) 192-207 [2019-07-00; online 2019-07-00]
PLA and Single Cell Proteomics [Service]
DOI Crossref
Surface activated polyethylene separator promoting Li+ ion transport in gel polymer electrolytes and cycling stability of Li-metal anode
Qiu Z, Shi L, Wang Z, ..., Zhao Y, Yuan S
Chemical Engineering Journal 368 (-) 321-330 [2019-07-00; online 2019-07-00]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Influence of ABO Locus on PFA-100 Collagen-ADP Closure Time Is Not Totally Dependent on the Von Willebrand Factor. Results of a GWAS on GAIT-2 Project Phenotypes.
Pujol-Moix N, Martinez-Perez A, Sabater-Lleal M, ..., Souto JC, Soria JM
Int J Mol Sci 20 (13) - [2019-06-30; online 2019-06-30]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Insights into the Exfoliation Process of V2O5·nH2O Nanosheet Formation Using Real-Time 51V NMR
Etman AS, Pell AJ, Svedlindh P, ..., Sun J, Bernin D
ACS Omega 4 (6) 10899-10905 [2019-06-30; online 2019-06-24]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.
Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A
pmc
Genes 10 (7) - [2019-06-28; online 2019-06-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.
Landegren N, Rosen LB, Freyhult E, ..., Anderson M, Kämpe O
pmc
Elife 8 (-) - [2019-06-27; online 2019-06-27]
Bioinformatics Support and Infrastructure [Service]
DOI Crossref
Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication
Yau WL, Nguyen-Dinh V, Larsson E, ..., Överby AK, Lundmark R
J Virol 93 (18) - [2019-06-26; online 2019-08-28]
Cryo-EM [Service]
PubMed DOI Crossref
Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.
Floyd JS, Bloch KM, Brody JA, ..., Alfirevic A, PREDICTION-ADR Consortium and EUDRAGENE
PLoS ONE 14 (6) e0218115 [2019-06-26; online 2019-06-26]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
A Role for the VPS Retromer in Brucella Intracellular Replication Revealed by Genomewide siRNA Screening
Casanova A, Low SH, Québatte M, ..., Ben-Tekaya H, Dehio C
mSphere 4 (3) - [2019-06-26; online 2019-06-26]
PubMed DOI Crossref
Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.
Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B
pmc
MBio 10 (3) - [2019-06-25; online 2019-06-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data.
Shungin D, Haworth S, Divaris K, ..., Timpson NJ, Johansson I
pmc
Nat Commun 10 (1) 2773 [2019-06-24; online 2019-06-24]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.
Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T
pmc
Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Single-nuclei transcriptomic analysis of the subthalamic nucleus reveals different Pitx2-positive subpopulations
Papathanou M, Björklund ÅK, Martis-Thiele MM, Wallén-Mackenzie Å
- - (-) - [2019-06-20; online 2019-06-20]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative]
DOI Crossref
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B
Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]
Bioinformatics Long-term Support WABI [Collaborative]
DOI Crossref
Correlative STED super-resolution light and electron microscopy on resin sections
Wurm CA, Schwarz H, Jans DC, ..., Humbel B, Jakobs S
J. Phys. D: Appl. Phys. - (-) - [2019-06-19; online 2019-06-19]
Advanced Light Microscopy (ALM) [Technology development]
PubMed DOI Crossref
A Call for Blood-In Human Immunology.
Brodin P, Duffy D, Quintana-Murci L
Immunity 50 (6) 1335-1336 [2019-06-18; online 2019-06-20]
Mass Cytometry [Technology development]
DOI Crossref
Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Bomkamp C, Tripathy SJ, Bengtsson Gonzales C, ..., Craig AM, Pavlidis P
PLoS Comput. Biol. 15 (6) e1007113 [2019-06-18; online 2019-06-18]
Eukaryotic Single Cell Genomics (ESCG) [Service]
PubMed DOI Crossref
Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival
Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A
The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]
Advanced Light Microscopy (ALM) [Collaborative] Chemical Proteomics & Proteogenomics [Technology development]
DOI Crossref
Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination
Dahlberg J, Sun L, Persson Waller K, ..., Agenäs S, Dicksved J
PLoS ONE 14 (6) e0218257 [2019-06-13; online 2019-06-13]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.
Smythe AB, Holovachov O, Kocot KM
pmc
BMC Evol. Biol. 19 (1) 121 [2019-06-13; online 2019-06-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Modeling Motor Neuron Resilience in ALS Using Stem Cells.
Allodi I, Nijssen J, Benitez JA, ..., Kiehn O, Hedlund E
pmc
Stem Cell Reports 12 (6) 1329-1341 [2019-06-11; online 2019-05-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Spatiotemporal structure of cell fate decisions in murine neural crest
Soldatov R, Kaucka M, Kastriti ME, ..., Kharchenko PV, Adameyko I
Science 364 (6444) eaas9536 [2019-06-07; online 2019-06-06]
Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP‐1
Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, ..., Höglund J, Laurila A
Mol Ecol - (-) - [2019-06-07; online 2019-06-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.
Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM
pmc
Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]
Autoimmunity Profiling [Technology development] Chemical Proteomics & Proteogenomics [Technology development] Plasma Profiling [Technology development]
DOI Crossref
Serum Metabolite Markers of Dementia Through Quantitative NMR Analysis: The Importance of Threonine-Linked Metabolic Pathways
Figueira J, Adolfsson R, Nordin Adolfsson A, Nyberg L, Öhman A
JAD 69 (3) 763-774 [2019-06-04; online 2019-06-04]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2.
Anandapadamanaban M, Kyriakidis NC, Csizmók V, ..., Wahren-Herlenius M, Sunnerhagen M
J. Biol. Chem. - (-) - [2019-06-03; online 2019-06-03]
Protein Science Facility (PSF) [Collaborative]
DOI Crossref
Recombinant dermatan sulfate is a potent activator of heparin cofactor II-dependent inhibition of thrombin
Tykesson E, Maccarana M, Thorsson H, ..., Ellervik U, Westergren-Thorsson G
- 29 (6) 446-451 [2019-06-01; online 2019-04-23]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species
Baskaran P, Ekblad A, Soucémarianadin LN, ..., Schleucher J, Lindahl BD
FEMS Microbiol. Ecol. 95 (6) - [2019-06-01; online 2019-04-25]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions
de Vries PS, Brown MR, Bentley AR, ..., Rao DC, Morrison AC
Am. J. Epidemiol. 188 (6) 1033-1054 [2019-06-01; online 2019-01-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells
Tibbitt CA, Stark JM, Martens L, ..., Saeys Y, Coquet JM
Immunity - (-) - [2019-06-00; online 2019-06-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Assembly mechanisms of the bacterial cytoskeletal protein FilP
Javadi A, Söderholm N, Olofsson A, Flärdh K, Sandblad L
Life Sci. Alliance 2 (3) e201800290 [2019-06-00; online 2019-06-26]
Cryo-EM [Collaborative]
PubMed DOI Crossref
Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.
Lundin J, Markljung E, Baranowska Körberg I, ..., Lindstrand A, Nordenskjöld A
pmc
Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Can markers of biological age predict dependency in old age?
Jylhävä J, Jiang M, Foebel AD, Pedersen NL, Hägg S
pmc
Biogerontology 20 (3) 321-329 [2019-06-00; online 2019-01-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.
Hill J, Rastas P, Hornett EA, ..., Nylin S, Wheat CW
pmc
Sci Adv 5 (6) eaau3648 [2019-06-00; online 2019-06-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Alterations in the metabolism of phospholipids, bile acids and branched-chain amino acids predicts development of type 2 diabetes in black South African women: a prospective cohort study
Zeng Y, Mtintsilana A, Goedecke JH, ..., Olsson T, Chorell E
Metabolism 95 (-) 57-64 [2019-06-00; online 2019-06-00]
Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
The effects of male social environment on sperm phenotype and genome integrity
Silva WTAF, Sáez‐Espinosa P, Torijo‐Boix S, ..., Gómez‐Torres MJ, Immler S
J Evol Biol 32 (6) 535-544 [2019-06-00; online 2019-03-25]
Genome Engineering Zebrafish [Service]
DOI Crossref
A catalog of genetic loci associated with kidney function from analyses of a million individuals
Wuttke M, None , Li Y, ..., Pattaro C, None
Nat Genet 51 (6) 957-972 [2019-06-00; online 2019-05-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
β-Mannosidosis caused by a novel homozygous intragenic inverted duplication in MANBA
Blomqvist M, Smeland MF, Lindgren J, ..., Riise Stensland HMF, Asin-Cayuela J
Cold Spring Harb Mol Case Stud 5 (3) a003954 [2019-06-00; online 2019-03-18]
Clinical Genomics Stockholm [Service]
DOI Crossref
DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures
Zhang H, Söderholm N, Sandblad L, Wiklund K, Andersson M
Microsc Microanal 25 (3) 711-719 [2019-06-00; online 2019-03-21]
Cryo-EM [Technology development]
PubMed DOI Crossref
A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer.
Shen Q, Polom K, Williams C, ..., Roviello F, Kamali-Moghaddam M
pmc
EBioMedicine 44 (-) 322-333 [2019-06-00; online 2019-05-28]
PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.
Das J, Verma D, Gustafsson M, Lerm M
pmc
Epigenetics 14 (6) 589-601 [2019-06-00; online 2019-04-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.
Maffezzini C, Laine I, Dallabona C, ..., Wredenberg A, Wedell A
pmc
Mol Genet Genomic Med 7 (6) e654 [2019-06-00; online 2019-03-28]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Gene fusion involving the insulin‐like growth factor 1 receptor in an ALK ‐negative inflammatory myofibroblastic tumour
Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F
Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]
Clinical Genomics Lund [Service]
DOI Crossref
Bax to the future – A novel, high-yielding approach for purification and expression of full-length Bax protein for structural studies
Dingeldein APG, Lindberg MJ, Ådén J, ..., Stoll R, Gröbner G
Protein Expression and Purification 158 (-) 20-26 [2019-06-00; online 2019-06-00]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Toxic Activation of an AAA+ Protease by the Antibacterial Drug Cyclomarin A
Maurer M, Linder D, Franke KB, ..., Bukau B, Mogk A
Cell Chem Biol - (-) - [2019-06-00; online 2019-06-00]
Cryo-EM [Service]
DOI Crossref
Magnesium induces preconditioning of the neonatal brain via profound mitochondrial protection
Koning G, Leverin AL, Nair S, ..., Mallard C, Hagberg H
J Cereb Blood Flow Metab 39 (6) 1038-1055 [2019-06-00; online 2017-12-05]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time
Klemm AH, Thomae AW, Wachal K, Dietzel S
Microsc Microanal 25 (3) 699-704 [2019-06-00; online 2019-02-06]
BioImage Informatics [Technology development]
PubMed DOI Crossref
Somatic alterations detected in diagnostic prostate biopsies provide an inadequate representation of multifocal prostate cancer.
Kristiansen A, Bergström R, Delahunt B, ..., Egevad L, Lindberg J
Prostate 79 (8) 920-928 [2019-06-00; online 2019-03-25]
Clinical Genomics Stockholm [Service]
DOI Crossref
Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers
Nadachowska‐Brzyska K, Burri R, Ellegren H
Mol Ecol 28 (9) 2290-2304 [2019-05-29; online 2019-05-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment.
Bedri SK, Nilsson OB, Fink K, ..., Grönlund H, Glaser A
pmc
PLoS ONE 14 (5) e0217208 [2019-05-29; online 2019-05-29]
Plasma Profiling [Collaborative]
DOI Crossref
A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing
Ku A, Ravi N, Yang M, ..., Lilja H, Ceder Y
PLoS ONE 14 (5) e0217507 [2019-05-29; online 2019-05-29]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
The viral protein corona directs viral pathogenesis and amyloid aggregation.
Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S
pmc
Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]
Chemical Proteomics & Proteogenomics [Technology development]
DOI Crossref
Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs
Scaletti E, Jemth A, Helleday T, Stenmark P
FEBS Lett - (-) - [2019-05-25; online 2019-05-25]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms.
Di Martino ML, Ek V, Hardt WD, Eriksson J, Sellin ME
pmc
MBio 10 (3) - [2019-05-21; online 2019-05-21]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Crystal structure of the catalytic domain of the Weissela oryzae botulinum-like toxin
Košenina S, Masuyer G, Zhang S, Dong M, Stenmark P
FEBS Lett - (-) - [2019-05-20; online 2019-05-20]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients
Idborg H, Zandian A, Ossipova E, ..., Svenungsson E, Jakobsson PJ
Front Immunol 10 (-) - [2019-05-17; online 2019-05-17]
Drug Discovery and Development (DDD) [Collaborative] Plasma Profiling [Collaborative]
PubMed DOI Crossref
Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.
Kashuba N, Kırdök E, Damlien H, ..., Persson P, Götherström A
pmc Dryad
Commun Biol 2 (-) 185 [2019-05-15; online 2019-05-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Adult Neural Progenitor Cells Transplanted into Spinal Cord Injury Differentiate into Oligodendrocytes, Enhance Myelination, and Contribute to Recovery.
Sankavaram SR, Hakim R, Covacu R, ..., Svensson M, Brundin L
pmc
Stem Cell Reports 12 (5) 950-966 [2019-05-14; online 2019-04-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Protic Ionic Liquids Based on the Alkyl-Imidazolium Cation: Effect of the Alkyl Chain Length on Structure and Dynamics
Abdurrokhman I, Elamin K, Danyliv O, ..., Swenson J, Martinelli A
J. Phys. Chem. B 123 (18) 4044-4054 [2019-05-09; online 2019-04-17]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.
Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T
pmc
J Clin Med 8 (5) - [2019-05-08; online 2019-05-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.
Nicoletti P, Barrett S, McEvoy L, ..., Alfirevic A, Pirmohamed M
Clin. Pharmacol. Ther. - (-) - [2019-05-07; online 2019-05-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Genetical Genomics of Tonic Immobility in the Chicken.
Fogelholm J, Inkabi S, Höglund A, ..., Henriksen R, Wright D
Genes 10 (5) - [2019-05-07; online 2019-05-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Mass Cytometry Identifies Distinct Subsets of Regulatory T Cells and Natural Killer Cells Associated With High Risk for Type 1 Diabetes.
Barcenilla H, Åkerman L, Pihl M, Ludvigsson J, Casas R
pmc
Front Immunol 10 (-) 982 [2019-05-03; online 2019-05-03]
Mass Cytometry [Service]
PubMed DOI Crossref
Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.
Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA
pmc
PLoS ONE 14 (5) e0216294 [2019-05-02; online 2019-05-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Software engineering for scientific big data analysis
Grüning BA, Lampa S, Vaudel M, Blankenberg D
Gigascience 8 (5) - [2019-05-01; online 2019-05-23]
Bioinformatics Support and Infrastructure [Collaborative]
PubMed DOI Crossref
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M
pmc
Gigascience 8 (5) - [2019-05-01; online 2019-01-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.
Tiukova IA, Pettersson ME, Hoeppner MP, ..., Söderberg J, Passoth V
pmc
PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]
Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Prompt apoptotic response to high glucose in SGLT-expressing renal cells
Nilsson LM, Zhang L, Bondar A, ..., Scott L, Aperia A
American Journal of Physiology-Renal Physiology 316 (5) F1078-F1089 [2019-05-01; online 2019-05-01]
Advanced Light Microscopy (ALM) [Service]
DOI Crossref
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Lampa S, Dahlö M, Alvarsson J, Spjuth O
Gigascience 8 (5) - [2019-05-01; online 2019-04-26]
Bioinformatics Support and Infrastructure [Technology development]
DOI Crossref
Interferon signature in patients with STAT1 gain‐of‐function mutation is epigenetically determined
Kaleviste E, Saare M, Leahy TR, ..., Peterson P, Kisand K
Eur. J. Immunol. 49 (5) 790-800 [2019-05-00; online 2019-03-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Axonemal doublet microtubules can split into two complete singlets in human sperm flagellum tips
Zabeo D, Croft JT, Höög JL
FEBS Lett 593 (9) 892-902 [2019-05-00; online 2019-04-19]
Cryo-EM [Service]
DOI Crossref
Molecular orientation distribution of regenerated cellulose fibers investigated with rotor synchronized solid state NMR spectroscopy
Svenningsson L, Sparrman T, Bialik E, Bernin D, Nordstierna L
Cellulose 26 (8) 4681-4692 [2019-05-00; online 2019-04-17]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Pervasive hybridizations in the history of wheat relatives.
Glémin S, Scornavacca C, Dainat J, ..., David J, Ranwez V
pmc
Sci Adv 5 (5) eaav9188 [2019-05-00; online 2019-05-01]
Bioinformatics Support and Infrastructure [Service]
DOI Crossref
How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers
Rettelbach A, Nater A, Ellegren H
Genetics 212 (1) 277-285 [2019-05-00; online 2019-03-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Mineralogical investigations of Jamaican hematite-rich and goethite-rich bauxites using XRD and solid state 27Al and 31P MAS NMR spectroscopy
Young NJ, Coley MD, Greenaway AM
Journal of Geochemical Exploration 200 (-) 54-76 [2019-05-00; online 2019-05-00]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Interannual variation in seasonal diatom sedimentation reveals the importance of late winter processes and their timing for sediment signal formation
Maier DB, Diehl S, Bigler C
Limnol Oceanogr 64 (3) 1186-1199 [2019-05-00; online 2019-01-31]
Cryo-EM [Service]
PubMed DOI Crossref
An Atlas of Vagal Sensory Neurons and Their Molecular Specialization
Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P
Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Spatial proteomics: a powerful discovery tool for cell biology
Lundberg E, Borner GHH
Nat Rev Mol Cell Biol 20 (5) 285-302 [2019-05-00; online 2019-01-18]
Cell Profiling [Collaborative]
PubMed DOI Crossref
Gene expression profile of extraocular muscles following resection strabismus surgery
Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F
Experimental Eye Research 182 (-) 182-193 [2019-05-00; online 2019-05-00]
Bioinformatics Support and Infrastructure [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
PKCζ facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model
Zang G, Mu Y, Gao L, Bergh A, Landström M
Oncogene 38 (22) 4215-4231 [2019-05-00; online 2019-01-31]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.
Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q
Nat Ecol Evol 3 (5) 834-844 [2019-05-00; online 2019-04-01]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Dynamic pH‐induced conformational changes of the PsbO protein in the fluctuating acidity of the thylakoid lumen
Carius AB, Rogne P, Duchoslav M, ..., Samuelsson G, Shutova T
Physiol Plantarum 166 (1) 288-299 [2019-05-00; online 2019-03-18]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Genotype‐free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data
Warmuth VM, Ellegren H
Mol Ecol Resour 19 (3) 586-596 [2019-05-00; online 2019-04-17]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Mic60 exhibits a coordinated clustered distribution along and across yeast and mammalian mitochondria
Stoldt S, Stephan T, Jans DC, ..., Hell SW, Jakobs S
Proc Natl Acad Sci USA - (-) 201820364 [2019-04-26; online 2019-04-26]
Advanced Light Microscopy (ALM) [Collaborative]
PubMed DOI Crossref
Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient
Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M
Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]
Bioinformatics Long-term Support WABI [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.
Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G
pmc
Cell Rep 27 (4) 1090-1102.e10 [2019-04-23; online 2019-04-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.
Zhang Z, Cheng H, Hong X, ..., Wang X, Hao K
pmc
Nucleic Acids Res. 47 (7) e39 [2019-04-23; online 2019-02-06]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Abramova A, Lind U, Blomberg A, Rosenblad MA
Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]
Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture.
Kharazmi M, Michaëlsson K, Schilcher J, ..., Wadelius M, Hallberg P
Calcif. Tissue Int. - (-) - [2019-04-20; online 2019-04-20]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
A proton T1-nuclear magnetic resonance dispersion study of water motion in snowflakes and hexagonal ice
Westlund PO
Molecular Physics 117 (7-8) 960-967 [2019-04-18; online 2018-10-30]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions
Sobol M, Klar J, Laan L, ..., Falk A, Dahl N
Mol Neurobiol 56 (10) 7113-7127 [2019-04-13; online 2019-04-13]
Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative]
PubMed DOI Crossref
The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.
Boman J, Frankl-Vilches C, da Silva Dos Santos M, ..., Gahr M, Suh A
pmc
Genes 10 (4) - [2019-04-13; online 2019-04-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure.
Sung YJ, de Las Fuentes L, Winkler TW, ..., Rao DC, Morrison AC
pmc
Hum. Mol. Genet. - (-) - [2019-04-10; online 2019-04-10]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.
Calvo-Garrido J, Maffezzini C, Schober FA, ..., Freyer C, Wredenberg A
pmc
Stem Cell Reports 12 (4) 696-711 [2019-04-09; online 2019-02-28]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.
Hu FJ, Lundqvist M, Uhlén M, Rockberg J
pmc
Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.
Wallberg A, Bunikis I, Pettersson OV, ..., Robinson GE, Webster MT
BMC Genomics 20 (1) 275 [2019-04-08; online 2019-04-08]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
DOI Crossref
Asthma and affective traits in adults: a genetically informative study
Lehto K, Pedersen NL, Almqvist C, Lu Y, Brew BK
Eur Respir J - (-) 1802142 [2019-04-07; online 2019-04-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
Science 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Parental Education and Genetics of BMI from Infancy to Old Age: A Pooled Analysis of 29 Twin Cohorts
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Front Immunol 10 (-) - [2019-04-05; online 2019-04-05]
Bioinformatics Long-term Support WABI [Collaborative]
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Pyridine-Fused 2-Pyridones via Povarov and A3 Reactions: Rapid Generation of Highly Functionalized Tricyclic Heterocycles Capable of Amyloid Fibril Binding
Singh P, Adolfsson DE, Ådén J, ..., Olofsson A, Almqvist F
J. Org. Chem. 84 (7) 3887-3903 [2019-04-05; online 2019-03-13]
Cryo-EM [Service] Swedish NMR Centre (SNC) [Service]
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The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
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Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.
Pekkinen M, Terhal PA, Botto LD, ..., Holthuis JC, Mäkitie O
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JCI Insight 4 (7) - [2019-04-04; online 2019-04-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.
Wang K, Sybers D, Maklad HR, ..., Lindås AC, Peeters E
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Nat Commun 10 (1) 1542 [2019-04-04; online 2019-04-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Silica-based diffusion probes for use in FRAP and NMR-diffusometry
Pihl M, Kolman K, Lotsari A, ..., Lorén N, Bordes R
Journal of Dispersion Science and Technology 40 (4) 555-562 [2019-04-03; online 2018-10-08]
Swedish NMR Centre (SNC) [Service]
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Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.
Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M
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Stem Cell Res Ther 10 (1) 115 [2019-04-03; online 2019-04-03]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets.
Sundling C, Rönnberg C, Yman V, ..., Persson KE, Färnert A
JCI Insight 5 (-) - [2019-04-02; online 2019-04-02]
Mass Cytometry [Service]
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Selection for longer lived sperm within ejaculate reduces reproductive ageing in offspring
Alavioon G, Cabrera Garcia A, LeChatelier M, Maklakov AA, Immler S
Evolution Letters 3 (2) 198-206 [2019-04-00; online 2019-02-14]
Genome Engineering Zebrafish [Service]
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Gain-of-function mutation of microRNA-140 in human skeletal dysplasia.
Grigelioniene G, Suzuki HI, Taylan F, ..., Sharp PA, Kobayashi T
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Nat. Med. 25 (4) 583-590 [2019-04-00; online 2019-02-25]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Outbreak of Methicillin‐resistant Staphylococcus aureus in a Hospital Center for Children's and Women's Health in a Swedish County
Gideskog M, Melhus Å
APMIS 127 (4) 181-186 [2019-04-00; online 2019-03-25]
NGI Uppsala (Uppsala Genome Center) [Service]
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Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11
La Fleur L, Falk-Sörqvist E, Smeds P, ..., Moens L, Botling J
Lung Cancer 130 (-) 50-58 [2019-04-00; online 2019-04-00]
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Backbone 1H, 13C, and 15N resonance assignments of BoMan26A, a β-mannanase of the glycoside hydrolase family 26 from the human gut bacterium Bacteroides ovatus
Wernersson S, Bågenholm V, Persson C, ..., Stålbrand H, Akke M
Biomol NMR Assign 13 (1) 213-218 [2019-04-00; online 2019-02-07]
Swedish NMR Centre (SNC) [Collaborative]
DOI Crossref
Multi-ancestry genome-wide gene–smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids
Bentley AR, None , Sung YJ, ..., None , None
Nat Genet 51 (4) 636-648 [2019-04-00; online 2019-03-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Post‐glacial colonization routes coincide with a life‐history breakpoint along a latitudinal gradient
Luquet E, Rödin Mörch P, Cortázar‐Chinarro M, ..., Höglund J, Laurila A
J Evol Biol 32 (4) 356-368 [2019-04-00; online 2019-02-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct
Ferreira MAR, Mathur R, Vonk JM, ..., Koppelman GH, Almqvist C
The American Journal of Human Genetics 104 (4) 665-684 [2019-04-00; online 2019-04-00]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species
Vallesi A, Sjödin A, Petrelli D, ..., Gutiérrez G, Villalobo E
Microb Ecol 77 (3) 587-596 [2019-04-00; online 2018-09-05]
NGI Uppsala (Uppsala Genome Center) [Service]
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Single-molecule genome assembly of the BasketWillow, Salix viminalis, reveals earliest stages of sex chromosome expansion
Almeida P, Proux-Wera E, Churcher A, ..., Berlin S, Mank JE
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Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative]
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Leukocytosis is associated with retinopathy of prematurity in extremely preterm infants.
Lundgren P, Klevebro S, Brodin P, ..., Hallberg B, Hellström A
Acta Paediatr. - (-) - [2019-03-28; online 2019-03-28]
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A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E
PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]
Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] Systems Biology [Collaborative]
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Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development
Vain T, Raggi S, Ferro N, ..., Pauwels L, Robert S
Proc Natl Acad Sci USA 116 (13) 6463-6472 [2019-03-26; online 2019-03-08]
Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish Metabolomics Centre (SMC) [Service]
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A novel human in vitro papillomavirus type 16 positive tonsil cancer cell line with high sensitivity to radiation and cisplatin.
Forslund O, Sugiyama N, Wu C, ..., Wennerberg J, Ekblad L
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BMC Cancer 19 (1) 265 [2019-03-25; online 2019-03-25]
NGI Uppsala (Uppsala Genome Center) [Service]
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Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1
Bauer SL, Chen J, Åström SU
PLoS ONE 14 (3) e0214102 [2019-03-21; online 2019-03-21]
Bioinformatics Support and Infrastructure [Service]
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Association of Chromosome 9p21 with Subsequent Coronary Heart Disease Events: A GENIUS-CHD Study of Individual Participant Data.
Patel RS, Schmidt AF, Tragante V, ..., Hingorani AD, Asselbergs FW
Circ Genom Precis Med - (-) - [2019-03-21; online 2019-03-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Subsequent Event Risk in Individuals with Established Coronary Heart Disease: Design and Rationale of the GENIUS-CHD Consortium.
Patel R, Tragante V, Schmidt AF, ..., Hingorani AD, Asselbergs FW
Circ Genom Precis Med - (-) - [2019-03-21; online 2019-03-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Characterization of Double Leached Waelz Oxide for Identification of Fluoride Mineral
Sar S, Sundqvist Ökvist L, Sparrman T, Engström F, Samuelsson C
Metals 9 (3) 361 [2019-03-20; online 2019-03-20]
Swedish NMR Centre (SNC) [Service]
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An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
Mäkeläinen S, Gòdia M, Hellsand M, ..., Andersson G, Bergström TF
PLoS Genet. 15 (3) e1007873 [2019-03-19; online 2019-03-19]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (Uppsala Genome Center) [Service]
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Current Status and Future Prospects of Clinically Exploiting Cancer-specific Metabolism—Why Is Tumor Metabolism Not More Extensively Translated into Clinical Targets and Biomarkers?
Muthu M, Nordström A
Int J Mol Sci 20 (6) 1385 [2019-03-19; online 2019-03-19]
Swedish Metabolomics Centre (SMC) [Service]
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The repertoire of maternal anti-viral antibodies in human newborns.
Pou C, Nkulikiyimfura D, Henckel E, ..., Bohlin K, Brodin P
Nat. Med. - (-) - [2019-03-18; online 2019-03-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Detecting selection signatures in three Iranian sheep breeds
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Anim Genet - (-) - [2019-03-18; online 2019-03-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors
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Bioinformatics Support and Infrastructure [Collaborative]
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Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains.
Behra PRK, Das S, Pettersson BMF, ..., Ennis DG, Kirsebom LA
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Sci Rep 9 (1) 4603 [2019-03-14; online 2019-03-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function
Sapir T, Segal M, Grigoryan G, ..., Segal M, Reiner O
Front Cell Neurosci 13 (-) - [2019-03-13; online 2019-03-13]
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Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.
Chyleński M, Ehler E, Somel M, ..., Juras A, Marciniak A
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Genes 10 (3) - [2019-03-11; online 2019-03-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.
van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K
Mol Ecol Resour - (-) - [2019-03-08; online 2019-03-08]
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Individual and stable autoantibody repertoires in healthy individuals.
Neiman M, Hellström C, Just D, ..., Uhlén M, Nilsson P
Autoimmunity - (-) 1-11 [2019-03-05; online 2019-03-05]
Autoimmunity Profiling [Collaborative]
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Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.
Cheng S, Pei Y, He L, ..., Jing N, Deng Q
Cell Rep 26 (10) 2593-2607.e3 [2019-03-05; online 2019-03-07]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation
Wu CC, Klaesson A, Buskas J, ..., Söderberg O, Wolf JBW
J Exp Biol 222 (5) jeb194431 [2019-03-01; online 2019-02-04]
BioImage Informatics [Service]
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A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts
Farias FHG, Dahlqvist J, Kozyrev SV, ..., Rönnblom L, Lindblad-Toh K
Eur J Hum Genet 27 (3) 432-441 [2019-03-01; online 2018-11-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification.
Nicoloff H, Hjort K, Levin BR, Andersson DI
Nat Microbiol 4 (3) 504-514 [2019-03-00; online 2019-02-11]
NGI Uppsala (Uppsala Genome Center) [Service]
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A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection.
Månberg A, Bradley F, Qundos U, ..., Nilsson P, Broliden K
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Mol. Cell Proteomics 18 (3) 461-476 [2019-03-00; online 2018-11-30]
Plasma Profiling [Collaborative]
DOI Crossref
Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum
Clergeot PH, Rode NO, Glémin S, ..., Ihrmark K, Olson Å
Genetics 211 (3) 963-976 [2019-03-00; online 2018-12-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Spontaneous calcium activity in metanephric mesenchymal cells regulates branching morphogenesis in the embryonic kidney
Fontana JM, Khodus GR, Unnersjö-Jess D, ..., Aperia A, Brismar H
The FASEB Journal 33 (3) 4089-4096 [2019-03-00; online 2019-03-00]
Advanced Light Microscopy (ALM) [Service]
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Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.
Jansen IE, Savage JE, Watanabe K, ..., Andreassen OA, Posthuma D
Nat. Genet. 51 (3) 404-413 [2019-03-00; online 2019-01-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.
Shrine N, Guyatt AL, Erzurumluoglu AM, ..., Tobin MD, Wain LV
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Nat. Genet. 51 (3) 481-493 [2019-03-00; online 2019-02-25]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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A Phenotypic Screening Assay Identifies Modulators of Diamond Blackfan Anemia
Siva K, Ek F, Chen J, ..., Lundbäck T, Flygare J
SLAS DISCOVERY: Advancing Life Sciences R&D 24 (3) 304-313 [2019-03-00; online 2019-02-20]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Chromosomal inversions associated with environmental adaptation in honeybees
Christmas MJ, Wallberg A, Bunikis I, ..., Wallerman O, Webster MT
Mol Ecol 28 (6) 1358-1374 [2019-03-00; online 2018-12-21]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
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Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.
Justice AE, Karaderi T, Highland HM, ..., North KE, Lindgren CM
Nat. Genet. 51 (3) 452-469 [2019-03-00; online 2019-02-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.
Kuruvilla J, Bayat N, Cristobal S
Proteomics 19 (5) e1800228 [2019-03-00; online 2019-02-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases.
Acosta-Herrera M, Kerick M, González-Serna D, ..., Mayes MD, Martin J
Ann. Rheum. Dis. 78 (3) 311-319 [2019-03-00; online 2018-12-20]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.
Newton PT, Li L, Zhou B, ..., Sävendahl L, Chagin AS
Nature 567 (7747) 234-238 [2019-03-00; online 2019-02-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.
Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B
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Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]
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Nanomedical Relevance of the Intermolecular Interaction Dynamics—Examples from Lysozymes and Insulins
Zhang R, Zhang N, Mohri M, ..., Nifantiev NE, Siebert HC
ACS Omega 4 (2) 4206-4220 [2019-02-28; online 2019-02-27]
Swedish NMR Centre (SNC) [Service]
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A genome-wide association study identifies new loci for factor VII and implicates factor VII in ischemic stroke etiology.
de Vries PS, Sabater-Lleal M, Huffman JE, ..., O'Donnell CJ, Smith NL
Blood 133 (9) 967-977 [2019-02-28; online 2019-01-14]
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Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
Andrade P, Pinho C, Pérez i de Lanuza G, ..., Andersson L, Carneiro M
Proc Natl Acad Sci USA - (-) 201820320 [2019-02-28; online 2019-02-28]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]
DOI Crossref
Exome sequencing in 51 early onset non-familial CRC cases
Thutkawkorapin J, Lindblom A, Tham E
Mol Genet Genomic Med - (-) e605 [2019-02-27; online 2019-02-27]
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Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract.
Sahara M, Santoro F, Sohlmér J, ..., Gruber P, Chien KR
Dev. Cell 48 (4) 475-490.e7 [2019-02-25; online 2019-01-31]
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DOI Crossref
Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes)
Košuthová A, Westberg M, Otálora MAG, Wedin M
MycoKeys 47 (-) 17-33 [2019-02-20; online 2019-02-20]
Bioinformatics Support and Infrastructure [Service]
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Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups
Pettersson ME, Jern P
Genes 10 (2) 162 [2019-02-20; online 2019-02-20]
NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
Immune-informed mucin hydrogels evade fibrotic foreign body response in vivo
Yan H, Seignez C, Hjorth M, ..., Phillipson M, Crouzier T
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Cell Profiling [Service]
DOI Crossref
Crystal Structure and Substrate Specificity of the 8-oxo-dGTP Hydrolase NUDT1 from Arabidopsis thaliana
Jemth AS, Scaletti E, Carter M, Helleday T, Stenmark P
Biochemistry 58 (7) 887-899 [2019-02-19; online 2019-01-07]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.
Wang D, Eraslan B, Wieland T, ..., Hahne H, Kuster B
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Mol. Syst. Biol. 15 (2) e8503 [2019-02-18; online 2019-02-18]
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PubMed DOI Crossref
Genetics and epigenetics in primary Sjögren's syndrome.
Imgenberg-Kreuz J, Rasmussen A, Sivils K, Nordmark G
Rheumatology (Oxford) - (-) - [2019-02-15; online 2019-02-15]
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DOI Crossref
Fine-Tuning of Sox17 and Canonical Wnt Coordinates the Permeability Properties of the Blood-Brain Barrier
Corada M, Orsenigo F, Bhat GP, ..., Magnusson P, Dejana E
Circ Res 124 (4) 511-525 [2019-02-15; online 2019-02-15]
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Association of the coronary artery disease risk gene GUCY1A3 with ischaemic events after coronary intervention.
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Cardiovasc. Res. - (-) - [2019-02-14; online 2019-02-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution
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Nature - (-) - [2019-02-13; online 2019-02-13]
Eukaryotic Single Cell Genomics (ESCG) [Service]
DOI Crossref
Zinc depletion does not necessarily induce ribosome hibernation in mycobacteria
Tobiasson V, Dow A, Prisic S, Amunts A
Proc Natl Acad Sci USA 116 (7) 2395-2397 [2019-02-12; online 2019-01-25]
Cryo-EM [Service]
DOI Crossref
Dynamics of Resistance Plasmids in Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization
Brolund A, Rajer F, Giske CG, ..., Titelman E, Sandegren L
Antimicrob Agents Chemother 63 (4) - [2019-02-11; online 2019-03-27]
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Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model
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G3 (Bethesda) 9 (4) 1165-1173 [2019-02-08; online 2019-02-08]
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Spatiotemporal dissection of the cell cycle regulated human proteome
Mahdessian D, Sullivan D, Danielsson F, ..., Lindskog C, Lundberg E
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Cell Profiling [Collaborative]
PubMed DOI Crossref
Mass cytometry identifies distinct CD4+ T cell clusters distinguishing HIV-1–infected patients according to antiretroviral therapy initiation
Bekele Y, Lakshmikanth T, Chen Y, ..., Brodin P, Chiodi F
JCI Insight 4 (3) - [2019-02-07; online 2019-02-07]
Mass Cytometry [Service]
DOI Crossref
Synthesis of Sulfonimidamide-Based Amino Acid Building Blocks with Orthogonal Protecting Groups
Chinthakindi PK, Benediktsdottir A, Ibrahim A, ..., Chen Y, Sandström A
Eur. J. Org. Chem. 2019 (5) 1045-1057 [2019-02-07; online 2019-01-02]
Drug Discovery and Development (DDD) [Technology development]
DOI Crossref
Interplay between Conformational Entropy and Solvation Entropy in Protein–Ligand Binding
Verteramo ML, Stenström O, Ignjatović MM, ..., Ryde U, Akke M
J. Am. Chem. Soc. 141 (5) 2012-2026 [2019-02-06; online 2019-01-08]
Swedish NMR Centre (SNC) [Service]
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Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques.
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Theor. Appl. Genet. - (-) - [2019-02-02; online 2019-02-02]
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Disentangling the genetics of lean mass.
Karasik D, Zillikens MC, Hsu YH, ..., Kiel DP, Ohlsson C
Am. J. Clin. Nutr. 109 (2) 276-287 [2019-02-01; online 2019-02-06]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Protein measurements in venous plasma, earlobe capillary plasma and in plasma stored on filter paper.
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Anal. Biochem. 566 (-) 146-150 [2019-02-01; online 2018-11-22]
PLA and Single Cell Proteomics [Technology development]
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IL-6 Signaling Blockade during CD40-Mediated Immune Activation Favors Antitumor Factors by Reducing TGF-β, Collagen Type I, and PD-L1/PD-1
Eriksson E, Milenova I, Wenthe J, ..., Alemany R, Loskog A
J.I. 202 (3) 787-798 [2019-02-01; online 2019-01-07]
NGI Uppsala (Uppsala Genome Center) [Service]
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Plasma Profiles of Inflammatory Markers Associated With Active Tuberculosis in Antiretroviral Therapy-Naive Human Immunodeficiency Virus-Positive Individuals
Olsson O, Björkman P, Jansson M, ..., Carlsson F, Skogmar S
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Bioinformatics Support and Infrastructure [Service]
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Structural Basis of Cross‐Reactivity of Anti–Citrullinated Protein Antibodies
Ge C, Xu B, Liang B, ..., Dobritzsch D, Holmdahl R
Arthritis Rheumatol 71 (2) 210-221 [2019-02-00; online 2019-01-04]
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PubMed DOI Crossref
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.
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PLoS Genet. 15 (2) e1007858 [2019-02-00; online 2019-02-08]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Corticosteroids protect infected cells against mycobacterial killing in vitro
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Biochemical and Biophysical Research Communications - (-) - [2019-02-00; online 2019-02-00]
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Cryo-EM [Service]
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NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia
Chen D, Camponeschi A, Wu Q, ..., Fogelstrand L, Mårtensson IL
Br J Haematol 184 (3) 418-423 [2019-02-00; online 2018-11-28]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Longitudinal changes in the genetic and environmental influences on the epigenetic clocks across old age: Evidence from two twin cohorts.
Jylhävä J, Hjelmborg J, Soerensen M, ..., Pedersen NL, Reynolds CA
pmc
EBioMedicine 40 (-) 710-716 [2019-02-00; online 2019-01-28]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Two Basidiomycete Fungi in the Cortex of Wolf Lichens
Tuovinen V, Ekman S, Thor G, ..., Spribille T, Johannesson H
Current Biology 29 (3) 476-483.e5 [2019-02-00; online 2019-02-00]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus
Almlöf JC, Nystedt S, Leonard D, ..., Sandling JK, Syvänen AC
Hum Genet 138 (2) 141-150 [2019-02-00; online 2019-02-01]
NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative]
PubMed DOI Crossref
Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.
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Nat. Genet. 51 (2) 245-257 [2019-02-00; online 2019-01-14]
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Insights into hydrothermal aging of phosphorus-poisoned Cu-SSZ-13 for NH3-SCR
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Applied Catalysis B: Environmental 241 (-) 205-216 [2019-02-00; online 2019-02-00]
Swedish NMR Centre (SNC) [Service]
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Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas
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Br J Cancer 120 (4) 435-443 [2019-02-00; online 2019-02-12]
Clinical Genomics Uppsala [Collaborative]
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A Chemical Screen Identifies Compounds Limiting the Toxicity of C9ORF72 Dipeptide Repeats
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Cell Chem Biol 26 (2) 235-243.e5 [2019-02-00; online 2019-02-00]
Chemical Biology Consortium Sweden (CBCS) [Service]
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The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients.
Mikus M, Johansson C, Acevedo N, Nilsson P, Scheynius A
pmc
Clin Transl Allergy 9 (-) 6 [2019-01-31; online 2019-01-31]
Autoimmunity Profiling [Collaborative]
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Pandemrix-induced narcolepsy is associated with genes related to immunity and neuronal survival.
Hallberg P, Smedje H, Eriksson N, ..., Wadelius M, Swedegene
EBioMedicine - (-) - [2019-01-30; online 2019-01-30]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Low Molecular Mass Myocardial Hyaluronan in Human Hypertrophic Cardiomyopathy
Lorén C, Dahl C, Do L, ..., Mörner S, Hellman U
Cells 8 (2) 97 [2019-01-29; online 2019-01-29]
Swedish NMR Centre (SNC) [Service]
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DOP15 Metabolomics coupled with pathway analysis characterise metabolic changes in treatment-naive ulcerative colitis patients
Diab J, Hansen T, Goll R, ..., Florholmen J, Forsdahl G
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Swedish Metabolomics Centre (SMC) [Collaborative]
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Ultrasensitive immunoprofiling of plasma extracellular vesicles identifies syndecan-1 as a potential tool for minimally invasive diagnosis of glioma.
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Clin. Cancer Res. - (-) - [2019-01-24; online 2019-01-24]
Bioinformatics Support and Infrastructure [Collaborative] Chemical Proteomics & Proteogenomics [Technology development]
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Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents.
Esberg A, Haworth S, Brunius C, Lif Holgerson P, Johansson I
pmc
Sci Rep 9 (1) 452 [2019-01-24; online 2019-01-24]
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Altered human oligodendrocyte heterogeneity in multiple sclerosis
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Nature - (-) - [2019-01-23; online 2019-01-23]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Systems-Level Immune Monitoring by Mass Cytometry.
Lakshmikanth T, Brodin P
Methods Mol. Biol. 1913 (-) 33-48 [2019-01-23; online 2019-01-23]
Mass Cytometry [Technology development]
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The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.
Lindefeldt M, Eng A, Darban H, ..., Dahlin M, Prast-Nielsen S
pmc
NPJ Biofilms Microbiomes 5 (-) 5 [2019-01-23; online 2019-01-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.
Kilpeläinen TO, Bentley AR, Noordam R, ..., Rao DC, Loos RJF
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Nat Commun 10 (1) 376 [2019-01-22; online 2019-01-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Transformation of mature mouse B cells into malignant plasma cells in vitro via introduction of defined genetic elements.
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Eur. J. Immunol. - (-) - [2019-01-21; online 2019-01-21]
Bioinformatics Support and Infrastructure [Collaborative]
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Structure of the DP1–DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases
Raia P, Carroni M, Henry E, ..., Delarue M, Sauguet L
PLoS Biol. 17 (1) e3000122 [2019-01-18; online 2019-01-18]
Cryo-EM [Collaborative]
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Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting.
Chauhan G, Adams HHH, Satizabal CL, ..., Debette S, Stroke Genetics Network (SiGN), the International Stroke Genetics Consortium (ISGC), METASTROKE, Alzheimer's Disease Genetics Consortium (ADGC), and the Neurology Working Group of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium
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Neurology - (-) - [2019-01-16; online 2019-01-16]
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Peri-arterial specification of vascular mural cells from naïve mesenchyme requires Notch signaling
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Development 146 (2) dev165589 [2019-01-15; online 2019-01-14]
Genome Engineering Zebrafish [Service]
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Diplodia Tip Blight on Its Way to the North: Drivers of Disease Emergence in Northern Europe
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Front Plant Sci 9 (-) - [2019-01-09; online 2019-01-09]
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Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity
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The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.
Caputo A, Nylander JAA, Foster RA
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Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.
Karkman A, Pärnänen K, Larsson DGJ
pmc
Nat Commun 10 (1) 80 [2019-01-08; online 2019-01-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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The Versatility of SMRT Sequencing.
Hestand MS, Ameur A
Genes 10 (1) - [2019-01-04; online 2019-01-04]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
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Analysis of colony phase variation switch in Acinetobacter baumannii clinical isolates
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PLoS ONE 14 (1) e0210082 [2019-01-04; online 2019-01-04]
Cryo-EM [Service]
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Systems-level patterns emerge
Brodin P
Nat Rev Immunol - (-) - [2019-01-03; online 2019-01-03]
Mass Cytometry [Technology development]
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Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies.
Morris AP, Le TH, Wu H, ..., Humphreys BD, Franceschini N
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Nat Commun 10 (1) 29 [2019-01-03; online 2019-01-03]
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Intrinsic blinking characteristics of single colloidal CdSe-CdS/ZnS core-multishell quantum dots
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Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J
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Clinical Genomics Stockholm [Service]
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Tracking the Epigenetic Clock Across the Human Life Course: A Meta-analysis of Longitudinal Cohort Data.
Marioni RE, Suderman M, Chen BH, ..., Deary IJ, Hägg S
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J. Gerontol. A Biol. Sci. Med. Sci. 74 (1) 57-61 [2019-01-01; online 2018-05-03]
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Single-Molecule Sequencing: Towards Clinical Applications.
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Trends Biotechnol. 37 (1) 72-85 [2019-01-01; online 2018-08-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]
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ZBED6 negatively regulates insulin production, neuronal differentiation, and cell aggregation in MIN6 cells
Wang X, Jiang L, Wallerman O, ..., Welsh N, Andersson L
The FASEB Journal 33 (1) 88-100 [2019-01-00; online 2019-01-00]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization
Orre LM, Vesterlund M, Pan Y, ..., Fredlund E, Lehtiö J
Molecular Cell 73 (1) 166-182.e7 [2019-01-00; online 2019-01-00]
Chemical Proteomics & Proteogenomics [Technology development]
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Mosaic loss of chromosome Y in leukocytes matters
Forsberg LA, Halvardson J, Rychlicka-Buniowska E, ..., Ingelsson M, Dumanski JP
Nat Genet 51 (1) 4-7 [2019-01-00; online 2018-10-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Tissue-specific hormone profiles from woody poplar roots under bending stress
De Zio E, Trupiano D, Karady M, ..., Ljung K, Scippa GS
Physiol Plantarum 165 (1) 101-113 [2019-01-00; online 2018-10-15]
Swedish Metabolomics Centre (SMC) [Service]
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Role of OmpA1 and OmpA2 in Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus serum resistance
Lindholm M, Min Aung K, Nyunt Wai S, Oscarsson J
Journal of Oral Microbiology 11 (1) 1536192 [2019-01-00; online 2018-10-26]
Cryo-EM [Service]
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The Iroquois homeobox proteins IRX3 and IRX5 have distinct roles in Wilms tumour development and human nephrogenesis.
Holmquist Mengelbier L, Lindell-Munther S, Yasui H, ..., Hopyan S, Gisselsson D
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J. Pathol. 247 (1) 86-98 [2019-01-00; online 2018-11-29]
NGI Uppsala (Uppsala Genome Center) [Service]
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Introducing ribosomal tandem repeat barcoding for fungi
Wurzbacher C, Larsson E, Bengtsson‐Palme J, ..., Kagami M, Nilsson RH
Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]
NGI Uppsala (Uppsala Genome Center) [Service]
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A Series of Analogues to the AT2 R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode
Isaksson R, Lindman J, Wannberg J, ..., Gising J, Larhed M
ChemistryOpen 8 (1) 114-125 [2019-01-00; online 2019-01-24]
Drug Discovery and Development (DDD) [Collaborative]
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Genetic risk for neuroticism predicts emotional health depending on childhood adversity
Lehto K, Karlsson I, Lundholm C, Pedersen NL
Psychol. Med. 49 (02) 260-267 [2019-01-00; online 2018-03-26]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile.
Durán RE, Barra-Sanhueza B, Salvà-Serra F, ..., Moore ERB, Seeger M
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Microbiol Resour Announc 8 (5) - [2019-01-00; online 2019-01-31]
NGI Uppsala (Uppsala Genome Center) [Service]
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Exploring rare and low-frequency variants in the Saguenay–Lac-Saint-Jean population identified genes associated with asthma and allergy traits
Morin A, Madore AM, Kwan T, ..., Pastinen T, Laprise C
Eur J Hum Genet 27 (1) 90-101 [2019-01-00; online 2018-09-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative]
DOI Crossref
A standardized protocol for comparable analysis of GSH/GSSG by UHPLC-ESI-MSMS for human plasma
Claeson AS, Gouveia-Figueira S, Stenlund H, Johansson AI
Journal of Chromatography B 1104 (-) 67-72 [2019-01-00; online 2019-01-00]
Swedish Metabolomics Centre (SMC) [Collaborative]
DOI Crossref
Auxin Function in the Brown Alga Dictyota dichotoma
Bogaert KA, Blommaert L, Ljung K, Beeckman T, De Clerck O
Plant Physiol. 179 (1) 280-299 [2019-01-00; online 2018-11-12]
Swedish Metabolomics Centre (SMC) [Service]
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Soil organic carbon depletion and degradation in surface soil after long-term non-growing season warming in High Arctic Svalbard
Semenchuk PR, Krab EJ, Hedenström M, ..., Ancin-Murguzur FJ, Cooper EJ
Science of The Total Environment 646 (-) 158-167 [2019-01-00; online 2019-01-00]
Swedish NMR Centre (SNC) [Collaborative]
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Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease
Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M
Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2019-00-00; online 2019-00-00]
Systems Biology [Collaborative]
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Understanding the mechanism of low temperature deactivation of Cu/SAPO-34 exposed to various amounts of water vapor in the NH3-SCR reaction
Woo J, Bernin D, Ahari H, ..., Zammit M, Olsson L
Catal. Sci. Technol. 9 (14) 3623-3636 [2019-00-00; online 2019-00-00]
Swedish NMR Centre (SNC) [Collaborative]
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Automated Cell Processing for Mass Cytometry Experiments.
Mikes J, Olin A, Lakshmikanth T, Chen Y, Brodin P
Methods Mol. Biol. 1989 (-) 111-123 [2019-00-00]
Mass Cytometry [Technology development]
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Methyl sulfonamide substituents improve the pharmacokinetic properties of bicyclic 2-pyridone based Chlamydia trachomatis inhibitors
Kulén M, Núñez-Otero C, Cairns AG, ..., Gylfe Å, Almqvist F
Med. Chem. Commun. 10 (11) 1966-1987 [2019-00-00; online 2019-00-00]
Drug Discovery and Development (DDD) [Service]
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Efficient and catalyst free synthesis of acrylic plastic precursors: methyl propionate and methyl methacrylate synthesis through reversible CO2 capture
Khokarale SG, Mikkola JP
Green Chem. 21 (8) 2138-2147 [2019-00-00; online 2019-00-00]
Swedish NMR Centre (SNC) [Service]
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Molecular dynamics involving proton exchange of a protic ionic liquid–water mixture studied by NMR spectroscopy
Hasani M, Nordstierna L, Martinelli A
Phys. Chem. Chem. Phys. 21 (39) 22014-22021 [2019-00-00; online 2019-00-00]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Metal free synthesis of ethylene and propylene carbonate from alkylene halohydrin and CO2 at room temperature
Khokarale SG, Mikkola JP
RSC Adv. 9 (58) 34023-34031 [2019-00-00; online 2019-00-00]
Swedish NMR Centre (SNC) [Service]
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Cryo-EM structure of the yeast respiratory supercomplex
Rathore S, Berndtsson J, Marin-Buera L, ..., Brzezinski P, Ott M
Nat Struct Mol Biol - (-) - [2018-12-31; online 2018-12-31]
Cryo-EM [Collaborative]
PubMed DOI Crossref
Invasive cervical tumors with high and low HPV titer represent molecular subgroups with different disease etiology.
Cui T, Enroth S, Ameur A, ..., Lindquist D, Gyllensten U
Carcinogenesis - (-) - [2018-12-28; online 2018-12-28]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
DOI Crossref
Endosperm-specific transcriptome analysis by applying the INTACT system
Del Toro-De León G, Köhler C
Plant Reprod 32 (1) 55-61 [2018-12-26; online 2018-12-26]
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B cell alterations during BAFF inhibition with belimumab in SLE.
Ramsköld D, Parodis I, Lakshmikanth T, ..., Gunnarsson I, Malmström V
EBioMedicine - (-) - [2018-12-25; online 2018-12-25]
Mass Cytometry [Service]
PubMed DOI Crossref
Sensitive ADAR editing reporter in cancer cells enables high-throughput screening of small molecule libraries
Fritzell K, Xu LD, Otrocka M, Andréasson C, Öhman M
Nucleic Acids Res - (-) - [2018-12-22; online 2018-12-22]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
DOI Crossref
An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression
Haider Z, Larsson P, Landfors M, ..., Hultdin M, Degerman S
Cancer Med - (-) - [2018-12-21; online 2018-12-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Bandaru MK, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M
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Bioinformatics Support and Infrastructure [Service]
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Valorisation of humic acids by hydrothermal conversion into carbonaceous materials: physical and functional properties
Kozyatnyk I, Latham KG, Jansson S
ACS Sustainable Chem. Eng. - (-) - [2018-12-20; online 2018-12-20]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia.
Chase A, Pellagatti A, Singh S, ..., Boultwood J, Cross NCP
Leukemia - (-) - [2018-12-20; online 2018-12-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Deep Learning in Image Cytometry: A Review
Gupta A, Harrison PJ, Wieslander H, ..., Sintorn IM, Wählby C
Cytometry - (-) - [2018-12-19; online 2018-12-19]
BioImage Informatics [Collaborative]
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Association of Genetic Risk Factors for Psychiatric Disorders and Traits of These Disorders in a Swedish Population Twin Sample
Taylor MJ, Martin J, Lu Y, ..., Larsson H, Lichtenstein P
JAMA Psychiatry - (-) - [2018-12-19; online 2018-12-19]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Red Fluorescent Chlamydia trachomatis Applied to Live Cell Imaging and Screening for Antibacterial Agents
Mojica SA, Eriksson AU, Davis RA, ..., Elofsson M, Gylfe Å
Front Microbiol 9 (-) - [2018-12-18; online 2018-12-18]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.
van der Valk T, Díez-Del-Molino D, Marques-Bonet T, Guschanski K, Dalén L
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NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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A multigene typing system for human adenoviruses reveals a new genotype in a collection of Swedish clinical isolates.
Kaján GL, Lipiec A, Bartha D, Allard A, Arnberg N
PLoS ONE 13 (12) e0209038 [2018-12-14; online 2018-12-14]
NGI Uppsala (Uppsala Genome Center) [Service]
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Proteome Integral Stability Alteration assay dramatically increases throughput and sensitivity in profiling factor-induced proteome changes
Gaetani M, Sabatier P, Saei AA, ..., Lundstrom S, Zubarev RA
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Chemical Proteomics & Proteogenomics [Technology development]
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Allele-Specific Methylation of SPDEF: A Novel Moderator of Psychosocial Stress and Substance Abuse.
Tay N, Macare C, Liu Y, ..., Schumann G, IMAGEN Consortium
Am J Psychiatry - (-) appiajp201817121360 [2018-12-11; online 2018-12-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.
Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY
pmc
Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]
Clinical Genomics Lund [Service]
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Cotranslational Folding of a Pentarepeat β-Helix Protein.
Notari L, Martínez-Carranza M, Farías-Rico JA, Stenmark P, von Heijne G
J. Mol. Biol. 430 (24) 5196-5206 [2018-12-07; online 2018-10-27]
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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.
Peters K, Bradbury J, Bergmann S, ..., Zanetti G, Steinbeck C
Gigascience - (-) - [2018-12-07; online 2018-12-07]
Bioinformatics Support and Infrastructure [Collaborative]
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Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability
Thuresson AC, Soussi Zander C, Zhao JJ, ..., Öhrner Y, Feuk L
Clin Genet 95 (3) 436-439 [2018-12-07; online 2018-12-07]
Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Carbon’s Three-Center, Four-Electron Tetrel Bond, Treated Experimentally
Karim A, Schulz N, Andersson H, ..., Keller S, Erdélyi M
J. Am. Chem. Soc. - (-) - [2018-12-07; online 2018-12-07]
Swedish NMR Centre (SNC) [Service]
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A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.
Ni G, Simone D, Palma D, ..., Turner S, Dopson M
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Front Microbiol 9 (-) 2945 [2018-12-05; online 2018-12-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
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Porous Cellulose Nanofiber-Based Microcapsules for Biomolecular Sensing
Paulraj T, Wennmalm S, Riazanova AV, ..., Crespo GA, Svagan AJ
ACS Appl. Mater. Interfaces 10 (48) 41146-41154 [2018-12-05; online 2018-11-09]
Advanced Light Microscopy (ALM) [Collaborative]
PubMed DOI Crossref
Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR.
Taylan F, Bang B, Öfverholm II, ..., Zachariadis V, Nordgren A
Clin. Chem. - (-) - [2018-12-05; online 2018-12-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Crystal Structures and Cytotoxicity of ent-Kaurane-Type Diterpenoids from Two Aspilia Species
Yaouba S, Valkonen A, Coghi P, ..., Erdélyi M, Yenesew A
Molecules 23 (12) 3199 [2018-12-04; online 2018-12-04]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Image Analysis in Digital Pathology: Combining Automated Assessment of Ki67 Staining Quality with Calculation of Ki67 Cell Proliferation Index
Bengtsson E, Ranefall P
Cytometry - (-) - [2018-12-03; online 2018-12-03]
BioImage Informatics [Technology development]
PubMed DOI Crossref
Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.
Gossing M, Smialowska A, Nielsen J
FEMS Yeast Res. 18 (8) - [2018-12-01; online 2018-09-01]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative]
PubMed DOI Crossref
Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.
Nilsson E, Benrick A, Kokosar M, ..., Ling C, Stener-Victorin E
J. Clin. Endocrinol. Metab. 103 (12) 4465-4477 [2018-12-01; online 2018-08-17]
Bioinformatics Support and Infrastructure [Collaborative]
PubMed DOI Crossref
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J
BioProject SRA
Microbiome 6 (1) - [2018-12-00; online 2018-09-28]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Individual Genetic Variation Might Predict Acute Skin Reactions in Women Undergoing Adjuvant Breast Cancer Radiotherapy.
Oliva D, Nilsson M, Strandéus M, ..., Laytragoon-Lewin N, Lewin F
Anticancer Res. 38 (12) 6763-6770 [2018-12-00; online 2018-12-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
A Chemical Screen Identifies Compounds Limiting the Toxicity of C9ORF72 Dipeptide Repeats
Corman A, Jung B, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O
Cell Chem Biol - (-) - [2018-12-00; online 2018-12-00]
Chemical Biology Consortium Sweden (CBCS) [Service]
DOI Crossref
ClpB mutants of Francisella tularensis subspecies holarctica and tularensis are defective for type VI secretion and intracellular replication
Alam A, Golovliov I, Javed E, Sjöstedt A
Sci Rep 8 (1) - [2018-12-00; online 2018-07-27]
Cryo-EM [Service]
PubMed DOI Crossref
A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901
Konasani VR, Jin C, Karlsson NG, Albers E
Sci Rep 8 (1) - [2018-12-00; online 2018-10-02]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
Bhosale R, Giri J, Pandey BK, ..., Bennett MJ, Swarup R
Nat Commun 9 (1) - [2018-12-00; online 2018-04-12]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells
Kundu S, Ali MA, Handin N, ..., Hellström M, Sjöblom T
BioProject
Genome Med 10 (1) - [2018-12-00; online 2018-01-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface
Karlberg T, Hornyak P, Pinto AF, ..., Björkegren C, Schüler H
PDB PDB PDB PDB PDB
Nat Commun 9 (1) - [2018-12-00; online 2018-09-17]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
DOI Crossref
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
Sci Rep 8 (1) - [2018-12-00; online 2018-08-09]
Bioinformatics Long-term Support WABI [Collaborative]
PubMed DOI Crossref
A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons
Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J
GEO
Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Ulvan lyase from Formosa agariphila and its applicability in depolymerisation of ulvan extracted from three different Ulva species
Konasani VR, Jin C, Karlsson NG, Albers E
Algal Research 36 (-) 106-114 [2018-12-00; online 2018-12-00]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome
Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S
BioProject SRA
Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Chemical Proteomics & Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin
Johansson HJ, Vallhov H, Holm T, ..., Lehtiö J, Scheynius A
Sci Rep 8 (1) - [2018-12-00; online 2018-06-15]
Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Chemical Proteomics & Proteogenomics [Collaborative] Cryo-EM [Service]
DOI Crossref
Structure of a functional obligate complex III2IV2 respiratory supercomplex from Mycobacterium smegmatis
Wiseman B, Nitharwal RG, Fedotovskaya O, ..., Brzezinski P, Högbom M
Nat Struct Mol Biol 25 (12) 1128-1136 [2018-12-00; online 2018-12-05]
Cryo-EM [Service]
PubMed DOI Crossref
Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells
Page BDG, Valerie NCK, Wright RHG, ..., Beato M, Helleday T
PDB PDB
Nat Commun 9 (1) - [2018-12-00; online 2018-01-17]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants
Delgado-Vega AM, Martínez-Bueno M, Oparina NY, ..., Kozyrev SV, Alarcón-Riquelme ME
Sci Rep 8 (1) - [2018-12-00; online 2018-06-08]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage
Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S
Nat Commun 9 (1) - [2018-12-00; online 2018-05-22]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
PubMed DOI Crossref
Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing
Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K
Nat Commun 9 (1) - [2018-12-00; online 2018-12-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Intelligent image-based in situ single-cell isolation
Brasko C, Smith K, Molnar C, ..., Tamas G, Horvath P
Nat Commun 9 (1) - [2018-12-00; online 2018-01-15]
DOI Crossref
Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma
Andrejeva D, Kugler JM, Nguyen HT, ..., Loya AC, Cohen SM
BMC Cancer 18 (1) - [2018-12-00; online 2018-11-28]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Analysis of porcine body size variation using re-sequencing data of miniature and large pigs
Reimer C, Rubin CJ, Sharifi AR, ..., Schlather M, Simianer H
Dryad SRA SRA SRA SRA SRA BioProject
BMC Genomics 19 (1) - [2018-12-00; online 2018-09-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records
Hines HN, Onsbring H, Ettema TJG, Esteban GF
Protist 169 (6) 875-886 [2018-12-00; online 2018-12-00]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL
Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]
Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia
Shiozawa Y, Malcovati L, Gallì A, ..., Ogawa S, Cazzola M
Nat Commun 9 (1) - [2018-12-00; online 2018-09-07]
Clinical Genomics Uppsala [Service]
PubMed DOI Crossref
A randomized controlled cross-over trial investigating the effect of anti-inflammatory diet on disease activity and quality of life in rheumatoid arthritis: the Anti-inflammatory Diet In Rheumatoid Arthritis (ADIRA) study protocol
Winkvist A, Bärebring L, Gjertsson I, Ellegård L, Lindqvist HM
Nutr J 17 (1) - [2018-12-00; online 2018-04-20]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins
Spåhr H, Chia T, Lingford JP, ..., Filipovska A, Rackham O
Nat Commun 9 (1) - [2018-12-00; online 2018-06-07]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Anti-Rift Valley fever virus activity in vitro, pre-clinical pharmacokinetics and oral bioavailability of benzavir-2, a broad-acting antiviral compound
Islam MK, Strand M, Saleeb M, ..., Elofsson M, Evander M
Sci Rep 8 (1) - [2018-12-00; online 2018-01-31]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]
PubMed DOI Crossref
The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.
Synnott NC, Madden SF, Bykov VJN, ..., Wiman KG, Duffy MJ
pmc
Transl Oncol 11 (6) 1343-1349 [2018-12-00; online 2018-09-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Effects of predation stress and food ration on perch gut microbiota
Zha Y, Eiler A, Johansson F, Svanbäck R
SRA
Microbiome 6 (1) - [2018-12-00; online 2018-02-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Interaction of Toluene with Polar Stationary Phases under Conditions Typical of Hydrophilic Interaction Chromatography Probed by Saturation Transfer Difference Nuclear Magnetic Resonance Spectroscopy
Shamshir A, Dinh NP, Jonsson T, ..., Ashiq MJ, Irgum K
Journal of Chromatography A - (-) - [2018-12-00; online 2018-12-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage
Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S
PDB GEO
Nat Commun 9 (1) - [2018-12-00; online 2018-03-16]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]
DOI Crossref
A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
Obudulu O, Mähler N, Skotare T, ..., Trygg J, Tuominen H
BMC Genomics 19 (1) - [2018-12-00; online 2018-01-03]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Genome sequencing and conservation genomics in the Scandinavian wolverine population
Ekblom R, Brechlin B, Persson J, ..., Flagstad Ø, Ellegren H
Conservation Biology 32 (6) 1301-1312 [2018-12-00; online 2018-09-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes
Franceschini N, None , Giambartolomei C, ..., Casas JP, O’Donnell CJ
Nat Commun 9 (1) - [2018-12-00; online 2018-12-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients
Houtman M, Ekholm L, Hesselberg E, ..., Lundberg IE, Padyukov L
Arthritis Res. Ther. 20 (1) - [2018-12-00; online 2018-08-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
A novel derivative of the fungal antimicrobial peptide plectasin is active against Mycobacterium tuberculosis
Tenland E, Krishnan N, Rönnholm A, ..., Robertson BD, Godaly G
Tuberculosis 113 (-) 231-238 [2018-12-00; online 2018-12-00]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]
DOI Crossref
Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins
Söderholm N, Javadi A, Flores IS, Flärdh K, Sandblad L
Sci Rep 8 (1) - [2018-12-00; online 2018-11-08]
Cryo-EM [Service]
PubMed DOI Crossref
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M
Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Enteric Species F Human Adenoviruses use Laminin-Binding Integrins as Co-Receptors for Infection of Ht-29 Cells
Rajan A, Persson BD, Frängsmyr L, ..., Gall J, Arnberg N
Sci Rep 8 (1) - [2018-12-00; online 2018-07-03]
Cryo-EM [Service]
DOI Crossref
Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Schmidt A, Marabita F, Kiani NA, ..., Lahesmaa R, Tegnér J
BMC Biol. 16 (1) - [2018-12-00; online 2018-05-07]
Chemical Proteomics & Proteogenomics [Collaborative]
PubMed DOI Crossref
Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
Bornelöv S, Seroussi E, Yosefi S, ..., Andersson L, Friedman-Einat M
BioProject
BMC Genomics 19 (1) - [2018-12-00; online 2018-04-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR
Baltrušis P, Halvarsson P, Höglund J
International Journal for Parasitology: Drugs and Drug Resistance 8 (3) 411-419 [2018-12-00; online 2018-12-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive
Norling M, Jareborg N, Dainat J
BMC Res Notes 11 (1) - [2018-12-00; online 2018-08-13]
Bioinformatics Support and Infrastructure [Technology development]
PubMed DOI Crossref
Oxidatively stressed mitochondria-mimicking membranes: A molecular insight into their organization during apoptosis
Dingeldein APG, Sparrman T, Gröbner G
Biochimica et Biophysica Acta (BBA) - Biomembranes 1860 (12) 2644-2654 [2018-12-00; online 2018-12-00]
Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J
Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Chemical Proteomics & Proteogenomics [Technology development]
DOI Crossref
Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Elbere I, Silamikelis I, Ustinova M, ..., Schiöth HB, Klovins J
Clin Epigenetics 10 (1) - [2018-12-00; online 2018-12-13]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing
Onuț-Brännström I, Benjamin M, Scofield DG, ..., Lindström ES, Johannesson H
GENBANK
Sci Rep 8 (1) - [2018-12-00; online 2018-03-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans
Bélteky J, Agnvall B, Bektic L, ..., Jensen P, Guerrero-Bosagna C
Genet. Sel. Evol. 50 (1) - [2018-12-00; online 2018-04-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades
Wieloch T, Ehlers I, Yu J, ..., Gessler A, Schleucher J
Sci Rep 8 (1) - [2018-12-00; online 2018-03-22]
Swedish NMR Centre (SNC) [Service]
DOI Crossref
Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate
Giri J, Bhosale R, Huang G, ..., Swarup R, Bennett MJ
Nat Commun 9 (1) - [2018-12-00; online 2018-04-12]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
van der Valk T, Sandoval-Castellanos E, Caillaud D, ..., Dalén L, Guschanski K
GENBANK
Sci Rep 8 (1) - [2018-12-00; online 2018-04-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
A major locus controls local adaptation and adaptive life history variation in a perennial plant
Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK
SRA
Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements
Svedberg J, Hosseini S, Chen J, ..., Lascoux M, Johannesson H
BioProject
Nat Commun 9 (1) - [2018-12-00; online 2018-10-12]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination
Gustafsson NMS, Färnegårdh K, Bonagas N, ..., Olin T, Helleday T
PDB
Nat Commun 9 (1) - [2018-12-00; online 2018-09-24]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Collaborative]
PubMed DOI Crossref
A drug screening assay on cancer cells chronically adapted to acidosis
Pellegrini P, Serviss JT, Lundbäck T, ..., Linder S, De Milito A
Cancer Cell Int 18 (1) - [2018-12-00; online 2018-09-25]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
De Wit P, Durland E, Ventura A, Langdon CJ
BioProject Dryad
BMC Genomics 19 (1) - [2018-12-00; online 2018-02-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster
Zare A, Johansson AM, Karlsson E, Delhomme N, Stenberg P
FEBS Lett 592 (24) 4078-4086 [2018-12-00; online 2018-11-15]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Comprehensive analysis of CTNNB1 in adrenocortical carcinomas: Identification of novel mutations and correlation to survival
Maharjan R, Backman S, Åkerström T, Hellman P, Björklund P
Sci Rep 8 (1) 8610 [2018-12-00; online 2018-06-05]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique
Cholleti H, Hayer J, Fafetine J, Berg M, Blomström AL
GENBANK
Virol J 15 (1) - [2018-12-00; online 2018-04-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders
Walters RK, None , Polimanti R, ..., Edenberg HJ, Agrawal A
Nat Neurosci 21 (12) 1656-1669 [2018-12-00; online 2018-11-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
A Chemical Screen Identifies Compounds Limiting the Toxicity of C9ORF72 Dipeptide Repeats
Corman A, Jung B, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O
Cell Chem Biol - (-) - [2018-12-00; online 2018-12-00]
Cell Profiling [Service]
DOI Crossref
Using High Content Imaging to Quantify Target Engagement in Adherent Cells
Axelsson H, Almqvist H, Seashore-Ludlow B
J Vis Exp - (141) - [2018-11-29; online 2018-11-29]
Chemical Biology Consortium Sweden (CBCS) [Technology development]
PubMed DOI Crossref
Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers.
Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M
pmc
Front Microbiol 9 (-) 2880 [2018-11-27; online 2018-11-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
The shape of the ribosome exit tunnel affects cotranslational protein folding
Kudva R, Tian P, Pardo-Avila F, ..., Bernstein HD, von Heijne G
Elife 7 (-) - [2018-11-26; online 2018-11-26]
Cryo-EM [Service]
DOI Crossref
Modelling of zero-inflation improves inference of metagenomic gene count data
Jonsson V, Österlund T, Nerman O, Kristiansson E
Stat Methods Med Res - (-) 096228021881135 [2018-11-25; online 2018-11-25]
Systems Biology [Technology development]
DOI Crossref
A Quantitative Analysis of Colonic Mucosal Oxylipins and Endocannabinoids in Treatment-Naïve and Deep Remission Ulcerative Colitis Patients and the Potential Link With Cytokine Gene Expression
Diab J, Al-Mahdi R, Gouveia-Figueira S, ..., Florholmen J, Forsdahl G
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Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping
Broberg M, Dubey M, Sun MH, ..., Brandström Durling M, Karlsson M
Front Microbiol 9 (-) 2844 [2018-11-22; online 2018-11-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis.
Mayrhofer M, De Laere B, Whitington T, ..., Grönberg H, Lindberg J
pmc
Genome Med 10 (1) 85 [2018-11-21; online 2018-05-11]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M
MBio 9 (6) - [2018-11-20; online 2018-11-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.
Franzén B, Alexeyenko A, Kamali-Moghaddam M, ..., Landegren U, Lewensohn R
Mol Oncol 13 (2) 376-391 [2018-11-19; online 2018-11-19]
Bioinformatics Support and Infrastructure [Collaborative] PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay
Seashore-Ludlow B, Axelsson H, Almqvist H, ..., Jonsson M, Lundbäck T
Biochemistry - (-) - [2018-11-19; online 2018-11-19]
Chemical Biology Consortium Sweden (CBCS) [Technology development]
PubMed DOI Crossref
Effect of CTLA4-Ig (abatacept) Treatment on T cells and B cells in Peripheral Blood of Patients with Polymyositis and Dermatomyositis.
Tang Q, Ramsköld D, Krystufkova O, ..., Lundberg IE, Malmström V
Scand. J. Immunol. - (-) e12732 [2018-11-19; online 2018-11-19]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Service]
PubMed DOI Crossref
Genome-Wide Association Studies of Estimated Fatty Acid Desaturase Activity in Serum and Adipose Tissue in Elderly Individuals: Associations with Insulin Sensitivity
Marklund M, Morris A, Mahajan A, ..., Lind L, Risérus U
Nutrients 10 (11) 1791 [2018-11-17; online 2018-11-17]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Expression profiling and in situ screening of circular RNAs in human tissues.
Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L
Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development]
PubMed DOI Crossref
Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters.
Pedersen JN, Bombar D, Paerl RW, Riemann L
pmc
Front Microbiol 9 (-) 2759 [2018-11-16; online 2018-11-16]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia
Papakonstantinou N, Ntoufa S, Tsagiopoulou M, ..., Rosenquist R, Stamatopoulos K
Int. J. Cancer - (-) - [2018-11-16; online 2018-11-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation
Visnes T, Cázares-Körner A, Hao W, ..., Boldogh I, Helleday T
Science 362 (6416) 834-839 [2018-11-16; online 2018-11-15]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).
Salgado MG, van Velzen R, Nguyen TV, ..., Lundin D, Pawlowski K
pmc
Front Plant Sci 9 (-) 1629 [2018-11-14; online 2018-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.
De Wit P, Yamada K, Panova M, André C, Johannesson K
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Sci Rep 8 (1) 16824 [2018-11-14; online 2018-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
Akhter S, Kretzschmar WW, Nordal V, ..., Emanuelsson O, Sundström JF
Front Plant Sci 9 (-) - [2018-11-13; online 2018-11-13]
Bioinformatics Support and Infrastructure [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Satiety Factors Oleoylethanolamide, Stearoylethanolamide, and Palmitoylethanolamide in Mother’s Milk Are Strongly Associated with Infant Weight at Four Months of Age—Data from the Odense Child Cohort
Bruun S, Gouveia-Figueira S, Domellöf M, ..., Fowler C, Zachariassen G
Nutrients 10 (11) 1747 [2018-11-13; online 2018-11-13]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G
GEO
Nat Med - (-) - [2018-11-12; online 2018-11-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Parallel plumage colour evolution and introgressive hybridization in wheatears.
Schweizer M, Warmuth V, Alaei Kakhki N, ..., Suh A, Burri R
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NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
DOI Crossref
Asexual reproduction and growth rate: independent and plastic life history traits in Neurospora crassa
Anderson JL, Nieuwenhuis BPS, Johannesson H
ISME J 13 (3) 780-788 [2018-11-09; online 2018-11-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
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Nitrogen utilization during germination of somatic embryos of Norway spruce: revealing the importance of supplied glutamine for nitrogen metabolism
Carlsson J, Egertsdotter U, Ganeteg U, Svennerstam H
Trees - (-) - [2018-11-09; online 2018-11-09]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
New tools for automated high-resolution cryo-EM structure determination in RELION-3
Zivanov J, Nakane T, Forsberg BO, ..., Lindahl E, Scheres SH
Elife 7 (-) - [2018-11-09; online 2018-11-09]
Cryo-EM [Technology development]
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The biology of the cell: insights from mass cytometry.
Brodin P
FEBS J. - (-) - [2018-11-03; online 2018-11-03]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]
DOI Crossref
Vandermonde Factorization of Hankel Matrix for Complex Exponential Signal Recovery—Application in Fast NMR Spectroscopy
Ying J, Cai JF, Guo D, ..., Chen Z, Qu X
IEEE Trans. Signal Process. 66 (21) 5520-5533 [2018-11-01; online 2018-11-01]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Computational and Statistical Analysis of Array-Based DNA Methylation Data.
Nordlund J, Bäcklin C, Raine A
Methods Mol. Biol. 1878 (-) 173-191 [2018-11-01; online 2018-11-01]
NGI Uppsala (SNP&SEQ Technology Platform) [Technology development]
PubMed DOI Crossref
Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle
Lind AE, Lewis WH, Spang A, ..., Embley TM, Ettema TJG
BioProject
ISME J 12 (11) 2655-2667 [2018-11-00; online 2018-07-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.
Salmén F, Ståhl PL, Mollbrink A, ..., Frisén J, Lundeberg J
Nat Protoc 13 (11) 2501-2534 [2018-11-00; online 2018-10-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers.
Valind A, Wessman S, Pal N, ..., Sandstedt B, Gisselsson D
Pediatr Blood Cancer 65 (11) e27301 [2018-11-00; online 2018-07-03]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.
Mahajan A, Taliun D, Thurner M, ..., Boehnke M, McCarthy MI
pmc mid
Nat. Genet. 50 (11) 1505-1513 [2018-11-00; online 2018-10-08]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
LMO7 and LIMCH1 interact with LRIG proteins in lung cancer, with prognostic implications for early-stage disease.
Karlsson T, Kvarnbrink S, Holmlund C, ..., Johansson M, Hedman H
Lung Cancer 125 (-) 174-184 [2018-11-00; online 2018-09-24]
Clinical Genomics Uppsala [Collaborative]
DOI Crossref
Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens
Srinivas V, Lebrette H, Lundin D, ..., Sjöberg BM, Högbom M
Nature 563 (7731) 416-420 [2018-11-00; online 2018-10-31]
Chemical Proteomics & Proteogenomics [Collaborative]
PubMed DOI Crossref
VEGF receptor-2/neuropilin 1 trans-complex formation between endothelial and tumor cells is an independent predictor of pancreatic cancer survival
Morin E, Sjöberg E, Tjomsland V, ..., Sjöblom T, Claesson-Welsh L
J. Pathol 246 (3) 311-322 [2018-11-00; online 2018-09-04]
Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Service]
PubMed DOI Crossref
Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.
Nazaryan-Petersen L, Eisfeldt J, Pettersson M, ..., Tümer Z, Lindstrand A
pmc
PLoS Genet. 14 (11) e1007780 [2018-11-00; online 2018-11-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders
Ligthart S, Vaez A, Võsa U, ..., Frayling TM, Slagboom EP
The American Journal of Human Genetics 103 (5) 691-706 [2018-11-00; online 2018-11-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Upregulated BMP-Smad signaling activity in the glucuronyl C5-epimerase knock out MEF cells
Batool T, Fang J, Jansson V, ..., Moustakas A, Li JP
Cellular Signalling - (-) - [2018-11-00; online 2018-11-00]
PLA and Single Cell Proteomics [Collaborative]
PubMed DOI Crossref
Gene-level associations in suicide attempter families show overrepresentation of synaptic genes and genes differentially expressed in brain development
Sokolowski M, Wasserman J, Wasserman D
Am. J. Med. Genet. - (-) - [2018-10-31; online 2018-10-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Cigarette smoking affects microRNAs and inflammatory biomarkers in healthy individuals and an association to single nucleotide polymorphisms is indicated
Andersson BÅ, Sayardoust S, Löfgren S, Rutqvist LE, Laytragoon-Lewin N
Biomarkers - (-) 1-17 [2018-10-30; online 2018-10-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.
Xu J, Gruber PJ, Chien KR
Stem Cells - (-) - [2018-10-30; online 2018-10-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR
Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Protein Profiling in Serum and Cerebrospinal Fluid Following Complex Surgery on the Thoracic Aorta Identifies Biological Markers of Neurologic Injury
Lindblom RPF, Shen Q, Axén S, ..., Kamali-Moghaddam M, Thelin S
J. of Cardiovasc. Trans. Res. - (-) - [2018-10-26; online 2018-10-26]
Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Collaborative]
PubMed DOI Crossref
Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.
Tanaka N, Katayama S, Reddy A, ..., Oya M, Uhlén P
Cancer Med - (-) - [2018-10-26; online 2018-10-26]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.
Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL
pmc
Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]
Chemical Proteomics & Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci
Drobin K, Assadi G, Hong MG, ..., D’Amato M, Halfvarson J
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Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Collaborative] Plasma Profiling [Collaborative]
PubMed DOI Crossref
Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays
Giacomello S, Lundeberg J
Nat Protoc - (-) - [2018-10-23; online 2018-10-23]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative]
PubMed DOI Crossref
XLSY: Extra-Large NMR Spectroscopy
Pustovalova Y, Mayzel M, Orekhov VY
Angew. Chem. Int. Ed. 57 (43) 14043-14045 [2018-10-22; online 2018-10-01]
Swedish NMR Centre (SNC) [Technology development]
DOI Crossref
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ
PLoS Comput. Biol. 14 (10) e1006541 [2018-10-18; online 2018-10-18]
Systems Biology [Technology development]
DOI Crossref
Halogen Bond Asymmetry in Solution
Lindblad S, Mehmeti K, Veiga AX, ..., Gräfenstein J, Erdélyi M
J. Am. Chem. Soc. 140 (41) 13503-13513 [2018-10-17; online 2018-09-20]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.
Joost S, Jacob T, Sun X, ..., Sur I, Kasper M
Cell Rep 25 (3) 585-597.e7 [2018-10-16; online 2018-10-18]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J
Cancer Res. 78 (20) 5970-5979 [2018-10-15; online 2018-08-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.
Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K
pmc
Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Systems Biology [Service]
PubMed DOI Crossref
Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds
Šafarič L, Shakeri Yekta S, Liu T, ..., Bastviken D, Björn A
SRA
Microorganisms 6 (4) 105 [2018-10-11; online 2018-10-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP
Jemth AS, Gustafsson R, Bräutigam L, ..., Stenmark P, Helleday T
PDB PDB
Nucleic Acids Res - (-) - [2018-10-10; online 2018-10-10]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
An orthotopic glioblastoma animal model suitable for high-throughput screenings
Pudelko L, Edwards S, Balan M, ..., Helleday T, Bräutigam L
Neuro Oncol 20 (11) 1475-1484 [2018-10-09; online 2018-05-10]
Advanced Light Microscopy (ALM) [Collaborative]
PubMed DOI Crossref
Chorea, psychosis, acanthocytosis, and prolonged survival associated with
Paucar M, Pajak A, Freyer C, ..., Wredenberg A, Svenningsson P
pmc
Neurology 91 (15) 710-712 [2018-10-09; online 2018-09-14]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data
Ameur A, Che H, Martin M, ..., Feuk L, Gyllensten U
Genes 9 (10) 486 [2018-10-09; online 2018-10-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative]
DOI Crossref
Silica-based diffusion probes for use in FRAP and NMR-diffusometry
Pihl M, Kolman K, Lotsari A, ..., Lorén N, Bordes R
Journal of Dispersion Science and Technology - (-) 1-8 [2018-10-08; online 2018-10-08]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Enhanced validation of antibodies for research applications.
Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M
pmc BioProject BioProject
Nat Commun 9 (1) 4130 [2018-10-08; online 2018-10-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation.
Ferreira CR, Xia ZJ, Clément A, ..., Gahl WA, Freeze HH
pmc
Am. J. Hum. Genet. 103 (4) 553-567 [2018-10-04; online 2018-10-06]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.
Willforss J, Chawade A, Levander F
J. Proteome Res. - (-) - [2018-10-02; online 2018-10-02]
Bioinformatics Support and Infrastructure [Technology development]
PubMed DOI Crossref
A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.
Dusart P, Fagerberg L, Perisic L, ..., Odeberg J, Butler LM
pmc
Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]
Bioinformatics Compute and Storage [Service] Cell Profiling [Service]
PubMed DOI Crossref
Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It
Bolívar P, Mugal CF, Rossi M, ..., Dutoit L, Ellegren H
SRA
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Development and Validation of a Novel RNA Sequencing-Based Prognostic Score for Acute Myeloid Leukemia.
Wang M, Lindberg J, Klevebring D, ..., Grönberg H, Rantalainen M
pmc
J. Natl. Cancer Inst. 110 (10) 1094-1101 [2018-10-01; online 2018-03-06]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Rapid Increase in Carriage Rates of Enterobacteriaceae Producing Extended-Spectrum β-Lactamases in Healthy Preschool Children, Sweden
Kaarme J, Riedel H, Schaal W, ..., Nevéus T, Melhus Å
Emerg. Infect. Dis. 24 (10) 1874-1881 [2018-10-00; online 2018-10-00]
NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells.
Maturi V, Enroth S, Heldin CH, Moustakas A
pmc
J. Cell. Physiol. 233 (10) 7113-7127 [2018-10-00; online 2018-05-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]
DOI Crossref
The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water
Orman-Ligeza B, Morris EC, Parizot B, ..., Beeckman T, Draye X
Current Biology 28 (19) 3165-3173.e5 [2018-10-00; online 2018-10-00]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads
Krzewińska M, Kılınç GM, Juras A, ..., Storå J, Götherström A
Sci Adv 4 (10) eaat4457 [2018-10-00; online 2018-10-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Using Scipion for stream image processing at Cryo-EM facilities
Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, ..., Conesa P, Carazo JM
Journal of Structural Biology - (-) - [2018-10-00; online 2018-10-00]
Cryo-EM [Technology development]
PubMed DOI Crossref
STAT3 differential scanning fluorimetry and differential scanning light scattering assays: Addressing a missing link in the characterization of STAT3 inhibitor interactions
Desroses M, Busker S, Astorga-Wells J, ..., Grandér D, Page BDG
Journal of Pharmaceutical and Biomedical Analysis 160 (-) 80-88 [2018-10-00; online 2018-10-00]
Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits.
Evangelou E, Warren HR, Mosen-Ansorena D, ..., Caulfield MJ, Million Veteran Program
Nat. Genet. 50 (10) 1412-1425 [2018-10-00; online 2018-09-17]
Bioinformatics Compute and Storage [Service]
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Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia
Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B
Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
DOI Crossref
Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation
Liu X, Karrenberg S
Mol Ecol 27 (19) 3889-3904 [2018-10-00; online 2018-04-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Partial genomic survival of cave bears in living brown bears.
Barlow A, Cahill JA, Hartmann S, ..., Shapiro B, Hofreiter M
Nat Ecol Evol 2 (10) 1563-1570 [2018-10-00; online 2018-08-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to Sunitinib
Dyczynski M, Yu Y, Otrocka M, ..., De Milito A, Pokrovskaja Tamm K
Cancer Letters 435 (-) 32-43 [2018-10-00; online 2018-10-00]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias.
Pettersson M, Vaz R, Hammarsjö A, ..., Grigelioniene G, Lindstrand A
Hum. Mutat. 39 (10) 1456-1467 [2018-10-00; online 2018-08-22]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Backbone 1H, 13C, and 15N resonance assignments of the ligand binding domain of the human wildtype glucocorticoid receptor and the F602S mutant variant
Köhler C, Carlström G, Tångefjord S, ..., Edman K, Akke M
Biomol NMR Assign 12 (2) 263-268 [2018-10-00; online 2018-04-17]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
Poongavanam V, Danelius E, Peintner S, ..., Ermondi G, Kihlberg J
ACS Omega 3 (9) 11742-11757 [2018-09-30; online 2018-09-24]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Interferon-α enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T].
Hagberg N, Rönnblom L
Ann. Rheum. Dis. - (-) - [2018-09-29; online 2018-09-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins
Wang Y, Karlsson R, Lampa E, ..., Pedersen NL, Hägg S
Epigenetics - (-) - [2018-09-28; online 2018-09-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.
Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M
pmc BioProject
Front Microbiol 9 (-) 2308 [2018-09-28; online 2018-09-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Male sex and the pattern of recurrent myeloid mutations are strong independent predictors of blood transfusion intensity in patients with myelodysplastic syndromes
Rydén J, Edgren G, Karimi M, ..., Hellström-Lindberg E, Höglund P
Leukemia - (-) - [2018-09-28; online 2018-09-28]
Clinical Genomics Uppsala [Service]
PubMed DOI Crossref
Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins
Reichenbach T, Kalyani D, Gandini R, ..., Aspeborg H, Divne C
PLoS ONE 13 (9) e0204703 [2018-09-27; online 2018-09-27]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Genotyping of Phytophthora infestans in eastern-Africa reveals a dominating invasive European lineage
Njoroge AW, Andersson B, Lees AK, ..., Yuen J, Pelle R
Phytopathology - (-) - [2018-09-25; online 2018-09-25]
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PubMed DOI Crossref
High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.
Ritter CD, Zizka A, Roger F, ..., Nilsson RH, Antonelli A
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PeerJ 6 (-) e5661 [2018-09-25; online 2018-09-25]
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Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype.
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Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]
PubMed DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH