Publications 2018

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

pii: S0002-9297(18)30314-8 pmc: PMC6174323

Am. J. Hum. Genet. 103 (4) 553-567 [2018-10-04; online 2018-10-06]

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

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

pii: 10.1038/s41598-018-32859-4 pmc: PMC6168570

Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]

Bioinformatics Compute and Storage [Service] Cell Profiling [Service]

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] Bioinformatics Support, Infrastructure and Training [Technology development]

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

pii: 4916692 pmc: PMC6186516

J. Natl. Cancer Inst. 110 (10) 1094-1101 [2018-10-01; online 2018-03-06]

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

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: ERP001377

- 35 (10) 2475-2486 [2018-10-01; online 2018-08-02]

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

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]

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] National Genomics Infrastructure [Service]

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]

Partial genomic survival of cave bears in living brown bears.

Barlow A, Cahill JA, Hartmann S, ..., Shapiro B, Hofreiter M

pii: 10.1038/s41559-018-0654-8

Nat Ecol Evol 2 (10) 1563-1570 [2018-10-00; online 2018-08-27]

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

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] National Genomics Infrastructure [Service]

Exploring photoinactivation of microbial biofilms using laser scanning microscopy and confined 2-photon excitation

Thomsen H, Graf FE, Farewell A, Ericson MB

J. Biophotonics 11 (10) e201800018 [2018-10-00; online 2018-06-19]

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

EGA: EGAS00001001795

Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]

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

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

pii: 10.1038/s41588-018-0205-x

Nat. Genet. 50 (10) 1412-1425 [2018-10-00; online 2018-09-17]

Bioinformatics Compute and Storage [Service]

Use of Vascular Assessments and Novel Biomarkers to Predict Cardiovascular Events in Type 2 Diabetes: The SUMMIT VIP Study

Shore AC, Colhoun HM, Natali A, ..., Björkbacka H, Nilsson J

Dia Care 41 (10) 2212-2219 [2018-10-00; online 2018-07-30]

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]

Chemical Proteomics [Collaborative] Protein Science Facility (PSF) [Service]

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]

Associations of Circulating Protein Levels With Lipid Fractions in the General Population

Figarska SM, Gustafsson S, Sundström J, ..., Lind L, Ingelsson E

Arterioscler Thromb Vasc Biol 38 (10) 2505-2518 [2018-10-00; online 2018-10-00]

Plasma levels of the proprotein convertase furin and incidence of diabetes and mortality

Fernandez C, Rysä J, Almgren P, ..., Ruskoaho H, Melander O

J Intern Med 284 (4) 377-387 [2018-10-00; online 2018-07-02]

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] National Genomics Infrastructure [Service]

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]

Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells.

Maturi V, Enroth S, Heldin CH, Moustakas A

pmc: PMC6055758

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] National Genomics Infrastructure [Service]

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] National Genomics Infrastructure [Service]

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]

Interferon-α enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T].

Hagberg N, Rönnblom L

pii: annrheumdis-2018-213836

Ann. Rheum. Dis. - (-) - [2018-09-29; online 2018-09-29]

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

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]

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.

Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M

pmc: PMC6172326 BioProject: PRJNA473625

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] National Genomics Infrastructure [Service]

Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

Wang Y, Karlsson R, Lampa E, ..., Pedersen NL, Hägg S

EBI: E-MTAB-7309

Epigenetics - (-) - [2018-09-28; online 2018-09-28]

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

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]

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

pii: 5661 pmc: PMC6161700

PeerJ 6 (-) e5661 [2018-09-25; online 2018-09-25]

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

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]

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

Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype.

Frykholm C, Klar J, Tomanovic T, Ameur A, Dahl N

pii: 10.1038/s41431-018-0256-6

Eur. J. Hum. Genet. - (-) - [2018-09-24; online 2018-09-24]

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

NMR Determination of the Binding Constant of Ionic Species: A Caveat

Schulz N, Schindler S, Huber SM, Erdelyi M

J. Org. Chem. 83 (18) 10881-10886 [2018-09-21; online 2018-08-15]

Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

Bravo AG, Peura S, Buck M, ..., Björn E, Bertilsson S

Appl Environ Microbiol 84 (23) - [2018-09-21; online 2018-11-15]

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

System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA)

Saei AA, Beusch C, Sabatier P, ..., Schuler H, Zubarev R

- - (-) - [2018-09-21; online 2018-09-21]

Chemical Proteomics [Collaborative]

Introducing ribosomal tandem repeat barcoding for fungi

Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH

ENA: PRJEB26696 GENBANK: MH356537 GENBANK: MH356538 GENBANK: MH356539 GENBANK: MH356540 GENBANK: MH356541 GENBANK: MH356542 GENBANK: MH356543 GENBANK: MH356544 GENBANK: MH356545

Mol Ecol Resour. 19 (1) 118-127 [2018-09-21; online 2018-09-21]

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

Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations

Pellagatti A, Armstrong RN, Steeples V, ..., Smith S, Boultwood J

Blood 132 (12) 1225-1240 [2018-09-20; online 2018-06-21]

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.

Yu S, Jordán-Pla A, Gañez-Zapater A, ..., Östlund Farrants AK, Visa N

pii: 5025902 pmc: PMC6144808 GEO: GSE95236

Nucleic Acids Res. 46 (16) 8557-8573 [2018-09-19; online 2018-06-04]

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

ProTargetMiner: A proteome signature library of anticancer molecules for functional discovery

Saei AA, Chernobrovkin A, Sabatier P, ..., Vegvari A, Zubarev R

- - (-) - [2018-09-18; online 2018-09-18]

Chemical Proteomics [Technology development]

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing

Dyrdak R, Mastafa M, Hodcroft E, Neher R, Albert J

- - (-) - [2018-09-18; online 2018-09-18]

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

Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability.

Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Lundberg ES

Clin. Genet. - (-) - [2018-09-16; online 2018-09-16]

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

Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.

Sun L, Vella P, Schnell R, ..., Schneider G, Römling U

pii: S0022-2836(18)30758-7 PDB: 5OJH PDB: 5OLT

J. Mol. Biol. 430 (18 Pt B) 3170-3189 [2018-09-14; online 2018-07-12]

Continuous Immune Cell Differentiation Inferred From Single-Cell Measurements Following Allogeneic Stem Cell Transplantation.

Chen Y, Lakshmikanth T, Olin A, ..., Remberger M, Brodin P

pmc: PMC6143687

Front Mol Biosci 5 (-) 81 [2018-09-12; online 2018-09-12]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

TP53 outperforms other androgen receptor biomarkers to predict abiraterone or enzalutamide outcome in metastatic castration-resistant prostate cancer.

De Laere B, Oeyen S, Mayrhofer M, ..., Lindberg J, Dirix LY

pii: 1078-0432.CCR-18-1943

Clin. Cancer Res. - (-) - [2018-09-12; online 2018-09-12]

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

Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.

Petitpré C, Wu H, Sharma A, ..., Hadjab S, Lallemend F

pii: 10.1038/s41467-018-06033-3 pmc: PMC6135759 GEO: GSE117055

Nat Commun 9 (1) 3691 [2018-09-12; online 2018-09-12]

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

How Does the Sweet Violet ( Viola odorata L.) Fight Pathogens and Pests - Cyclotides as a Comprehensive Plant Host Defense System.

Slazak B, Kapusta M, Strömstedt AA, ..., Kuta E, Göransson U

pmc: PMC6141879

Front Plant Sci 9 (-) 1296 [2018-09-11; online 2018-09-11]

National Resource for Mass Spectrometry Imaging [Service]

Contribution of allelic imbalance to colorectal cancer.

Palin K, Pitkänen E, Turunen M, ..., Taipale J, Aaltonen LA

pii: 10.1038/s41467-018-06132-1 pmc: PMC6131244 European Nucleotide Archive: PRJEB25645 European Genome-phenome Archive: EGAS00001002966 European Genome-phenome Archive: EGAS00001003010 Zenodo: https://doi.org/10.5281/zenodo.1222172

Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Graells T, Ishak H, Larsson M, Guy L

FEMS Microbiol. Ecol. - (-) - [2018-09-10; online 2018-09-10]

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

Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.

Krzewińska M, Kjellström A, Günther T, ..., Storå J, Götherström A

pii: S0960-9822(18)30844-3 European Nucleotide Archive: PRJEB27220

Curr. Biol. 28 (17) 2730-2738.e10 [2018-09-10; online 2018-08-23]

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

Neuroblastoma with flat genomic profile: a question of representativity?

Valind A, Öra I, Mertens F, Gisselsson D

BMJ Case Reports - (-) bcr-2018-225568 [2018-09-08; online 2018-09-08]

Higher Energy Collisional Dissociation Mass Spectrometry of Sulfated O-Linked Oligosaccharides.

Issa SMA, Vitiazeva V, Hayes CA, Karlsson NG

J. Proteome Res. 17 (9) 3259-3267 [2018-09-07; online 2018-08-13]

Glycoproteomics [Technology development]

Attached stratified mucus separates bacteria from the epithelial cells in COPD lungs

Fernández-Blanco JA, Fakih D, Arike L, ..., Ermund A, Hansson GC

JCI Insight 3 (17) - [2018-09-06; online 2018-09-06]

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 [2018-09-05; online 2018-09-05]

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

The Thomsen-Friedenreich Antigen: A Highly Sensitive and Specific Predictor of Microsatellite Instability in Gastric Cancer.

Mereiter S, Polom K, Williams C, ..., Magalhães A, Reis CA

pii: jcm7090256 pmc: PMC6162870

J Clin Med 7 (9) - [2018-09-05; online 2018-09-05]

Inflammatory markers in women with postpartum depressive symptoms

Bränn E, Fransson E, White RA, ..., Sundström-Poromaa I, Skalkidou A

J Neuro Res - (-) - [2018-09-05; online 2018-09-05]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC

pii: 5061551 pmc: PMC6152947

Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]

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

Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids

Narrowe AB, Spang A, Stairs CW, ..., Miller CS, Ettema TJG

Genome Biol Evol 10 (9) 2380-2393 [2018-09-01; online 2018-08-27]

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

Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain.

Bazov I, Sarkisyan D, Kononenko O, ..., Yakovleva T, Bakalkin G

pii: 4049562

Cereb. Cortex 28 (9) 3129-3142 [2018-09-01; online 2017-10-03]

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

FADD (Fas-Associated Protein With Death Domain), Caspase-3, and Caspase-8 and Incidence of Ischemic Stroke

Muhammad IF, Borné Y, Melander O, ..., Söderholm M, Engström G

Stroke 49 (9) 2224-2226 [2018-09-00; online 2018-09-00]

Multi-ethnic genome-wide association study for atrial fibrillation.

Roselli C, Chaffin MD, Weng LC, ..., Lunetta KL, Ellinor PT

pii: 10.1038/s41588-018-0133-9 pmc: PMC6136836 mid: NIHMS986675

Nat. Genet. 50 (9) 1225-1233 [2018-09-00; online 2018-06-11]

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

Ein Fall von Pankreaskarzinom

Löhr JM, Kordes M, Gustafsson-Liljefors M, ..., Permert J, Jäger D

Forum 33 (4) 232-235 [2018-09-00; online 2018-08-14]

Clinical Genomics Stockholm [Collaborative]

Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer

Djureinovic D, Dodig-Crnkovic T, Hellström C, ..., Schwenk JM, Micke P

Lung Cancer - (-) - [2018-09-00; online 2018-09-00]

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

Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation

Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O

Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]

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

Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.

Johansson US, Irestedt M, Qu Y, Ericson PGP

pii: S1055-7903(17)30880-1

Mol. Phylogenet. Evol. 126 (-) 17-22 [2018-09-00; online 2018-04-06]

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

Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditis elegans PAQR-2 and Its Mammalian Homolog AdipoR2

Bodhicharla R, Devkota R, Ruiz M, Pilon M

Genetics 210 (1) 189-201 [2018-09-00; online 2018-07-11]

Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

Dutoit L, Mugal CF, Bolívar P, ..., Gustafsson L, Ellegren H

BioProject: PRJEB2984 SRA: ERP001377

Mol Ecol 27 (18) 3572-3581 [2018-09-00; online 2018-09-04]

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

The molecular genetic basis of herbivory between butterflies and their host plants.

Nallu S, Hill JA, Don K, ..., Wheat CW, Kronforst MR

pii: 10.1038/s41559-018-0629-9 pmc: PMC6149523 mid: NIHMS979338 SRA: SRP134094 Transcriptome Shotgun Assembly Sequence Database: GGJX00000000 Transcriptome Shotgun Assembly Sequence Database: GGKA00000000 Transcriptome Shotgun Assembly Sequence Database: GGJQ00000000 Transcriptome Shotgun Assembly Sequence Database: GGJO00000000 Transcriptome Shotgun Assembly Sequence Database: GGJY00000000 Transcriptome Shotgun Assembly Sequence Database: GGJZ00000000 Transcriptome Shotgun Assembly Sequence Database: GGKB00000000 Transcriptome Shotgun Assembly Sequence Database: GGKC00000000

Nat Ecol Evol 2 (9) 1418-1427 [2018-09-00; online 2018-08-03]

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

Screening for Inhibitors of Acetaldehyde Dehydrogenase (AdhE) from Enterohemorrhagic Escherichia coli (EHEC)

Zetterström CE, Uusitalo P, Qian W, ..., Grundström C, Elofsson M

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (8) 815-822 [2018-09-00; online 2018-04-09]

Chemical Biology Consortium Sweden (CBCS) [Service]

Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.

Vetukuri RR, Kushwaha SK, Sen D, ..., Lamour KH, Grenville-Briggs LJ

GENBANK: NSDL00000000

Mol. Plant Microbe Interact. 31 (9) 903-905 [2018-09-00; online 2018-08-03]

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

Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment

Dyczynski M, Vesterlund M, Björklund AC, ..., Tamm KP, Nilsson R

Cell Death Dis 9 (9) - [2018-09-00; online 2018-08-28]

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest

Castaño C, Alday JG, Lindahl BD, ..., Pera J, Bonet JA

Forest Ecology and Management 424 (-) 420-427 [2018-09-00; online 2018-09-00]

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

Broad spectrum developmental role of Brachypodium AUX1

van der Schuren A, Voiniciuc C, Bragg J, ..., Pauly M, Hardtke CS

New Phytol 219 (4) 1216-1223 [2018-09-00; online 2018-06-27]

Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

Höijer I, Tsai YC, Clark TA, ..., Gyllensten U, Ameur A

GitHub: https://github.com/NationalGenomicsInfrastructure/HTT-repeat-analysis

Human Mutation 39 (9) 1262-1272 [2018-09-00; online 2018-07-12]

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

Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism

Gupta AA, Reinartz I, Karunanithy G, ..., Schug A, Wolf-Watz M

Journal of Molecular Biology 430 (18) 3157-3169 [2018-09-00; online 2018-09-00]

The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.

Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M

pii: IAI.00244-18 pmc: PMC6105892

Infect. Immun. 86 (9) - [2018-09-00; online 2018-08-22]

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

Autoantibody profiling reveals four protein candidate autoantigens associated with systemic lupus erythematosus.

Frostegård J, Hellström C, Nilsson P, Frostegård AG, Ajeganova S

Lupus 27 (10) 1670-1678 [2018-09-00; online 2018-07-24]

Autoimmunity and Serology Profiling [Service]

STK25 regulates oxidative capacity and metabolic efficiency in adipose tissue

Sütt S, Cansby E, Paul A, ..., Enerbäck S, Mahlapuu M

- 238 (3) 187-202 [2018-09-00; online 2018-09-00]

A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions

Franzén B, Kamali-Moghaddam M, Alexeyenko A, ..., Landegren U, Lewensohn R

Mol Oncol 12 (9) 1415-1428 [2018-09-00; online 2018-08-09]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Technology development]

Interactions between monomeric CCTδ and p150 Glued : A novel function for CCTδ at the cell periphery distinct from the protein folding activity of the molecular chaperone CCT

Echbarthi M, Vallin J, Grantham J

Experimental Cell Research 370 (1) 137-149 [2018-09-00; online 2018-09-00]

The endoplasmic reticulum-resident collagen chaperone Hsp47 interacts with and promotes the secretion of decorin, fibromodulin, and lumican.

Ishikawa Y, Rubin K, Bächinger HP, Kalamajski S

pii: RA117.000758 pmc: PMC6120207

J. Biol. Chem. 293 (35) 13707-13716 [2018-08-31; online 2018-07-12]

PLA and Single Cell Proteomics [Service]

A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant.

Rozman Grinberg I, Lundin D, Sahlin M, ..., Hofer A, Sjöberg BM

pii: RA118.004991

J. Biol. Chem. - (-) - [2018-08-30; online 2018-08-30]

Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression

Klum S, Zaouter C, Alekseenko Z, ..., Muhr J, Bergsland M

EMBO Rep. - (-) e46635 [2018-08-30; online 2018-08-30]

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

Eleven percent intact PGM3 in a severely immunodeficient patient with a novel splice-site mutation, a case report.

Lundin KE, Wang Q, Hamasy A, ..., Ekwall O, Smith CIE

pii: 10.1186/s12887-018-1258-9 pmc: PMC6114780

BMC Pediatr 18 (1) 285 [2018-08-29; online 2018-08-29]

Clinical Genomics Stockholm [Collaborative]

Patient-derived xenograft models reveal intratumor heterogeneity and temporal stability in neuroblastoma

Braekeveldt N, von Stedingk K, Fransson S, ..., Påhlman S, Bexell D

Cancer Res - (-) canres.0527.2018 [2018-08-28; online 2018-08-28]

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

Exploratory Profiling of Urine MicroRNAs in the dy Mouse Model of LAMA2-CMD: Relation to Disease Progression.2J/dy2J

Moreira Soares Oliveira B, Gawlik KI, Durbeej M, Holmberg J

pmc: PMC6140833

PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]

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

Human plasma cell derived monoclonal antibodies to post-translationally modified proteins recognize amino acid motifs rather than specific proteins.

Steen J, Forsström B, Sahlström P, ..., Klareskog L, Malmström V

Arthritis & rheumatology (Hoboken, N.J.) - (-) - [2018-08-27; online 2018-08-27]

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

Life history of Parnips and the evolutionary origin of gall wasps

Ronquist F, Nylander JAA, Vårdal H, Nieves-Aldrey JL

JHR 65 (-) 91-110 [2018-08-27; online 2018-08-27]

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

A Protein-Based Encapsulation System with Calcium-Controlled Cargo Loading and Detachment

Lizatović R, Assent M, Barendregt A, ..., Wennmalm S, André I

Angew. Chem. Int. Ed. 57 (35) 11334-11338 [2018-08-27; online 2018-07-30]

Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.

Tan DJX, Chattopadhyay B, Garg KM, ..., Irestedt M, Rheindt FE

pii: 10.1038/s41598-018-31074-5 pmc: PMC6109123 BioProject: PRJNA392017

Sci Rep 8 (1) 12804 [2018-08-24; online 2018-08-24]

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

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project.

Omenn GS, Lane L, Overall CM, ..., Baker MS, Deutsch EW

J. Proteome Res. - (-) - [2018-08-23; online 2018-08-23]

Translational Plasma Profiling [Collaborative]

Stereotypic Immune System Development in Newborn Children.

Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P

pii: S0092-8674(18)30848-1 FlowRepository: FR-FCM-ZYKQ Mendeley: 10.17632/ynhdrcxtcc.1

Cell 174 (5) 1277-1292.e14 [2018-08-23; online 2018-08-25]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Translational Plasma Profiling [Service]

Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype

Goudarzi KM, Espinoza JA, Guo M, ..., Lindström MS, Hägerstrand D

Cancer Res - (-) canres.0320.2018 [2018-08-22; online 2018-08-22]

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

Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.

He L, Vanlandewijck M, Mäe MA, ..., Lendahl U, Betsholtz C

pii: sdata2018160 pmc: PMC6103262 GEO: GSE98816 GEO: GSE99235 GEO: GSE99058 figshare: https://doi.org/10.6084/m9.figshare.c.4077260).

Sci Data 5 (1) 180160 [2018-08-21; online 2018-08-21]

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

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq.

Muñoz-Manchado AB, Bengtsson Gonzales C, Zeisel A, ..., Linnarsson S, Hjerling-Leffler J

pii: S2211-1247(18)31156-2 pmc: PMC6117871

Cell Rep 24 (8) 2179-2190.e7 [2018-08-21; online 2018-08-23]

Eukaryotic Single Cell Genomics (ESCG) [Service]

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.

Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F

pmc: PMC6161686

RNA Biol 15 (7) 937-954 [2018-08-21; online 2018-08-21]

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

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

Sullivan DP, Winsnes CF, Åkesson L, ..., Szantner A, Lundberg E

Nat Biotechnol 36 (9) 820-828 [2018-08-20; online 2018-08-20]

BioImage Informatics [Collaborative] Cell Profiling [Collaborative]

Ibrutinib induces rapid down-regulation of inflammatory markers and altered transcription of chronic lymphocytic leukaemia-related genes in blood and lymph nodes

Palma M, Krstic A, Peña Perez L, ..., Månsson R, Smith CIE

Br J Haematol - (-) - [2018-08-20; online 2018-08-20]

Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Collaborative]

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G

pii: S1534-5807(18)30558-6 pmc: PMC6104814 GEO: GSE95194 GEO: GSE95093

Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]

The structure-activity relationship of the salicylimide derived inhibitors of UDP-sugar producing pyrophosphorylases

Decker D, Öberg C, Kleczkowski LA

Plant Signal Behav - (-) 1-3 [2018-08-20; online 2018-08-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Sulfonimidamides: Synthesis and Applications in Preparative Organic Chemistry

Nandi GC, Arvidsson PI

Adv. Synth. Catal. 360 (16) 2976-3001 [2018-08-17; online 2018-05-25]

Drug Discovery and Development (DDD) [Technology development]

BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence

Rosa J, Fernandez-Gonzalez E, Ducani C, Högberg B

PLoS ONE 13 (8) e0202057 [2018-08-17; online 2018-08-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

Pharmacokinetic Properties of the Nephrotoxin Orellanine in Rats.

Najar D, Haraldsson B, Thorsell A, ..., Nyström J, Ebefors K

pii: toxins10080333 pmc: PMC6116018

Toxins (Basel) 10 (8) - [2018-08-17; online 2018-08-17]

Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Peura S, Buck M, Aalto SL, ..., Nykänen H, Eiler A

SRA: SRP076290

MBio 9 (4) - [2018-08-14; online 2018-08-14]

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

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das S, Pettersson F, Behra PRK, ..., Ennis DG, Kirsebom L

Sci. Rep. 8 (1) - [2018-08-13; online 2018-08-13]

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

Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes

Salami F, Lee HS, Freyhult E, ..., Lernmark Å, Törn C

Diabetes - (-) db180355 [2018-08-13; online 2018-08-13]

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

Nutritional Metabolomics: Postprandial Response of Meals Relating to Vegan, Lacto-Ovo Vegetarian, and Omnivore Diets

Rådjursöga M, Lindqvist H, Pedersen A, ..., Ellegård L, Winkvist A

Nutrients 10 (8) 1063 [2018-08-10; online 2018-08-10]

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR-Cas9-based approach

von der Heyde B, Emmanouilidou A, Klingström T, ..., Brooke HL, den Hoed M

- - (-) - [2018-08-09; online 2018-08-09]

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

Molecular Architecture of the Mouse Nervous System.

Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S

pii: S0092-8674(18)30789-X pmc: PMC6086934 SRA: SRP135960

Cell 174 (4) 999-1014.e22 [2018-08-09; online 2018-08-11]

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

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF

pii: 10.1038/s41598-018-29920-7 pmc: PMC6085348 European Nucleotide Archive: PRJEB20562

Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]

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

SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion.

Quintana MDP, Ch'ng JH, Zandian A, ..., Chan S, Wahlgren M

pii: PONE-D-18-10007 pmc: PMC6084945

PLoS ONE 13 (8) e0201669 [2018-08-09; online 2018-08-09]

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

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

Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K

pii: 10.1186/s13058-018-1022-y GEO: GSE97293 GEO: GSE97177

Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]

Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.

Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J

pii: S2211-1247(18)31107-0 GEO: GSE78928

Cell Rep 24 (6) 1397-1406 [2018-08-07; online 2018-08-09]

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

A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution.

Papoli Yazdi H, Ellegren H

pii: 5067707

Genome Biol Evol - (-) - [2018-08-07; online 2018-08-07]

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

Proteomic Biomarkers for Incident Aortic Stenosis Requiring Valvular Replacement

Ljungberg J, Janiec M, Bergdahl IA, ..., Fall T, Söderberg S

Circulation 138 (6) 590-599 [2018-08-07; online 2018-08-07]

Modeling the structural implications of an alternatively spliced Exoc3l2, a paralog of the tunneling nanotube-forming M-Sec

O’Callaghan P, Zarb Y, Noborn F, Kreuger J

PLoS ONE 13 (8) e0201557 [2018-08-07; online 2018-08-07]

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

Thermodynamics of Hg(II) Bonding to Thiol Groups in Suwannee River Natural Organic Matter Resolved by Competitive Ligand Exchange, Hg LIII-Edge EXAFS and 1H NMR Spectroscopy

Song Y, Jiang T, Liem-Nguyen V, ..., Björn E, Skyllberg U

Environ. Sci. Technol. 52 (15) 8292-8301 [2018-08-07; online 2018-07-07]

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.

Nascimento FJA, Lallias D, Bik HM, Creer S

pii: 10.1038/s41598-018-30179-1 pmc: PMC6078945 figshare: doi:10.6084/m9.figshare.4993667

Sci Rep 8 (1) 11737 [2018-08-06; online 2018-08-06]

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

Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source

Liu T, Sun L, Nordberg Å, Schnürer A

Microorganisms 6 (3) 80 [2018-08-05; online 2018-08-05]

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

Impact in Plasma Metabolome as Effect of Lifestyle Intervention for Weight-Loss Reveals Metabolic Benefits in Metabolically Healthy Obese Women

Almanza-Aguilera E, Brunius C, Bernal-Lopez MR, ..., Landberg R, Andres-Lacueva C

J. Proteome Res. 17 (8) 2600-2610 [2018-08-03; online 2018-06-07]

Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma

Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM

SLAS DISCOVERY: Advancing Life Sciences R&D - (-) 247255521879141 [2018-08-03; online 2018-08-03]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service]

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits

Redondo MA, Boberg J, Stenlid J, Oliva J

ISME J - (-) - [2018-08-02; online 2018-08-02]

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

Sulfonyl Fluorides (SFs): More Than Click Reagents?

Chinthakindi PK, Arvidsson PI

Eur. J. Org. Chem. 2018 (27-28) 3648-3666 [2018-08-01; online 2018-07-06]

Drug Discovery and Development (DDD) [Technology development]

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling

Lopez-Fernandez M, Broman E, Turner S, ..., Bertilsson S, Dopson M

BioProject: PRJNA431355 SRA: SRP131350

FEMS Microbiol. Ecol. 94 (8) - [2018-08-01; online 2018-06-19]

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

CD93 promotes β1 integrin activation and fibronectin fibrillogenesis during tumor angiogenesis.

Lugano R, Vemuri K, Yu D, ..., Dejana E, Dimberg A

pii: 97459 pmc: PMC6063507

J. Clin. Invest. 128 (8) 3280-3297 [2018-08-01; online 2018-06-25]

Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Service]

RNA velocity of single cells.

La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV

pii: 10.1038/s41586-018-0414-6 pmc: PMC6130801 mid: EMS78511

Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]

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

Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy

Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC

SRA: SRP102619

Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]

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

An imidazole based H-Phe-Phe-NH 2 peptidomimetic with anti-allodynic effect in spared nerve injury mice

Skogh A, Lesniak A, Sköld C, ..., Hallberg M, Sandström A

Bioorganic & Medicinal Chemistry Letters 28 (14) 2446-2450 [2018-08-00; online 2018-08-00]

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

Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.

Lin Y, van Duyvenvoorde HA, Liu H, ..., Wit JM, Larsson O

pii: EJE-18-0176

Eur. J. Endocrinol. 179 (2) 85-95 [2018-08-00; online 2018-05-22]

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

Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.

Thörnqvist L, Ohlin M

pii: S2352-3409(18)30478-5 pmc: PMC5992955 European Nucleotide Archive: PRJEB18926

Data Brief 19 (-) 337-352 [2018-08-00; online 2018-05-04]

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

Effect of the paste-anode interface under impressed current cathodic protection in concrete structures

Zhang EQ, Tang L, Bernin D, Jansson H

Materials and Corrosion 69 (8) 1104-1116 [2018-08-00; online 2018-03-06]

Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips

Bra¨nnstro¨m K, Gharibyan AL, Islam T, ..., Pamren A, Olofsson A

Data Brief 19 (-) 1166-1170 [2018-08-00; online 2018-08-00]

Cryo-EM [Technology development]

Delineating closely related dinoflagellate lineages using phylotranscriptomics.

Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K

J. Phycol. 54 (4) 571-576 [2018-08-00; online 2018-06-13]

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

Epigenetics in pediatric acute lymphoblastic leukemia.

Nordlund J, Syvänen AC

pii: S1044-579X(17)30091-3

Semin. Cancer Biol. 51 (-) 129-138 [2018-08-00; online 2017-09-05]

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

Sex-specific manifestation of genetic risk for attention deficit hyperactivity disorder in the general population.

Martin J, Taylor MJ, Rydell M, ..., Thapar A, Lichtenstein P

pmc: PMC6055636

J Child Psychol Psychiatry 59 (8) 908-916 [2018-08-00; online 2018-02-16]

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

Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

Birgisson H, Tsimogiannis K, Freyhult E, Kamali-Moghaddam M

Transl Oncol 11 (4) 1034-1043 [2018-08-00; online 2018-08-00]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Characterization of Swedish Campylobacter coli clade 2 and clade 3 water isolates.

Nilsson A, Skarp A, Johansson C, ..., Engstrand L, Rautelin H

pmc: PMC6079167

Microbiologyopen 7 (4) e00583 [2018-08-00; online 2018-02-09]

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

Detailed analysis of the plasma extracellular vesicle proteome after separation from lipoproteins

Karimi N, Cvjetkovic A, Jang SC, ..., Lötvall J, Lässer C

Cell. Mol. Life Sci. 75 (15) 2873-2886 [2018-08-00; online 2018-02-13]

Centre for Cellular Imaging [Service] Glycoproteomics [Service]

A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 – Review of the literature

Gudmundsson S, Annerén G, Marcos-Alcalde Í, ..., Gómez-Puertas P, Bondeson ML

European Journal of Medical Genetics - (-) - [2018-08-00; online 2018-08-00]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage.

Matic LP, Jesus Iglesias M, Vesterlund M, ..., Odeberg J, Hedin U

pii: S2452-302X(18)30096-2 pmc: PMC6115646

JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]

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

Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

Cedernaes J, Schönke M, Westholm JO, ..., Zierath JR, Benedict C

Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]

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

Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

Sundell GN, Arnold R, Ali M, ..., Chi CN, Ivarsson Y

Mol. Syst. Biol. 14 (8) e8129 [2018-08-00; online 2018-08-20]

Drug Discovery and Development (DDD) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.

Lee JJ, Wedow R, Okbay A, ..., Benjamin DJ, Cesarini D

pii: 10.1038/s41588-018-0147-3

Nat. Genet. 50 (8) 1112-1121 [2018-08-00; online 2018-07-23]

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

Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation.

Gliga AR, Engström K, Kippler M, ..., Raqib R, Broberg K

pii: 10.1007/s00204-018-2239-3 pmc: PMC6063321

Arch. Toxicol. 92 (8) 2487-2500 [2018-08-00; online 2018-06-08]

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

A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.

Jerlström Hultqvist J, Warsi O, Söderholm A, ..., Selmer M, Andersson DI

pii: 10.1038/s41559-018-0568-5

Nat Ecol Evol 2 (8) 1321-1330 [2018-08-00; online 2018-05-28]

Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates

Nilsson L, Pamrén A, Islam T, ..., Gharibyan AL, Olofsson A

Journal of Molecular Biology 430 (17) 2722-2733 [2018-08-00; online 2018-08-00]

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.

Markussen T, Happel EM, Teikari JE, ..., Middelboe M, Kisand V

Environ. Microbiol. 20 (8) 3083-3099 [2018-08-00; online 2018-09-19]

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

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.

Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF

pii: sdata2018146 pmc: PMC6067050 European Nucleotide Archive: PRJEB22997 SRA: SRP058493 figshare: https://doi.org/10.6084/m9.figshare.c.3831631 SRA: SRP077551

Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]

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

Regulation of Neuronal Na,K-ATPase by Extracellular Scaffolding Proteins

Liebmann T, Fritz N, Kruusmägi M, ..., Aperia A, Brismar H

Int J Mol Sci 19 (8) 2214 [2018-07-29; online 2018-07-29]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service]

Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat

Sigeman H, Ponnikas S, Videvall E, ..., Naurin S, Hansson B

Genes 9 (8) 373 [2018-07-26; online 2018-07-26]

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

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.

Berner C, Bertos-Fortis M, Pinhassi J, Legrand C

pmc: PMC6068395 SRA: SRP120581

Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]

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

A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.

Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA

pii: 10.1038/s41419-018-0865-6 pmc: PMC6057880

Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]

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

The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis.

Haapasalo K, Koskinen LLE, Suvilehto J, ..., Jokiranta TS, Saavalainen P

pii: IAI.00304-18

Infect. Immun. - (-) - [2018-07-23; online 2018-07-23]

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

Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics.

Pett C, Nasir W, Sihlbom C, ..., Nilsson J, Westerlind U

Angew. Chem. Int. Ed. Engl. 57 (30) 9320-9324 [2018-07-20; online 2018-06-20]

Glycoproteomics [Technology development]

Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs

Blomström AL, Ye X, Fossum C, Wallgren P, Berg M

Viruses 10 (7) 382 [2018-07-20; online 2018-07-20]

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

Mebendazole stimulates CD14+ myeloid cells to enhance T-cell activation and tumour cell killing.

Rubin J, Mansoori S, Blom K, ..., Nygren P, Larsson R

pii: 25713 pmc: PMC6089388

Oncotarget 9 (56) 30805-30813 [2018-07-20; online 2018-07-20]

Drug Discovery and Development (DDD) [Service]

Disruption of a GATA1-binding motif upstream of XG/PBDX abolishes Xga expression and resolves the Xg blood group system.

Möller M, Lee YQ, Vidovic K, ..., Storry JR, Olsson ML

pii: blood-2018-03-842542

Blood 132 (3) 334-338 [2018-07-19; online 2018-05-10]

Targeted and Structural Proteomics [Collaborative]

Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.

Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M

pii: 10.1007/s00248-018-1229-6 BioProject: PRJNA323408

Microb. Ecol. - (-) - [2018-07-17; online 2018-07-17]

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

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.

Saravanan R, Holdbrook DA, Petrlova J, ..., Malmsten M, Schmidtchen A

pii: 10.1038/s41467-018-05242-0 pmc: PMC6050251

Nat Commun 9 (1) 2762 [2018-07-17; online 2018-07-17]

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A

SRA: SRP131660 Zenodo: 10.5281/zenodo.1162653

PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]

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

Microdeletion of 7p12.1p13, including IKZF1, causes intellectual impairment, overgrowth, and susceptibility to leukaemia.

Järviaho T, Zachariadis V, Tesi B, ..., Harila-Saari A, Nordgren A

Br. J. Haematol. - (-) - [2018-07-13; online 2018-07-13]

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

Bacterial Outer Membrane Vesicles Induce Vitronectin Release Into the Bronchoalveolar Space Conferring Protection From Complement-Mediated Killing

Paulsson M, Che KF, Ahl J, ..., Lindén A, Riesbeck K

Front Microbiol 9 (-) - [2018-07-13; online 2018-07-13]

Biaryl sulfonamide motifs up- or down-regulate ion channel activity by activating voltage sensors

Liin SI, Lund PE, Larsson JE, ..., Wallner B, Elinder F

J. Gen. Physiol. - (-) jgp.201711942 [2018-07-12; online 2018-07-12]

Chemical Biology Consortium Sweden (CBCS) [Service]

Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.

Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U

pii: 10.1038/s41388-018-0400-3

Oncogene - (-) - [2018-07-11; online 2018-07-11]

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

Untargeted 1H NMR-Based Metabolomics Analysis of Urine and Serum Profiles after Consumption of Lentils, Chickpeas, and Beans: An Extended Meal Study To Discover Dietary Biomarkers of Pulses

Madrid-Gambin F, Brunius C, Garcia-Aloy M, ..., Landberg R, Andres-Lacueva C

J. Agric. Food Chem. 66 (27) 6997-7005 [2018-07-11; online 2018-06-19]

Autoantibody profiling in intraocular fluid of patients with uveitis.

Ten Berge JC, Schreurs MW, van Rosmalen J, Rothova A

pii: S0014-4835(18)30007-1

Exp. Eye Res. 176 (-) 141-146 [2018-07-10; online 2018-07-10]

Autoimmunity and Serology Profiling [Service]

Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury.

Kapur R, Kim M, Rebetz J, ..., Speck ER, Semple JW

pii: bloodadvances.2018018903 pmc: PMC6039664

Blood Adv 2 (13) 1651-1663 [2018-07-10; online 2018-07-12]

Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice

Torell F, Bennett K, Cereghini S, ..., Trygg J, Lundstedt T

J. Proteome Res. 17 (7) 2293-2306 [2018-07-06; online 2018-06-06]

Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages.

Baskaran S, Mayrhofer M, Kultima HG, ..., Isaksson A, Nelander S

pii: 4860173

Neuro-oncology 20 (8) 1080-1091 [2018-07-05; online 2018-02-21]

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

Multimodal Chemical Imaging of Amyloid Plaque Polymorphism Reveals Aβ Aggregation Dependent Anionic Lipid Accumulations and Metabolism

Michno W, Kaya I, Nyström S, ..., Zetterberg H, Hanrieder J

Anal. Chem. 90 (13) 8130-8138 [2018-07-03; online 2018-06-00]

Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103−CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium

Gibbs A, Buggert M, Edfeldt G, ..., Broliden K, Tjernlund A

- 218 (3) 453-465 [2018-07-02; online 2017-12-20]

BioImage Informatics [Collaborative]

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A

pii: 5035166 pmc: PMC6030852 GEO: GSE112698

Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]

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

OLMα2 Cells Bidirectionally Modulate Learning

Siwani S, França ASC, Mikulovic S, ..., Tort ABL, Kullander K

Neuron 99 (2) 404-412.e3 [2018-07-00; online 2018-07-00]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service]

Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.

Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A

pmc: PMC6011928 GENBANK: KJ701175 GENBANK: MG356789 GENBANK: MG356790 GENBANK: MG012806 GENBANK: MG012840 GENBANK: MG385064 GENBANK: MG385074

Microb Biotechnol 11 (4) 680-693 [2018-07-00; online 2017-12-04]

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

Increased Neuronal Differentiation of Neural Progenitor Cells Derived from Phosphovimentin-Deficient Mice

Chen M, Puschmann TB, Marasek P, ..., Wilhelmsson U, Pekny M

Mol Neurobiol 55 (7) 5478-5489 [2018-07-00; online 2017-09-27]

Genotype-Phenotype Correlation of PLOD2 Skeletal Dysplasias Using Structural Information.

Tham E, Grigelionis G, Hammarsjö A, Grigelioniene G

J. Bone Miner. Res. 33 (7) 1377-1378 [2018-07-00; online 2018-06-07]

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

A heterogeneous response of liver and skeletal muscle fat to the combination of a Paleolithic diet and exercise in obese individuals with type 2 diabetes: a randomised controlled trial

Otten J, Stomby A, Waling M, ..., Hauksson J, Olsson T

Diabetologia 61 (7) 1548-1559 [2018-07-00; online 2018-04-26]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Calcium-activated Chloride Channel Regulator 1 (CLCA1) Controls Mucus Expansion in Colon by Proteolytic Activity

Nyström EEL, Birchenough GMH, van der Post S, ..., Hansson GC, Johansson MEV

EBioMedicine 33 (-) 134-143 [2018-07-00; online 2018-07-00]

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.

Savage JE, Jansen PR, Stringer S, ..., Wright MJ, Posthuma D

pii: 10.1038/s41588-018-0152-6

Nat. Genet. 50 (7) 912-919 [2018-07-00; online 2018-06-25]

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

Porosity measurements in suspension plasma sprayed YSZ coatings using NMR cryoporometry and X-ray microscopy

Klement U, Ekberg J, Creci S, Kelly ST

J Coat Technol Res 15 (4) 753-757 [2018-07-00; online 2018-03-13]

Assessment of titanium dioxide nanoparticle toxicity in the rainbow trout (Onchorynchus mykiss) liver and gill cell lines RTL-W1 and RTgill-W1 under particular consideration of nanoparticle stability and interference with fluorometric assays

Lammel T, Sturve J

NanoImpact 11 (-) 1-19 [2018-07-00; online 2018-07-00]

The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey

Nygren K, Dubey M, Zapparata A, ..., Jensen DF, Karlsson M

SRA: SRX3389264 SRA: SRX3389265 SRA: SRX3389266 SRA: SRX3389267 SRA: SRX3389268 SRA: SRX3389269

Evol Appl 11 (6) 931-949 [2018-07-00; online 2018-03-14]

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

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning B, Dale R, Sjödin A, ..., Valieris R, Köster J

Nat Methods 15 (7) 475-476 [2018-07-00; online 2018-07-02]

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

Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

Holzwarth K, Köhler R, Philipsen L, ..., Niesner RA, Hauser AE

Cytometry 93 (9) 876-888 [2018-07-00; online 2018-08-14]

BioImage Informatics [Collaborative]

Identification of inhibitors of Tartrate-resistant acid phosphatase (TRAP/ACP5) activity by small-molecule screening

Reithmeier A, Lundbäck T, Haraldsson M, ..., Gustavsson AL, Andersson G

Chem Biol Drug Des 92 (1) 1255-1271 [2018-07-00; online 2018-03-30]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cytotoxic properties reveals structural diversity and novel glycan modifications.

Persson A, Gomez Toledo A, Vorontsov E, ..., Nilsson J, Larson G

pii: RA118.002971 pmc: PMC6028968

J. Biol. Chem. 293 (26) 10202-10219 [2018-06-29; online 2018-05-08]

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.

Garcia SL, Buck M, Hamilton JJ, ..., McMahon KD, Eiler A

pii: 3/3/e00202-18 pmc: PMC5976882

mSphere 3 (3) - [2018-06-27; online 2018-05-30]

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

appreci8: a pipeline for precise variant calling integrating 8 tools

Sandmann S, Karimi M, de Graaf AO, ..., Jansen JH, Dugas M

- - (-) - [2018-06-26; online 2018-06-26]

The contribution of common genetic risk variants for ADHD to a general factor of childhood psychopathology.

Brikell I, Larsson H, Lu Y, ..., Lichtenstein P, Martin J

pii: 10.1038/s41380-018-0109-2

Mol. Psychiatry - (-) - [2018-06-22; online 2018-06-22]

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

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution

Persson H, Kirik U, Thörnqvist L, ..., Levander F, Ohlin M

Front Immunol 9 (-) - [2018-06-21; online 2018-06-21]

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.

Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J

pii: 10.1038/s41467-018-04724-5 pmc: PMC6010471 European Genome-phenome Archive: EGAS0000100300

Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]

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

Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry

Kong Z, Jia S, Chabes AL, ..., Moritz T, Chabes A

Nucleic Acids Res 46 (11) e66-e66 [2018-06-20; online 2018-03-15]

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.

Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T

pii: 10.1038/s41598-018-27627-3 pmc: PMC6008462

Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]

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

Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks

De Vadder F, Grasset E, Mannerås Holm L, ..., Olofsson LE, Bäckhed F

Proc Natl Acad Sci USA 115 (25) 6458-6463 [2018-06-19; online 2018-06-04]

Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.

Feitosa MF, Kraja AT, Chasman DI, ..., Province MA, Levy D

pii: PONE-D-18-04838 dbGaP: phs000930

PLoS ONE 13 (6) e0198166 [2018-06-18; online 2018-06-18]

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

Poly(alkylidenimine) Dendrimers Functionalized with the Organometallic Moiety [Ru(η5-C5H5)(PPh3)2]+ as Promising Drugs Against Cisplatin-Resistant Cancer Cells and Human Mesenchymal Stem Cells

Gouveia M, Figueira J, Jardim M, ..., Rissanen K, Rodrigues J

Molecules 23 (6) 1471 [2018-06-17; online 2018-06-17]

Stabilized Cyclic Peptides as Scavengers of Autoantibodies: Neutralization of Anticitrullinated Protein/Peptide Antibodies in Rheumatoid Arthritis

Gunasekera S, Fernandes-Cerqueira C, Wennmalm S, ..., Jakobsson PJ, Göransson U

ACS Chem. Biol. 13 (6) 1525-1535 [2018-06-15; online 2018-04-09]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

Investigating Holocene human population history in North Asia using ancient mitogenomes.

Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A

pii: 10.1038/s41598-018-27325-0 pmc: PMC5997703 Popset: 1405681532

Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]

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

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

Nat Med - (-) - [2018-06-11; online 2018-06-11]

High-throughput Genome Engineering (HTGE) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

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

Cárdenas CA, González-Aravena M, Font A, ..., Malmberg M, Bongcam-Rudloff E

pii: 4935 pmc: PMC5994334

PeerJ 6 (-) e4935 [2018-06-07; online 2018-06-07]

Higher Concentrations of BCAAs and 3-HIB Are Associated with Insulin Resistance in the Transition from Gestational Diabetes to Type 2 Diabetes

Andersson-Hall U, Gustavsson C, Pedersen A, ..., Joelsson L, Holmäng A

Journal of Diabetes Research 2018 (-) 1-12 [2018-06-05; online 2018-06-05]

Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer

Karlsson J, Valind A, Holmquist Mengelbier L, ..., Bexell D, Gisselsson D

Nat Genet 50 (7) 944-950 [2018-06-04; online 2018-06-04]

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

Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers

Nilsson LKJ, Sharma A, Bhatnagar RK, Bertilsson S, Terenius O

BioProject: PRJEB23603

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-03-29]

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

Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

Schmidt R, Durling MB, de Jager V, ..., Karlsson M, Garbeva P

BioProject: PRJNA375977

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-04-30]

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

Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells

Maturi V, Morén A, Enroth S, Heldin CH, Moustakas A

Mol Oncol 12 (7) 1153-1174 [2018-06-00; online 2018-05-21]

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

Topology of membrane proteins — predictions, limitations and variations

Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A

Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]

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

Expression of ribosomal and actin network proteins and immunochemotherapy resistance in diffuse large B cell lymphoma patients

Bram Ednersson S, Stenson M, Stern M, ..., Hasselblom S, Andersson PO

Br J Haematol 181 (6) 770-781 [2018-06-00; online 2018-05-16]

Centre for Cellular Imaging [Service] Glycoproteomics [Service]

Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS.

Karlsson CAQ, Järnum S, Winstedt L, ..., Linder A, Malmström JA

pii: RA117.000525 pmc: PMC5986240

Mol. Cell Proteomics 17 (6) 1097-1111 [2018-06-00; online 2018-03-06]

Targeted and Structural Proteomics [Technology development]

Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees

Edwards KD, Takata N, Johansson M, ..., Ljung K, Eriksson ME

Plant, Cell & Environment 41 (6) 1468-1482 [2018-06-00; online 2018-04-15]

Liquid Norbornadiene Photoswitches for Solar Energy Storage

Dreos A, Wang Z, Udmark J, ..., Nielsen MB, Moth-Poulsen K

Adv. Energy Mater. 8 (18) 1703401 [2018-06-00; online 2018-03-25]

Neuronal Aβ42 is enriched in small vesicles at the presynaptic side of synapses

Yu Y, Jans DC, Winblad B, Tjernberg LO, Schedin-Weiss S

Life Sci. Alliance 1 (3) e201800028 [2018-06-00; online 2018-06-14]

Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14

Holechek J, Lease R, Thorsell AG, ..., Schüler H, Ferraris D

Bioorganic & Medicinal Chemistry Letters 28 (11) 2050-2054 [2018-06-00; online 2018-06-00]

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

Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Science of The Total Environment 625 (-) 1234-1246 [2018-06-00; online 2018-06-00]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol

Porseryd T, Reyhanian Caspillo N, Volkova K, ..., Olsson PE, Porsch-Hällström I

General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]

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

Paternally expressed imprinted genes associate with hybridization barriers in Capsella

Lafon-Placette C, Hatorangan MR, Steige KA, ..., Slotte T, Köhler C

GEO: GSE103209

NPLANTS 4 (6) 352-357 [2018-06-00; online 2018-05-28]

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

PubMed

A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep.

Pasandideh M, Rahimi-Mianji G, Gholizadeh M

J. Genet. 97 (2) 493-503 [2018-06-00; online 2018-06-23]

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

Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics

Šimura J, Antoniadi I, Široká J, ..., Ljung K, Novák O

Plant Physiol. 177 (2) 476-489 [2018-06-00; online 2018-04-27]

A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin creases

Stattin EL, Johansson J, Gudmundsson S, ..., Bondeson ML, Wilbe M

Am J Med Genet 176 (6) 1405-1410 [2018-06-00; online 2018-04-16]

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

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.

Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P

pii: 10.1038/s41593-018-0141-1

Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]

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

The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation

Brännström K, Islam T, Gharibyan AL, ..., Pamrén A, Olofsson A

Journal of Molecular Biology 430 (13) 1940-1949 [2018-06-00; online 2018-06-00]

Diminished CXCR5 expression in peripheral blood of patients with Sjögren's syndrome may relate to both genotype and salivary gland homing

Aqrawi LA, Ivanchenko M, Björk A, ..., Skarstein K, Wahren-Herlenius M

Clin Exp Immunol 192 (3) 259-270 [2018-06-00; online 2018-03-24]

Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award.

Mirgorodskaya E, Karlsson NG, Sihlbom C, Larson G, Nilsson CL

pii: 10.1007/s13361-018-1912-3 pmc: PMC6003999

J. Am. Soc. Mass Spectrom. 29 (6) 1065-1074 [2018-06-00; online 2018-04-11]

γ-glutamyl transpeptidase deficiency caused by a large homozygous intragenic deletion in GGT1.

Darin N, Leckström K, Sikora P, ..., Almén G, Asin-Cayuela J

pii: 10.1038/s41431-018-0122-6 pmc: PMC5974402

Eur. J. Hum. Genet. 26 (6) 808-817 [2018-06-00; online 2018-02-26]

Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Stockholm [Service]

Mechanistic study of hydrothermally aged Cu/SSZ-13 catalysts for ammonia-SCR

Leistner K, Kumar A, Kamasamudram K, Olsson L

Catalysis Today 307 (-) 55-64 [2018-06-00; online 2018-06-00]

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

Equilibrative nucleoside transporter 1 gene polymorphisms and clinical outcomes following acute coronary syndromes: findings from the PLATelet inhibition and patient Outcomes (PLATO) study.

Parker WAE, Eriksson N, Becker RC, ..., Storey RF, PLATO Investigators

Platelets - (-) 1-10 [2018-05-31; online 2018-05-31]

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

Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.

Eriksson D, Bianchi M, Landegren N, ..., Rosengren Pielberg G, Kämpe O

pii: 10.1038/s41598-018-26842-2 pmc: PMC5976627

Sci Rep 8 (1) 8395 [2018-05-30; online 2018-05-30]

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

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).

Blåhed IM, Königsson H, Ericsson G, Spong G

pii: PONE-D-17-39125 pmc: PMC5976195 Zenodo: https://doi.org/10.5281/zenodo.1237474

PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]

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

Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

Davies G, Lam M, Harris SE, ..., Lencz T, Deary IJ

pii: 10.1038/s41467-018-04362-x pmc: PMC5974083

Nat Commun 9 (1) 2098 [2018-05-29; online 2018-05-29]

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

A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility

Wei B, Jolma A, Sahu B, ..., Taipale M, Taipale J

Nat Biotechnol 36 (6) 521-529 [2018-05-21; online 2018-05-21]

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.

Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N

pii: 10.1186/s12864-018-4746-2 pmc: PMC5960078 GEO: GSE95236

BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]

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

A mass spectrometry imaging approach for investigating how drug-drug interactions influence drug blood-brain barrier permeability.

Vallianatou T, Strittmatter N, Nilsson A, ..., Goodwin RJA, Andrén PE

pii: S1053-8119(18)30015-6

Neuroimage 172 (-) 808-816 [2018-05-15; online 2018-01-10]

National Resource for Mass Spectrometry Imaging [Technology development]

A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia.

Chen X, Gustafsson S, Whitington T, ..., Frostegård J, Magnusson PKE

pii: 4935077

Hum. Mol. Genet. 27 (10) 1809-1818 [2018-05-15; online 2018-03-17]

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

Quantitation of Endogenous Metabolites in Mouse Tumors Using Mass-Spectrometry Imaging.

Swales JG, Dexter A, Hamm G, ..., Critchlow SE, Goodwin RJA

Anal. Chem. 90 (10) 6051-6058 [2018-05-15; online 2018-04-26]

National Resource for Mass Spectrometry Imaging [Service]

Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

Castaño C, Lindahl BD, Alday JG, ..., Pera J, Bonet JA

New Phytol - (-) - [2018-05-14; online 2018-05-14]

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

Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.

Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S

pii: 10.1007/s00234-018-2033-1 pmc: PMC5995995

Neuroradiology - (-) - [2018-05-14; online 2018-05-14]

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

Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.

Zhou A, Taylor AE, Karhunen V, ..., Llewellyn DJ, Hyppönen E

pii: 10.1038/s41598-018-25919-2 pmc: PMC5951917

Sci Rep 8 (1) 7526 [2018-05-14; online 2018-05-14]

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

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Rossi Sebastiano M, Doak BC, Backlund M, ..., Matsson P, Kihlberg J

J. Med. Chem. 61 (9) 4189-4202 [2018-05-10; online 2018-04-02]

Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]

Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.

Vdovikova S, Gilfillan S, Wang S, ..., Wai SN, Hurtado A

pii: 10.1038/s41598-018-25308-9 pmc: PMC5943334

Sci Rep 8 (1) 7434 [2018-05-09; online 2018-05-09]

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

Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.

de Oliveira Otto MC, Lemaitre RN, Sun Q, ..., Siscovick DS, Mozaffarian D

pii: PONE-D-18-05019 pmc: PMC5940220

PLoS ONE 13 (5) e0196951 [2018-05-08; online 2018-05-08]

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

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K

pii: 25329 pmc: PMC5963621 GEO: GSE97293

Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]

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

Multiplexed Antigen Bead Arrays for the Assessment of Antibody Selectivity and Epitope Mapping.

Ayoglu B, Nilsson P, Schwenk JM

Methods Mol. Biol. 1785 (-) 239-248 [2018-05-02; online 2018-05-02]

Autoimmunity and Serology Profiling [Technology development] Translational Plasma Profiling [Technology development]

The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.

Steiner EM, Lyngsø J, Guy JE, ..., Schneider G, Schnell R

PDB: 6EWY

Proteins - (-) - [2018-05-02; online 2018-05-02]

High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding.

Sjöberg R, Andersson E, Hellström C, ..., Nilsson P, Ayoglu B

Methods Mol. Biol. 1785 (-) 231-238 [2018-05-02; online 2018-05-02]

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

BAP1 induces cell death via interaction with 14-3-3 in neuroblastoma.

Sime W, Niu Q, Abassi Y, ..., Fu H, Massoumi R

pii: 10.1038/s41419-018-0500-6 pmc: PMC5913307

Cell Death Dis 9 (5) 458 [2018-05-01; online 2018-05-01]

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.

Westbury MV, Hartmann S, Barlow A, ..., Dalén L, Hofreiter M

pii: 4924857 pmc: PMC5913678

Mol. Biol. Evol. 35 (5) 1225-1237 [2018-05-01; online 2018-03-13]

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

Array profiling reveals contribution of Cthrc1 to growth of the denervated rat urinary bladder.

Zhu B, Ekman M, Svensson D, ..., Uvelius B, Swärd K

Am. J. Physiol. Renal Physiol. 314 (5) F893-F905 [2018-05-01; online 2018-01-10]

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

O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K

pii: 1721764115

Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]

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

Pretreatment of anaerobic digester samples by hydrochloric acid for solution-state 1 H and 13 C NMR spectroscopic characterization of organic matter

Shakeri Yekta S, Hedenström M, Stehr JE, ..., Hertkorn N, Björn A

Chemosphere 199 (-) 201-209 [2018-05-00; online 2018-05-00]

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Wray NR, Ripke S, Mattheisen M, ..., Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium

pii: 10.1038/s41588-018-0090-3 pmc: PMC5934326 mid: NIHMS943355

Nat. Genet. 50 (5) 668-681 [2018-05-00; online 2018-04-26]

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

Sulfasalazine-Induced Agranulocytosis Is Associated With the Human Leukocyte Antigen Locus

Wadelius M, Eriksson N, Kreutz R, ..., Hallberg P, None

Clin Pharmacol Ther 103 (5) 843-853 [2018-05-00; online 2017-09-28]

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

Molecular barcoding of viral vectors enables mapping and optimization of mRNAtrans-splicing

Davidsson M, Díaz-Fernández P, Torroba M, ..., Lundberg C, Björklund T

RNA 24 (5) 673-687 [2018-05-00; online 2018-01-31]

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

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells

Guzzi N, Cieśla M, Ngoc PCT, ..., Hsieh AC, Bellodi C

Cell 173 (5) 1204-1216.e26 [2018-05-00; online 2018-05-00]

Inflammatory biomarker profiling in classical orthostatic hypotension: Insights from the SYSTEMA cohort

Johansson M, Ricci F, Aung N, ..., Melander O, Fedorowski A

International Journal of Cardiology 259 (-) 192-197 [2018-05-00; online 2018-05-00]

Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

Bolin S, Borgenvik A, Persson CU, ..., Weishaupt H, Swartling FJ

Oncogene 37 (21) 2850-2862 [2018-05-00; online 2018-03-07]

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

Uterine progesterone signaling is a target for metformin therapy in PCOS-like rats

Hu M, Zhang Y, Feng J, ..., Shao LR, Billig H

- 237 (2) 123-137 [2018-05-00; online 2018-05-00]

Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis

Suhm T, Kaimal JM, Dawitz H, ..., Andréasson C, Ott M

Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]

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

Identification of novel diagnostic biomarkers for deep venous thrombosis

Memon AA, Sundquist K, PirouziFard M, ..., Sundquist J, Zöller B

Br J Haematol 181 (3) 378-385 [2018-05-00; online 2018-04-19]

Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry-Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS.

Li L, Andrén PE, Sweedler JV

pii: 10.1007/s13361-018-1939-5

J. Am. Soc. Mass Spectrom. 29 (5) 801-806 [2018-05-00; online 2018-04-07]

National Resource for Mass Spectrometry Imaging [Service]

Kynurenine pathway is altered in patients with SLE and associated with severe fatigue

Åkesson K, Pettersson S, Ståhl S, ..., Svenungsson E, Idborg H

Lupus Sci Med 5 (1) e000254 [2018-05-00; online 2018-05-23]

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies

Pent M, Hiltunen M, Põldmaa K, ..., Ryberg M, Bahram M

www.mg-rast.org: mgp20495

Environ Microbiol 20 (5) 1641-1650 [2018-05-00; online 2018-03-25]

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

Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling.

Roswall P, Bocci M, Bartoschek M, ..., Eriksson U, Pietras K

pii: nm.4494 pmc: PMC5896729 mid: EMS75725

Nat. Med. 24 (4) 463-473 [2018-05-00; online 2018-03-12]

Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling.

Lund H, Pieber M, Parsa R, ..., Zhang XM, Harris RA

pii: 10.1038/s41590-018-0091-5

Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]

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

Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen

Felten J, Vahala J, Love J, ..., Mellerowicz EJ, Sundberg B

New Phytol 218 (3) 999-1014 [2018-05-00; online 2018-03-12]

Potentials and pitfalls of inverse fluorescence correlation spectroscopy

Wennmalm S

Methods 140-141 (-) 23-31 [2018-05-00; online 2018-05-00]

Advanced Light Microscopy (ALM) [Technology development]

Increasing sorghum yields by seed treatment with an aqueous extract of the plant Eclipta alba may involve a dual mechanism of hydropriming and suppression of fungal pathogens

Zida PE, Néya BJ, Stokholm MS, ..., Sérémé P, Lund OS

Crop Protection 107 (-) 48-55 [2018-05-00; online 2018-05-00]

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

Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature

Imgenberg-Kreuz J, Sandling JK, Björk A, ..., Syvänen AC, Nordmark G

Scand J Immunol 87 (5) e12662 [2018-05-00; online 2018-04-18]

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

DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus.

Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, ..., Syvänen AC, Sandling JK

pii: annrheumdis-2017-212379 pmc: PMC5909746

Ann. Rheum. Dis. 77 (5) 736-743 [2018-05-00; online 2018-02-01]

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

Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis

Pěnčík A, Casanova-Sáez R, Pilařová V, ..., Ljung K, Novák O

- 69 (10) 2569-2579 [2018-04-27; online 2018-03-03]

Rebooting Human Immunology.

Davis MM, Brodin P

Annu. Rev. Immunol. 36 (-) 843-864 [2018-04-26; online 2018-02-28]

Mass Cytometry [Collaborative]

Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging

Bernhem K, Blom H, Brismar H

Dryad: https://doi.org/10.5061/dryad.kc42g

PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]

Advanced Light Microscopy (ALM) [Technology development] Bioinformatics Compute and Storage [Service]

Experimental validation of predicted cancer genes using FRET

Guala D, Bernhem K, Blal HA, ..., Brismar H, Sonnhammer ELL

Methods Appl. Fluoresc. 6 (3) 035007 [2018-04-25; online 2018-04-25]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service]

Repeated evolution of self-compatibility for reproductive assurance.

Nieuwenhuis BPS, Tusso S, Bjerling P, ..., Wolf JBW, Immler S

pii: 10.1038/s41467-018-04054-6 pmc: PMC5915400

Nat Commun 9 (1) 1639 [2018-04-24; online 2018-04-24]

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

Autophagic flux blockage by accumulation of weakly basic tenovins leads to elimination of B-Raf mutant tumour cells that survive vemurafenib

Ladds MJGW, Pastor-Fernández A, Popova G, ..., Bhatia R, Laín S

OSF: https://osf.io/sreqf/?view_only=bd0c5cd611be481984ef164d5d15df3d

PLoS ONE 13 (4) e0195956 [2018-04-23; online 2018-04-23]

Drug Discovery and Development (DDD) [Service]

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B

Genes 9 (4) 225 [2018-04-23; online 2018-04-23]

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

Human erythrocyte-derived nanovesicles can readily be loaded with doxorubicin and act as anticancer agents.

Dubois L, Löf L, Larsson A, ..., Ronquist G, Ronquist KG

Cancer Res Front 4 (1) 13-26 [2018-04-20; online 2018-04-20]

PLA and Single Cell Proteomics [Technology development]

Eleven loci with new reproducible genetic associations with allergic disease risk.

Ferreira MAR, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

pii: S0091-6749(18)30558-X

J. Allergy Clin. Immunol. - (-) - [2018-04-19; online 2018-04-19]

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

Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.

Dussex N, von Seth J, Robertson BC, Dalén L

pii: genes9040220 pmc: PMC5924562 European Nucleotide Archive: PRJEB25924

Genes 9 (4) - [2018-04-19; online 2018-04-19]

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

A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome.

Bonfiglio F, Henström M, Nag A, ..., Zhernakova A, D'Amato M

GENBANK: rs17112758

Neurogastroenterol. Motil. - (-) e13358 [2018-04-19; online 2018-04-19]

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

Data quality of whole genome bisulfite sequencing on Illumina platforms.

Raine A, Liljedahl U, Nordlund J

pii: PONE-D-17-37428 pmc: PMC5905984 BioProject: PRJNA407440 GEO: GSE89213

PLoS ONE 13 (4) e0195972 [2018-04-18; online 2018-04-18]

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

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J

Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]

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

Genetic and Environmental Contributions to the Covariation Between Cardiometabolic Traits.

Chen X, Kuja-Halkola R, Chang Z, ..., Pedersen NL, Magnusson PKE

pii: JAHA.117.007806

J Am Heart Assoc 7 (9) - [2018-04-18; online 2018-04-18]

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

Complete Remission with Reduction of High-Risk Clones following Haploidentical NK-Cell Therapy against MDS and AML

Björklund AT, Carlsten M, Sohlberg E, ..., Ljunggren HG, Malmberg KJ

Clin. Cancer Res. 24 (8) 1834-1844 [2018-04-15; online 2018-02-14]

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

Granule-stored MUC5B mucins are packed by the non-covalent formation of N-terminal head-to-head tetramers

Trillo-Muyo S, Nilsson HE, Recktenwald CV, ..., Hebert H, Hansson GC

J. Biol. Chem. 293 (15) 5746-5754 [2018-04-13; online 2018-02-13]

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.

Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E

pii: 24808 pmc: PMC5929421 GEO: GSE109367

Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]

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

Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding.

Gustafsson R, Zhang S, Masuyer G, Dong M, Stenmark P

pii: toxins10040153 pmc: PMC5923319 PDB: 6ES1

Toxins (Basel) 10 (4) - [2018-04-12; online 2018-04-12]

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.

Morgunova E, Yin Y, Das PK, ..., Nilsson L, Taipale J

pii: 32963 pmc: PMC5896879

Elife 7 (-) - [2018-04-11; online 2018-04-11]

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

Active and inactive β1 integrins segregate into distinct nanoclusters in focal adhesions

Spiess M, Hernandez-Varas P, Oddone A, ..., Lakadamyali M, Strömblad S

J. Cell Biol. - (-) jcb.201707075 [2018-04-09; online 2018-04-09]

Expression levels of long non-coding RNAs are prognostic for AML outcome.

Mer AS, Lindberg J, Nilsson C, ..., Lehmann S, Rantalainen M

pii: 10.1186/s13045-018-0596-2 pmc: PMC5889529

J Hematol Oncol 11 (1) 52 [2018-04-07; online 2018-04-07]

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

Allele-selective RUNX1 binding regulates P1 blood group status by transcriptional control of A4GALT.

Westman JS, Stenfelt L, Vidovic K, ..., Kjellström S, Olsson ML

pii: blood-2017-08-803080

Blood 131 (14) 1611-1616 [2018-04-05; online 2018-02-08]

Female-specific Association Between Variants on Chromosome 9 and Self-reported Diagnosis of Irritable Bowel Syndrome.

Bonfiglio F, Zheng T, Garcia-Etxebarria K, ..., Zhernakova A, D'Amato M

pii: S0016-5085(18)30407-4

Gastroenterology - (-) - [2018-04-04; online 2018-04-04]

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

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

Gelali E, Custodio J, Girelli G, ..., Crosetto N, Bienko M

Methods Mol. Biol. 1766 (-) 303-333 [2018-04-02; online 2018-04-02]

Advanced FISH Technologies [Technology development]

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor

Boerema AP, Aibara S, Paul B, ..., Lindahl E, Amunts A

PDB: 6ERI EMDB: EMD-3941 EMDB: EMD-3942 EMDB: EMD-3943

NPLANTS 4 (4) 212-217 [2018-04-00; online 2018-04-02]

Effects of fixation on electrophysiology and structure of human jejunal villi

Casselbrant A, Helander HF

Microsc Res Tech 81 (4) 376-383 [2018-04-00; online 2018-01-11]

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Correction

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr Relat Cancer 25 (4) X1-X2 [2018-04-00; online 2018-04-00]

Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.

Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P

pii: S2352-3964(18)30094-X pmc: PMC5952343

EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]

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

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Wang H, Sikora P, Rutgersson C, ..., Larsson DGJ, Norder H

International Journal of Hygiene and Environmental Health 221 (3) 479-488 [2018-04-00; online 2018-04-00]

Bioinformatics Compute and Storage [Service] Clinical Genomics Gothenburg [Collaborative]

RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Onsbring H, Jamy M, Ettema TJG

GENBANK: GGGV00000000 SRA: SRP132767 data.mendeley.com: https://doi.org/10.17632/nmgz3m3ptn.1

Current Biology 28 (8) 1281-1288.e3 [2018-04-00; online 2018-04-00]

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

GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4 + T Cells and Is Immunosuppressive in Type 1 Diabetes

Bhandage AK, Jin Z, Korol SV, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 30 (-) 283-294 [2018-04-00; online 2018-04-00]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

Identification of Poly(ADP-Ribose) Polymerase Macrodomain Inhibitors Using an AlphaScreen Protocol

Ekblad T, Verheugd P, Lindgren AE, ..., Elofsson M, Schüler H

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (4) 353-362 [2018-04-00; online 2018-01-09]

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

Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in

Han X, Sun R, Sandalova T, Achour A

pii: rsob.170248 pmc: PMC5936713

Open Biol 8 (4) - [2018-04-00; online 2018-04-20]

Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.

Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H

pii: pp.17.01590 pmc: PMC5884607

Plant Physiol. 176 (4) 2851-2870 [2018-04-00; online 2018-02-27]

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

The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.

Thörnqvist L, Ohlin M

pii: S0161-5890(18)30043-9 European Nucleotide Archive: PRJEB18926

Mol. Immunol. 96 (-) 61-68 [2018-04-00; online 2018-02-28]

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

Identification of Potential MR-Derived Biomarkers for Tumor Tissue Response to 177Lu-Octreotate Therapy in an Animal Model of Small Intestine Neuroendocrine Tumor.

Montelius M, Spetz J, Jalnefjord O, ..., Ljungberg M, Forssell-Aronsson E

pii: S1936-5233(17)30374-1 pmc: PMC5772005

Transl Oncol 11 (2) 193-204 [2018-04-00; online 2018-01-11]

Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion

Unnersjö-Jess D, Scott L, Sevilla SZ, ..., Blom H, Brismar H

Kidney International 93 (4) 1008-1013 [2018-04-00; online 2018-04-00]

Advanced Light Microscopy (ALM) [Technology development] Bioinformatics Compute and Storage [Service]

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods

Krizsan SJ, Mateos-Rivera A, Bertilsson S, ..., Gidlund H, Huhtanen P

Ecol Evol 8 (8) 4183-4196 [2018-04-00; online 2018-03-31]

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

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

Mahajan A, Wessel J, Willems SM, ..., Rotter JI, McCarthy MI

pii: 10.1038/s41588-018-0084-1 pmc: PMC5898373 mid: NIHMS938867

Nat. Genet. 50 (4) 559-571 [2018-04-00; online 2018-04-09]

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

Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Vanderpool D, Bracewell RR, McCutcheon JP

Mol Ecol 27 (8) 2077-2094 [2018-04-00; online 2017-11-23]

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

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, ..., MEGASTROKE Consortium , MEGASTROKE Consortium:

pii: 10.1038/s41588-018-0058-3

Nat. Genet. 50 (4) 524-537 [2018-04-00; online 2018-03-12]

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

Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids

Bergenholm D, Gossing M, Wei Y, Siewers V, Nielsen J

Biotechnol. Bioeng. 115 (4) 932-942 [2018-04-00; online 2018-01-24]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes.

Klaesson A, Grannas K, Ebai T, ..., Söderberg O, Landegren U

pii: 10.1038/s41598-018-23582-1 pmc: PMC5876389

Sci Rep 8 (1) 5400 [2018-03-29; online 2018-03-29]

PLA and Single Cell Proteomics [Technology development]

Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.

Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A

pmc: PMC5874392 ArrayExpress: E-MTAB-5143

Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]

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

Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

Valdiosera C, Günther T, Vera-Rodríguez JC, ..., Smith CI, Jakobsson M

BioProject: PRJEB23467

Proc Natl Acad Sci USA 115 (13) 3428-3433 [2018-03-27; online 2018-03-12]

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

Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents.

Ciuculete DM, Boström AE, Tuunainen AK, ..., Mwinyi J, Schiöth HB

pii: S0022-3956(17)31054-3

J Psychiatr Res 102 (-) 44-51 [2018-03-26; online 2018-03-26]

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

AMYCNE: Confident copy number assessment using whole genome sequencing data.

Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A

pii: PONE-D-17-18300 pmc: PMC5868770

PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]

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

Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome

Ramqvist T, Näsman A, Franzén B, ..., Dalianis T, Munck-Wikland E

Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

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

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM

SRA: SRP132598 SRA: SRP132591

New Phytol - (-) - [2018-03-24; online 2018-03-24]

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

A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.

Jiang J, Thalamuthu A, Ho JE, ..., Sachdev PS, Mather KA

pmc: PMC5876753

Front Genet 9 (-) 97 [2018-03-23; online 2018-03-23]

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

Peptide ion channel toxins from the bootlace worm, the longest animal on Earth.

Jacobsson E, Andersson HS, Strand M, ..., Tytgat J, Göransson U

pii: 10.1038/s41598-018-22305-w pmc: PMC5864730

Sci Rep 8 (1) 4596 [2018-03-22; online 2018-03-22]

National Resource for Mass Spectrometry Imaging [Service]

Introduction of Intrinsic Kinetics of Protein–Ligand Interactions and Their Implications for Drug Design

Linkuvienė V, Talibov VO, Danielson UH, Matulis D

J. Med. Chem. 61 (6) 2292-2302 [2018-03-22; online 2018-02-21]

Drug Discovery and Development (DDD) [Service]

Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.

Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J

pii: S0092-8674(18)30148-X pmc: PMC5871719 GEO: GSE93976

Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]

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

A Space Efficient Direct Access Data Compression Approach for Mass Spectrometry Imaging.

Källback P, Nilsson A, Shariatgorji M, Andrén PE

Anal. Chem. 90 (6) 3676-3682 [2018-03-20; online 2018-03-08]

National Resource for Mass Spectrometry Imaging [Technology development]

Molecular mechanism of ATP versus GTP selectivity of adenylate kinase

Rogne P, Rosselin M, Grundström C, ..., Sauer UH, Wolf-Watz M

Proc Natl Acad Sci USA 115 (12) 3012-3017 [2018-03-20; online 2018-03-05]

ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.

Bremer HD, Landegren N, Sjöberg R, ..., Kämpe O, Hansson-Hamlin H

pii: 10.1038/s41598-018-23034-w pmc: PMC5859008

Sci Rep 8 (1) 4852 [2018-03-19; online 2018-03-19]

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

Myopathy With SQSTM1 and TIA1 Variants: Clinical and Pathological Features.

Niu Z, Pontifex CS, Berini S, ..., Pfeffer G, Milone M

pmc: PMC5868303

Front Neurol 9 (-) 147 [2018-03-19; online 2018-03-19]

Cell Profiling [Service]

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res 46 (5) 2159-2168 [2018-03-16; online 2018-02-01]

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

Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.

Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A

pii: PONE-D-17-41609 pmc: PMC5856271

PLoS ONE 13 (3) e0193547 [2018-03-16; online 2018-03-16]

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

Clinical Presentation of a Complex Neurodevelopmental Disorder Caused by Mutations in ADNP.

Van Dijck A, Vulto-van Silfhout AT, Cappuyns E, ..., Vandeweyer G, Kooy RF

pii: S0006-3223(18)31303-9 pmc: PMC6139063 mid: NIHMS980073

Biol. Psychiatry - (-) - [2018-03-15; online 2018-03-15]

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

Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness

Minina EA, Moschou PN, Vetukuri RR, ..., Hofius D, Bozhkov PV

- 69 (6) 1415-1432 [2018-03-14; online 2018-01-20]

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

Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H

pmc: PMC5861219 European Nucleotide Archive: ERP012528

Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]

High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.

Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G

pii: PONE-D-17-38103 pmc: PMC5846771 SRA: SRP121435

PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]

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

Increased thermal stability of nanocellulose composites by functionalization of the sulfate groups on cellulose nanocrystals with azetidinium ions

Börjesson M, Sahlin K, Bernin D, Westman G

J. Appl. Polym. Sci. 135 (10) 45963 [2018-03-10; online 2017-11-08]

Darkened leaves use different metabolic strategies for senescence and survival

Law SR, Chrobok D, Juvany M, ..., Gardestrom P, Keech O

Plant Physiol. - (-) pp.00062.2018 [2018-03-09; online 2018-03-09]

Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.

Coleman JRI, Bryois J, Gaspar HA, ..., Posthuma D, Breen G

pii: 10.1038/s41380-018-0040-6

Mol. Psychiatry - (-) - [2018-03-08; online 2018-03-08]

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

Genome-wide analysis yields new loci associating with aortic valve stenosis.

Helgadottir A, Thorleifsson G, Gretarsdottir S, ..., Holm H, Stefansson K

pii: 10.1038/s41467-018-03252-6 pmc: PMC5840367

Nat Commun 9 (1) 987 [2018-03-07; online 2018-03-07]

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

Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis.

Leonard D, Svenungsson E, Dahlqvist J, ..., Criswell LA, Rönnblom L

pii: annrheumdis-2017-212614

Ann. Rheum. Dis. - (-) - [2018-03-07; online 2018-03-07]

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

Global analysis of A-to-I RNA editing reveals association with common disease variants

Franzén O, Ermel R, Sukhavasi K, ..., Schadt EE, Björkegren JLM

PeerJ 6 (-) e4466 [2018-03-06; online 2018-03-06]

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

DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia.

Borssén M, Nordlund J, Haider Z, ..., Lönnerholm G, Degerman S

pii: 466 pmc: PMC5836434

Clin Epigenetics 10 (-) 31 [2018-03-05; online 2018-03-05]

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

The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Hafstrand I, Doorduijn EM, Sun R, ..., van Hall T, Achour A

pii: jimmunol.1700228

J. Immunol. - (-) - [2018-03-05; online 2018-03-05]

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV

pii: PONE-D-17-39048 pmc: PMC5834160 ENA: PRJEB22154

PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]

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

A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.

Sung YJ, Winkler TW, de Las Fuentes L, ..., Rao DC, Chasman DI

pii: S0002-9297(18)30017-X

Am. J. Hum. Genet. 102 (3) 375-400 [2018-03-01; online 2018-02-15]

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

Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.

James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I

pii: 4792999

Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]

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

Genetic variants influencing phenotypic variance heterogeneity.

Ek WE, Rask-Andersen M, Karlsson T, ..., Gyllensten U, Johansson Å

pii: 4792998

Hum. Mol. Genet. 27 (5) 799-810 [2018-03-01; online 2018-01-13]

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

Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Lillie M, Sheng ZY, Honaker CF, ..., Siegel PB, Carlborg Ö

Poult. Sci. 97 (3) 781-790 [2018-03-01; online 2017-12-20]

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

Striatal Tyrosine Hydroxylase Is Stimulated via TAAR1 by 3-Iodothyronamine, But Not by Tyramine or β-Phenylethylamine.

Zhang X, Mantas I, Alvarsson A, ..., Chergui K, Svenningsson P

pmc: PMC5837966

Front Pharmacol 9 (-) 166 [2018-03-01; online 2018-03-01]

National Resource for Mass Spectrometry Imaging [Service]

Sexual dimorphism in the width of the mouse synaptonemal complex

Agostinho A, Kouznetsova A, Hernández-Hernández A, ..., Brismar H, Höög C

J Cell Sci 131 (5) jcs212548 [2018-03-01; online 2018-02-02]

The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Balasundaram SV, Hess J, Durling MB, ..., Eastwood DC, Skrede I

BioProject: PRJNA412961 Dryad: https://doi.org/10.5061/dryad.28sb6

ISME J 12 (3) 791-801 [2018-03-00; online 2018-01-05]

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

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr Relat Cancer 25 (3) 367-380 [2018-03-00; online 2018-03-00]

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans

Mardinoglu A, Wu H, Bjornson E, ..., Taskinen MR, Borén J

Cell Metabolism 27 (3) 559-571.e5 [2018-03-00; online 2018-03-00]

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Marathe NP, Janzon A, Kotsakis SD, ..., Kristiansson E, Larsson DGJ

Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]

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

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Bravo AG, Zopfi J, Buck M, ..., Poté J, Cosio C

BioProject: PRJEB20838

ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]

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

Cleaner fish escape salmon farms and hybridize with local wrasse populations

Faust E, Halvorsen KT, Andersen P, Knutsen H, André C

BioProject: PRJNA415388 Dryad: https://doi.org/10.5061/dryad.tv553

R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]

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

Affinity of charcoals for different forms of radioactive organic iodine

Aneheim E, Bernin D, Foreman MRS

Nuclear Engineering and Design 328 (-) 228-240 [2018-03-00; online 2018-03-00]

Proteomic Profiling for Cardiovascular Biomarker Discovery in Orthostatic Hypotension

Johansson M, Ricci F, Aung N, ..., Melander O, Fedorowski A

Hypertension 71 (3) 465-472 [2018-03-00; online 2018-03-00]

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence

Hagenbo A, Kyaschenko J, Clemmensen KE, Lindahl BD, Fransson P

J Ecol 106 (2) 490-501 [2018-03-00; online 2018-02-13]

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

Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.

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

pii: S1055-7903(17)30354-8

Mol. Phylogenet. Evol. 120 (-) 28-32 [2018-03-00; online 2017-12-02]

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

Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.

Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y

pii: PPATHOGENS-D-17-02350 pmc: PMC5851638

PLoS Pathog. 14 (3) e1006936 [2018-03-00; online 2018-03-02]

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

Galectin-3 levels relate in children to total body fat, abdominal fat, body fat distribution, and cardiac size

Dencker M, Arvidsson D, Karlsson MK, ..., Andersen LB, Thorsson O

Eur J Pediatr 177 (3) 461-467 [2018-03-00; online 2018-01-11]

CEP128 Localizes to the Subdistal Appendages of the Mother Centriole and Regulates TGF-β/BMP Signaling at the Primary Cilium

Mönnich M, Borgeskov L, Breslin L, ..., Larsen LA, Pedersen LB

Cell Rep 22 (10) 2584-2592 [2018-03-00; online 2018-03-00]

Advanced Light Microscopy (ALM) [Service] Cell Profiling [Collaborative]

Cardiovascular disease in systemic lupus erythematosus is associated with increased levels of biomarkers reflecting receptor-activated apoptosis

Wigren M, Svenungsson E, Mattisson IY, ..., Fredrikson GN, Nilsson J

Atherosclerosis 270 (-) 1-7 [2018-03-00; online 2018-03-00]

Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

Costeira-Paulo J, Gault J, Popova G, ..., Marklund EG, Landreh M

Cell Chem Biol 25 (3) 309-317.e4 [2018-03-00; online 2018-03-00]

Drug Discovery and Development (DDD) [Collaborative]

Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides.

Duarte M, Subedi P, Yilmaz E, ..., Laurell T, Ekström S

J. Mol. Recognit. 31 (3) - [2018-03-00; online 2017-10-12]

Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative

Brueffer C, Vallon-Christersson J, Grabau D, ..., Borg Å, Saal LH

JCO Precision Oncology - (2) 1-18 [2018-03-00; online 2018-03-00]

Current applications of antibody microarrays.

Chen Z, Dodig-Crnković T, Schwenk JM, Tao SC

pii: 9184 pmc: PMC5830343

Clin Proteomics 15 (-) 7 [2018-02-28; online 2018-02-28]

Translational Plasma Profiling [Collaborative]

Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level.

Charkoftaki G, Rattray NJW, Andrén PE, ..., Johnson CH, Vasiliou V

pii: 10.1186/s40246-018-0142-x pmc: PMC5828306

Hum Genomics 12 (1) 10 [2018-02-27; online 2018-02-27]

National Resource for Mass Spectrometry Imaging [Service]

The ZBED6–IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals

Younis S, Schönke M, Massart J, ..., Zierath JR, Andersson L

SRA: SRP128271

Proc Natl Acad Sci USA 115 (9) E2048-E2057 [2018-02-27; online 2018-02-12]

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

Brain Tissue Sample Stabilization and Extraction Strategies for Neuropeptidomics.

Fridjonsdottir E, Nilsson A, Wadensten H, Andrén PE

Methods Mol. Biol. 1719 (-) 41-49 [2018-02-25; online 2018-02-25]

National Resource for Mass Spectrometry Imaging [Technology development]

The STAT4 SLE risk allele rs7574865[T] is associated with increased IL-12-induced IFN-γ production in T cells from patients with SLE

Hagberg N, Joelsson M, Leonard D, ..., Bryceson YT, Rönnblom L

pii: annrheumdis-2017-212794

Ann. Rheum. Dis. - (-) - [2018-02-23; online 2018-02-23]

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

Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Bachmann JA, Tedder A, Laenen B, Steige KA, Slotte T

BioProject: PRJEB24927

G3 (Bethesda) 8 (4) 1327-1333 [2018-02-23; online 2018-02-23]

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

A molecular atlas of cell types and zonation in the brain vasculature.

Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C

pii: nature25739 GEO: GSE98816 GEO: GSE99058 GEO: GSE99235

Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]

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

Disruption of Accumbens and Thalamic White Matter Connectivity Revealed by Diffusion Tensor Tractography in Young Men with Genetic Risk for Obesity

Olivo G, Latini F, Wiemerslage L, Larsson EM, Schiöth HB

Front Hum Neurosci 12 (-) - [2018-02-22; online 2018-02-22]

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

In Situ Target Engagement Studies in Adherent Cells

Axelsson H, Almqvist H, Otrocka M, ..., Lundbäck T, Seashore-Ludlow B

ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development]

Structural and Biophysical Characterization of Human EXTL3: Domain Organization, Glycosylation, and Solution Structure.

Awad W, Kjellström S, Svensson Birkedal G, Mani K, Logan DT

Biochemistry 57 (7) 1166-1177 [2018-02-20; online 2018-02-05]

Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.

Quintana MDP, Ch'ng JH, Moll K, ..., Qundos U, Wahlgren M

pii: 10.1038/s41598-018-21026-4 pmc: PMC5818650

Sci Rep 8 (1) 3262 [2018-02-19; online 2018-02-19]

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

Two novel colorectal cancer risk loci in the region on chromosome 9q22.32

Thutkawkorapin J, Mahdessian H, Barber T, ..., Jiao X, Lindblom A

Oncotarget 9 (13) - [2018-02-16; online 2018-01-30]

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

Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation

Wang X, Omar O, Vazirisani F, Thomsen P, Ekström K

PLoS ONE 13 (2) e0193059 [2018-02-15; online 2018-02-15]

Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density.

Byström S, Eklund M, Hong MG, ..., Schwenk JM, Gabrielson M

pii: 10.1186/s13058-018-0940-z pmc: PMC5813412

Breast Cancer Res. 20 (1) 14 [2018-02-14; online 2018-02-14]

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

Irreversible inhibition of cytosolic thioredoxin reductase 1 as a mechanistic basis for anticancer therapy.

Stafford WC, Peng X, Olofsson MH, ..., Linder S, Arnér ESJ

pii: 10/428/eaaf7444

Sci Transl Med 10 (428) - [2018-02-14; online 2018-02-16]

Advancing the immunoaffinity platform AFFIRM to targeted measurements of proteins in serum in the pg/ml range.

Säll A, Corbee D, Vikström S, ..., Persson H, Waldemarson S

pii: PONE-D-17-23519 pmc: PMC5810979 PeptideAtlas: PASS00852

PLoS ONE 13 (2) e0189116 [2018-02-13; online 2018-02-13]

Drug Discovery and Development (DDD) [Technology development]

Educated natural killer cells show dynamic movement of the activating receptor NKp46 and confinement of the inhibitory receptor Ly49A

Staaf E, Hedde PN, Bagawath Singh S, ..., Gratton E, Johansson S

Sci. Signal. 11 (517) eaai9200 [2018-02-13; online 2018-02-13]

Advanced Light Microscopy (ALM) [Service]

Dispersed Uniform Nanoparticles from a Macroscopic Organosilica Powder

Church TL, Bernin D, Garcia-Bennett AE, Hedin N

Langmuir 34 (6) 2274-2281 [2018-02-13; online 2018-02-05]

Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma.

Hu D, Ansari D, Pawłowski K, ..., Marko-Varga G, Andersson R

pii: 23929 pmc: PMC5839402

Oncotarget 9 (11) 9789-9807 [2018-02-09; online 2018-01-03]

The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

Couturier M, Lindås AC

Front Microbiol 9 (-) - [2018-02-08; online 2018-02-08]

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

A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer.

Wendel U, Persson N, Risinger C, ..., Jansson B, Blixt O

pii: PONE-D-17-37995 pmc: PMC5805250

PLoS ONE 13 (2) e0191872 [2018-02-08; online 2018-02-08]

Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.

Agudelo LZ, Ferreira DMS, Cervenka I, ..., Berggren P, Ruas JL

pii: S1550-4131(18)30053-6

Cell Metab. 27 (2) 378-392.e5 [2018-02-06; online 2018-02-08]

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

MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of estrogen and NGF signaling

Dzieran J, Rodriguez Garcia A, Westermark UK, ..., Lehtiö J, Arsenian-Henriksson M

Proc Natl Acad Sci USA 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel V, Hjerde E, Sterck L, ..., Binzer-Panchal M, Lantz H

F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

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

CheckQC: Quick quality control of Illumina sequencing runs

Åslin M, Brandt M, Dahlberg J

JOSS 3 (22) 556 [2018-02-05; online 2018-02-05]

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

Interferon γ treatment increases endocannabinoid and related N-acylethanolamine levels in T84 human colon carcinoma cells

Alhouayek M, Rankin L, Gouveia-Figueira S, Fowler CJ

British Journal of Pharmacology - (-) - [2018-02-05; online 2018-02-05]

Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit.

Rozman Grinberg I, Lundin D, Hasan M, ..., Logan DT, Sjöberg BM

pii: 31529 pmc: PMC5794259

Elife 7 (-) - [2018-02-01; online 2018-02-01]

Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.

Inturi R, Mun K, Singethan K, Schreiner S, Punga T

pii: JVI.01154-17 pmc: PMC5774890

J. Virol. 92 (3) - [2018-02-01; online 2018-01-17]

PLA and Single Cell Proteomics [Service]

De novo mutations implicate novel genes in systemic lupus erythematosus

Pullabhatla V, Roberts AL, Lewis MJ, ..., Syvänen AC, Vyse TJ

Hum Mol Genet 27 (3) 421-429 [2018-02-01; online 2017-11-21]

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

Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis

Darolti I, Wright AE, Pucholt P, Berlin S, Mank JE

BioProject: PRJEB15050

Mol Ecol 27 (3) 694-708 [2018-02-00; online 2018-01-22]

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

Formation of mercury methylation hotspots as a consequence of forestry operations

Eklöf K, Bishop K, Bertilsson S, ..., Kronberg RM, Bravo AG

Science of The Total Environment 613-614 (-) 1069-1078 [2018-02-00; online 2018-02-00]

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

Bacterial secretion of D-arginine controls environmental microbial biodiversity.

Alvarez L, Aliashkevich A, de Pedro MA, Cava F

pii: ismej2017176 pmc: PMC5776457

ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]

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

Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration

Pettersson-Klein AT, Izadi M, Ferreira DMS, ..., Griffin PR, Ruas JL

Mol Metab - (-) - [2018-02-00; online 2018-02-00]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders.

Stamouli S, Anderlid BM, Willfors C, ..., Tammimies K, Bölte S

pii: S183242741700069X

Twin Res Hum Genet 21 (1) 1-11 [2018-02-00; online 2018-01-08]

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

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, Boberg J, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

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

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.

McDonald MC, Ahren D, Simpfendorfer S, Milgate A, Solomon PS

Mol. Plant Pathol. 19 (2) 432-439 [2018-02-00; online 2017-03-12]

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

Red meat intake in chronic kidney disease patients: Two sides of the coin

Mafra D, Borges NA, Cardozo LFMdF, ..., Lindholm B, Stenvinkel P

Nutrition 46 (-) 26-32 [2018-02-00; online 2018-02-00]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

A convenient transesterification method for synthesis of AT2 receptor ligands with improved stability in human liver microsomes

Wannberg J, Isaksson R, Bremberg U, ..., Hallberg M, Larhed M

Bioorganic & Medicinal Chemistry Letters 28 (3) 519-522 [2018-02-00; online 2018-02-00]

Drug Discovery and Development (DDD) [Collaborative]

Human NUDT22 Is a UDP-Glucose/Galactose Hydrolase Exhibiting a Unique Structural Fold

Carter M, Jemth AS, Carreras-Puigvert J, ..., Helleday T, Stenmark P

PDB: 5LOR PDB: 5LOU

Structure 26 (2) 295-303.e6 [2018-02-00; online 2018-02-00]

Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

Borges F, Parent JS, van Ex F, ..., Köhler C, Martienssen RA

GEO: GSE106117 GEO: GSE106112 GEO: GSE106113 GEO: GSE106114 GEO: GSE106115 SRA: SRP121332 BioProject: PRJNA415632

Nat Genet 50 (2) 186-192 [2018-02-00; online 2018-01-15]

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

A DNA methylation biomarker of alcohol consumption.

Liu C, Marioni RE, Hedman ÅK, ..., Ingelsson E, Levy D

pii: mp2016192 pmc: PMC5575985 mid: NIHMS855941 dbGaP: phs000930

Mol. Psychiatry 23 (2) 422-433 [2018-02-00; online 2016-11-15]

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

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

Martinez G, Wolff P, Wang Z, ..., Slotkin RK, Köhler C

GEO: GSE84122

Nat Genet 50 (2) 193-198 [2018-02-00; online 2018-01-15]

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

Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases

Dubreuil C, Jin X, Barajas-López JdD, ..., Small I, Strand Å

Plant Physiol. 176 (2) 1199-1214 [2018-02-00; online 2017-06-16]

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.

Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S

pii: 10.1038/s41593-017-0056-2

Nat. Neurosci. 21 (2) 290-299 [2018-02-00; online 2018-01-15]

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

The Influence of Heat Treatments on the Porosity of Suspension Plasma-Sprayed Yttria-Stabilized Zirconia Coatings

Ekberg J, Ganvir A, Klement U, Creci S, Nordstierna L

J Therm Spray Tech 27 (3) 391-401 [2018-02-00; online 2018-01-04]

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile

Undabarrena A, Salvà-Serra F, Jaén-Luchoro D, ..., Seeger M, Cámara B

GENBANK: CP023720 BioProject: PRJNA411856

Marine Genomics - (-) - [2018-02-00; online 2018-02-00]

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

Megakaryocytes harbour the del(5q) abnormality despite complete clinical and cytogenetic remission induced by lenalidomide treatment

Scharenberg C, Jansson M, Saft L, Hellström-Lindberg E

Br J Haematol 180 (4) 526-533 [2018-02-00; online 2018-01-29]

Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.

Leal L, Talla V, Källman T, ..., Vila R, Backström N

BioProject: PRJEB24745 ArrayExpress: E‐MTAB‐6454

Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]

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

Dispersal timing determines the importance of priority effects in bacterial communities

Svoboda P, Lindström ES, Ahmed Osman O, Langenheder S

ISME J 12 (2) 644-646 [2018-02-00; online 2017-10-20]

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

Vascular Endothelial Growth Factor D, Pulmonary Congestion, and Incidence of Heart Failure

Borné Y, Gränsbo K, Nilsson J, ..., Smith JG, Engström G

Journal of the American College of Cardiology 71 (5) 580-582 [2018-02-00; online 2018-02-00]

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus

Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L

Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]

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

Quantitative image analysis of protein expression and colocalisation in skin sections

Zhang H, Ericsson M, Virtanen M, ..., Vahlquist A, Törmä H

Exp Dermatol 27 (2) 196-199 [2018-02-00; online 2018-01-09]

BioImage Informatics [Service]

A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts

Kmiec B, Branca RMM, Murcha MW, ..., Glaser E, Teixeira PF

Molecular Plant 11 (2) 342-345 [2018-02-00; online 2018-02-00]

Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B

Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

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

Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.

Löfdahl A, Rydell-Törmänen K, Larsson-Callerfelt A, Wenglén C, Westergren-Thorsson G

pii: 10.1038/s41598-018-20430-0 pmc: PMC5792547

Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]

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

A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.

Kokosar M, Benrick A, Perfilyev A, ..., Ling C, Stener-Victorin E

pii: 10.1038/s41598-017-17919-5 pmc: PMC5790004

Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]

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

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, Thorell K, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

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

Innate immune alterations are elicited in microglial cells before plaque deposition in the Alzheimer's disease mouse model 5xFAD.

Boza-Serrano A, Yang Y, Paulus A, Deierborg T

pii: 10.1038/s41598-018-19699-y pmc: PMC5784016

Sci Rep 8 (1) 1550 [2018-01-24; online 2018-01-24]

The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome

Tian P, Steward A, Kudva R, ..., Clarke J, Best R

- - (-) - [2018-01-24; online 2018-01-24]

Demography and mating system shape the genome-wide impact of purifying selection inArabis alpina

Laenen B, Tedder A, Nowak MD, ..., Coupland G, Slotte T

Proc Natl Acad Sci USA 115 (4) 816-821 [2018-01-23; online 2018-01-04]

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

Genetical genomics of growth in a chicken model.

Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D

pii: 10.1186/s12864-018-4441-3 pmc: PMC5782384 ArrayExpress: E-MTAB-5572

BMC Genomics 19 (1) 72 [2018-01-23; online 2018-01-23]

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

Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome

Gupta S, Ylä-Anttila P, Callegari S, ..., Delecluse HJ, Masucci MG

PLoS Pathog. 14 (1) e1006852 [2018-01-22; online 2018-01-22]

Proteogenomics [Service]

Alpha-actinin of the chlorarchiniophyte Bigelowiella natans

Backman L

PeerJ 6 (-) e4288 [2018-01-17; online 2018-01-17]

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.

Jiang X, O'Reilly PF, Aschard H, ..., Kraft P, Kiel DP

pii: 10.1038/s41467-017-02662-2 pmc: PMC5772647

Nat Commun 9 (1) 260 [2018-01-17; online 2018-01-17]

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

Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity

Narwal M, Jemth AS, Gustafsson R, ..., Helleday T, Stenmark P

PDB: 5MZE PDB: 5MZF PDB: 5MZG PDB: 6EHH

Biochemistry - (-) - [2018-01-16; online 2018-01-16]

Spotty Carotid Plaques Are Associated with Inflammation and the Occurrence of Cerebrovascular Symptoms

Halak S, Östling G, Edsfeldt A, ..., Gonçalves I, Asciutto G

Cerebrovasc Dis Extra 8 (1) 16-25 [2018-01-15; online 2018-01-15]

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Jenjaroenpun P, Wongsurawat T, Pereira R, ..., Nielsen J, Nookaew I

Nucleic Acids Res - (-) - [2018-01-13; online 2018-01-13]

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

Meta-analysis of exome array data identifies six novel genetic loci for lung function.

Jackson VE, Latourelle JC, Wain LV, ..., Tobin MD, London SJ

pmc: PMC6081985

Wellcome Open Res 3 (-) 4 [2018-01-12; online 2018-01-12]

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

Rapid hybrid speciation in Darwin’s finches

Lamichhaney S, Han F, Webster MT, ..., Grant BR, Grant PR

SRA: PRJNA392917 TreeBASE: S21803

Science 359 (6372) 224-228 [2018-01-12; online 2017-11-23]

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

Identification of shared genetic variants between schizophrenia and lung cancer.

Zuber V, Jönsson EG, Frei O, ..., Mills IG, Andreassen OA

pii: 10.1038/s41598-017-16481-4 pmc: PMC5766533

Sci Rep 8 (1) 674 [2018-01-12; online 2018-01-12]

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

The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators.

Jers C, Ravikumar V, Lezyk M, ..., Wai SN, Mijakovic I

pmc: PMC5768985

Front. Cell. Infect. Microbiol. 7 (-) 537 [2018-01-11; online 2018-01-11]

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.

Nassa G, Giurato G, Cimmino G, ..., Weisz A, Tarallo R

pii: 10.1038/s41598-017-18985-5 pmc: PMC5765118

Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]

Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues.

Adamczyk B, Jin C, Polom K, ..., Roviello F, Karlsson NG

pii: 10.1038/s41598-017-18299-6 pmc: PMC5762837

Sci Rep 8 (1) 242 [2018-01-10; online 2018-01-10]

Glycoproteomics [Technology development]

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M

BioProject: PRJEB21940

PLoS Biol. 16 (1) e2003703 [2018-01-09; online 2018-01-09]

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

A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors

Faraz M, Herdenberg C, Holmlund C, Henriksson R, Hedman H

J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]

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

Discovering viral genomes in human metagenomic data by predicting unknown protein families.

Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL

pii: 10.1038/s41598-017-18341-7 pmc: PMC5758519 European Nucleotide Archive: PRJEB17838

Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]

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

Comprehensive Mass Spectrometric Survey of Streptococcus pyogenes Subcellular Proteomes.

Wilk L, Happonen L, Malmström J, Herwald H

J. Proteome Res. 17 (1) 600-617 [2018-01-05; online 2017-12-04]

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.

Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C

pii: 10.1186/s12864-017-4407-x pmc: PMC5753508

BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]

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

Evaluating vacquinol-1 in rats carrying glioblastoma models RG2 and NS1

Ahlstedt J, Förnvik K, Zolfaghari S, ..., Salford LG, Redebrandt HN

Oncotarget - (-) - [2018-01-03; online 2018-01-03]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice

Loganathan K, Salem Said E, Winterrowd E, ..., Quaggin SE, Jeansson M

PLoS ONE 13 (1) e0189433 [2018-01-02; online 2018-01-02]

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

Differential impact of RB status on E2F1 reprogramming in human cancer.

McNair C, Xu K, Mandigo AC, ..., Brown M, Knudsen KE

pii: 93566 pmc: PMC5749518

J. Clin. Invest. 128 (1) 341-358 [2018-01-02; online 2017-12-04]

Clinical Genomics Stockholm [Service]

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy

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Bioinformatics 34 (1) 137-138 [2018-01-01; online 2017-09-04]

Advanced Light Microscopy (ALM) [Technology development] Bioinformatics Compute and Storage [Service]

The ATPase activity of Asna1/TRC40 is required for pancreatic progenitor cell survival

Norlin S, Parekh V, Edlund H

Development 145 (1) dev154468 [2018-01-01; online 2017-11-27]

Cytokine Autoantibody Screening in the Swedish Addison Registry Identifies Patients With Undiagnosed APS1

Eriksson D, Dalin F, Eriksson GN, ..., Munoz KD, None

J Clin Endocrinol Metab 103 (1) 179-186 [2018-01-01; online 2017-10-20]

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

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE

pii: 10.1038/s41437-017-0026-1 pmc: PMC5837122

Heredity (Edinb) 120 (2) 138-153 [2018-01-00; online 2017-12-11]

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

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone

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Ecol Evol 8 (2) 1019-1030 [2018-01-00; online 2017-12-14]

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

Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

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Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]

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

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Turcot V, Lu Y, Highland HM, ..., MAGIC Investigators , Understanding Society Scientific Group

pii: 10.1038/s41588-017-0011-x pmc: PMC5945951 mid: NIHMS920811

Nat. Genet. 50 (1) 26-41 [2018-01-00; online 2017-12-22]

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

Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents.

Jokinen J, Boström AE, Dadfar A, ..., Åsberg M, Schiöth HB

pii: S2352-3964(17)30499-1 pmc: PMC5828554

EBioMedicine 27 (-) 123-133 [2018-01-00; online 2017-12-18]

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

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

Suh A, Smeds L, Ellegren H

Mol Ecol 27 (1) 99-111 [2018-01-00; online 2017-12-12]

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

Characterization of gamma-tubulin filaments in mammalian cells

Lindström L, Alvarado-Kristensson M

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1865 (1) 158-171 [2018-01-00; online 2018-01-00]

Genomic consequences of intensive inbreeding in an isolated wolf population

Kardos M, Åkesson M, Fountain T, ..., Wikenros C, Ellegren H

BioProject: PRJEB20635

Nat Ecol Evol 2 (1) 124-131 [2018-01-00; online 2017-11-20]

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

MicroRNA expression profiles in non‑epithelial ovarian tumors.

Chang RK, Li X, Mu N, ..., Larsson C, Lui WO

pmc: PMC5743337

Int. J. Oncol. 52 (1) 55-66 [2018-01-00; online 2017-11-10]

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

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

Salvatore M, Shu N, Elofsson A

pmc: PMC5734273

Protein Sci. 27 (1) 195-201 [2018-01-00; online 2017-10-24]

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

Leucocyte recruitment and molecular fortification of keratinocytes triggered by streptococcal M1 protein.

Persson ST, Hauri S, Malmström J, Herwald H

Cell. Microbiol. 20 (1) - [2018-01-00; online 2017-10-19]

Surface treatment of cellulose nanocrystals (CNC): effects on dispersion rheology

Sahlin K, Forsgren L, Moberg T, ..., Rigdahl M, Westman G

Cellulose 25 (1) 331-345 [2018-01-00; online 2017-11-28]

Perspectives on NMR studies of CO2 adsorption

Bernin D, Hedin N

Current Opinion in Colloid & Interface Science 33 (-) 53-62 [2018-01-00; online 2018-01-00]

Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations

Lodé L, Ameur A, Coste T, ..., Lavabre-Bertrand T, Soussi T

Haematologica 103 (1) e13-e16 [2018-01-00; online 2017-10-27]

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

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration

Schroeder BO, Birchenough GMH, Ståhlman M, ..., Hansson GC, Bäckhed F

Cell Host & Microbe 23 (1) 27-40.e7 [2018-01-00; online 2018-01-00]

Natural product inspired library synthesis - Identification of 2,3-diarylbenzofuran and 2,3-dihydrobenzofuran based inhibitors of Chlamydia trachomatis

Saleeb M, Mojica S, Eriksson AU, ..., Gylfe Å, Elofsson M

European Journal of Medicinal Chemistry 143 (-) 1077-1089 [2018-01-00; online 2018-01-00]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique

Cholleti H, Hayer J, Mulandane FC, ..., Berg M, Blomström AL

Infect Ecol Epidemiol 8 (1) 1478585 [2018-01-00; online 2018-05-28]

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

Homozygosity for a missense variant in COMP gene associated with severe pseudoachondroplasia

Tariq M, Khan TN, Lundin L, ..., Dahl N, Klar J

Clin Genet 93 (1) 182-186 [2018-01-00; online 2017-11-21]

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

Optimising methods for the recovery and quantification of di- and tripeptides in soil

J�mtg�rd S, Robinson N, Moritz T, Colgrave ML, Schmidt S

Soil Res. - (-) - [2018-00-00; online 2018-00-00]

Orange is the new white: rapid curing of an ethylene-glycidyl methacrylate copolymer with a Ti-bisphenolate type catalyst

Mauri M, Svenningsson L, Hjertberg T, ..., Prieto O, Müller C

Polym. Chem. 9 (13) 1710-1718 [2018-00-00; online 2018-00-00]

Hepatitis E Virus Genotype 3 Genomes from RNA-Positive but Serologically Negative Plasma Donors Have CUG as the Start Codon for ORF3

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Intervirology 61 (2) 96-103 [2018-00-00; online 2018-10-02]

Clinical Genomics Gothenburg [Collaborative]

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RSC Adv. 8 (65) 37503-37507 [2018-00-00; online 2018-00-00]

Drug Discovery and Development (DDD) [Technology development]

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Solorzano L, Almeida GM, Mesquita B, ..., Oliveira C, Wählby C

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BioImage Informatics [Technology development]

High purity and viability cell separation of a bacterivorous jakobid flagellate based on a steep velocity gradient induced soft inertial force

Deng P, Fu CJ, Wu Z

RSC Adv. 8 (62) 35512-35520 [2018-00-00; online 2018-00-00]

Microbial Single Cell Genomics [Service]

Improved Reconstruction of Low Intensity Magnetic Resonance Spectroscopy With Weighted Low Rank Hankel Matrix Completion

Guo D, Qu X

IEEE Access 6 (-) 4933-4940 [2018-00-00; online 2018-00-00]

Efficient C–C coupling of bio-based furanics and carbonyl compounds to liquid hydrocarbon precursors over lignosulfonate derived acidic carbocatalysts

Konwar LJ, Samikannu A, Mäki-Arvela P, Mikkola JP

Catal. Sci. Technol. 8 (9) 2449-2459 [2018-00-00; online 2018-00-00]

Effect of food intake on biomarkers for cardiovascular disease and inflammation analyzed with the Proseek Multiplex CVD II kit

Dencker M, GAAyrdinger Y, BjAAlrgell O, Hlebowicz J

gmr 17 (1) - [2018-00-00; online 2018-00-00]

Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus

Swenson U, Nylander JAA, Munzinger J

Aust. Systematic Bot. 31 (2) 120 [2018-00-00; online 2018-00-00]

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

The CO2 capturing ability of cellulose dissolved in NaOH(aq) at low temperature

Gunnarsson M, Bernin D, Östlund Å, Hasani M

Green Chem. 20 (14) 3279-3286 [2018-00-00; online 2018-00-00]

Effect of various structure directing agents (SDAs) on low-temperature deactivation of Cu/SAPO-34 during NH3-SCR reaction

Woo J, Leistner K, Bernin D, ..., Zammit M, Olsson L

Catal. Sci. Technol. 8 (12) 3090-3106 [2018-00-00; online 2018-00-00]

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

High-fidelity spectroscopy reconstruction in accelerated NMR

Qu X, Qiu T, Guo D, ..., Orekhov V, Chen Z

Chem. Commun. 54 (78) 10958-10961 [2018-00-00; online 2018-00-00]

Swedish NMR Centre (SNC) [Technology development]

An unexpected re-arrangement of the antibiotic carbapenem core to new 1,4-diazepin-5-one scaffolds

Peters BK, Razuwika R, Samipillai M, ..., Govender T, Naicker T

RSC Adv. 8 (1) 190-193 [2018-00-00; online 2018-00-00]

Drug Discovery and Development (DDD) [Collaborative]

Solid and fluid segments within the same molecule of stratum corneum ceramide lipid

Pham QD, Mojumdar EH, Gooris GS, ..., Sparr E, Topgaard D

Quart. Rev. Biophys. 51 (-) - [2018-00-00; online 2018-06-05]