Bioinformatics Support, Infrastructure and Training (439 publications)

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei

Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Johannesson H, Rosling A

Sci Rep 10 (1) - [2020-12-00; online 2020-01-28]

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

DOI Crossref

A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice

Purhonen J, Grigorjev V, Ekiert R, ..., Fellman V, Kallijärvi J

Nat Commun 11 (1) - [2020-12-00; online 2020-01-16]

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

PubMed DOI Crossref

A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver

Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C

Thromb. Haemost. - (-) - [2019-12-30; online 2019-12-30]

Bioinformatics 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] Systems Biology [Collaborative]

PubMed DOI Crossref

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.

Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N

Ann. Bot. - (-) - [2019-12-24; online 2019-12-24]

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

PubMed DOI Crossref

Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox

Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L

Phil. Trans. R. Soc. B 374 (1788) 20190212 [2019-12-23; online 2019-11-04]

Bioinformatics 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]

PubMed DOI Crossref

Gene Expression Alterations during Development of Castration-Resistant Prostate Cancer Are Detected in Circulating Tumor Cells.

Josefsson A, Larsson K, Freyhult E, Damber J, Welén K

Cancers (Basel) 12 (1) - [2019-12-21; online 2019-12-21]

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

PubMed DOI Crossref

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J

Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

DOI Crossref

Plasma Lipidome and Prediction of Type 2 Diabetes in the Population-Based Malmö Diet and Cancer Cohort

Fernandez C, Surma MA, Klose C, ..., Simons K, Melander O

Dia Care - (-) dc191199 [2019-12-08; online 2019-12-08]

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

DOI Crossref

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats

Dong Y, Sanford RA, Inskeep WP, ..., Fried GA, Fouke BW

Astrobiology 19 (12) 1442-1458 [2019-12-01; online 2019-12-01]

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

PubMed DOI Crossref

Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G

Sci Rep 9 (1) - [2019-12-00; online 2019-03-20]

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

DOI Crossref

Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment

Schuster J, Laan L, Klar J, ..., Birnir B, Dahl N

Neurobiology of Disease 132 (-) 104583 [2019-12-00; online 2019-12-00]

Bioinformatics 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]

PubMed DOI Crossref

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish

Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson ML

Sci Rep 9 (1) - [2019-12-00; online 2019-07-24]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Gelali E, Girelli G, Matsumoto M, ..., Crosetto N, Bienko M

Nat Commun 10 (1) - [2019-12-00; online 2019-04-09]

Advanced FISH Technologies [Technology development] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

DOI Crossref

Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder

Tammimies K, Li D, Rabkina I, ..., Choque-Olsson N, Bölte S

Sci Rep 9 (1) - [2019-12-00; online 2019-07-08]

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

DOI Crossref

Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data

Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A

Sci Rep 9 (1) - [2019-12-00; online 2019-02-20]

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

PubMed DOI Crossref

ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes

Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C

GEO

Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]

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

PubMed DOI Crossref

Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å

Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]

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

PubMed DOI Crossref

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M

Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]

Bioinformatics 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]

PubMed DOI Crossref

The genomic footprint of sexual conflict.

Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G

Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]

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

DOI Crossref

Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes

Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C

Sci Rep 9 (1) - [2019-12-00; online 2019-06-03]

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

PubMed DOI Crossref

Breast cancer quantitative proteome and proteogenomic landscape

Johansson HJ, None , Socciarelli F, ..., Børresen-Dale AL, Lehtiö J

Nat Commun 10 (1) - [2019-12-00; online 2019-04-08]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]

PubMed DOI Crossref

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J

Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]

Bioinformatics 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]

PubMed DOI Crossref

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Rojas-Macias MA, Mariethoz J, Andersson P, ..., Lisacek F, Karlsson NG

Nat Commun 10 (1) - [2019-12-00; online 2019-07-22]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Glycoproteomics [Technology development]

DOI Crossref

Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T

GEO

Nat Commun 10 (1) - [2019-12-00; online 2019-02-04]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Collaborative]

PubMed DOI Crossref

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D

Genome Med 11 (1) - [2019-12-00; online 2019-11-07]

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

PubMed DOI Crossref

The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.

Tractenberg RE, Lindvall JM, Attwood TK, Via A

pmc

PLoS ONE 14 (11) e0225256 [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

DOI Crossref

Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

Raethong N, Wang H, Nielsen J, Vongsangnak W

Computational and Structural Biotechnology Journal 18 (-) 1-8 [2019-11-26]

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

PubMed DOI Crossref

TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells

Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M

Front Immunol 10 (-) - [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cell Profiling [Collaborative] Proteogenomics [Technology development]

PubMed DOI Crossref

Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.

Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K

Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]

Bioinformatics 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]

PubMed DOI Crossref

Daytime melatonin levels in saliva are associated with inflammatory markers and anxiety disorders.

Sundberg I, Rasmusson AJ, Ramklint M, ..., Ekselius L, Cunningham JL

Psychoneuroendocrinology - (-) 104514 [2019-11-14; online 2019-11-14]

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

DOI Crossref

On-demand virtual research environments using microservices

Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O

- 5 (-) e232 [2019-11-11; online 2019-11-11]

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

PubMed DOI Crossref

Leveraging European infrastructures to access 1 million human genomes by 2022.

Saunders G, Baudis M, Becker R, ..., Blomberg N, Scollen S

Nat. Rev. Genet. 20 (11) 693-701 [2019-11-00; online 2019-08-27]

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

PubMed DOI Crossref

The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.

Stjelja S, Fogelqvist J, Tellgren-Roth C, Dixelius C

pmc

Sci Rep 9 (1) 15753 [2019-10-31; online 2019-10-31]

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

PubMed DOI Crossref

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540.

Tiukova IA, Jiang H, Dainat J, ..., Gu Z, Passoth V

Microorganisms 7 (11) - [2019-10-26; online 2019-10-26]

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

DOI Crossref

Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity

Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR

- - (-) - [2019-10-22; online 2019-10-22]

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

DOI Crossref

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

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

- - (-) - [2019-10-17; online 2019-10-17]

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

PubMed DOI Crossref

Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.

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

Pharmacogenomics J. - (-) - [2019-10-15; online 2019-10-15]

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

DOI Crossref

Interoperable and scalable data analysis with microservices: applications in metabolomics

Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O

- 35 (19) 3752-3760 [2019-10-01; online 2019-03-09]

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

PubMed DOI Crossref

Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.

Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N

pmc

Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]

Bioinformatics 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]

DOI Crossref

Whole genome sequencing of apparently mutation-negative MEN1 patients

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

- - (-) - [2019-10-00; online 2019-10-00]

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

DOI Crossref

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

Kurland S, Wheat CW, Paz Celorio Mancera M, ..., Ryman N, Laikre L

Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]

Bioinformatics 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]

DOI Crossref

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities

Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N

Water Research 162 (-) 437-445 [2019-10-00; online 2019-10-00]

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

PubMed DOI Crossref

Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.

Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C

Cancer Med - (-) - [2019-09-30; online 2019-09-30]

Bioinformatics 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]

DOI Crossref

Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota

Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C

MBio 10 (5) - [2019-09-10; online 2019-09-10]

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

PubMed DOI Crossref

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.

Pederson ERA, Warshan D, Rasmussen U

pmc

G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]

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]

PubMed DOI Crossref

The bio.tools registry of software tools and data resources for the life sciences.

Ison J, Ienasescu H, Chmura P, ..., Løngreen P, Brunak S

pmc

Genome Biol. 20 (1) 164 [2019-08-12; online 2019-08-12]

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

PubMed DOI Crossref

Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species

Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N

Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]

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

DOI Crossref

Evolved for success in novel environments: The round goby genome

Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S

- - (-) - [2019-07-19; online 2019-07-19]

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

DOI Crossref

GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files

Wik E, Olin H, Haughey C, Klasson L, Dainat J

JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]

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

PubMed DOI Crossref

Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality

Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A

Experimental Cell Research 383 (1) 111469 [2019-07-00; online 2019-07-00]

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

PubMed DOI Crossref

Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.

Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM

Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]

Bioinformatics 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] Systems Biology [Collaborative]

PubMed DOI Crossref

Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.

Landegren N, Rosen LB, Freyhult E, ..., Anderson M, Kämpe O

pmc

Elife 8 (-) - [2019-06-27; online 2019-06-27]

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

DOI Crossref

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B

Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]

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

DOI Crossref

Single-nuclei transcriptomic analysis of the subthalamic nucleus reveals different Pitx2-positive subpopulations

Papathanou M, Björklund ÅK, Martis-Thiele MM, Wallén-Mackenzie Å

- - (-) - [2019-06-20; online 2019-06-20]

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

DOI Crossref

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination

Dahlberg J, Sun L, Persson Waller K, ..., Agenäs S, Dicksved J

PLoS ONE 14 (6) e0218257 [2019-06-13; online 2019-06-13]

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

DOI Crossref

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

Lampa S, Dahlö M, Alvarsson J, Spjuth O

Gigascience 8 (5) - [2019-05-01; online 2019-04-26]

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

PubMed DOI Crossref

Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.

Tiukova IA, Pettersson ME, Hoeppner MP, ..., Söderberg J, Passoth V

pmc

PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]

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

DOI Crossref

Software engineering for scientific big data analysis

Grüning BA, Lampa S, Vaudel M, Blankenberg D

Gigascience 8 (5) - [2019-05-01; online 2019-05-23]

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

PubMed DOI Crossref

PKCζ facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model

Zang G, Mu Y, Gao L, Bergh A, Landström M

Oncogene 38 (22) 4215-4231 [2019-05-00; online 2019-01-31]

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

PubMed DOI Crossref

Gene expression profile of extraocular muscles following resection strabismus surgery

Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F

Experimental Eye Research 182 (-) 182-193 [2019-05-00; online 2019-05-00]

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

PubMed DOI Crossref

Pervasive hybridizations in the history of wheat relatives.

Glémin S, Scornavacca C, Dainat J, ..., David J, Ranwez V

pmc

Sci Adv 5 (5) eaav9188 [2019-05-00; online 2019-05-01]

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

PubMed DOI Crossref

Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient

Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M

Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]

Bioinformatics 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]

PubMed DOI Crossref

The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement

Abramova A, Lind U, Blomberg A, Rosenblad MA

Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]

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

DOI Crossref

Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions

Sobol M, Klar J, Laan L, ..., Falk A, Dahl N

Mol Neurobiol 56 (10) 7113-7127 [2019-04-13; online 2019-04-13]

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

DOI Crossref

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Drysdale R, Cook CE, Petryszak R, ..., McEntyre J, None

- - (-) - [2019-04-05; online 2019-04-05]

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

DOI Crossref

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis

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Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]

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Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

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Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]

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Modelling of zero-inflation improves inference of metagenomic gene count data

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Nat Med - (-) - [2018-11-12; online 2018-11-12]

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Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.

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Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]

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Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

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

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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]

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

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

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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]

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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

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

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Life history of Parnips and the evolutionary origin of gall wasps

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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

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

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Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

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

pmc GEO GEO

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

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

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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]

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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]

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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

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PubMed DOI Crossref

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

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

pmc

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

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

GEO GEO

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

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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

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

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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]

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PubMed DOI Crossref

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]

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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]

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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

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

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

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

pmc GEO

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]

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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]

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PubMed DOI Crossref

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

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

pmc

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

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PubMed DOI Crossref

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]

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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]

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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

pmc GEO

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]

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

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

pmc

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]

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Garcia M, Juhos S, Larsson M, ..., Nystedt B, Käller M

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

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

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

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

pmc

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

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

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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]

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O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K

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]

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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]

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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]

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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

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]

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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]

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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

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]

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Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.

Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y

pmc

PLoS Pathog. 14 (3) e1006936 [2018-03-00; online 2018-03-02]

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

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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]

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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]

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Bacterial secretion of D-arginine controls environmental microbial biodiversity.

Alvarez L, Aliashkevich A, de Pedro MA, Cava F

pmc

ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]

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

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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]

PubMed DOI Crossref

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

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]

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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]

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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

pmc

Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]

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

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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

pmc

Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]

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

PubMed DOI Crossref

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]

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MicroRNA expression profiles in non‑epithelial ovarian tumors.

Chang RK, Li X, Mu N, ..., Larsson C, Lui WO

pmc

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]

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The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

Salvatore M, Shu N, Elofsson A

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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]

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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]

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Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases

Lehmann P, Pruisscher P, Koštál V, ..., Wheat CW, Gotthard K

Journal of Experimental Biology - (-) - [2017-12-01; online 2017-11-27]

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

PubMed DOI Crossref

Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration

Elewa A, Wang H, Talavera-López C, ..., Andersson B, Simon A

SRA BioProject

Nat Commun 8 (1) - [2017-12-00; online 2017-12-22]

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]

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Dog ownership and the risk of cardiovascular disease and death – a nationwide cohort study

Mubanga M, Byberg L, Nowak C, ..., Ingelsson E, Fall T

Sci Rep 7 (1) - [2017-12-00; online 2017-11-17]

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

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Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

Lauss M, Donia M, Harbst K, ..., Svane IM, Jönsson G

Nat Commun 8 (1) - [2017-12-00; online 2017-11-23]

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

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Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea

Hüttner S, Nguyen TT, Granchi Z, ..., Thanh VN, Olsson L

Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-11-13]

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

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RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG

BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]

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]

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Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells

Piltti J, Bygdell J, Fernández-Echevarría C, Marcellino D, Lammi MJ

Sci Rep 7 (1) - [2017-12-00; online 2017-06-16]

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

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Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition

Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M

Sci Rep 7 (1) - [2017-12-00; online 2017-09-04]

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

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Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Pečnerová P, Palkopoulou E, Wheat CW, ..., Díez-del-Molino D, Dalén L

Evolution Letters - (-) - [2017-11-28; online 2017-11-28]

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

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Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.

Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L

BioProject

Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]

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]

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Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths

Kirik U, Persson H, Levander F, Greiff L, Ohlin M

Front Immunol 8 (-) - [2017-11-13; online 2017-11-13]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

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RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole

Martis MM, Tarbiat B, Tydén E, Jansson DS, Höglund J

BioProject

PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]

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

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Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity

Resjö S, Brus M, Ali A, ..., Grenville-Briggs L, Andreasson E

Mol Cell Proteomics 16 (11) 1958-1971 [2017-11-00; online 2017-09-21]

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

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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U

Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]

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

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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

Hubalek V, Buck M, Tan B, ..., Bertilsson S, Eiler A

mSystems 2 (5) e00038-17 [2017-10-31; online 2017-10-31]

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

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Effects of long-term low oxygen tension in human chondrosarcoma cells

Piltti J, Bygdell J, Qu C, Lammi MJ

J. Cell. Biochem. - (-) - [2017-10-18; online 2017-10-18]

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

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The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G

GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]

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

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The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.

Johansson A, Claesson R, Höglund Åberg C, Haubek D, Oscarsson J

GENBANK GENBANK GENBANK GENBANK GENBANK

J. Periodont. Res. 52 (5) 903-912 [2017-10-00; online 2017-04-10]

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

PubMed DOI Crossref

Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.

Cimdins A, Simm R, Li F, ..., Brauner A, Römling U

pmc

Microbiologyopen 6 (5) - [2017-10-00; online 2017-09-15]

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

PubMed DOI Crossref

Antibody Affinity Against 2009 A/H1N1 Influenza and Pandemrix Vaccine Nucleoproteins Differs Between Childhood Narcolepsy Patients and Controls.

Lind A, Freyhult E, Ramelius A, ..., Elding Larsson H, Lernmark Å

Viral Immunol. 30 (8) 590-600 [2017-10-00; online 2017-08-10]

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

PubMed DOI Crossref

Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.

Verma D, Parasa VR, Raffetseder J, ..., Netea M, Lerm M

pmc

Sci Rep 7 (1) 12305 [2017-09-26; online 2017-09-26]

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]

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Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.

Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF

Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]

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

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The regulation of hydroxysteroid 17β-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.

Hilborn E, Stål O, Alexeyenko A, Jansson A

pmc

Oncotarget 8 (37) 62183-62194 [2017-09-22; online 2017-07-10]

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

PubMed DOI Crossref

Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.

Celauro E, Mukaj A, Fierro-González JC, Wittung-Stafshede P

Biochem. Biophys. Res. Commun. 491 (1) 147-153 [2017-09-09; online 2017-07-12]

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

PubMed DOI Crossref

A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero-Mendieta S, Grabherr M, Lantz H, ..., Webster MT, Vilà C

SRA GENBANK BioProject

PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]

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]

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The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.

Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV

pmc BioProject

Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]

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]

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Genome scale metabolic modeling of cancer

Nilsson A, Nielsen J

Metabolic Engineering 43 (-) 103-112 [2017-09-00; online 2017-09-00]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

PubMed DOI Crossref

Cerium oxide nanoparticles inhibit differentiation of neural stem cells.

Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B

pmc

Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]

Advanced Light Microscopy (ALM) [Collaborative] 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]

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SubCons: a new ensemble method for improved human subcellular localization predictions.

Salvatore M, Warholm P, Shu N, Basile W, Elofsson A

Bioinformatics 33 (16) 2464-2470 [2017-08-15; online 2017-04-14]

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

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Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3

Bersani C, Sivars L, Haeggblom L, ..., Ramqvist T, Dalianis T

Oncotarget - (-) - [2017-07-18; online 2017-02-09]

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

PubMed DOI Crossref

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A

pmc GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

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

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Identifying Bird Remains Using Ancient DNA Barcoding

Dalén L, Lagerholm V, Nylander J, ..., Irestedt M, Stewart J

Genes 8 (6) 169 [2017-06-21; online 2017-06-21]

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

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Systems Biology of Metabolism

Nielsen J

Annu. Rev. Biochem. 86 (1) 245-275 [2017-06-20; online 2017-06-20]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

PubMed DOI Crossref

Protein expression in tension wood formation monitored at high tissue resolution in Populus

Bygdell J, Srivastava V, Obudulu O, ..., Mellerowicz EJ, Wingsle G

- 68 (13) 3405-3417 [2017-06-15; online 2017-06-13]

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

PubMed DOI Crossref

Four simple recommendations to encourage best practices in research software

Jiménez RC, Kuzak M, Alhamdoosh M, ..., Watson-Haigh NS, Crouch S

F1000Res 6 (-) 876 [2017-06-13; online 2017-06-13]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

PubMed DOI Crossref

A community proposal to integrate proteomics activities in ELIXIR

Vizcaíno JA, Walzer M, Jiménez RC, ..., Martens L, Kohlbacher O

F1000Res 6 (-) 875 [2017-06-13; online 2017-06-13]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

PubMed DOI Crossref

Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).

Grenville-Briggs LJ, Kushwaha SK, Cleary MR, ..., Chawade A, Vetukuri RR

pmc

Genom Data 12 (-) 155-156 [2017-06-00; online 2017-05-12]

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

PubMed DOI Crossref

The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.

Videvall E, Cornwallis CK, Ahrén D, ..., Valkiūnas G, Hellgren O

Mol. Ecol. 26 (11) 2939-2958 [2017-06-00; online 2017-04-08]

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

PubMed DOI Crossref

Lower inflammatory markers in women with antenatal depression brings the M1/M2 balance into focus from a new direction

Edvinsson Å, Bränn E, Hellgren C, ..., Cunningham JL, Sundström-Poromaa I

Psychoneuroendocrinology 80 (-) 15-25 [2017-06-00; online 2017-06-00]

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

PubMed DOI Crossref

Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ

pmc

Genome Announc 5 (21) - [2017-05-25; online 2017-05-25]

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]

PubMed DOI Crossref

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.

Lahtvee P, Sánchez BJ, Smialowska A, ..., Gatto F, Nielsen J

Cell Syst 4 (5) 495-504.e5 [2017-05-24; online 2017-03-29]

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

PubMed DOI Crossref

ProQ3D: improved model quality assessments using deep learning.

Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

Bioinformatics 33 (10) 1578-1580 [2017-05-15; online 2017-01-06]

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

PubMed DOI Crossref

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.

Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB

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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

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RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.

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The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

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Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.

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Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages

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Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach

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PLoS ONE 11 (7) e0159105 [2016-07-19; online 2016-07-19]

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

PubMed DOI Crossref

Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.

Gatto F, Schulze A, Nielsen J

Cell Rep 16 (3) 878-895 [2016-07-19; online 2016-07-12]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

PubMed DOI Crossref

Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.

Martínez-Redondo V, Jannig PR, Correia JC, ..., Dahlman-Wright K, Ruas JL

pmc

J. Biol. Chem. 291 (29) 15169-15184 [2016-07-15; online 2016-05-28]

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

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Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

Reischauer S, Stone OA, Villasenor A, ..., Andersson O, Stainier DY

SRA GENBANK

Nature 535 (7611) 294-298 [2016-07-14; online 2016-07-15]

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

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Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J

pmc

Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J

Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]

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

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Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

Teleman J, Chawade A, Sandin M, Levander F, Malmström J

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J. Proteome Res. 15 (7) 2143-2151 [2016-07-01; online 2016-05-26]

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

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A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.

Humble E, Martinez-Barrio A, Forcada J, ..., Wolf JB, Hoffman JI

GENBANK

Mol Ecol Resour 16 (4) 909-921 [2016-07-00; online 2015-12-20]

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]

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Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.

Hagey DW, Zaouter C, Combeau G, ..., Huss M, Muhr J

pmc

Genome Res. 26 (7) 908-917 [2016-07-00; online 2016-05-20]

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

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The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.

Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V

Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]

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]

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PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

Fernandez-Ricaud L, Kourtchenko O, Zackrisson M, Warringer J, Blomberg A

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BMC Bioinformatics 17 (-) 249 [2016-06-23; online 2016-06-23]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

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Read-based phasing of related individuals.

Garg S, Martin M, Marschall T

pmc

Bioinformatics 32 (12) i234-i242 [2016-06-15; online 2016-06-17]

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

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Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

Gatto F, Volpi N, Nilsson H, ..., Basso U, Nielsen J

Cell Rep 15 (8) 1822-1836 [2016-05-24; online 2016-05-18]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B

pmc

PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]

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]

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Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.

Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A

Bioinformatics 32 (10) 1571-1573 [2016-05-15; online 2016-01-23]

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

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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Nilsson RH, Alm Rosenblad M, Martín MP, ..., Wurzbacher C, Abarenkov K

MycoKeys 13 (-) 21-33 [2016-05-13; online 2016-05-13]

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

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Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.

Pečnerová P, Díez-Del-Molino D, Vartanyan S, Dalén L

pmc

Sci Rep 6 (-) 25274 [2016-05-04; online 2016-05-04]

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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

Martinez Barrio A, Lamichhaney S, Fan G, ..., Xu X, Andersson L

pmc Dryad SRA SRA SRA

Elife 5 (-) - [2016-05-03; online 2016-05-03]

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

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Regulating retrotransposon activity through the use of alternative transcription start sites.

Persson J, Steglich B, Smialowska A, ..., Nielsen O, Ekwall K

pmc

EMBO Rep. 17 (5) 753-768 [2016-05-00; online 2016-02-22]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Bioinformatics and Expression Analysis (BEA) [Service]

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The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

Engel P, Kwong WK, McFrederick Q, ..., vanEngelsdorp D, Dainat B

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MBio 7 (2) e02164-e02115 [2016-04-26; online 2016-04-26]

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

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EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer.

Husa AM, Magić Ž, Larsson M, Fornander T, Pérez-Tenorio G

pmc

Oncotarget 7 (16) 21362-21380 [2016-04-19; online 2016-02-13]

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

PubMed DOI Crossref

Improved topology prediction using the terminal hydrophobic helices rule.

Peters C, Tsirigos KD, Shu N, Elofsson A

Bioinformatics 32 (8) 1158-1162 [2016-04-15; online 2015-12-09]

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

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Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.

Spoerry C, Seele J, Valentin-Weigand P, Baums CG, von Pawel-Rammingen U

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J. Biol. Chem. 291 (15) 7915-7925 [2016-04-08; online 2016-02-11]

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

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Transcriptomics resources of human tissues and organs.

Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J

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Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]

Bioinformatics Support, Infrastructure and Training [Technology development] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Technology development] Tissue Profiling [Collaborative]

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Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.

Rodríguez SA, Grochová D, McKenna T, ..., Erdos MR, Eriksson M

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Aging Cell 15 (2) 267-278 [2016-04-00; online 2015-12-22]

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

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Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes.

Andersson Hall U, Edin F, Pedersen A, Madsen K

Appl Physiol Nutr Metab 41 (4) 430-437 [2016-04-00; online 2015-12-17]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Swedish NMR Centre (SNC) [Collaborative]

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RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.

Christel S, Fridlund J, Buetti-Dinh A, ..., Watkin EL, Dopson M

FEMS Microbiol. Lett. 363 (7) - [2016-04-00; online 2016-03-10]

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

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VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.

Li X, Padhan N, Sjöström EO, ..., Jansson L, Claesson-Welsh L

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Nat Commun 7 (-) 11017 [2016-03-23; online 2016-03-23]

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

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In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo.

Tjernlund A, Burgener A, Lindvall JM, ..., McElrath MJ, Corey L

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PLoS ONE 11 (3) e0149907 [2016-03-17; online 2016-03-17]

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

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Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.

Zepeda Mendoza ML, Lundberg J, Ivarsson M, ..., Sallstedt T, Dalen L

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PLoS ONE 11 (3) e0151577 [2016-03-17; online 2016-03-17]

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

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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

Steige K, Reimegård J, Rebernig CA, ..., Scofield DG, Slotte T

bioRxiv - (-) - [2016-03-16; online 2016-03-16]

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The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, ..., Zhao J, Mons B

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Sci Data 3 (-) 160018 [2016-03-15; online 2016-03-15]

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

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Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.

Celorio-Mancera Mde L, Wheat CW, Huss M, ..., Nylin S, Janz N

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BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]

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Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.

Gatto F, Nielsen J

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J Hematol Oncol 9 (-) 15 [2016-03-02; online 2016-03-02]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

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Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients.

Kirchner H, Sinha I, Gao H, ..., Dahlman-Wright K, Zierath JR

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Mol Metab 5 (3) 171-183 [2016-03-00; online 2016-01-02]

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Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

Shah F, Nicolás C, Bentzer J, ..., Persson P, Tunlid A

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New Phytol. 209 (4) 1705-1719 [2016-03-00; online 2015-11-04]

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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

Wang J, Street NR, Scofield DG, Ingvarsson PK

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Genetics 202 (3) 1185-1200 [2016-03-00; online 2016-01-02]

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

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A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients

Lind AL, Wu D, Freyhult E, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 11 (2) e0149821 [2016-02-25; online 2016-02-25]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] PLA and Single Cell Proteomics [Technology development]

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Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal.

Karimpour M, Surowiec I, Wu J, ..., Zivkovic AM, Nording ML

Anal. Chim. Acta 908 (-) 121-131 [2016-02-18; online 2016-01-31]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

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Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.

Obudulu O, Bygdell J, Sundberg B, ..., Trygg J, Wingsle G

pmc

BMC Genomics 17 (-) 119 [2016-02-18; online 2016-02-18]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

Olsen JL, Rouzé P, Verhelst B, ..., Reusch TB, Van de Peer Y

Bioinformatics Support, Infrastructure and Training

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