Bioinformatics Support, Infrastructure and Training

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Publications

2020 (113)

2019 (744)

2018 (669)

2017 (697)

2016 (671)

2015 (431)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (4566)


Facilities

Journals

444 publications

Year 2020

PubMed DOI Crossref
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] Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
DOI Crossref
Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma
Mitra S, Lauss M, Cabrita R, ..., Brown KM, Jönsson G
Mol Oncol 14 (5) 933-950 [2020-05-00; online 2020-03-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Building blocks are synthesized on demand during the yeast cell cycle
Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J
Proc Natl Acad Sci USA 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Comparative analysis of genome-wide DNA methylation in Neurospora
Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H
Epigenetics - (-) 1-16 [2020-03-31; online 2020-03-31]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles
Nunez JCB, Flight PA, Neil KB, ..., Blomberg A, Rand DM
Proc Natl Acad Sci USA - (-) 201918232 [2020-02-25; online 2020-02-25]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B
F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Year 2019

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]
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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]
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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
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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
Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB
Front Immunol 10 (-) - [2019-04-05; online 2019-04-05]
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DOI Crossref
Single-molecule genome assembly of the BasketWillow, Salix viminalis, reveals earliest stages of sex chromosome expansion
Almeida P, Proux-Wera E, Churcher A, ..., Berlin S, Mank JE
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PubMed DOI Crossref
A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E
PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]
Bioinformatics 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] Systems Biology [Collaborative]
DOI Crossref
Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1
Bauer SL, Chen J, Åström SU
PLoS ONE 14 (3) e0214102 [2019-03-21; online 2019-03-21]
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PubMed DOI Crossref
An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
Mäkeläinen S, Gòdia M, Hellsand M, ..., Andersson G, Bergström TF
PLoS Genet. 15 (3) e1007873 [2019-03-19; online 2019-03-19]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors
Gaudenzi G, Dethlefsen O, Walfridsson J, Hermanson O
- - (-) - [2019-03-16; online 2019-03-16]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function
Sapir T, Segal M, Grigoryan G, ..., Segal M, Reiner O
Front Cell Neurosci 13 (-) - [2019-03-13; online 2019-03-13]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
Andrade P, Pinho C, Pérez i de Lanuza G, ..., Andersson L, Carneiro M
Proc Natl Acad Sci USA - (-) 201820320 [2019-02-28; online 2019-02-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes)
Košuthová A, Westberg M, Otálora MAG, Wedin M
MycoKeys 47 (-) 17-33 [2019-02-20; online 2019-02-20]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
DOI Crossref
Plasma Profiles of Inflammatory Markers Associated With Active Tuberculosis in Antiretroviral Therapy-Naive Human Immunodeficiency Virus-Positive Individuals
Olsson O, Björkman P, Jansson M, ..., Carlsson F, Skogmar S
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Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Ultrasensitive immunoprofiling of plasma extracellular vesicles identifies syndecan-1 as a potential tool for minimally invasive diagnosis of glioma.
Indira Chandran V, Welinder C, Månsson AS, ..., Sundgren PC, Belting M
Clin. Cancer Res. - (-) - [2019-01-24; online 2019-01-24]
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Transformation of mature mouse B cells into malignant plasma cells in vitro via introduction of defined genetic elements.
Högstrand K, Lindvall JM, Sundblad A, Grandien A
Eur. J. Immunol. - (-) - [2019-01-21; online 2019-01-21]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.
Caputo A, Nylander JAA, Foster RA
FEMS Microbiol. Lett. - (-) - [2019-01-09; online 2019-01-09]
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DOI Crossref
Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease
Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M
Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2019-00-00; online 2019-00-00]
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Year 2018

DOI Crossref
Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Bandaru MK, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M
- - (-) - [2018-12-20; online 2018-12-20]
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PubMed DOI Crossref
PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.
Peters K, Bradbury J, Bergmann S, ..., Zanetti G, Steinbeck C
Gigascience - (-) - [2018-12-07; online 2018-12-07]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.
Nilsson E, Benrick A, Kokosar M, ..., Ling C, Stener-Victorin E
J. Clin. Endocrinol. Metab. 103 (12) 4465-4477 [2018-12-01; online 2018-08-17]
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PubMed DOI Crossref
Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.
Gossing M, Smialowska A, Nielsen J
FEMS Yeast Res. 18 (8) - [2018-12-01; online 2018-09-01]
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PubMed DOI Crossref
A major locus controls local adaptation and adaptive life history variation in a perennial plant
Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK
SRA
Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]
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PubMed DOI Crossref
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J
Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]
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EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive
Norling M, Jareborg N, Dainat J
BMC Res Notes 11 (1) - [2018-12-00; online 2018-08-13]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M
Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]
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PubMed DOI Crossref
RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL
Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]
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Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing
Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K
Nat Commun 9 (1) - [2018-12-00; online 2018-12-04]
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PubMed DOI Crossref
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome
Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S
BioProject SRA
Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]
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PubMed DOI Crossref
A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons
Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J
GEO
Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]
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DOI Crossref
Modelling of zero-inflation improves inference of metagenomic gene count data
Jonsson V, Österlund T, Nerman O, Kristiansson E
Stat Methods Med Res - (-) 096228021881135 [2018-11-25; online 2018-11-25]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M
MBio 9 (6) - [2018-11-20; online 2018-11-20]
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PubMed DOI Crossref
Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.
Franzén B, Alexeyenko A, Kamali-Moghaddam M, ..., Landegren U, Lewensohn R
Mol Oncol 13 (2) 376-391 [2018-11-19; online 2018-11-19]
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Expression profiling and in situ screening of circular RNAs in human tissues.
Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L
Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
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Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
Akhter S, Kretzschmar WW, Nordal V, ..., Emanuelsson O, Sundström JF
Front Plant Sci 9 (-) - [2018-11-13; online 2018-11-13]
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Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G
GEO
Nat Med - (-) - [2018-11-12; online 2018-11-12]
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PubMed DOI Crossref
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR
Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]
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Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays
Giacomello S, Lundeberg J
Nat Protoc - (-) - [2018-10-23; online 2018-10-23]
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RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ
PLoS Comput. Biol. 14 (10) e1006541 [2018-10-18; online 2018-10-18]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.
Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K
pmc
Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]
Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Service]
PubMed DOI Crossref
De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data
Ameur A, Che H, Martin M, ..., Feuk L, Gyllensten U
Genes 9 (10) 486 [2018-10-09; online 2018-10-09]
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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]
PubMed DOI Crossref
Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia
Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B
Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.
Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC
pmc
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]
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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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
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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
pmc
PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]
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DOI Crossref
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]
PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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]
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]
PubMed DOI Crossref
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
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]
PubMed DOI Crossref
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]
DOI Crossref
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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Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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]
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]
PubMed DOI Crossref
Clonal relatedness in tumour pairs of breast cancer patients.
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]
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]
PubMed DOI Crossref
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]
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
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]
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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PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
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
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]
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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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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
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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
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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]
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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]
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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]
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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
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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
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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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Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.
Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y
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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
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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]
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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]
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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]
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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
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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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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]

Year 2017

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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]
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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]
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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]
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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]
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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
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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]
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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]
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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]
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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]
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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]
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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]
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The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.
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Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.
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Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.
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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
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Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
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Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.
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Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.
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Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
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Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
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Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715
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Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.
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Green listed—a CRISPR screen tool
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Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.
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Frequent low-level mutations of protein kinase D2 in angiolipoma
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Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology
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Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]
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Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.
Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ
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Genome Announc 5 (12) - [2017-03-23; online 2017-03-23]
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NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.
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BMC Bioinformatics 18 (Suppl 5) 118 [2017-03-23; online 2017-03-23]
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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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Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]
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Towards a whole-genome sequence for rye (Secale cereale L.).
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Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE.
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Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays
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Mol Cell Proteomics 16 (3) 502-511 [2017-03-00; online 2017-01-22]
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High GC content causes orphan proteins to be intrinsically disordered.
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PLoS Comput. Biol. 13 (3) e1005375 [2017-03-00; online 2017-03-29]
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Defining the human copper proteome and analysis of its expression variation in cancers.
Blockhuys S, Celauro E, Hildesjö C, ..., Fierro-González JC, Wittung-Stafshede P
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RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.
Alkasalias T, Alexeyenko A, Hennig K, ..., Gad AK, Pavlova T
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Proc. Natl. Acad. Sci. U.S.A. 114 (8) E1413-E1421 [2017-02-21; online 2017-02-07]
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The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.
Adrian-Kalchhauser I, Svensson O, Kutschera VE, ..., Blomberg A, Burkhardt-Holm P
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BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]
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microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.
Zhou Y, Frings O, Branca RM, ..., Agami R, Orre LM
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Oncogene 36 (6) 731-745 [2017-02-09; online 2016-08-01]
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Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy.
Dalin MG, Engström PG, Ivarsson EG, ..., Andersson B, Bergo MO
Int. J. Cardiol. 228 (-) 742-748 [2017-02-01; online 2016-11-26]
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The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.
Abrouk M, Balcárková B, Šimková H, ..., Doležel J, Valárik M
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Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora
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Proc Natl Acad Sci USA 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]
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Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.
Cimdins A, Lüthje P, Li F, ..., Brauner A, Römling U
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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
Vizlin-Hodzic D, Zhai Q, Illes S, ..., Ågren H, Funa K
Transl Psychiatry 7 (1) e1010 [2017-01-24; online 2017-01-24]
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NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.
Masoumi KC, Daams R, Sime W, ..., Levander F, Massoumi R
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Mol. Biol. Cell 28 (2) 346-355 [2017-01-15; online 2016-11-30]
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Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes
Le Rhun A, Lécrivain AL, Reimegård J, ..., Della Beffa C, Charpentier E
Nucleic Acids Res - (-) gkw1316 [2017-01-12; online 2017-01-12]
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Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.
Kee N, Volakakis N, Kirkeby A, ..., Parmar M, Perlmann T
Cell Stem Cell 20 (1) 29-40 [2017-01-05; online 2016-10-27]
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Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells.
Marabita F, Islam MS
Pancreas 46 (1) 97-101 [2017-01-00; online 2016-07-29]
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Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.
Pauter AM, Trattner S, Gonzalez-Bengtsson A, ..., Dethlefsen O, Jacobsson A
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Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.
Ma W, Gabriel TS, Martis MM, ..., Banaei-Moghaddam AM, Houben A
New Phytol. 213 (2) 916-928 [2017-01-00; online 2016-07-29]
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Year 2016

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Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
Corcoran MM, Phad GE, Néstor VB, ..., Martin M, Karlsson Hedestam GB
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Nat Commun 7 (-) 13642 [2016-12-20; online 2016-12-20]
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Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.
Hambäck PA, Weingartner E, Dalén L, Wirta H, Roslin T
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Ecol Evol 6 (23) 8431-8439 [2016-12-00; online 2016-10-26]
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Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction
Kjellqvist S, Klose C, Surma MA, ..., Melander O, Fernandez C
J Am Heart Assoc 5 (12) e004503 [2016-12-00; online 2016-11-29]
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Validation and development of MTH1 inhibitors for treatment of cancer.
Warpman Berglund U, Sanjiv K, Gad H, ..., Scobie M, Helleday T
Ann. Oncol. 27 (12) 2275-2283 [2016-12-00; online 2016-11-08]
Advanced Mass Spectrometry Proteomics [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Chemical Proteomics [Service] Clinical Proteomics Mass spectrometry [Collaborative] Drug Discovery and Development (DDD) [Collaborative]
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Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.
Lampa S, Alvarsson J, Spjuth O
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J Cheminform 8 (-) 67 [2016-11-24; online 2016-11-24]
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A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis.
Mukwaya A, Lindvall JM, Xeroudaki M, ..., Jensen LD, Lagali N
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Sci Data 3 (-) 160103 [2016-11-22; online 2016-11-22]
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WhatsHap: fast and accurate read-based phasing
Martin M, Patterson M, Garg S, ..., Schoenhuth A, Marschall T
bioRxiv - (-) - [2016-11-02; online 2016-11-02]
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Deletion of FtsH11 protease has impact on chloroplast structure and function in Arabidopsis thaliana when grown under continuous light.
Wagner R, von Sydow L, Aigner H, ..., Clarke A, Funk C
Plant Cell Environ. 39 (11) 2530-2544 [2016-11-00; online 2016-08-02]
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Computational pan-genomics: status, promises and challenges.
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Brief. Bioinformatics - (-) - [2016-10-21; online 2016-10-21]
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Integrative analysis of human omics data using biomolecular networks.
Robinson JL, Nielsen J
Mol Biosyst 12 (10) 2953-2964 [2016-10-20; online 2016-08-12]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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Massive and parallel expression profiling using microarrayed single-cell sequencing.
Vickovic S, Ståhl PL, Salmén F, ..., Frisén J, Lundeberg J
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Nat Commun 7 (-) 13182 [2016-10-14; online 2016-10-14]
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Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.
Bagnoud A, Chourey K, Hettich RL, ..., Schwyn B, Bernier-Latmani R
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Nat Commun 7 (-) 12770 [2016-10-14; online 2016-10-14]
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ProQ3: Improved model quality assessments using Rosetta energy terms.
Uziela K, Shu N, Wallner B, Elofsson A
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Sci Rep 6 (-) 33509 [2016-10-04; online 2016-10-04]
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Factors regulating capillary remodeling in a reversible model of inflammatory corneal angiogenesis
Mukwaya A, Peebo B, Xeroudaki M, ..., Jensen L, Lagali N
Sci Rep 6 (1) - [2016-10-00; online 2016-08-26]
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Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.
Lindblad O, Cordero E, Puissant A, ..., Rönnstrand L, Kazi JU
Oncogene 35 (39) 5119-5131 [2016-09-29; online 2016-03-22]
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Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes.
Lindqvist CM, Lundmark A, Nordlund J, ..., Berglund EC, Syvänen AC
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Oncotarget 7 (39) 64071-64088 [2016-09-27; online 2016-09-04]
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Combinatorial identification of DNA methylation patterns over age in the human brain.
Torabi Moghadam B, Dabrowski M, Kaminska B, Grabherr MG, Komorowski J
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BMC Bioinformatics 17 (1) 393 [2016-09-23; online 2016-09-23]
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Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa
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Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes
Buck M, Nilsson LKJ, Brunius C, ..., Hopkins R, Terenius O
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The distribution of α-kleisin during meiosis in the holocentromeric plant Luzula elegans.
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The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Lindholm ME, Giacomello S, Werne Solnestam B, ..., Kjellqvist S, Sundberg CJ
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PLoS Genet. 12 (9) e1006294 [2016-09-00; online 2016-09-22]
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Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach
Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C
New Biotechnology 33 (5) 503-513 [2016-09-00; online 2016-09-00]
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The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.
Rydén M, Hrydziuszko O, Mileti E, ..., Daub CO, Arner P
Cell Rep 16 (9) 2317-2326 [2016-08-30; online 2016-08-23]
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Large-scale ligand-based predictive modelling using support vector machines.
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Compounds from the marine sponge Cribrochalina vasculum offer a way to target IGF-1R mediated signaling in tumor cells
Zovko A, Novak M, Hååg P, ..., Lewensohn R, Viktorsson K
Oncotarget 7 (31) 50258-50276 [2016-08-02; online 2016-07-01]
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Töpel M, Zizka A, Calió MF, ..., Silvestro D, Antonelli A
Syst Biol - (-) syw064 [2016-08-02; online 2016-08-02]
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MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.
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Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.
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ISME J 10 (8) 1902-1914 [2016-08-00; online 2016-01-20]
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Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes.
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Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells.
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Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.
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Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.
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Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.
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Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.
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Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]
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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
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Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]
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Dinosaur: A Refined Open-Source Peptide MS Feature Detector.
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A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.
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Mol Ecol Resour 16 (4) 909-921 [2016-07-00; online 2015-12-20]
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Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.
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The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.
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PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.
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Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.
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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.
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Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
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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)
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Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.
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Regulating retrotransposon activity through the use of alternative transcription start sites.
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The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.
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EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer.
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Improved topology prediction using the terminal hydrophobic helices rule.
Peters C, Tsirigos KD, Shu N, Elofsson A
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Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.
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Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.
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Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes.
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RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.
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VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.
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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.
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Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.
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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids
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The FAIR Guiding Principles for scientific data management and stewardship.
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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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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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Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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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]
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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
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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
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BMC Genomics 17 (-) 119 [2016-02-18; online 2016-02-18]
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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
BioProject GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK 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