Bioinformatics Support, Infrastructure and Training (449 publications)

PubMed DOI Crossref

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

Halvorsen M, Huh R, Oskolkov N, ..., Sullivan PF, Szatkiewicz JP

Nat Commun 11 (1) - [2020-12-00; online 2020-04-15]

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

DOI Crossref

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N

Clin Epigenetics 12 (1) - [2020-12-00; online 2020-01-08]

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

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]

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

DOI Crossref

Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s disease

Tiklová K, Nolbrant S, Fiorenzano A, ..., Perlmann T, Parmar M

Nat Commun 11 (1) - [2020-12-00; online 2020-05-15]

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

DOI Crossref

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Almeida P, Proux-Wera E, Churcher A, ..., Berlin S, Mank JE

BMC Biol. 18 (1) - [2020-12-00; online 2020-06-30]

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

DOI Crossref

Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

Sakthikumar S, Roy A, Haseeb L, ..., Lindblad-Toh K, Forsberg-Nilsson K

Genome Biol. 21 (1) - [2020-12-00; online 2020-06-09]

Bioinformatics Long-term Support WABI [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]

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

GEO

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

The genomic footprint of sexual conflict.

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

Breast cancer quantitative proteome and proteogenomic landscape

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

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

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

GEO

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

Tractenberg RE, Lindvall JM, Attwood TK, Via A

pmc

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

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

DOI Crossref

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

Raethong N, Wang H, Nielsen J, Vongsangnak W

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

On-demand virtual research environments using microservices

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.

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

pmc

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

Interoperable and scalable data analysis with microservices: applications in metabolomics

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

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

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

PubMed DOI Crossref

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

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

pmc

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

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

DOI Crossref

Whole genome sequencing of apparently mutation-negative MEN1 patients

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

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

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

DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

Pederson ERA, Warshan D, Rasmussen U

pmc

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

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

PubMed DOI Crossref

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

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

pmc

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

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

PubMed DOI Crossref

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

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

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

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

DOI Crossref

Evolved for success in novel environments: The round goby genome

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

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

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

DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

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

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

PubMed DOI Crossref

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

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

pmc

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

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

DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

DOI Crossref

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

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

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

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

DOI Crossref

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

Lampa S, Dahlö M, Alvarsson J, Spjuth O

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Life history of Parnips and the evolutionary origin of gall wasps

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

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

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

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

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Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

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

pmc GEO GEO

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

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

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

SRA

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

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

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

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

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

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

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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

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

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

GEO GEO

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

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

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

SRA

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

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Delineating closely related dinoflagellate lineages using phylotranscriptomics.

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Bioconda: sustainable and comprehensive software distribution for the life sciences

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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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pmc GEO

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

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

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

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Hilborn E, Stål O, Alexeyenko A, Jansson A

pmc

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

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

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SRA GENBANK 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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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

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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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Nilsson A, Nielsen J

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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

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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

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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]

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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

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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

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

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

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

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

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

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

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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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pmc ClinicalTrials.gov ClinicalTrials.gov

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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.

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Spatially resolved transcriptome profiling in model plant species.

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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.

Rineau F, Lmalem H, Ahren D, ..., Martin F, Colpaert JV

Mycorrhiza 27 (4) 383-396 [2017-05-00; online 2017-01-09]

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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.

Tobiasson M, Abdulkadir H, Lennartsson A, ..., Hellström-Lindberg E, Ungerstedt J

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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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Nucleic Acids Res 45 (6) 3253-3265 [2017-04-07; online 2017-02-08]

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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.

Jeggari A, Alexeyenko A

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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.

Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J

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Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative] Proteogenomics [Technology development]

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Towards a whole-genome sequence for rye (Secale cereale L.).

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GENBANK GENBANK GENBANK

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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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High GC content causes orphan proteins to be intrinsically disordered.

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Defining the human copper proteome and analysis of its expression variation in cancers.

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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]

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

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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]

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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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

Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T

BioProject BioProject

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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Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]

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

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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.

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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

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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

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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]

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

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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

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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]

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

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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

Antonelli A, Hettling H, Condamine FL, ..., Oxelman B, Vos RA

Syst Biol - (-) syw066 [2016-09-10; online 2016-09-10]

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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.

Ma W, Schubert V, Martis MM, ..., Cheng Z, Houben A

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

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