Bioinformatics Support, Infrastructure and Training

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Publications

2021 (156)

2020 (580)

2019 (722)

2018 (643)

2017 (697)

2016 (660)

2015 (427)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (5126)


Infrastructure Units

Journals

SciLifeLab Infrastructure Unit Since 2021.

Started: 2021

Ended: Current

502 publications

Year 2021

PubMed DOI Crossref
Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
Zaghlool A, Niazi A, Björklund ÅK, ..., Ameur A, Feuk L
Sci Rep 11 (1) 4076 [2021-12-00; online 2021-02-18]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations
von Seth J, Dussex N, Díez-del-Molino D, ..., Götherström A, Dalén L
Nat Commun 12 (1) 2393 [2021-12-00; online 2021-04-26]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation
Norin U, Rintisch C, Meng L, ..., Bäckdahl L, Holmdahl R
Nat Commun 12 (1) 610 [2021-12-00; online 2021-01-27]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Large-scale identification of protein histidine methylation in human cells.
Kapell S, Jakobsson ME
NAR Genom Bioinform 3 (2) lqab045 [2021-06-00; online 2021-05-22]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A combined approach for single-cell mRNA and intracellular protein expression analysis.
Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ
Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.
Jönsson E, Ljung L, Norrman E, ..., Dahlqvist J, Dahlqvist SR
Rheumatology (Oxford) - (-) - [2021-05-16; online 2021-05-16]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A plasma lipid signature predicts incident coronary artery disease.
Ottosson F, Emami Khoonsari P, Gerl MJ, ..., Melander O, Fernandez C
Int. J. Cardiol. 331 (-) 249-254 [2021-05-15; online 2021-02-03]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A
Mar Biotechnol - (-) - [2021-05-01; online 2021-05-01]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.
Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O
Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]
PubMed DOI Crossref
Complete Genome Sequence of an Antimicrobial-Producing Bacillus velezensis Sam8H1 Isolate from the Makgadikgadi Saltpans of Botswana.
Modikwe G, Manoharan L, Mabutho G, ..., Lebogang L, Zhou N
Microbiol Resour Announc 10 (17) - [2021-04-29; online 2021-04-29]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.
Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M
Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Divergent airway microbiomes in lung transplant recipients with or without pulmonary infection.
Påhlman LI, Manoharan L, Aspelund AS
Respir. Res. 22 (1) 118 [2021-04-23; online 2021-04-23]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.
Rosengren MK, Sigurðardóttir H, Eriksson S, ..., Solé M, Lindgren G
BMC Genomics 22 (1) 267 [2021-04-14; online 2021-04-14]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Genetic barriers to historical gene flow between cryptic species of alpine bumblebees revealed by comparative population genomics.
Christmas MJ, Jones JC, Olsson A, ..., Geib JC, Webster MT
Mol. Biol. Evol. - (-) - [2021-04-06; online 2021-04-06]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure
PubMed DOI Crossref
Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection
Morgell A, Reisz JA, Ateeb Z, ..., Chen MS, D’Alessandro A
J. Proteome Res. 20 (5) 2725-2738 [2021-03-15; online 2021-03-15]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology
PubMed DOI Crossref
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
Schneider AN, Sundh J, Sundström G, ..., Hurry V, Street NR
mSystems 6 (1) - [2021-02-16; online 2021-02-16]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns.
Ugalde-Morales E, Grassmann F, Humphreys K, ..., Hall P, Czene K
Int. J. Cancer 148 (4) 884-894 [2021-02-15; online 2020-09-05]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.
Stratmann S, Yones SA, Mayrhofer M, ..., Cavelier L, Holmfeldt L
Blood Adv 5 (3) 900-912 [2021-02-09; online 2021-02-10]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.
Rengefors K, Gollnisch R, Sassenhagen I, ..., Bassham S, Ahrén D
Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]
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
Monocytes in sarcoidosis are potent TNF producers and predict disease outcome.
Lepzien R, Liu S, Czarnewski P, ..., Grunewald J, Smed-Sörensen A
Eur. Respir. J. - (-) 2003468 [2021-01-14; online 2021-01-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J
Cell Res 31 (5) 554-568 [2021-01-08; online 2021-01-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Year 2020

PubMed DOI Crossref
Genetic Risk Score for Serum 25-Hydroxyvitamin D Concentration Helps to Guide Personalized Vitamin D Supplementation in Healthy Finnish Adults.
Sallinen RJ, Dethlefsen O, Ruotsalainen S, ..., Kaunisto MA, Kallioniemi O
J. Nutr. - (-) - [2020-12-31; online 2020-12-31]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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 Compute and Storage [Service] 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] Systems Biology [Collaborative]
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 Compute and Storage [Service] 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]
PubMed DOI Crossref
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.
Appelberg S, Gupta S, Svensson Akusjärvi S, ..., Mirazimi A, Neogi U
Emerg Microbes Infect 9 (1) 1748-1760 [2020-12-00; online 2020-07-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed 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, Mazzaferro E, ..., Brooke HL, den Hoed M
Sci Rep 10 (1) 11831 [2020-12-00; online 2020-07-16]
BioImage Informatics Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [Service] 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]
PubMed DOI Crossref
The methylation landscape and its role in domestication and gene regulation in the chicken.
Höglund A, Henriksen R, Fogelholm J, ..., Jensen P, Wright D
Nat Ecol Evol 4 (12) 1713-1724 [2020-12-00; online 2020-09-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth.
Manoharan L, Brundin M, Rakhimova O, Chávez de Paz L, Romani Vestman N
J Clin Med 9 (12) 3877 [2020-11-28; online 2020-11-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.
Olsson Lindvall M, Angerfors A, Andersson B, ..., Stanne TM, Jern C
Thromb. Haemost. - (-) - [2020-11-17; online 2020-11-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size.
Tyson Y, Hillman C, Majenburg N, ..., Mohaddes M, Hailer NP
Acta Orthop - (-) 1-8 [2020-11-12; online 2020-11-12]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M
mSystems 5 (6) - [2020-11-10; online 2020-11-10]
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]
DOI Crossref
Drought legacy affects microbial community trait distributions related to moisture along a savanna‐grassland precipitation gradient
Leizeaga A, Hicks LC, Manoharan L, Hawkes CV, Rousk J
J Ecol - (-) - [2020-11-05; online 2020-11-05]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Metabolic characterization of plasma and cyst fluid from cystic precursors to pancreatic cancer patients reveal metabolic signatures of bacterial infection.
Morgell A, Reisz JA, Ateeb Z, ..., Sällberg Chen M, D'Alessandro A
medRxiv - (-) - [2020-11-04; online 2020-11-04]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.
Kalsoom Khan F, Kluting K, Tångrot J, ..., Ryberg M, Rosling A
IMA Fungus 11 (1) 23 [2020-11-03; online 2020-11-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenetic alterations in skin homing CD4 +CLA+ T cells of atopic dermatitis patients.
Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A
Sci Rep 10 (1) 18020 [2020-10-22; online 2020-10-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder.
Li D, Choque-Olsson N, Jiao H, ..., Bölte S, Tammimies K
npj Genom. Med. 5 (1) 45 [2020-10-12; online 2020-10-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A
Mol Ecol Resour 21 (1) 263-286 [2020-10-10; online 2020-10-10]
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 (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Sources of variation in cell-type RNA-Seq profiles.
Gustafsson J, Held F, Robinson JL, ..., Jörnsten R, Nielsen J
PLoS ONE 15 (9) e0239495 [2020-09-21; online 2020-09-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells.
Niklasson CU, Fredlund E, Monni E, ..., Bronner ME, Mohlin S
Dev. Dyn. - (-) - [2020-09-17; online 2020-09-17]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Reconstruction of the birth of a male sex chromosome present in Atlantic herring.
Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L
Proc. Natl. Acad. Sci. U.S.A. 117 (39) 24359-24368 [2020-09-16; online 2020-09-16]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Transcriptome analysis of EPO and GFP HEK293 Cell-lines Reveal Shifts in Energy and ER Capacity Support Improved Erythropoietin Production in HEK293F Cells
Saghaleyni R, Malm M, Zrimec J, ..., Robinson JL, Rockberg J
- - (-) - [2020-09-16; online 2020-09-16]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Integration of molecular profiles in a longitudinal wellness profiling cohort.
Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L
Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]
Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Cellular Immunomonitoring [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]
PubMed DOI Crossref
Genome sequence of segmented filamentous bacteria present in the human intestine.
Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF
Commun Biol 3 (1) 485 [2020-09-04; online 2020-09-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed 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
Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]
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
Comparative analysis of genome-wide DNA methylation in Neurospora.
Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H
Epigenetics 15 (9) 972-987 [2020-09-00; online 2020-03-31]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.
Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B
Front Microbiol 11 (-) 2066 [2020-08-27; online 2020-08-27]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.
Nascimento Lemos L, Manoharan L, William Mendes L, ..., Satler Pylro V, Tsai SM
Environ Microbiol Rep 12 (6) 651-655 [2020-08-19; online 2020-08-19]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.
Ljunggren M, Theorell-Haglöw J, Freyhult E, ..., Janson C, Lindberg E
J Sleep Res 29 (4) e13041 [2020-08-00; online 2020-04-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L
Current Biology 30 (19) 3871-3879.e7 [2020-08-00; online 2020-08-00]
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
Prototypical pacemaker neurons interact with the resident microbiota.
Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG
Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?
Ebrahimi P, Luthman H, McGuigan FE, Akesson KE
Epigenetics - (-) 1-14 [2020-07-21; online 2020-07-21]
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
Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.
Wallén-Mackenzie Å, Dumas S, Papathanou M, ..., König N, Björklund ÅK
Commun Biol 3 (1) 338 [2020-07-03; online 2020-07-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]
PubMed DOI Crossref
A framework to assess the quality and impact of bioinformatics training across ELIXIR.
Gurwitz KT, Singh Gaur P, Bellis LJ, ..., Morgan SL, Rustici G
PLoS Comput. Biol. 16 (7) e1007976 [2020-07-00; online 2020-07-23]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed 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) 78 [2020-06-30; online 2020-06-30]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed 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) 127 [2020-06-09; online 2020-06-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed 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) 2434 [2020-05-15; online 2020-05-15]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed 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 Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed 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. U.S.A. 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
DOI Crossref
Guidelines for curriculum and course development in higher education and training
Tractenberg RE, Lindvall JM, Attwood T, Via A
- - (-) - [2020-04-03; online 2020-04-03]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
An atlas of human metabolism.
Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J
Sci Signal 13 (624) - [2020-03-24; online 2020-03-24]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed 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. U.S.A. 117 (10) 5376-5385 [2020-03-10; online 2020-02-25]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.
Phad GE, Pushparaj P, Tran K, ..., Wyatt RT, Karlsson Hedestam GB
J. Exp. Med. 217 (2) - [2020-02-03; online 2019-11-11]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed 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
Diabetes Care 43 (2) 366-373 [2020-02-00; online 2019-12-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [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 Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.
Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR
Nat Commun 11 (1) 470 [2020-01-24; online 2020-01-24]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.
Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N
Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome sequencing of apparently mutation-negative MEN1 patients.
Backman S, Bajic D, Crona J, ..., Skogseid B, Stålberg P
Eur. J. Endocrinol. 182 (1) 35-45 [2020-01-00; online 2019-10-29]
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]

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. 120 (02) 229-242 [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]
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]
PubMed 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
Neurobiol. Dis. 132 (-) 104583 [2019-12-00; online 2019-08-21]
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]
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
Genome Biol. 20 (1) 164 [2019-12-00; online 2019-08-12]
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
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]
PubMed 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 [2019-12-00; online 2019-04-30]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development] Integrated Microscopy Technologies Stockholm [Service]
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]
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) 68 [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
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]
PubMed 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; online 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] Global Proteomics and Proteogenomics [Technology development] Spatial Proteomics [Collaborative]
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 112 (-) 104514 [2019-11-14; online 2019-11-14]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Biomarkers [Service]
PubMed DOI Crossref
On-demand virtual research environments using microservices.
Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O
PeerJ Comput Sci 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
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]
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
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
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
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
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]
PubMed 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) 9810 [2019-07-08; online 2019-07-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
DOI Crossref
GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files
Wik E, Olin H, Haughey C, Klasson L, Dainat J
JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]
Bioinformatics 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
Elife 8 (-) - [2019-06-27; online 2019-06-27]
Autoimmunity and Serology Profiling [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
DOI Crossref
Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis
Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T
Front. Cell. Infect. Microbiol. 9 (-) - [2019-06-21; online 2019-06-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B
Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]
Bioinformatics 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]
PubMed 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) 8169 [2019-06-03; online 2019-06-03]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
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
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
Sci Adv 5 (5) eaav9188 [2019-05-00; online 2019-05-01]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient
Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M
Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Abramova A, Lind U, Blomberg A, Rosenblad MA
Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions
Sobol M, Klar J, Laan L, ..., Falk A, Dahl N
Mol Neurobiol 56 (10) 7113-7127 [2019-04-13; online 2019-04-13]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Drysdale R, Cook CE, Petryszak R, ..., McEntyre J, None
- - (-) - [2019-04-05; online 2019-04-05]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis
Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB
Front Immunol 10 (-) - [2019-04-05; online 2019-04-05]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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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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]
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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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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]
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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
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DOI Crossref
The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function
Sapir T, Segal M, Grigoryan G, ..., Segal M, Reiner O
Front Cell Neurosci 13 (-) - [2019-03-13; online 2019-03-13]
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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]
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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) 2379 [2019-02-20; online 2019-02-20]
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DOI Crossref
Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes)
Košuthová A, Westberg M, Otálora MAG, Wedin M
MycoKeys 47 (-) 17-33 [2019-02-20; online 2019-02-20]
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Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development.
Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T
Nat Commun 10 (1) 581 [2019-02-04; online 2019-02-04]
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Plasma Profiles of Inflammatory Markers Associated With Active Tuberculosis in Antiretroviral Therapy-Naive Human Immunodeficiency Virus-Positive Individuals
Olsson O, Björkman P, Jansson M, ..., Carlsson F, Skogmar S
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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]
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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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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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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]
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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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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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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
Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]
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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]
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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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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
Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]
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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
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]
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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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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]
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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
Nat Med - (-) - [2018-11-12; online 2018-11-12]
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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]
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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
Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]
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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]
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Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia
Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B
Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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]
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Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.
Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC
Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]
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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]
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A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions
Franzén B, Kamali-Moghaddam M, Alexeyenko A, ..., Landegren U, Lewensohn R
Mol Oncol 12 (9) 1415-1428 [2018-09-00; online 2018-08-09]
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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]
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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
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]
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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
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
Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]
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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
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]
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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
Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]
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PubMed DOI Crossref
Clonal relatedness in tumour pairs of breast cancer patients.
Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K
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
Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]
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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]
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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]
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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
PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]
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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
Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]
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PubMed DOI Crossref
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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Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.
Garcia SL, Buck M, Hamilton JJ, ..., McMahon KD, Eiler A
mSphere 3 (3) - [2018-06-27; online 2018-05-30]
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PubMed DOI Crossref
Topology of membrane proteins — predictions, limitations and variations
Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A
Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]
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PubMed DOI Crossref
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
BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]
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Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S
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Zhu B, Ekman M, Svensson D, ..., Uvelius B, Swärd K
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Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K
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Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis
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Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]
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La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J
Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]
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Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A
Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]
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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]
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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
ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]
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Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y
PLoS Pathog. 14 (3) e1006936 [2018-03-00; online 2018-03-02]
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F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]
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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]
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Bacterial secretion of D-arginine controls environmental microbial biodiversity.
Alvarez L, Aliashkevich A, de Pedro MA, Cava F
ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]
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The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.
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Mol. Plant Pathol. 19 (2) 432-439 [2018-02-00; online 2017-03-12]
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Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]
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Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B
Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]
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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.
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Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]
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Year 2017

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Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases
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Journal of Experimental Biology - (-) - [2017-12-01; online 2017-11-27]
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Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration
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Nat Commun 8 (1) - [2017-12-00; online 2017-12-22]
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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]
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Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea
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Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-11-13]
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Sci Rep 7 (1) - [2017-12-00; online 2017-06-16]
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Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M
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Evolution Letters - (-) - [2017-11-28; online 2017-11-28]
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Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.
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Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]
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PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]
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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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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
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Effects of long-term low oxygen tension in human chondrosarcoma cells
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The Evolution of Dark Matter in the Mitogenome of Seed Beetles
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Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]
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Johansson A, Claesson R, Höglund Åberg C, Haubek D, Oscarsson J
J. Periodont. Res. 52 (5) 903-912 [2017-10-00; online 2017-04-10]
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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]
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Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF
Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]
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Hilborn E, Stål O, Alexeyenko A, Jansson A
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.
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]
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Montero-Mendieta S, Grabherr M, Lantz H, ..., Webster MT, Vilà C
PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]
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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
Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]
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Nilsson A, Nielsen J
Metabolic Engineering 43 (-) 103-112 [2017-09-00; online 2017-09-00]
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Cerium oxide nanoparticles inhibit differentiation of neural stem cells.
Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B
Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]
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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]
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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]
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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
PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]
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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]
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Annu. Rev. Biochem. 86 (1) 245-275 [2017-06-20; online 2017-06-20]
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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
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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]
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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]
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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
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.
Videvall E, Cornwallis CK, Ahrén D, ..., Valkiūnas G, Hellgren O
Mol. Ecol. 26 (11) 2939-2958 [2017-06-00; online 2017-04-08]
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Lower inflammatory markers in women with antenatal depression brings the M1/M2 balance into focus from a new direction
Edvinsson Å, Bränn E, Hellgren C, ..., Cunningham JL, Sundström-Poromaa I
Psychoneuroendocrinology 80 (-) 15-25 [2017-06-00; online 2017-06-00]
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Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.
Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ
Genome Announc 5 (21) - [2017-05-25; online 2017-05-25]
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Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.
Lahtvee P, Sánchez BJ, Smialowska A, ..., Gatto F, Nielsen J
Cell Syst 4 (5) 495-504.e5 [2017-05-24; online 2017-03-29]
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ProQ3D: improved model quality assessments using deep learning.
Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A
Bioinformatics 33 (10) 1578-1580 [2017-05-15; online 2017-01-06]
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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.
Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB
J Transl Med 15 (1) 102 [2017-05-11; online 2017-05-11]
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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
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Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
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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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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
Reimegård J, Kundu S, Pendle A, ..., Sundström JF, Emanuelsson O
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
Moreno AD, Tellgren-Roth C, Soler L, ..., Olsson L, Geijer C
Genome Announc 5 (14) e00138-17 [2017-04-06; online 2017-04-06]
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Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.
Nielsen JC, Grijseels S, Prigent S, ..., Workman M, Nielsen J
Nat Microbiol 2 (-) 17044 [2017-04-03; online 2017-04-03]
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Green listed—a CRISPR screen tool
Panda SK, Boddul SV, Jiménez-Andrade GY, ..., Fernandez-Ricaud L, Wermeling F
Bioinformatics 33 (7) 1099-1100 [2017-04-01; online 2016-12-19]
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Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.
Kalanxhi E, Risberg K, Barua IS, ..., Flatmark K, Ree AH
Cancer Res Treat 49 (2) 374-386 [2017-04-00; online 2016-08-05]
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Frequent low-level mutations of protein kinase D2 in angiolipoma
Hofvander J, Arbajian E, Stenkula KG, ..., Hornick JL, Mertens F
J. Pathol 241 (5) 578-582 [2017-04-00; online 2017-02-27]
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Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology
Viļuma A, Mikko S, Hahn D, ..., Andersson G, Bergström TF
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
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
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
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] Global Proteomics and Proteogenomics [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Towards a whole-genome sequence for rye (Secale cereale L.).
Bauer E, Schmutzer T, Barilar I, ..., Schön CC, Scholz U
Plant J. 89 (5) 853-869 [2017-03-00; online 2016-11-27]
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Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE.
Levin M, Levander F, Palmason R, Greiff L, Ohlin M
J. Allergy Clin. Immunol. 139 (3) 1026-1030 [2017-03-00; online 2016-08-09]
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Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays
Larssen P, Wik L, Czarnewski P, ..., Gabrielsson S, Kamali-Moghaddam M
Mol Cell Proteomics 16 (3) 502-511 [2017-03-00; online 2017-01-22]
Affinity Proteomics Uppsala [Technology development] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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High GC content causes orphan proteins to be intrinsically disordered.
Basile W, Sachenkova O, Light S, Elofsson A
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
Metallomics 9 (2) 112-123 [2017-02-22; online 2016-12-13]
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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
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
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
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
International Journal of Cardiology 228 (-) 742-748 [2017-02-00; online 2017-02-00]
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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
Plant Biotechnol. J. 15 (2) 249-256 [2017-02-00; online 2016-08-12]
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Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora
Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T
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
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
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
J. Lipid Res. 58 (1) 111-123 [2017-01-00; online 2016-11-20]
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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

PubMed DOI Crossref
Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
Corcoran MM, Phad GE, Néstor VB, ..., Martin M, Karlsson Hedestam GB
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
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
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
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.
Computational Pan-Genomics Consortium
Brief. Bioinformatics - (-) - [2016-10-21; online 2016-10-21]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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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
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
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
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
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
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
Sci Rep 6 (1) - [2016-09-00; online 2016-03-10]
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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
Chromosome Res. 24 (3) 393-405 [2016-09-00; online 2016-06-14]
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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
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.
Alvarsson J, Lampa S, Schaal W, ..., Wikberg JE, Spjuth O
J Cheminform 8 (-) 39 [2016-08-10; online 2016-08-10]
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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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SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution
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.
Norling M, Karlsson-Lindsjö OE, Gourlé H, Bongcam-Rudloff E, Hayer J
PLoS ONE 11 (8) e0160334 [2016-08-01; online 2016-08-01]
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Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.
Stenson M, Pedersen A, Hasselblom S, ..., Pinto R, Andersson PO
Leuk. Lymphoma 57 (8) 1814-1822 [2016-08-00; online 2016-02-17]
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Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.
Eiler A, Mondav R, Sinclair L, ..., Woyke T, Bertilsson S
ISME J 10 (8) 1902-1914 [2016-08-00; online 2016-01-19]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Microbial Single Cell Genomics [Collaborative]
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Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes.
Buetti-Dinh A, Dethlefsen O, Friedman R, Dopson M
Microbiology (Reading, Engl.) 162 (8) 1422-1434 [2016-08-00; online 2016-05-28]
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Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells.
Astakhova L, Ngara M, Babich O, ..., Ernberg I, Matskova L
PLoS ONE 11 (7) e0154102 [2016-07-21; online 2016-07-21]
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DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning.
Svennerholm K, Rodsand P, Hellman U, ..., Ronquist G, Haney M
PLoS ONE 11 (7) e0159105 [2016-07-19; online 2016-07-19]
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Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.
Gatto F, Schulze A, Nielsen J
Cell Rep 16 (3) 878-895 [2016-07-19; online 2016-07-12]
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Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.
Martínez-Redondo V, Jannig PR, Correia JC, ..., Dahlman-Wright K, Ruas JL
J. Biol. Chem. 291 (29) 15169-15184 [2016-07-15; online 2016-05-28]
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Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.
Reischauer S, Stone OA, Villasenor A, ..., Andersson O, Stainier DY
Nature 535 (7611) 294-298 [2016-07-14; online 2016-07-15]
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Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.
Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J
Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J
Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]
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Dinosaur: A Refined Open-Source Peptide MS Feature Detector.
Teleman J, Chawade A, Sandin M, Levander F, Malmström J
J. Proteome Res. 15 (7) 2143-2151 [2016-07-01; online 2016-05-26]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.
Humble E, Martinez-Barrio A, Forcada J, ..., Wolf JB, Hoffman JI
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.
Hagey DW, Zaouter C, Combeau G, ..., Huss M, Muhr J
Genome Res. 26 (7) 908-917 [2016-07-00; online 2016-05-02]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.
Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V
Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]
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PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.
Fernandez-Ricaud L, Kourtchenko O, Zackrisson M, Warringer J, Blomberg A
BMC Bioinformatics 17 (-) 249 [2016-06-23; online 2016-06-23]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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Read-based phasing of related individuals.
Garg S, Martin M, Marschall T
Bioinformatics 32 (12) i234-i242 [2016-06-15; online 2016-06-17]
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Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.
Gatto F, Volpi N, Nilsson H, ..., Basso U, Nielsen J
Cell Rep 15 (8) 1822-1836 [2016-05-24; online 2016-05-18]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.
Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B
PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A
Bioinformatics 32 (10) 1571-1573 [2016-05-15; online 2016-01-23]
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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
Nilsson RH, Alm Rosenblad M, Martín MP, ..., Wurzbacher C, Abarenkov K
MycoKeys 13 (-) 21-33 [2016-05-13; online 2016-05-13]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.
Pečnerová P, Díez-Del-Molino D, Vartanyan S, Dalén L
Sci Rep 6 (-) 25274 [2016-05-04; online 2016-05-04]
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.
Martinez Barrio A, Lamichhaney S, Fan G, ..., Xu X, Andersson L
Elife 5 (-) - [2016-05-03; online 2016-05-03]
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Regulating retrotransposon activity through the use of alternative transcription start sites.
Persson J, Steglich B, Smialowska A, ..., Nielsen O, Ekwall K
EMBO Rep. 17 (5) 753-768 [2016-05-00; online 2016-02-22]
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The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.
Engel P, Kwong WK, McFrederick Q, ..., vanEngelsdorp D, Dainat B
MBio 7 (2) e02164-e02115 [2016-04-26; online 2016-04-26]
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EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer.
Husa AM, Magić Ž, Larsson M, Fornander T, Pérez-Tenorio G
Oncotarget 7 (16) 21362-21380 [2016-04-19; online 2016-02-13]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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Improved topology prediction using the terminal hydrophobic helices rule.
Peters C, Tsirigos KD, Shu N, Elofsson A
Bioinformatics 32 (8) 1158-1162 [2016-04-15; online 2015-12-09]
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Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.
Spoerry C, Seele J, Valentin-Weigand P, Baums CG, von Pawel-Rammingen U
J. Biol. Chem. 291 (15) 7915-7925 [2016-04-08; online 2016-02-11]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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Transcriptomics resources of human tissues and organs.
Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J
Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]
Bioinformatics Support, Infrastructure and Training [Technology development] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Technology development] Tissue Profiling [Collaborative]
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Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.
Rodríguez SA, Grochová D, McKenna T, ..., Erdos MR, Eriksson M
Aging Cell 15 (2) 267-278 [2016-04-00; online 2015-12-22]
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Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes.
Andersson Hall U, Edin F, Pedersen A, Madsen K
Appl Physiol Nutr Metab 41 (4) 430-437 [2016-04-00; online 2015-12-17]
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RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.
Christel S, Fridlund J, Buetti-Dinh A, ..., Watkin EL, Dopson M
FEMS Microbiol. Lett. 363 (7) - [2016-04-00; online 2016-03-10]
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VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.
Li X, Padhan N, Sjöström EO, ..., Jansson L, Claesson-Welsh L
Nat Commun 7 (-) 11017 [2016-03-23; online 2016-03-23]
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In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo.
Tjernlund A, Burgener A, Lindvall JM, ..., McElrath MJ, Corey L
PLoS ONE 11 (3) e0149907 [2016-03-17; online 2016-03-17]
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Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.
Zepeda Mendoza ML, Lundberg J, Ivarsson M, ..., Sallstedt T, Dalen L
PLoS ONE 11 (3) e0151577 [2016-03-17; online 2016-03-17]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids
Steige K, Reimegård J, Rebernig CA, ..., Scofield DG, Slotte T
bioRxiv - (-) - [2016-03-16; online 2016-03-16]
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PubMed DOI Crossref
The FAIR Guiding Principles for scientific data management and stewardship.
Wilkinson MD, Dumontier M, Aalbersberg IJ, ..., Zhao J, Mons B
Sci Data 3 (-) 160018 [2016-03-15; online 2016-03-15]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.
Celorio-Mancera Mde L, Wheat CW, Huss M, ..., Nylin S, Janz N
BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]
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Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.
Gatto F, Nielsen J
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
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
New Phytol. 209 (4) 1705-1719 [2016-03-00; online 2015-11-04]
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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.
Wang J, Street NR, Scofield DG, Ingvarsson PK
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]
Affinity Proteomics Uppsala [Technology development] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal.
Karimpour M, Surowiec I, Wu J, ..., Zivkovic AM, Nording ML
Anal. Chim. Acta 908 (-) 121-131 [2016-02-18; online 2016-01-31]
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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
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
Nature 530 (7590) 331-335 [2016-02-18; online 2016-01-28]
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Species identification of Swedish mosquitoes through DNA metabarcoding
Lilja T, Nylander JAA, Troell K, Lindström A
JOURNAL OF THE EUROPEAN MOSQUITO CONTROL ASSOCIATION 35 (-) 1-9 [2016-02-16; online 2016-02-16]
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Targeted Proteomics Approach for Precision Plant Breeding.
Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F
J. Proteome Res. 15 (2) 638-646 [2016-02-05; online 2015-12-26]
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Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1.
Landegren N, Sharon D, Freyhult E, ..., Snyder M, Kämpe O
Sci Rep 6 (-) 20104 [2016-02-01; online 2016-02-01]
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Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.
Huang Y, Chain FJ, Panchal M, ..., Milinski M, Feulner PG
Mol. Ecol. 25 (4) 943-958 [2016-02-00; online 2016-01-11]
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The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854.
Wrange AL, Charrier G, Thonig A, ..., Jonsson PR, André C
PLoS ONE 11 (1) e0147082 [2016-01-28; online 2016-01-28]
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Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.
Thureborn P, Franzetti A, Lundin D, Sjöling S
PeerJ 4 (-) e1593 [2016-01-19; online 2016-01-19]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities
Green H, Hasmats J, Kupershmidt I, ..., Peterson C, Lundeberg J
Clin. Cancer Res. 22 (2) 366-373 [2016-01-15; online 2015-09-16]
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Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.
Bersani C, Huss M, Giacomello S, ..., Lui W, Wiman KG
Oncotarget 7 (2) 1895-1911 [2016-01-12; online 2015-12-18]
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PGSB PlantsDB: updates to the database framework for comparative plant genome research.
Spannagl M, Nussbaumer T, Bader KC, ..., Gundlach H, Mayer KF
Nucleic Acids Res. 44 (D1) D1141-D1147 [2016-01-04; online 2015-11-04]
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Fat intake and breast milk fatty acid composition in farming and nonfarming women and allergy development in the offspring.
Jonsson K, Barman M, Moberg S, ..., Wold AE, Sandberg AS
Pediatr. Res. 79 (1-1) 114-123 [2016-01-00; online 2015-09-22]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).
Lamichhaney S, Fan G, Widemo F, ..., Liu X, Andersson L
Nat. Genet. 48 (1) 84-88 [2016-01-00; online 2015-11-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2015

PubMed DOI Crossref
Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors.
Mattsson A, Kärrman A, Pinto R, Brunström B
PLoS ONE 10 (12) e0143780 [2015-12-01; online 2015-12-01]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.
Manoharan L, Kushwaha SK, Hedlund K, Ahrén D
DNA Res. 22 (6) 451-460 [2015-12-00; online 2015-10-23]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.
Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium , Huminiecki L
PLoS Biol. 13 (12) e1002315 [2015-12-00; online 2015-12-18]
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PubMed DOI Crossref
Experiences with workflows for automating data-intensive bioinformatics
Spjuth O, Bongcam-Rudloff E, Hernández GC, ..., Siretskiy A, Vassilev D
Biol. Direct 10 (1) - [2015-12-00; online 2015-08-19]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.
Zubair S, Fischer A, Liljander A, ..., Bongcam-Rudloff E, Jores J
Stand Genomic Sci 10 (-) 109 [2015-11-20; online 2015-11-20]
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RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.
Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E
RNA Biol 13 (2) 177-195 [2015-11-19; online 2015-11-19]
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In search for symmetries in the metabolism of cancer.
Gatto F, Nielsen J
Wiley Interdiscip Rev Syst Biol Med 8 (1) 23-35 [2015-11-05; online 2015-11-05]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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Quantitative proteogenomics of human pathogens using DIA-MS.
Malmström L, Bakochi A, Svensson G, ..., Karlsson C, Malmström J
J Proteomics 129 (-) 98-107 [2015-11-03; online 2015-09-19]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma.
Fall T, Lundholm C, Örtqvist AK, ..., Ingelsson E, Almqvist C
JAMA Pediatr 169 (11) e153219 [2015-11-00; online 2015-11-02]
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Herring and Beef Meals Lead to Differences in Plasma 2-Aminoadipic Acid, β-Alanine, 4-Hydroxyproline, Cetoleic Acid, and Docosahexaenoic Acid Concentrations in Overweight Men.
Ross AB, Svelander C, Undeland I, Pinto R, Sandberg AS
J. Nutr. 145 (11) 2456-2463 [2015-11-00; online 2015-09-25]
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Assessing the consistency of public human tissue RNA-seq data sets.
Danielsson F, James T, Gomez-Cabrero D, Huss M
Brief. Bioinformatics 16 (6) 941-949 [2015-11-00; online 2015-04-02]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.
Burri R, Nater A, Kawakami T, ..., Török J, Ellegren H
Genome Res. 25 (11) 1656-1665 [2015-11-00; online 2015-09-09]
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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Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Née)
Sork VL, Smouse PE, Grivet D, Scofield DG
Evol Ecol 29 (6) 927-945 [2015-11-00; online 2015-11-12]
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Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.
Sanli K, Bengtsson-Palme J, Nilsson RH, ..., Blanck H, Eriksson KM
Front Microbiol 6 (-) 1192 [2015-10-30; online 2015-10-30]
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Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.
Dumesic PA, Rosenblad MA, Samuelsson T, ..., Yates JR, Madhani HD
Nucleic Acids Res. 43 (18) 9017-9027 [2015-10-15; online 2015-08-16]
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Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.
Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T
Mol. Biol. Evol. 32 (10) 2501-2514 [2015-10-00; online 2015-08-28]
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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The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.
Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DGJ, Johansson A
Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-12]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.
Dmitriev AA, Rosenberg EE, Krasnov GS, ..., Senchenko VN, Kashuba VI
Dis. Markers 2015 (-) 241301 [2015-09-28; online 2015-09-28]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).
Delhomme N, Sundström G, Zamani N, ..., Grabherr MG, Street NR
PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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HLA class I is most tightly linked to levels of tapasin compared with other antigen-processing proteins in glioblastoma.
Thuring C, Follin E, Geironson L, ..., Buus S, Paulsson KM
Br. J. Cancer 113 (6) 952-962 [2015-09-15; online 2015-08-28]
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Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.
Garcia SL, Buck M, McMahon KD, ..., Eiler A, Warnecke F
Mol. Ecol. 24 (17) 4449-4459 [2015-09-00; online 2015-07-17]
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BEX1 acts as a tumor suppressor in acute myeloid leukemia.
Lindblad O, Li T, Su X, ..., Rönnstrand L, Kazi JU
Oncotarget 6 (25) 21395-21405 [2015-08-28; online 2015-06-06]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.
Zuccolo A, Scofield DG, De Paoli E, Morgante M
Gene 568 (1) 89-99 [2015-08-15; online 2015-05-20]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.
Lee W, Alexeyenko A, Pernemalm M, ..., Lehtiö J, Pawitan Y
Biomed Res Int 2015 (-) 462549 [2015-08-03; online 2015-08-03]
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Representation of selected-reaction monitoring data in the mzQuantML data standard.
Qi D, Lawless C, Teleman J, ..., Hubbard S, Jones AR
Proteomics 15 (15) 2592-2596 [2015-08-00; online 2015-04-18]
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Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression.
Menzel M, Sletvold N, Ågren J, Hansson B
Mol. Biol. Evol. 32 (8) 2036-2047 [2015-08-00; online 2015-04-10]
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Identification of New Potential Interaction Partners for Human Cytoplasmic Copper Chaperone Atox1: Roles in Gene Regulation?
Öhrvik H, Wittung-Stafshede P
Int J Mol Sci 16 (8) 16728-16739 [2015-07-23; online 2015-07-23]
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Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.
Wallace-Salinas V, Brink DP, Ahrén D, Gorwa-Grauslund MF
BMC Genomics 16 (-) 514 [2015-07-09; online 2015-07-09]
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The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.
Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A
Nucleic Acids Res. 43 (W1) W401-W407 [2015-07-01; online 2015-05-15]
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Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries.
Herrmann B, Isaksson J, Ryberg M, ..., Gravningen K, Bruisten S
J. Clin. Microbiol. 53 (7) 2172-2179 [2015-07-00; online 2015-05-01]
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Proteomics for the detection of indirect markers of steroids treatment in bovine muscle.
Stella R, Biancotto G, Arrigoni G, ..., Angeletti R, James P
Proteomics 15 (13) 2332-2341 [2015-07-00; online 2015-03-12]
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Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency.
Prasad MA, Ungerbäck J, Åhsberg J, ..., Hagman J, Sigvardsson M
Blood 125 (26) 4052-4059 [2015-06-25; online 2015-04-04]
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The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.
Lindskog C, Linné J, Fagerberg L, ..., Pontén F, Uhlén M
BMC Genomics 16 (-) 475 [2015-06-25; online 2015-06-25]
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Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.
Alexeyenko A, Alkasalias T, Pavlova T, ..., Guven H, Klein G
J. Exp. Clin. Cancer Res. 34 (-) 62 [2015-06-18; online 2015-06-18]
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Transglutaminase 4 as a prostate autoantigen in male subfertility.
Landegren N, Sharon D, Shum AK, ..., Snyder M, Kämpe O
Sci Transl Med 7 (292) 292ra101 [2015-06-17; online 2015-06-19]
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Whiteboard: a framework for the programmatic visualization of complex biological analyses.
Sundström G, Zamani N, Grabherr MG, Mauceli E
Bioinformatics 31 (12) 2054-2055 [2015-06-15; online 2015-02-11]
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A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.
Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O
Gigascience 4 (-) 26 [2015-06-04; online 2015-06-04]
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PubMed
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Skoglund C, Carlsen AL, Weiner M, ..., Heegaard NH, Segelmark M
Clin. Exp. Rheumatol. 33 (2 Suppl 89) S-64-71 [2015-05-26; online 2015-05-26]
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Phylogeny, evolution and classification of gall wasps: the plot thickens.
Ronquist F, Nieves-Aldrey JL, Buffington ML, ..., Liljeblad J, Nylander JA
PLoS ONE 10 (5) e0123301 [2015-05-20; online 2015-05-20]
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Is label-free LC-MS/MS ready for biomarker discovery?
Sandin M, Chawade A, Levander F
Proteomics Clin Appl 9 (3-4) 289-294 [2015-04-00; online 2015-02-07]
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Site-specific programming of the host epithelial transcriptome by the gut microbiota.
Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F
Genome Biol. 16 (-) 62 [2015-03-28; online 2015-03-28]
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Discovery of molecular markers to discriminate corneal endothelial cells in the human body.
Yoshihara M, Ohmiya H, Hara S, ..., Tsujikawa M, Nishida K
PLoS ONE 10 (3) e0117581 [2015-03-25; online 2015-03-25]
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Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.
Hosseini S, Resjö S, Liu Y, ..., Andreasson E, Karlsson M
J Proteomics 117 (-) 24-40 [2015-03-18; online 2015-01-24]
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Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.
Vigil-Stenman T, Larsson J, Nylander JA, Bergman B
BMC Genomics 16 (-) 193 [2015-03-17; online 2015-03-17]
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FGF2 as a potential prognostic biomarker for proneural glioma patients.
Sooman L, Freyhult E, Jaiswal A, ..., Bergqvist M, Ekman S
Acta Oncol 54 (3) 385-394 [2015-03-00; online 2014-09-30]
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MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.
Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D
BMC Bioinformatics 16 (-) 65 [2015-02-28; online 2015-02-28]
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Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.
Chawade A, Sandin M, Teleman J, Malmström J, Levander F
J. Proteome Res. 14 (2) 676-687 [2015-02-06; online 2014-11-20]
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Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.
Leong SL, Lantz H, Pettersson OV, ..., Tellgren-Roth C, Schnürer J
Environ. Microbiol. 17 (2) 496-513 [2015-02-00; online 2014-08-22]
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Multi-omic data analysis using Galaxy.
Boekel J, Chilton JM, Cooke IR, ..., Moerland PD, Griffin TJ
Nat. Biotechnol. 33 (2) 137-139 [2015-02-00; online 2015-02-07]
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The statistical geometry of transcriptome divergence in cell-type evolution and cancer.
Liang C, FANTOM Consortium , Forrest AR, Wagner GP
Nat Commun 6 (-) 6066 [2015-01-14; online 2015-01-14]
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Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
Avican K, Fahlgren A, Huss M, ..., Dersch P, Fällman M
PLoS Pathog. 11 (1) e1004600 [2015-01-00; online 2015-01-15]
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A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.
Freyhult E, Gustafsson MG, Strömbergsson H
Mol Inform 34 (1) 44-52 [2015-01-00; online 2015-01-08]
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The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.
Lindqvist CM, Nordlund J, Ekman D, ..., Syvänen A, Berglund EC
Hum. Mutat. 36 (1) 118-128 [2015-01-00; online 2014-10-31]
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Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes
Silvar C, Martis MM, Nussbaumer T, ..., Ordon F, Perovic D
Plant Genome 8 (3) 0 [2015-00-00; online 2015-00-00]
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Year 2014

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Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.
Alkasalias T, Flaberg E, Kashuba V, ..., Klein G, Guven H
Proc. Natl. Acad. Sci. U.S.A. 111 (48) 17188-17193 [2014-12-02; online 2014-11-19]
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High opsin diversity in a non-visual infaunal brittle star.
Delroisse J, Ullrich-Lüter E, Ortega-Martinez O, ..., Mallefet J, Flammang P
BMC Genomics 15 (-) 1035 [2014-11-28; online 2014-11-28]
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Leachability and desorption of PCBs from soil and their dependency on pH and dissolved organic matter.
Badea SL, Mustafa M, Lundstedt S, Tysklind M
Sci. Total Environ. 499 (-) 220-227 [2014-11-15; online 2014-09-07]
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Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands.
Magnusson K, Simon R, Sjölander D, ..., Hammarström P, Nilsson KP
Prion 8 (4) 319-329 [2014-11-01; online 2014-11-01]
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Binning metagenomic contigs by coverage and composition.
Alneberg J, Bjarnason BS, de Bruijn I, ..., Andersson AF, Quince C
Nat. Methods 11 (11) 1144-1146 [2014-11-00; online 2014-09-15]
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Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions.
Einarsdottir BO, Bagge RO, Bhadury J, ..., Ny L, Nilsson JA
Oncotarget 5 (20) 9609-9618 [2014-10-30; online 2014-09-18]
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The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing
Lindholm ME, Huss M, Solnestam BW, ..., Lundeberg J, Sundberg CJ
The FASEB Journal 28 (10) 4571-4581 [2014-10-01; online 2014-07-11]
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Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.
Merid SK, Goranskaya D, Alexeyenko A
BMC Bioinformatics 15 (-) 308 [2014-09-19; online 2014-09-19]
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Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.
Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A
BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]
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Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
Westram AM, Galindo J, Alm Rosenblad M, ..., Panova M, Butlin RK
Mol. Ecol. 23 (18) 4603-4616 [2014-09-00; online 2014-08-13]
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Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.
Panova M, Johansson T, Canbäck B, ..., Tunlid A, André C
BMC Genomics 15 (-) 687 [2014-08-18; online 2014-08-18]
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A universal genomic coordinate translator for comparative genomics.
Zamani N, Sundström G, Meadows JR, ..., Haas BJ, Grabherr MG
BMC Bioinformatics 15 (-) 227 [2014-06-30; online 2014-06-30]
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Large tilts in transmembrane helices can be induced during tertiary structure formation.
Virkki M, Boekel C, Illergård K, ..., von Heijne G, Nilsson I
J. Mol. Biol. 426 (13) 2529-2538 [2014-06-26; online 2014-04-30]
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The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
Poelstra JW, Vijay N, Bossu CM, ..., Grabherr MG, Wolf JBW
Science 344 (6190) 1410-1414 [2014-06-20; online 2014-06-19]
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Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.
Alexeyenko A, Nystedt B, Vezzi F, ..., Wu CC, Lundeberg J
BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]
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Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.
Chawade A, Alexandersson E, Levander F
J. Proteome Res. 13 (6) 3114-3120 [2014-06-06; online 2014-04-29]
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Numerical compression schemes for proteomics mass spectrometry data.
Teleman J, Dowsey AW, Gonzalez-Galarza FF, ..., Deutsch EW, Levander F
Mol. Cell Proteomics 13 (6) 1537-1542 [2014-06-00; online 2014-03-29]
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miR-20b regulates expression of proteinase-activated receptor-1 (PAR-1) thrombin receptor in melanoma cells.
Saleiban A, Faxälv L, Claesson K, Jönsson JI, Osman A
Pigment Cell Melanoma Res 27 (3) 431-441 [2014-05-00; online 2014-01-11]
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Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.
Resjö S, Ali A, Meijer HJ, ..., Govers F, Andreasson E
J. Proteome Res. 13 (4) 1848-1859 [2014-04-04; online 2014-03-05]
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Brownstein CA, Beggs AH, Homer N, ..., Kohane IS, Margulies DM
Genome Biol. 15 (3) R53 [2014-03-25; online 2014-03-25]
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On the biogeography of Centipeda: a species-tree diffusion approach.
Nylinder S, Lemey P, De Bruyn M, ..., Walsh N, Anderberg AA
Syst. Biol. 63 (2) 178-191 [2014-03-00; online 2013-12-18]
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Functional tradeoffs underpin salinity-driven divergence in microbial community composition.
Dupont CL, Larsson J, Yooseph S, ..., Venter JC, Bergman B
PLoS ONE 9 (2) e89549 [2014-02-27; online 2014-02-27]
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Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children.
Browall S, Norman M, Tångrot J, ..., Normark S, Henriques-Normark B
J. Infect. Dis. 209 (3) 377-388 [2014-02-01; online 2013-09-07]
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Lipid mediator profiles differ between lung compartments in asthmatic and healthy humans.
Larsson N, Lundström SL, Pinto R, ..., Wheelock CE, Nording ML
Eur. Respir. J. 43 (2) 453-463 [2014-02-00; online 2013-09-17]
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Dating the diversification of the major lineages of Passeriformes (Aves).
Ericson PG, Klopfstein S, Irestedt M, Nguyen JM, Nylander JA
BMC Evol. Biol. 14 (-) 8 [2014-01-15; online 2014-01-15]
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HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
Branca RM, Orre LM, Johansson HJ, ..., Käll L, Lehtiö J
Nat. Methods 11 (1) 59-62 [2014-01-00; online 2013-11-19]
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Data processing methods and quality control strategies for label-free LC-MS protein quantification.
Sandin M, Teleman J, Malmström J, Levander F
Biochim. Biophys. Acta 1844 (1 Pt A) 29-41 [2014-01-00; online 2013-04-10]
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Year 2013

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Automated quality control system for LC-SRM setups.
Teleman J, Waldemarson S, Malmström J, Levander F
J Proteomics 95 (-) 77-83 [2013-12-16; online 2013-04-16]
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Linkage analysis in familial non-Lynch syndrome colorectal cancer families from Sweden.
Kontham V, von Holst S, Lindblom A
PLoS ONE 8 (12) e83936 [2013-12-11; online 2013-12-11]
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Protein expansion is primarily due to indels in intrinsically disordered regions.
Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A
Mol. Biol. Evol. 30 (12) 2645-2653 [2013-12-00; online 2013-09-17]
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Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.
Åhsberg J, Ungerbäck J, Strid T, ..., Qian H, Sigvardsson M
J. Biol. Chem. 288 (46) 33449-33461 [2013-11-15; online 2013-10-01]
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Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.
Meerupati T, Andersson KM, Friman E, ..., Tunlid A, Ahrén D
PLoS Genet. 9 (11) e1003909 [2013-11-00; online 2013-11-14]
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Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.
Butler È, Alsterfjord M, Olofsson TC, ..., Malmström J, Vásquez A
BMC Microbiol. 13 (-) 235 [2013-10-22; online 2013-10-22]
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Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.
Nookaew I, Thorell K, Worah K, ..., Nielsen J, Lundin SB
BMC Med Genomics 6 (-) 41 [2013-10-11; online 2013-10-11]
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Molecular characterization of the α-subunit of Na⁺/K⁺ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.
Lind U, Alm Rosenblad M, Wrange AL, ..., Havenhand J, Blomberg A
PLoS ONE 8 (10) e77069 [2013-10-09; online 2013-10-09]
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Structural diversity of signal recognition particle RNAs in plastids.
Rosenblad MA, Träger C, Schünemann D
Plant Signal Behav 8 (10) doi: 10.4161/psb.26848 [2013-10-00; online 2014-02-05]
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Improved production of membrane proteins in Escherichia coli by selective codon substitutions.
Nørholm MH, Toddo S, Virkki MT, ..., von Heijne G, Daley DO
FEBS Lett. 587 (15) 2352-2358 [2013-08-02; online 2013-06-19]
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Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
Andersson KM, Meerupati T, Levander F, ..., Ahrén D, Tunlid A
Appl. Environ. Microbiol. 79 (16) 4993-5004 [2013-08-00; online 2013-06-19]
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Response of Acidithiobacillus caldus toward suboptimal pH conditions.
Mangold S, Rao Jonna V, Dopson M
Extremophiles 17 (4) 689-696 [2013-07-00; online 2013-05-29]
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Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.
Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O
Gigascience 2 (1) 9 [2013-06-25; online 2013-06-25]
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Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.
Sooman L, Lennartsson J, Gullbo J, ..., Blomquist E, Ekman S
Med. Oncol. 30 (3) 638 [2013-06-20; online 2013-06-20]
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The impact of splicing on protein domain architecture.
Light S, Elofsson A
Curr. Opin. Struct. Biol. 23 (3) 451-458 [2013-06-00; online 2013-04-09]
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The Norway spruce genome sequence and conifer genome evolution.
Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S
Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-22]
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A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits.
Hansen K, Perry BA, Dranginis AW, Pfister DH
Mol. Phylogenet. Evol. 67 (2) 311-335 [2013-05-00; online 2013-02-14]
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An adaptive alignment algorithm for quality-controlled label-free LC-MS.
Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F
Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]
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Membrane protein shaving with thermolysin can be used to evaluate topology predictors.
Bendz M, Skwark M, Nilsson D, ..., Käll L, Elofsson A
Proteomics 13 (9) 1467-1480 [2013-05-00; online 2013-03-21]
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Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.
Light S, Sagit R, Ekman D, Elofsson A
Biochim. Biophys. Acta 1834 (5) 890-897 [2013-05-00; online 2013-01-22]
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The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, ..., Eisenacher M, HUPO-PSI Group
Database (Oxford) 2013 (-) bat009 [2013-03-12; online 2013-03-12]
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Origin and evolution of medium chain alcohol dehydrogenases.
Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B
Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]
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Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).
Persson B, Kallberg Y
Chem. Biol. Interact. 202 (1-3) 111-115 [2013-02-25; online 2012-12-04]
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Evolution of sperm structure and energetics in passerine birds.
Rowe M, Laskemoen T, Johnsen A, Lifjeld JT
Proc. Biol. Sci. 280 (1753) 20122616 [2013-02-22; online 2013-01-04]
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FANTOM: Functional and taxonomic analysis of metagenomes.
Sanli K, Karlsson FH, Nookaew I, Nielsen J
BMC Bioinformatics 14 (-) 38 [2013-02-01; online 2013-02-01]
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Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.
Nookaew I, Svensson PA, Jacobson P, ..., Nielsen J, Carlsson LM
J. Clin. Endocrinol. Metab. 98 (2) E370-E378 [2013-02-00; online 2012-12-25]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Teschendorff AE, Marabita F, Lechner M, ..., Gomez-Cabrero D, Beck S
Bioinformatics 29 (2) 189-196 [2013-01-15; online 2012-11-24]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Year 2012

PubMed DOI Crossref
Evolution from the prokaryotic to the higher plant chloroplast signal recognition particle: the signal recognition particle RNA is conserved in plastids of a wide range of photosynthetic organisms.
Träger C, Rosenblad MA, Ziehe D, ..., Aronsson H, Schünemann D
Plant Cell 24 (12) 4819-4836 [2012-12-00; online 2012-12-28]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.
Olsson N, Wallin S, James P, Borrebaeck CA, Wingren C
Protein Sci. 21 (12) 1897-1910 [2012-12-00; online 2012-10-05]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns.
Moummou H, Kallberg Y, Tonfack LB, Persson B, van der Rest B
BMC Plant Biol. 12 (-) 219 [2012-11-20; online 2012-11-20]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
Nookaew I, Papini M, Pornputtapong N, ..., Uhlén M, Nielsen J
Nucleic Acids Res. 40 (20) 10084-10097 [2012-11-01; online 2012-09-12]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.
Pinto RC, Gerber L, Eliasson M, Sundberg B, Trygg J
Anal. Chem. 84 (20) 8675-8681 [2012-10-16; online 2012-09-18]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.
Papini M, Nookaew I, Uhlén M, Nielsen J
Microb. Cell Fact. 11 (-) 136 [2012-10-09; online 2012-10-09]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function.
Kallberg Y, Segerstolpe Å, Lackmann F, Persson B, Wieslander L
PLoS ONE 7 (9) e43786 [2012-09-12; online 2012-09-12]
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DOI Crossref
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
Nilsson RH, Tedersoo L, Abarenkov K, ..., Larsson E, Kõljalg U
MycoKeys 4 (-) 37-63 [2012-09-05; online 2012-09-05]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
The evolution of filamin-a protein domain repeat perspective.
Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A
J. Struct. Biol. 179 (3) 289-298 [2012-09-00; online 2012-03-15]
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PubMed DOI Crossref
Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway.
Arabi A, Ullah K, Branca RM, ..., Lehtiö J, Sangfelt O
Nat Commun 3 (-) 976 [2012-08-07; online 2012-08-07]
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PubMed DOI Crossref
Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry.
Olsson N, James P, Borrebaeck CA, Wingren C
Mol. Cell Proteomics 11 (8) 342-354 [2012-08-00; online 2012-05-01]
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Polyploidy and the evolution of complex traits.
Huminiecki L, Conant GC
Int J Evol Biol 2012 (-) 292068 [2012-07-30; online 2012-07-30]
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Automated selected reaction monitoring software for accurate label-free protein quantification.
Teleman J, Karlsson C, Waldemarson S, ..., Malmström J, Levander F
J. Proteome Res. 11 (7) 3766-3773 [2012-07-06; online 2012-06-05]
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Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?
Lundin D, Severin I, Logue JB, ..., Andersson AF, Lindström ES
Environ Microbiol Rep 4 (3) 367-372 [2012-06-00; online 2012-04-23]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Multimodel pathway enrichment methods for functional evaluation of expression regulation.
Kirik U, Cifani P, Albrekt AS, ..., Heyden A, Levander F
J. Proteome Res. 11 (5) 2955-2967 [2012-05-04; online 2012-04-05]
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Manipulating the genetic code for membrane protein production: what have we learnt so far?
Nørholm MH, Light S, Virkki MT, ..., von Heijne G, Daley DO
Biochim. Biophys. Acta 1818 (4) 1091-1096 [2012-04-00; online 2011-09-03]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
A dimerized single-chain variable fragment system for the assessment of neutralizing activity of phage display-selected antibody fragments specific for cytomegalovirus.
Carlsson F, Trilling M, Perez F, Ohlin M
J. Immunol. Methods 376 (1-2) 69-78 [2012-02-28; online 2011-12-14]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Characterization of the lipid droplet proteome of a clonal insulin-producing β-cell line (INS-1 832/13).
Larsson S, Resjö S, Gomez MF, James P, Holm C
J. Proteome Res. 11 (2) 1264-1273 [2012-02-03; online 2012-01-25]
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