Bioinformatics Support, Infrastructure and Training

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SciLifeLab Infrastructure Unit since 2021.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2021

Ended: Current

Year 2024

DOI Crossref
Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells
Arcoverde Cerveira R, Lenart K, Martin M, ..., Ols S, Loré K
Immunoinformatics (Amst) 16 (-) 100046 [2024-12-00; online 2024-12-00]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion.
Christ W, Kapell S, Sobkowiak MJ, ..., El Andaloussi S, Ezzat K
ACS Chem Neurosci 15 (22) 4095-4104 [2024-11-20; online 2024-11-07]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Service]
DOI Crossref
A comprehensive human embryo reference tool using single-cell RNA-sequencing data
Zhao C, Plaza Reyes A, Schell JP, ..., Petropoulos S, Lanner F
Nat Methods - (-) - [2024-11-14; online 2024-11-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Prospective Screening of Cancer Syndromes in Patients with Mesenchymal Tumors.
Öfverholm I, Lin Y, Mondini J, ..., Haglund de Flon F, Wallander K
Cancers (Basel) 16 (22) 3816 [2024-11-13; online 2024-11-13]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling.
Raouraoua N, Mirabello C, Véry T, ..., Lensink MF, Brysbaert G
Nat Comput Sci - (-) - [2024-11-11; online 2024-11-11]
Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
Spatial Multiomics Reveals Intratumoral Immune Heterogeneity with Distinct Cytokine Networks in Lung Cancer Brain Metastases.
Christensson G, Bocci M, Kazi JU, ..., Gonzalez Velozo H, Hagerling C
Cancer Res Commun 4 (11) 2888-2902 [2024-11-01; online 2024-10-14]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
The TβRI promotes migration and metastasis through thrombospondin 1 and ITGAV in prostate cancer cells.
Mu Y, Wallenius A, Zang G, ..., Mateus A, Landström M
Oncogene 43 (45) 3321-3334 [2024-11-00; online 2024-09-20]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Androgen receptor pathway inhibitors and taxanes in metastatic prostate cancer: an outcome-adaptive randomized platform trial.
De Laere B, Crippa A, Discacciati A, ..., Grönberg H, Lindberg J
Nat. Med. 30 (11) 3291-3302 [2024-11-00; online 2024-08-20]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Changes in circulating extracellular vesicle cargo are associated with cognitive decline after major surgery: an observational case-control study.
Mkrtchian S, Eldh M, Ebberyd A, ..., Eriksson LI, Gómez-Galán M
Br J Anaesth - (-) - [2024-10-18; online 2024-10-18]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.
Rubalcava-Gracia D, Bubb K, Levander F, ..., Koolmeister C, Larsson NG
Nucleic Acids Res. 52 (18) 11266-11282 [2024-10-14; online 2024-08-01]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] CRISPR Functional Genomics [Service]
PubMed DOI Crossref
GCKIII Kinases Control Hepatocellular Lipid Homeostasis via Shared Mode of Action.
Cansby E, Caputo M, Andersson E, ..., Hoy AJ, Mahlapuu M
J. Lipid Res. - (-) 100669 [2024-10-10; online 2024-10-10]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.
Mirabello C, Wallner B, Nystedt B, Azinas S, Carroni M
Nat Commun 15 (1) 8724 [2024-10-09; online 2024-10-09]
Bioinformatics Support, Infrastructure and Training [Technology development] Cryo-EM [Service]
PubMed DOI Crossref
Estradiol-mediated enhancement of the human ectocervical epithelial barrier correlates with desmoglein-1 expression in the follicular menstrual phase.
Bradley F, Stern A, Franzén Boger M, ..., Fowke KR, Broliden K
Front Endocrinol (Lausanne) 15 (-) 1454006 [2024-10-08; online 2024-10-08]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.
Mirabello C, Wallner B
Bioinformatics 40 (10) - [2024-10-01; online 2024-09-30]
Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
A research data management (RDM) community for ELIXIR.
D'Anna F, Jareborg N, Jetten M, ..., Vondrasek J, Andrabi M
F1000Res 13 (-) - [2024-09-30; online 2024-09-30]
Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Multiomic biomarkers after cardiac arrest.
Stopa V, Lileikyte G, Bakochi A, ..., Nielsen N, Devaux Y
Intensive Care Med Exp 12 (1) 83 [2024-09-27; online 2024-09-27]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Multi-omics analysis of aggregative multicellularity.
Edelbroek B, Westholm JO, Bergquist J, Söderbom F
iScience 27 (9) 110659 [2024-09-20; online 2024-08-03]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.
Mc Cartney AM, Formenti G, Mouton A, ..., Waterhouse RM, Mazzoni CJ
NPJ Biodivers 3 (1) 28 [2024-09-17; online 2024-09-17]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exposure of Colon-Derived Epithelial Monolayers to Fecal Luminal Factors from Patients with Colon Cancer and Ulcerative Colitis Results in Distinct Gene Expression Patterns.
Magnusson MK, Bas Forsberg A, Verveda A, ..., Simrén M, Öhman L
Int J Mol Sci 25 (18) - [2024-09-13; online 2024-09-13]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chalmers Mass Spectrometry Infrastructure [Collaborative]
PubMed DOI Crossref
Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference.
Lobo V, Nowak I, Fernandez C, ..., Angeletti D, Sarshad AA
Nucleic Acids Res. 52 (16) 9917-9935 [2024-09-09; online 2024-07-12]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dantrolene corrects cellular disease features of Darier disease and may be a novel treatment.
Hunt M, Wang N, Pupinyo N, ..., Bachar-Wikstrom E, Wikstrom JD
EMBO Mol Med 16 (9) 1986-2001 [2024-09-00; online 2024-07-26]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Contemporary intergeneric hybridization and backcrossing among birds-of-paradise.
Thörn F, Soares AER, Müller IA, ..., Blom MPK, Irestedt M
Evolution Letters 8 (5) 680-694 [2024-09-00; online 2024-06-08]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma.
Olsen TK, Otte J, Mei S, ..., Kharchenko PV, Baryawno N
Mol. Cancer 23 (1) 180 [2024-08-31; online 2024-08-31]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A charged tail on anti-α-Synuclein antibodies does not enhance their affinity to α-Synuclein fibrils.
Petersen I, Godec A, Ranjbarian F, ..., Mirabello C, Hultqvist G
PLoS ONE 19 (8) e0308521 [2024-08-29; online 2024-08-29]
Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics.
Sonavane S, Hassan S, Chatterjee U, ..., Reimegård J, Rising A
Sci Adv 10 (33) eadn0597 [2024-08-16; online 2024-08-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Spatial omics [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.
Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S
BMC Genomics 25 (1) 772 [2024-08-08; online 2024-08-08]
Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.
Rashid U, Wu C, Shiller J, ..., Thomson S, Deng CH
Bioinformatics 40 (8) - [2024-08-02; online 2024-07-30]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV.
Narayanan A, Kieri O, Vesterbacka J, ..., Ray S, Nowak P
Sci Rep 14 (1) 17820 [2024-08-01; online 2024-08-01]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.
Unneberg P, Larsson M, Olsson A, ..., Meyer B, Wallberg A
Nat Commun 15 (1) 6297 [2024-08-01; online 2024-08-01]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
DOI Crossref
Species-specific erosion of genetic diversity in grassland butterflies depends on landscape land cover
Nolen ZJ, Rundlöf M, Runemark A
Biological Conservation 296 (-) 110694 [2024-08-00; online 2024-08-00]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album).
Schneider K, Steward RA, Celorio-Mancera MP, ..., Wheat CW, Nylin S
Mol. Ecol. 33 (16) e17479 [2024-08-00; online 2024-07-22]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.
Wallerstein J, Han X, Levkovets M, ..., Agback T, Orekhov V
Commun Biol 7 (1) 868 [2024-07-16; online 2024-07-16]
Bioinformatics Support, Infrastructure and Training [Technology development] Swedish NMR Centre (SNC) [Technology development]
PubMed DOI Crossref
Temporal dynamics of woolly mammoth genome erosion prior to extinction.
Dehasque M, Morales HE, Díez-Del-Molino D, ..., Vartanyan S, Dalén L
Cell 187 (14) 3531-3540.e13 [2024-07-11; online 2024-06-27]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.
Papachristos K, Sayadi A, Arnqvist G
Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-28]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Utilising ancient DNA to understand crop population dynamics across a millennium: A case study of archaeological barley (Hordeum vulgare L.) from Gran Canaria, Spain
Hagenblad J, Morales J, Leino MW, ..., Rodríguez-Rodríguez AC, Santana J
Journal of Archaeological Science 167 (-) 106001 [2024-07-00; online 2024-07-00]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
GABA-mediated inhibition of human CD4+ T cell functions is enhanced by insulin but impaired by high glucose levels.
Jin Z, Hammoud H, Bhandage AK, ..., Kamali-Moghaddam M, Birnir B
EBioMedicine 105 (-) 105217 [2024-07-00; online 2024-06-28]
Affinity Proteomics Uppsala [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Spatial Mass Spectrometry [Collaborative]
PubMed DOI Crossref
Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice.
Holl D, Hau WF, Julien A, ..., Dias DO, Göritz C
Nat. Neurosci. 27 (7) 1285-1298 [2024-07-00; online 2024-06-07]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Integrated Microscopy Technologies Stockholm [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.
Rönn T, Perfilyev A, Oskolkov N, Ling C
Sci Rep 14 (1) 14637 [2024-06-25; online 2024-06-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Quantification and Profiling of Early and Late Differentiation Stage T Cells in Mantle Cell Lymphoma Reveals Immunotherapeutic Targets in Subsets of Patients.
Lokhande L, Nilsson D, de Matos Rodrigues J, ..., Jerkeman M, Ek S
Cancers (Basel) 16 (13) - [2024-06-21; online 2024-06-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Hearing loss and its association with the proteome of perilymph, cerebrospinal fluid, and tumor tissue in patients with vestibular schwannoma.
Edvardsson Rasmussen J, Li P, Laurell G, Bergquist J, Eriksson PO
Sci Rep 14 (1) 14118 [2024-06-19; online 2024-06-19]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma.
Öfverholm I, Wallander K, Haglund C, ..., Lin Y, Haglund de Flon F
Clin. Cancer Res. 30 (12) 2647-2658 [2024-06-14; online 2024-04-04]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.
Lobo V, Shcherbinina E, Westholm JO, ..., Anastasakis DG, Sarshad AA
Sci Data 11 (1) 617 [2024-06-12; online 2024-06-12]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Glycoproteomics and MS Proteomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice.
Masarapu Y, Cekanaviciute E, Andrusivova Z, ..., Costes SV, Giacomello S
Nat Commun 15 (1) 4778 [2024-06-11; online 2024-06-11]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Long-term impact of digital media on brain development in children.
Nivins S, Sauce B, Liebherr M, Judd N, Klingberg T
Sci Rep 14 (1) 13030 [2024-06-06; online 2024-06-06]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support.
Amoedo-Leite C, Parv K, Testini C, ..., Christoffersson G, Phillipson M
Nat Cardiovasc Res 3 (6) 685-700 [2024-06-00; online 2024-06-06]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci.
Wu PC, McGowan EC, Lee YQ, ..., Hansson J, Olsson ML
Transfusion 64 (6) 1083-1096 [2024-06-00; online 2024-04-21]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Childhood screening for type 1 diabetes comparing automated multiplex Antibody Detection by Agglutination-PCR (ADAP) with single plex islet autoantibody radiobinding assays.
Lind A, Freyhult E, de Jesus Cortez F, ..., Lernmark Å, Better Diabetes Diagnosis (BDD) study group
EBioMedicine 104 (-) 105144 [2024-06-00; online 2024-05-08]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Bacterial diversity in semen from stallions in three European countries evaluated by 16S sequencing.
Malaluang P, Niazi A, Guo Y, ..., Aurich C, Morrell JM
Vet Res Commun 48 (3) 1409-1421 [2024-06-00; online 2024-02-02]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
An endothelial regulatory module links blood pressure regulation with elite athletic performance.
Fegraeus K, Rosengren MK, Naboulsi R, ..., Meadows JRS, Lindgren G
PLoS Genet. 20 (6) e1011285 [2024-06-00; online 2024-06-17]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing.
Engvall K, Uvdal H, Björn N, Åvall-Lundqvist E, Gréen H
NPJ Precis Oncol 8 (1) 102 [2024-05-16; online 2024-05-16]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Gothenburg [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.
Mohamadnejad Sangdehi F, Jamsandekar MS, Enbody ED, Pettersson ME, Andersson L
BMC Genomics 25 (1) 459 [2024-05-10; online 2024-05-10]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.
Gutiérrez-Valencia J, Zervakis P, Postel Z, ..., Arroyo J, Slotte T
Mol. Biol. Evol. 41 (5) - [2024-05-03; online 2024-05-06]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
PARKIN is not required to sustain OXPHOS function in adult mammalian tissues.
Filograna R, Gerlach J, Choi H, ..., Svenningsson P, Larsson N
NPJ Parkinsons Dis 10 (1) 93 [2024-04-29; online 2024-04-29]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Cyanotoxin Occurrence and Diversity in 98 Cyanobacterial Blooms from Swedish Lakes and the Baltic Sea.
Dirks C, Cappelli P, Blomqvist M, ..., Pekar H, Zuberovic Muratovic A
Mar Drugs 22 (5) - [2024-04-27; online 2024-04-27]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
HIV-2 mediated effects on target and bystander cells induce plasma proteome remodeling.
Johansson E, Nazziwa J, Freyhult E, ..., Jansson M, SWEGUB CORE group
iScience 27 (4) 109344 [2024-04-19; online 2024-02-28]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi.
Roberts KT, Steward RA, Süess P, Lehmann P, Wheat CW
Mol. Ecol. - (-) e17348 [2024-04-10; online 2024-04-10]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.
Lundtoft C, Knight A, Meadows JRS, ..., Lindblad-Toh K, Dahlqvist J
RMD Open 10 (2) - [2024-04-04; online 2024-04-04]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.
David G, Bertolotti A, Layer R, ..., Jensen H, Husby A
Genome Biol Evol 16 (4) - [2024-04-02; online 2024-03-15]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck.
Nilsson J, Eriksson P, Naguib MM, ..., Larson G, Ellström P
Glycobiology 34 (3) - [2024-04-01; online 2023-12-21]
Bioinformatics Support, Infrastructure and Training [Collaborative] Glycoproteomics and MS Proteomics [Collaborative]
DOI Crossref
Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations
Saha A, Kurland S, Kutschera VE, ..., Ryman N, Laikre L
Conserv Genet 25 (2) 513-531 [2024-04-00; online 2024-01-20]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Designing efficient randstrobes for sequence similarity analyses.
Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K
Bioinformatics 40 (4) - [2024-03-29; online 2024-04-05]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.
ElBeck Z, Hossain MB, Siga H, ..., Végvári Á, Betsholtz C
Nat Commun 15 (1) 2358 [2024-03-20; online 2024-03-20]
BioImage Informatics [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.
Suarez C, Rosenqvist T, Dimitrova I, ..., Hermansson M, Persson F
Microbiome 12 (1) 51 [2024-03-12; online 2024-03-12]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Identification of microbial pathogens in Neolithic Scandinavian humans.
Bergfeldt N, Kırdök E, Oskolkov N, ..., Storå J, Götherström A
Sci Rep 14 (1) 5630 [2024-03-07; online 2024-03-07]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.
Höglund A, Henriksen R, Churcher AM, ..., Jensen P, Wright D
PLoS Genet. 20 (3) e1010719 [2024-03-00; online 2024-03-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult.
Di Nunzio G, Hellberg S, Zhang Y, ..., Olofsson PS, Malin SG
Nat Cardiovasc Res 3 (3) 356-371 [2024-03-00; online 2024-03-11]
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Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs.
Ås J, Bertulyte I, Norgren N, ..., Wadelius M, Hallberg P
PLoS ONE 19 (2) e0299075 [2024-02-29; online 2024-02-29]
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Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.
Kvedaraite E, Lourda M, Mouratidou N, ..., Henter JI, Svensson M
Nat Commun 15 (1) 1752 [2024-02-26; online 2024-02-26]
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Differential gene expression in two consecutive pregnancies between same sex siblings and implications on maternal constraint.
Kallak TK, Serapio S, Visser N, ..., Skalkidou A, Ahlsson F
Sci Rep 14 (1) 4210 [2024-02-20; online 2024-02-20]
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Nigral transcriptomic profiles in Engrailed-1 hemizygous mouse models of Parkinson's disease reveal upregulation of oxidative phosphorylation-related genes associated with delayed dopaminergic neurodegeneration.
Belfiori LF, Dueñas Rey A, Ralbovszki DM, ..., Brolin KA, Swanberg M
Front Aging Neurosci 16 (-) 1337365 [2024-02-05; online 2024-02-05]
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PubMed DOI Crossref
A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.
Höglund J, Dias G, Olsen RA, ..., Talla V, Backström N
Genome Biol Evol 16 (2) - [2024-02-01; online 2024-02-18]
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Vaginal candida infection is associated with host molecular signatures of neutrophil activation in the adjacent ectocervical mucosa in Kenyan sex workers
Hasselrot T, Boger MF, Kaldhusdal V, ..., Czarnewski P, Broliden K
American J Rep Immunol 91 (2) - [2024-02-00; online 2024-01-31]
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Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome.
Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen A
Arthritis & rheumatology (Hoboken, N.J.) 76 (2) 255-267 [2024-02-00; online 2023-12-18]
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Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles.
Geng K, Merino LG, Veiga RG, ..., Brinkman EK, Kutter C
Life Sci. Alliance 7 (2) - [2024-02-00; online 2023-11-20]
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A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.
Lindelöf L, Rantapää-Dahlqvist S, Lundtoft C, ..., Svenungsson E, Eriksson O
J. Autoimmun. 143 (-) 103166 [2024-02-00; online 2024-01-13]
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Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.
Grujčić V, Saarenpää S, Sundh J, ..., Foster RA, Andersson AF
PLoS ONE 19 (1) e0296672 [2024-01-19; online 2024-01-19]
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WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.
Bouyssié D, Altıner P, Capella-Gutierrez S, ..., Winkelhardt D, Schwämmle V
J. Proteome Res. 23 (1) 418-429 [2024-01-05; online 2023-12-01]
Bioinformatics Support, Infrastructure and Training [Technology development]
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Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite.
Cīrulis A, Nordén AK, Churcher AM, ..., Zadesenets KS, Abbott JK
Genome Biol Evol 16 (1) - [2024-01-05; online 2023-12-29]
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Mutation of the cyclooxygenase 2 gene promoter and anastomotic leakage in colorectal cancer patients: retrospective cohort study.
Grahn O, Holmgren K, Hong MG, Sund M, Rutegård M
BJS Open 8 (1) - [2024-01-03; online 2024-01-30]
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Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.
Hunt G, Vaid R, Pirogov S, ..., Reimegård J, Mannervik M
Genome Biol. 25 (1) 2 [2024-01-02; online 2024-01-02]
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Functional annotation of a divergent genome using sequence and structure-based similarity.
Svedberg D, Winiger RR, Berg A, ..., Vossbrinck CR, Barandun J
BMC Genomics 25 (1) 6 [2024-01-02; online 2024-01-02]
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A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.
Latz MAC, Andersson A, Brugel S, ..., Torstensson A, Andersson AF
Sci Data 11 (1) 18 [2024-01-02; online 2024-01-02]
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The functional role of CST1 and CCL26 in asthma development.
Hoyer A, Chakraborty S, Lilienthal I, ..., Katayama S, Söderhäll C
Immun Inflamm Dis 12 (1) e1162 [2024-01-00; online 2024-01-25]
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Population genomics of the muskox' resilience in the near absence of genetic variation.
Pečnerová P, Lord E, Garcia-Erill G, ..., Moltke I, Siegismund HR
Mol. Ecol. 33 (2) e17205 [2024-01-00; online 2023-11-16]
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New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.
Bittner MJ, Bannon CC, Rowland E, ..., Paerl RW, Riemann L
ISME COMMUN. 4 (1) ycad016 [2024-01-00; online 2024-01-10]
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Year 2023

PubMed DOI Crossref
Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut.
Wang J, Chen H, Li Y, ..., Qu C, Shan S
Plants (Basel) 13 (1) - [2023-12-20; online 2023-12-20]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.
Hafstað V, Häkkinen J, Larsson M, ..., Vallon-Christersson J, Persson H
BMC Genomics 24 (1) 783 [2023-12-18; online 2023-12-18]
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Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).
Landi M, Shah T, Falquet L, ..., Bongcam-Rudloff E, Gisel A
Sci Data 10 (1) 887 [2023-12-09; online 2023-12-09]
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PubMed DOI Crossref
The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15.
Ozden B, Kryshtafovych A, Karaca E
Proteins 91 (12) 1636-1657 [2023-12-00; online 2023-10-20]
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Tertiary structure assessment at CASP15.
Simpkin AJ, Mesdaghi S, Sánchez Rodríguez F, ..., Keegan RM, Rigden DJ
Proteins 91 (12) 1616-1635 [2023-12-00; online 2023-09-25]
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Screening for Circulating Inflammatory Proteins Does Not Reveal Plasma Biomarkers of Constant Tinnitus.
Cederroth CR, Hong MG, Freydin MB, ..., Bulla J, Williams FMK
J Assoc Res Otolaryngol 24 (6) 593-606 [2023-12-00; online 2023-12-11]
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DOI Crossref
FAIR+E pathogen data for surveillance and research: lessons from COVID-19
Neves A, Cuesta I, Hjerde E, ..., Waheed Z, Blomberg N
Front Public Health 11 (-) - [2023-11-21; online 2023-11-21]
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Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.
Estravis Barcala M, van der Valk T, Chen Z, ..., Nilsson O, Wu HX
Plant J. - (-) - [2023-11-10; online 2023-11-10]
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BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.
Höjer P, Frick T, Siga H, ..., Martin M, Ahmadian A
Nucleic Acids Res. - (-) - [2023-11-06; online 2023-11-06]
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Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice.
Aoun M, Coelho A, Krämer A, ..., Burkhardt H, Holmdahl R
J. Exp. Med. 220 (11) - [2023-11-06; online 2023-09-11]
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Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.
Fracasso I, Zaccone C, Oskolkov N, ..., Ventura M, Borruso L
Sci. Total Environ. 908 (-) 168159 [2023-11-01; online 2023-11-01]
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CGG toolkit: Software components for computational genomics.
Vasileiou D, Karapiperis C, Baltsavia I, ..., Enright AJ, Ouzounis CA
PLoS Comput. Biol. 19 (11) e1011498 [2023-11-00; online 2023-11-07]
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aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
Genome Biol. 24 (1) 242 [2023-10-23; online 2023-10-23]
Ancient DNA [Technology development] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.
Mastropasqua F, Oksanen M, Soldini C, ..., Bölte S, Tammimies K
Biol Open 12 (10) - [2023-10-15; online 2023-10-10]
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Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.
Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M
Clin. Cancer Res. 29 (20) 4139-4152 [2023-10-13; online 2023-08-04]
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Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication.
Chakraborty C, Nissen I, Vincent CA, ..., Hörnblad A, Remeseiro S
Nat Commun 14 (1) 6446 [2023-10-13; online 2023-10-13]
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Integrated Genomic and Transcriptomic Analysis Improves Disease Classification and Risk Stratification of MDS with Ring Sideroblasts.
Todisco G, Creignou M, Bernard E, ..., Papaemmanuil E, Hellström-Lindberg E
Clin. Cancer Res. 29 (20) 4256-4267 [2023-10-13; online 2023-07-27]
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Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses.
Ols S, Lenart K, Arcoverde Cerveira R, ..., King NP, Loré K
Immunity 56 (10) 2425-2441.e14 [2023-10-10; online 2023-09-08]
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Mitochondrial heteroplasmic shifts reveal a positive selection of breast cancer.
Li Y, Sundquist K, Vats S, ..., Sundquist J, Memon AA
J Transl Med 21 (1) 696 [2023-10-05; online 2023-10-05]
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Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.
Merino I, Guasca AO, Krmela A, ..., Schulzova V, Sitbon F
Front Plant Sci 14 (-) 1210850 [2023-10-04; online 2023-10-04]
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Copy number variations and their effect on the plasma proteome.
Schmitz D, Li Z, Lo Faro V, ..., Rafati N, Johansson Å
Genetics - (-) - [2023-10-04; online 2023-10-04]
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PubMed DOI Crossref
The dynamics of touch-responsive gene expression in cereals.
Darwish E, Ghosh R, Bentzer J, ..., Sirijovski N, Van Aken O
Plant J. 116 (1) 282-302 [2023-10-00; online 2023-06-08]
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Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation.
Mengal K, Kor G, Siino V, ..., Levander F, Niksirat H
Dev. Comp. Immunol. 147 (-) 104760 [2023-10-00; online 2023-06-16]
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PubMed DOI Crossref
Origin matters: Using a local reference genome improves measures in population genomics.
Thorburn DJ, Sagonas K, Binzer-Panchal M, ..., Lenz TL, Eizaguirre C
Mol Ecol Resour 23 (7) 1706-1723 [2023-10-00; online 2023-07-25]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).
Steffen K, Proux-Wéra E, Soler L, ..., Sundh J, Cárdenas P
G3 (Bethesda) 13 (10) - [2023-09-30; online 2023-08-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Oral fungal profiling and risk of nasopharyngeal carcinoma: a population-based case-control study.
Chen Y, Li W, Chang ET, ..., Zhang Z, Ye W
EBioMedicine 96 (-) 104813 [2023-09-28; online 2023-09-28]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
The microbial biodiversity at the archeological site of Tel Megiddo (Israel).
Zhang Y, Ruff SE, Oskolkov N, ..., Mason CE, Elhaik E
Front Microbiol 14 (-) 1253371 [2023-09-22; online 2023-09-22]
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Strict self-isolation did not protect Swedish cancer patients on active treatment from the risk of becoming seropositive for SARS-CoV-2.
Ginman B, Pahnke S, Freyhult E, ..., Enblad G, Glimelius I
Acta Oncol - (-) 1-9 [2023-09-20; online 2023-09-20]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Ki67 and prostate specific antigen are prognostic in metastatic hormone naïve prostate cancer.
Spyratou V, Freyhult E, Bergh A, ..., Welén K, Josefsson A
Acta Oncol - (-) 1-9 [2023-09-15; online 2023-09-15]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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In vivo gene expression profile of Haemophilus influenzae during human pneumonia.
Polland L, Rydén H, Su Y, Paulsson M
Microbiol Spectr 11 (5) e0163923 [2023-09-14; online 2023-09-14]
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Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster.
Corthals K, Andersson V, Churcher A, Reimegård J, Enjin A
Sci Rep 13 (1) 15202 [2023-09-14; online 2023-09-14]
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Sustained and intermittent hypoxia differentially modulate primary monocyte immunothrombotic responses to IL-1β stimulation.
Wahlund CJE, Çaglayan S, Czarnewski P, Hansen JB, Snir O
Front Immunol 14 (-) 1240597 [2023-09-11; online 2023-09-11]
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PLK1 as a cooperating partner for BCL2-mediated antiapoptotic program in leukemia.
Shah K, Nasimian A, Ahmed M, ..., Lock RB, Kazi JU
Blood Cancer J 13 (1) 139 [2023-09-07; online 2023-09-07]
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PubMed DOI Crossref
Stratified genetic analysis reveals sex differences in MPO-ANCA-associated vasculitis.
Ekman D, Sennblad B, Knight A, ..., Lindblad-Toh K, Dahlqvist J
Rheumatology (Oxford) 62 (9) 3213-3218 [2023-09-01; online 2023-04-03]
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PubMed DOI Crossref
An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants.
Tran HC, Schmitt V, Lama S, ..., Delannoy E, Van Aken O
Science 381 (6661) eadg0995 [2023-09-00; online 2023-09-01]
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PubMed DOI Crossref
Highly multiplexed targeted sequencing strategy for infectious disease surveillance.
Hernández-Neuta I, Magoulopoulou A, Pineiro F, ..., Gulberg M, Nilsson M
BMC Biotechnol. 23 (1) 31 [2023-08-23; online 2023-08-23]
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PubMed DOI Crossref
Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour.
Zhang H, Konjusha D, Rafati N, Tararuk T, Hallböök F
Cell Oncol (Dordr) - (-) - [2023-08-22; online 2023-08-22]
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PubMed DOI Crossref
Molecular and spatial landmarks of early mouse skin development.
Jacob T, Annusver K, Czarnewski P, ..., Björklund ÅK, Kasper M
Dev. Cell - (-) - [2023-08-13; online 2023-08-13]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.
Almamoun R, Pierozan P, Manoharan L, Karlsson O
Ecotoxicol Environ Saf 262 (-) 115321 [2023-08-05; online 2023-08-05]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
Borry M, Forsythe A, Andrades Valtueña A, ..., Warinner C, Fellows Yates JA
F1000Res 12 (-) 926 [2023-08-02; online 2023-08-02]
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PubMed DOI Crossref
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.
Vromman M, Anckaert J, Bortoluzzi S, ..., Vandesompele J, Volders PJ
Nat. Methods 20 (8) 1159-1169 [2023-08-00; online 2023-07-13]
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PubMed DOI Crossref
Historical RNA expression profiles from the extinct Tasmanian tiger.
Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR
Genome Res. 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PVT1 interacts with polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma.
Nylund P, Garrido-Zabala B, Párraga AA, ..., Kalushkova A, Wiklund HJ
Haematologica - (-) - [2023-07-27; online 2023-07-27]
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An Okinawan-Based Nordic Diet Leads to Profound Effects on Gut Microbiota and Plasma Metabolites Linked to Glucose and Lipid Metabolism.
Manoharan L, Roth B, Bang C, Stenlund H, Ohlsson B
Nutrients 15 (14) - [2023-07-24; online 2023-07-24]
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Serum proteome profiles in patients treated with targeted temperature management after out-of-hospital cardiac arrest.
Lileikyte G, Bakochi A, Ali A, ..., Malmström J, Nielsen N
Intensive Care Med Exp 11 (1) 43 [2023-07-17; online 2023-07-17]
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Autologous hematopoietic stem cell transplantation significantly alters circulating ceramides in peripheral blood of relapsing-remitting multiple sclerosis patients.
Vaivade A, Wiberg A, Khoonsari PE, ..., Burman J, Kultima K
Lipids Health Dis 22 (1) 97 [2023-07-07; online 2023-07-07]
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Unmodified rabies mRNA vaccine elicits high cross-neutralizing antibody titers and diverse B cell memory responses.
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Nat Commun 14 (1) 3713 [2023-06-22; online 2023-06-22]
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Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.
Lauterbur ME, Cavassim MIA, Gladstein AL, ..., Schrider DR, Gronau I
Elife 12 (-) - [2023-06-21; online 2023-06-21]
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Disease phenotype prediction in multiple sclerosis.
Herman S, Arvidsson McShane S, Zjukovskaja C, ..., Spjuth O, Kultima K
iScience 26 (6) 106906 [2023-06-16; online 2023-05-19]
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The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.
Yazdi HP, Olito C, Kawakami T, ..., Hansson B, Cornwallis CK
PLoS Genet. 19 (6) e1010801 [2023-06-00; online 2023-06-30]
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Pathogenic antibody response to glucose-6-phosphate isomerase targets a modified epitope uniquely exposed on joint cartilage.
Li T, Ge C, Krämer A, ..., Gjertsson I, Holmdahl R
Ann. Rheum. Dis. 82 (6) 799-808 [2023-06-00; online 2023-03-01]
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Díaz de Ståhl T, Shamikh A, Mayrhofer M, ..., Sandgren J, Nistér M
J Transl Med 21 (1) 342 [2023-05-23; online 2023-05-23]
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The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis.
Kokkinou E, Soini T, Pandey RV, ..., Rolandsdotter H, Mjösberg J
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Gollnisch R, Wallenius J, Gribble KE, Ahrén D, Rengefors K
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-20]
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Characterization of the Mitochondrial Genetic Landscape in Abdominal Aortic Aneurysm.
Vats S, Sundquist K, Li Y, ..., Gottsäter A, Memon AA
J Am Heart Assoc 12 (8) e029248 [2023-04-18; online 2023-04-07]
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Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19.
Yu M, Charles A, Cagigi A, ..., Loré K, Smed-Sörensen A
Nat Commun 14 (1) 2164 [2023-04-15; online 2023-04-15]
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Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation.
Petkova M, Kraft M, Stritt S, ..., Betsholtz C, Mäkinen T
J. Exp. Med. 220 (4) - [2023-04-03; online 2023-01-23]
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Microbial gene activity in straw residue amendments reveals carbon sequestration mechanisms in agricultural soils
Kozjek K, Manoharan L, Urich T, Ahrén D, Hedlund K
Soil Biology and Biochemistry 179 (-) 108994 [2023-04-00; online 2023-04-00]
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Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers.
Edfeldt G, Kaldhusdal V, Czarnewski P, ..., Kwon DS, Broliden K
Microbiome 11 (1) 67 [2023-03-31; online 2023-03-31]
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Analysis of human lung mast cells by single cell RNA sequencing.
Rönnberg E, Ravindran A, Mazzurana L, ..., Mjösberg J, Nilsson G
Front Immunol 14 (-) 1151754 [2023-03-30; online 2023-03-30]
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Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce.
Chen ZQ, Klingberg A, Hallingbäck HR, Wu HX
BMC Genomics 24 (1) 147 [2023-03-27; online 2023-03-27]
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A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration.
Subramanian E, Elewa A, Brito G, ..., Andersson O, Simon A
Dev. Cell 58 (6) 450-460.e6 [2023-03-27; online 2023-03-08]
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Micro-scale spatial preference and temporal cyclicity linked to foraging in harbour porpoises
Stedt J, Wahlberg M, Carlström J, ..., Oskolkov N, Carlsson P
Mar. Ecol. Prog. Ser. 708 (-) 143-161 [2023-03-23; online 2023-03-23]
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Serum immuno-oncology markers carry independent prognostic information in patients with newly diagnosed metastatic breast cancer, from a prospective observational study.
Gunnarsdottir FB, Bendahl PO, Johansson A, ..., Bergenfelz C, Larsson AM
Breast Cancer Res. 25 (1) 29 [2023-03-21; online 2023-03-21]
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DNA methylation changes and increased mRNA expression of coagulation proteins, factor V and thrombomodulin in Fuchs endothelial corneal dystrophy.
Westin IM, Landfors M, Giannopoulos A, ..., Degerman S, Golovleva I
Cell. Mol. Life Sci. 80 (3) 62 [2023-02-11; online 2023-02-11]
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Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data.
Gustafsson J, Anton M, Roshanzamir F, ..., Robinson JL, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 120 (6) e2217868120 [2023-02-07; online 2023-01-31]
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A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.
Sarhan MS, Wurst C, Tzankov A, ..., Zink A, Maixner F
BMC Biol. 21 (1) 9 [2023-02-07; online 2023-02-07]
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Larval transcriptomes reflect the evolutionary history of plant-insect associations.
de la Paz Celorio-Mancera M, Steward RA, Pruisscher P, ..., Wheat CW, Nylin S
Evolution 77 (2) 519-533 [2023-02-04; online 2023-01-11]
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Proteogenomics decodes the evolution of human ipsilateral breast cancer.
De Marchi T, Pyl PT, Sjöström M, ..., Malmstöm J, Niméus E
Commun Biol 6 (1) 139 [2023-02-02; online 2023-02-02]
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Immune gene expression in the mosquito vector Culex quinquefasciatus during an avian malaria infection
García‐Longoria L, Ahrén D, Berthomieu A, ..., Rivero A, Hellgren O
Mol Ecol 32 (4) 904-919 [2023-02-00; online 2022-12-14]
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Identification of biomarkers and outcomes of endocrine disruption in human ovarian cortex using In Vitro Models.
Li T, Vazakidou P, Leonards PEG, ..., van Duursen M, Damdimopoulou P
Toxicology 485 (-) 153425 [2023-02-00; online 2023-01-05]
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An annotated high-content fluorescence microscopy dataset with Hoechst 33342-stained nuclei and manually labelled outlines.
Arvidsson M, Rashed SK, Aits S
Data Brief 46 (-) 108769 [2023-02-00; online 2022-11-21]
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High cardiomyocyte diversity in human early prenatal heart development.
Sylvén C, Wärdell E, Månsson-Broberg A, ..., Björklund Å, Giacomello S
iScience 26 (1) 105857 [2023-01-20; online 2022-12-21]
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Cerebellar granule neurons induce Cyclin D1 before the onset of motor symptoms in Huntington's disease mice.
Bauer S, Chen CY, Jonson M, ..., Magadi SS, Jackson WS
Acta Neuropathol Commun 11 (1) 17 [2023-01-20; online 2023-01-20]
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Single-cell analysis of myeloid cells in HPV+ tonsillar cancer.
Jimenez DG, Altunbulakli C, Swoboda S, ..., Greiff L, Lindstedt M
Front Immunol 13 (-) 1087843 [2023-01-19; online 2023-01-19]
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GotEnzymes: an extensive database of enzyme parameter predictions.
Li F, Chen Y, Anton M, Nielsen J
Nucleic Acids Res. 51 (D1) D583-D586 [2023-01-06; online 2022-09-29]
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ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.
Prager M, Lundin D, Ronquist F, Andersson AF
BMC Bioinformatics 24 (1) 6 [2023-01-05; online 2023-01-05]
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Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.
Immonen E, Sayadi A, Stojković B, ..., Wiberg RAW, Arnqvist G
Genome Biol Evol 15 (1) - [2023-01-04; online 2022-12-22]
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Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs.
Lingaas F, Tengvall K, Jansen JH, ..., Lindblad-Toh K, Wang C
PLoS Genet. 19 (1) e1010599 [2023-01-00; online 2023-01-24]
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Year 2022

PubMed DOI Crossref
Loss of Y in leukocytes as a risk factor for critical COVID-19 in men
Bruhn-Olszewska B, Davies H, Sarkisyan D, ..., Frithiof R, Dumanski JP
Genome Med 14 (1) 139 [2022-12-14; online 2022-12-14]
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Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.
Tengvall K, Sundström E, Wang C, ..., Andersson G, Lindblad-Toh K
Commun Biol 5 (1) 1348 [2022-12-08; online 2022-12-08]
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Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis.
von Berlin L, Westholm JO, Ratz M, Frisén J
Hippocampus - (-) - [2022-12-05; online 2022-12-05]
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Plasma protein biomarker profiling reveals major differences between acute leukaemia, lymphoma patients and controls.
Abu Sabaa A, Shen Q, Lennmyr EB, ..., Enblad G, Eriksson A
N Biotechnol 71 (-) 21-29 [2022-11-25; online 2022-06-29]
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Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery.
Mosquim Junior S, Siino V, Rydén L, Vallon-Christersson J, Levander F
Cancers (Basel) 14 (23) - [2022-11-23; online 2022-11-23]
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Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis.
Needhamsen M, Khoonsari PE, Zheleznyakova GY, ..., Ekman D, Jagodic M
Front Genet 13 (-) 1042483 [2022-11-17; online 2022-11-17]
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ID1 and CEBPA coordinate epidermal progenitor cell differentiation.
Kantzer CG, Yang W, Grommisch D, ..., Shirokova V, Genander M
Development 149 (22) - [2022-11-15; online 2022-11-16]
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Systems Biology in ELIXIR: modelling in the spotlight.
Martins Dos Santos V, Anton M, Szomolay B, ..., Evelo CT, Hancock JM
F1000Res 11 (-) 1265 [2022-11-07; online 2022-11-07]
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Read-Based Phasing and Analysis of Phased Variants with WhatsHap.
Martin M, Ebert P, Marschall T
Methods Mol. Biol. 2590 (-) 127-138 [2022-11-07; online 2022-11-07]
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The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.
Ament-Velásquez SL, Gilchrist C, Rêgo A, ..., Rafati N, Stelkens R
Mol. Biol. Evol. 39 (11) - [2022-11-03; online 2022-11-06]
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Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.
Sahraei SE, Sánchez-García M, Montoliu-Nerin M, ..., Rosendahl S, Rosling A
Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]
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Translatome profiling in fatal familial insomnia implicates TOR signaling in somatostatin neurons.
Bauer S, Dittrich L, Kaczmarczyk L, ..., Benfeitas R, Jackson WS
Life Sci. Alliance 5 (11) - [2022-11-00; online 2022-10-03]
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ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.
Schuster J, Klar J, Khalfallah A, ..., Birnir B, Dahl N
Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T
Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]
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PubMed
Pediatric Hip Disease Increases the Risk for Opioid Use in Adulthood: Long-term Burden of Pain and Depression.
Wadström MG, Hailer YD
Pain Physician 25 (7) E1153-E1160 [2022-10-00; online 2022-10-27]
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Osteoclasts directly influence castration-resistant prostate cancer cells.
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Clin Exp Metastasis 39 (5) 801-814 [2022-10-00; online 2022-08-16]
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Synergistic Effects of Sanglifehrin-Based Cyclophilin Inhibitor NV651 with Cisplatin in Hepatocellular Carcinoma.
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Cancers (Basel) 14 (19) 4553 [2022-09-20; online 2022-09-20]
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Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.
Stenberg H, Hellman S, Lindström L, ..., Hayer J, Malmberg M
BMC Vet Res 18 (1) 348 [2022-09-16; online 2022-09-16]
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Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.
Peña-Pérez L, Frengen N, Hauenstein J, ..., Lindstrand A, Månsson R
Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]
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Sir2 and Reb1 antagonistically regulate nucleosome occupancy in subtelomeric X-elements and repress TERRAs by distinct mechanisms.
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PLoS Genet. 18 (9) e1010419 [2022-09-00; online 2022-09-22]
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Plasma proteome profiling of healthy individuals across the life span in a Sicilian cohort with long-lived individuals.
Siino V, Ali A, Accardi G, ..., Levander F, Vasto S
Aging Cell 21 (9) e13684 [2022-09-00; online 2022-08-06]
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PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.
Toskas K, Yaghmaeian-Salmani B, Skiteva O, ..., Perlmann T, Holmberg J
Sci Adv 8 (34) eabo1543 [2022-08-26; online 2022-08-26]
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Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
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Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.
Söderhäll I, Fasterius E, Ekblom C, Söderhäll K
iScience 25 (8) 104850 [2022-08-19; online 2022-08-02]
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Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.
Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S
Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]
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Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.
Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H
Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]
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Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.
Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B
Am. J. Respir. Crit. Care Med. - (-) - [2022-08-10; online 2022-08-10]
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Ageing desexualizes the Drosophila brain transcriptome.
Malacrinò A, Brengdahl MI, Kimber CM, ..., Mirabello C, Friberg U
Proc. Biol. Sci. 289 (1980) 20221115 [2022-08-10; online 2022-08-10]
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Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.
Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K
Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
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The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.
Westerdahl H, Mellinger S, Sigeman H, ..., Wolf JBW, Strandh M
Mol Ecol Resour 22 (6) 2379-2395 [2022-08-00; online 2022-04-11]
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Human adaptation to arsenic in Bolivians living in the Andes.
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Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.
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Mol. Ecol. 31 (2) 498-511 [2022-01-00; online 2021-11-15]
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Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.
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Year 2021

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Whole-Exome Sequencing of HPV Positive Tonsillar and Base of Tongue Squamous Cell Carcinomas Reveals a Global Mutational Pattern along with Relapse-Specific Somatic Variants.
Ährlund-Richter A, Holzhauser S, Dalianis T, Näsman A, Mints M
Cancers (Basel) 14 (1) - [2021-12-24; online 2021-12-24]
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Immune-Proteome Profiling in Classical Hodgkin Lymphoma Tumor Diagnostic Tissue.
Gholiha AR, Hollander P, Löf L, ..., Kamali-Moghaddam M, Enblad G
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Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data.
Welén K, Rosendal E, Gisslén M, ..., Överby AK, Josefsson A
Eur. Urol. - (-) - [2021-12-15; online 2021-12-15]
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Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
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F1000Res 10 (-) 1238 [2021-12-03; online 2021-12-03]
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Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis.
Haytural H, Benfeitas R, Schedin-Weiss S, ..., Frykman S, Tjernberg LO
Sci Data 8 (1) 312 [2021-12-03; online 2021-12-03]
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Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought
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Applied Soil Ecology 168 (-) 104140 [2021-12-00; online 2021-12-00]
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Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium.
Sáinz-Jaspeado M, Smith RO, Plunde O, ..., Bäck M, Claesson-Welsh L
Circulation 144 (20) 1629-1645 [2021-11-16; online 2021-10-12]
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Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system.
Baniol M, Murganti F, Smialowska A, ..., Derks W, Bergmann O
Exp. Cell Res. 408 (2) 112880 [2021-11-15; online 2021-10-14]
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Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.
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Int J Mol Sci 22 (21) - [2021-11-06; online 2021-11-06]
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Tonsillar Cancer with High CD8+ T-Cell Infiltration Features Increased Levels of Dendritic Cells and Transcriptional Regulation Associated with an Inflamed Tumor Microenvironment.
Jimenez DG, Sobti A, Askmyr D, ..., Greiff L, Lindstedt M
Cancers (Basel) 13 (21) - [2021-10-25; online 2021-10-25]
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Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8.
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Comparison of sequencing data processing pipelines and application to underrepresented African human populations.
Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M
BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]
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Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.
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BMC Genomics 22 (1) 710 [2021-10-02; online 2021-10-02]
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Population genomics of the critically endangered kākāpō
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Cell Genomics 1 (1) 100002 [2021-10-00; online 2021-10-00]
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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A
Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]
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Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes.
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Sci Rep 11 (1) 15988 [2021-08-06; online 2021-08-06]
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Acta Neuropathol Commun 9 (1) 132 [2021-08-03; online 2021-08-03]
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Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.
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Genome-scale metabolic network reconstruction of model animals as a platform for translational research.
Wang H, Robinson JL, Kocabas P, ..., Zetterberg H, Nielsen J
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The enigmatic RNase MRP of kinetoplastids.
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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.
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Nat Commun 12 (1) 4253 [2021-07-12; online 2021-07-12]
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Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.
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Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector.
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Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.
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Toll-like receptor 4 methylation grade is linked to depressive symptom severity.
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X-chromosome variants are associated with aldosterone producing adenomas.
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Mörth C, Sabaa AA, Freyhult E, ..., Eriksson A, Enblad G
Cardiooncology 7 (1) 6 [2021-02-03; online 2021-02-03]
Affinity Proteomics Uppsala [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Dev. Dyn. 250 (2) 191-236 [2021-02-00; online 2020-09-26]
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Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.
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Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]
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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 [2021-01-27; 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
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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 [2021-01-00; online 2020-10-10]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [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]
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Epigenetics 16 (1) 92-105 [2021-01-00; 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]

Year 2020

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A biomimetic engineered bone platform for advanced testing of prosthetic implants.
Sladkova-Faure M, Pujari-Palmer M, Öhman-Mägi C, ..., Engqvist H, de Peppo GM
Sci Rep 10 (1) 22154 [2020-12-17; online 2020-12-17]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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Moose genomes reveal past glacial demography and the origin of modern lineages.
Dussex N, Alberti F, Heino MT, ..., Dalén L, Díez-Del-Molino D
BMC Genomics 21 (1) 854 [2020-12-02; online 2020-12-02]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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]
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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 [2020-12-00; online 2020-09-07]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
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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 Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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 Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
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The Human Adenovirus Type 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs.
Westergren Jakobsson A, Segerman B, Wallerman O, ..., Pettersson U, Akusjärvi G
J. Virol. - (-) - [2020-11-25; online 2020-11-25]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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]
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Evolution from adherent to suspension: systems biology of HEK293 cell line development.
Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J
Sci Rep 10 (1) 18996 [2020-11-04; online 2020-11-04]
Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
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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 Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer
Mehmeti-Ajradini M, Bergenfelz C, Larsson AM, ..., Bexell D, Leandersson K
Life Sci. Alliance 3 (11) e202000893 [2020-11-00; online 2020-09-21]
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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]
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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]
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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.
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Curr. Biol. 30 (19) 3871-3879.e7 [2020-10-05; online 2020-08-13]
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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 [2020-09-29; online 2020-09-16]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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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]
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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 Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Cellular Immunomonitoring [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]
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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]
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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]
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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]
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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]
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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.
Floudas D, Bentzer J, Ahrén D, ..., Persson P, Tunlid A
ISME J 14 (8) 2046-2059 [2020-08-00; online 2020-05-07]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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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]
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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]
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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M
Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]
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AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding.
Mujahed H, Miliara S, Neddermeyer A, ..., Lennartsson A, Lehmann S
Blood 136 (3) 339-352 [2020-07-16; online 2020-04-02]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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]
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Gurwitz KT, Singh Gaur P, Bellis LJ, ..., Morgan SL, Rustici G
PLoS Comput. Biol. 16 (7) e1007976 [2020-07-00; online 2020-07-23]
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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]
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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 Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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]
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In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma.
Babačić H, Lehtiö J, Pico de Coaña Y, Pernemalm M, Eriksson H
J Immunother Cancer 8 (1) e000204 [2020-05-00; online 2020-05-28]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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]
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Interactive proteogenomic exploration of response to Fusarium head blight in oat varieties with different resistance.
Willforss J, Leonova S, Tillander J, ..., Chawade A, Levander F
J Proteomics 218 (-) 103688 [2020-04-30; online 2020-02-14]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Drysdale R, Cook CE, Petryszak R, ..., Durinx C, McEntyre J
Bioinformatics 36 (8) 2636-2642 [2020-04-15; online 2020-01-18]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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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) 1842 [2020-04-15; online 2020-04-15]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] 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]
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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]
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Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.
Shafeeq S, Wang X, Lünsdorf H, Brauner A, Römling U
Microorganisms 8 (4) 522 [2020-04-05; online 2020-04-05]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [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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Guidelines for curriculum and course development in higher education and training
Tractenberg RE, Lindvall JM, Attwood T, Via A
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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. 20 (2) 179-191 [2020-04-00; 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]
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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]
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Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress.
Crawford T, Karamat F, Lehotai N, ..., Strand Å, Björklund S
Sci Rep 10 (1) 5073 [2020-03-19; online 2020-03-19]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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]
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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]
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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]
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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]
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The round goby genome provides insights into mechanisms that may facilitate biological invasions.
Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S
BMC Biol. 18 (1) 11 [2020-01-28; online 2020-01-28]
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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) 1303 [2020-01-28; online 2020-01-28]
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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]
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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) 322 [2020-01-16; online 2020-01-16]
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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]
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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 Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [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]
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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 Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [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
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 374 (1788) 20190212 [2019-12-23; online 2019-11-04]
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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]
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Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.
Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S
Arthritis Res. Ther. 21 (1) 288 [2019-12-16; online 2019-12-16]
Affinity Proteomics Stockholm [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
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Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
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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]
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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]
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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]
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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]
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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 and MS Proteomics [Technology development]
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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]
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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]
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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]
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Modelling of zero-inflation improves inference of metagenomic gene count data.
Jonsson V, Österlund T, Nerman O, Kristiansson E
Stat Methods Med Res 28 (12) 3712-3728 [2019-12-00; online 2018-11-25]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
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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]
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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]
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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]
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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]
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TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells.
Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M
Front Immunol 10 (-) 2708 [2019-11-26; online 2019-11-26]
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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]
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Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning.
Mogodiniyai Kasmaei K, Sundh J
Front Microbiol 10 (-) 2673 [2019-11-20; online 2019-11-20]
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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]
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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]
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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]
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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 [2019-11-07; online 2019-11-07]
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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]
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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]
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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]
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Interoperable and scalable data analysis with microservices: applications in metabolomics.
Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O
Bioinformatics 35 (19) 3752-3760 [2019-10-01; online 2019-03-10]
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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 Res. 162 (-) 437-445 [2019-10-01; online 2019-07-04]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
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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]
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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 [2019-10-00; online 2019-04-13]
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Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.
Kurland S, Wheat CW, de la Paz Celorio Mancera M, ..., Ryman N, Laikre L
Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]
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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]
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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]
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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]
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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]
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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 M
Sci Rep 9 (1) 10730 [2019-07-24; online 2019-07-24]
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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]
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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]
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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]
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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]
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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]
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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 (-) 216 [2019-06-21; online 2019-06-21]
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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]
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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]
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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]
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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. 25 (10) 3115-3127 [2019-05-15; online 2019-01-24]
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Software engineering for scientific big data analysis.
Grüning BA, Lampa S, Vaudel M, Blankenberg D
Gigascience 8 (5) - [2019-05-01; online 2019-05-24]
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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 2019-04-28]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Technology development]
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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]
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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]
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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]
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Gene expression profile of extraocular muscles following resection strabismus surgery.
Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F
Exp. Eye Res. 182 (-) 182-193 [2019-05-00; online 2019-04-03]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
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The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Abramova A, Lind U, Blomberg A, Rosenblad MA
Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Breast cancer quantitative proteome and proteogenomic landscape.
Johansson HJ, Socciarelli F, Vacanti NM, ..., Børresen-Dale AL, Lehtiö J
Nat Commun 10 (1) 1600 [2019-04-08; online 2019-04-08]
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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 (-) 660 [2019-04-05; online 2019-04-05]
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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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
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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]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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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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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 (-) 92 [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]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes).
Košuthová A, Westberg M, Tálora MAG, Wedin M
MycoKeys 47 (47) 17-33 [2019-02-20; online 2019-02-20]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.
Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A
Sci Rep 9 (1) 2379 [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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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 [2019-02-00; online 2019-01-07]
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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
Open Forum Infect Dis 6 (2) ofz015 [2019-02-00; online 2019-01-31]
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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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Introducing ribosomal tandem repeat barcoding for fungi.
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH
Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]
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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]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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 [2018-12-19; online 2018-12-19]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
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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]
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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) 5150 [2018-12-04; online 2018-12-04]
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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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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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EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive
Norling M, Jareborg N, Dainat J
BMC Res Notes 11 (1) - [2018-12-00; online 2018-08-13]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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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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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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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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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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Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.
Giacomello S, Lundeberg J
Nat Protoc 13 (11) 2425-2446 [2018-11-00; online 2018-10-26]
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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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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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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 [2018-10-00; online 2018-10-18]
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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]
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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]
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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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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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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]
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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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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]
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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]
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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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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 Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [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
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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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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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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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
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) 10813 [2018-07-17; online 2018-07-17]
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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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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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Topology of membrane proteins — predictions, limitations and variations
Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A
Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]
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Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol
Porseryd T, Reyhanian Caspillo N, Volkova K, ..., Olsson PE, Porsch-Hällström I
General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]
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PubMed DOI Crossref
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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PubMed DOI Crossref
Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.
Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S
Neuroradiology - (-) - [2018-05-14; online 2018-05-14]
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PubMed DOI Crossref
Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.
Vdovikova S, Gilfillan S, Wang S, ..., Wai SN, Hurtado A
Sci Rep 8 (1) 7434 [2018-05-09; online 2018-05-09]
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Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.
Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K
Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]
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O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function
Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K
Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]
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Array profiling reveals contribution of Cthrc1 to growth of the denervated rat urinary bladder.
Zhu B, Ekman M, Svensson D, ..., Uvelius B, Swärd K
Am. J. Physiol. Renal Physiol. 314 (5) F893-F905 [2018-05-01; online 2018-01-10]
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Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis
Suhm T, Kaimal JM, Dawitz H, ..., Andréasson C, Ott M
Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]
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Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.
La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J
Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]
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Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.
Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A
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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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) 903 [2018-03-02; online 2018-03-02]
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Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.
Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y
PLoS Pathog. 14 (3) e1006936 [2018-03-00; online 2018-03-02]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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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Ten steps to get started in Genome Assembly and Annotation
Dominguez Del Angel V, Hjerde E, Sterck L, ..., Binzer-Panchal M, Lantz H
F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]
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The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.
McDonald MC, Ahren D, Simpfendorfer S, Milgate A, Solomon PS
Mol. Plant Pathol. 19 (2) 432-439 [2018-02-00; online 2017-03-12]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.
Leal L, Talla V, Källman T, ..., Vila R, Backström N
Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Formation of mercury methylation hotspots as a consequence of forestry operations
Eklöf K, Bishop K, Bertilsson S, ..., Kronberg RM, Bravo AG
Science of The Total Environment 613-614 (-) 1069-1078 [2018-02-00; online 2018-02-00]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Bacterial secretion of D-arginine controls environmental microbial biodiversity.
Alvarez L, Aliashkevich A, de Pedro MA, Cava F
ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]
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DOI Crossref
Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA
Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B
Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]
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Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.
Löfdahl A, Rydell-Törmänen K, Larsson-Callerfelt A, Wenglén C, Westergren-Thorsson G
Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]
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A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.
Kokosar M, Benrick A, Perfilyev A, ..., Ling C, Stener-Victorin E
Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]
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Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases.
Lehmann P, Pruisscher P, Koštál V, ..., Wheat CW, Gotthard K
J Exp Biol 221 (Pt 2) - [2018-01-25; online 2018-01-25]
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A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors
Faraz M, Herdenberg C, Holmlund C, Henriksson R, Hedman H
J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]
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The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.
Salvatore M, Shu N, Elofsson A
Protein Sci. 27 (1) 195-201 [2018-01-00; online 2017-10-24]
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PubMed DOI Crossref
MicroRNA expression profiles in non‑epithelial ovarian tumors.
Chang RK, Li X, Mu N, ..., Larsson C, Lui WO
Int. J. Oncol. 52 (1) 55-66 [2018-01-00; online 2017-11-10]
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DOI Crossref
Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus
Swenson U, Nylander JAA, Munzinger J
Aust. Systematic Bot. 31 (2) 120 [2018-00-00; online 2018-00-00]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Year 2017

PubMed DOI Crossref
Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.
Elewa A, Wang H, Talavera-López C, ..., Andersson B, Simon A
Nat Commun 8 (1) 2286 [2017-12-22; online 2017-12-22]
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Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells
Piltti J, Bygdell J, Fernández-Echevarría C, Marcellino D, Lammi MJ
Sci Rep 7 (1) - [2017-12-00; online 2017-06-16]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG
BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]
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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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Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size.
Pečnerová P, Palkopoulou E, Wheat CW, ..., Díez-Del-Molino D, Dalén L
Evolution Letters 1 (6) 292-303 [2017-12-00; online 2017-11-28]
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Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea
Hüttner S, Nguyen TT, Granchi Z, ..., Thanh VN, Olsson L
Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-11-13]
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Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.
Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L
Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]
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Dog ownership and the risk of cardiovascular disease and death - a nationwide cohort study.
Mubanga M, Byberg L, Nowak C, ..., Ingelsson E, Fall T
Sci Rep 7 (1) 15821 [2017-11-17; online 2017-11-17]
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Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths
Kirik U, Persson H, Levander F, Greiff L, Ohlin M
Front Immunol 8 (-) - [2017-11-13; online 2017-11-13]
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RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole
Martis MM, Tarbiat B, Tydén E, Jansson DS, Höglund J
PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]
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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.
Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U
Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]
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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
Hubalek V, Buck M, Tan B, ..., Bertilsson S, Eiler A
mSystems 2 (5) e00038-17 [2017-10-31; online 2017-10-31]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Effects of long-term low oxygen tension in human chondrosarcoma cells
Piltti J, Bygdell J, Qu C, Lammi MJ
J. Cell. Biochem. - (-) - [2017-10-18; online 2017-10-18]
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PubMed DOI Crossref
The Evolution of Dark Matter in the Mitogenome of Seed Beetles
Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G
Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]
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The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.
Johansson A, Claesson R, Höglund Åberg C, Haubek D, Oscarsson J
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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Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.
Cimdins A, Simm R, Li F, ..., Brauner A, Römling U
Microbiologyopen 6 (5) - [2017-10-00; online 2017-09-15]
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Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.
Verma D, Parasa VR, Raffetseder J, ..., Netea M, Lerm M
Sci Rep 7 (1) 12305 [2017-09-26; online 2017-09-26]
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Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.
Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF
Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]
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The regulation of hydroxysteroid 17β-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.
Hilborn E, Stål O, Alexeyenko A, Jansson A
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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Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.
Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M
Sci Rep 7 (1) 10392 [2017-09-04; online 2017-09-04]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.
Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV
Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]
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A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
Montero-Mendieta S, Grabherr M, Lantz H, ..., Webster MT, Vilà C
PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome scale metabolic modeling of cancer.
Nilsson A, Nielsen J
Metab. Eng. 43 (Pt B) 103-112 [2017-09-00; online 2016-11-04]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Cerium oxide nanoparticles inhibit differentiation of neural stem cells.
Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B
Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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SubCons: a new ensemble method for improved human subcellular localization predictions.
Salvatore M, Warholm P, Shu N, Basile W, Elofsson A
Bioinformatics 33 (16) 2464-2470 [2017-08-15; online 2017-04-14]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3
Bersani C, Sivars L, Haeggblom L, ..., Ramqvist T, Dalianis T
Oncotarget - (-) - [2017-07-18; online 2017-02-09]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.
Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A
PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Identifying Bird Remains Using Ancient DNA Barcoding.
Dalén L, Lagerholm VK, Nylander JAA, ..., Irestedt M, Stewart JR
Genes 8 (6) 169 [2017-06-21; online 2017-06-21]
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Systems Biology of Metabolism.
Nielsen J
Annu. Rev. Biochem. 86 (1) 245-275 [2017-06-20; online 2017-03-08]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Protein expression in tension wood formation monitored at high tissue resolution in Populus
Bygdell J, Srivastava V, Obudulu O, ..., Mellerowicz EJ, Wingsle G
- 68 (13) 3405-3417 [2017-06-15; online 2017-06-13]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Four simple recommendations to encourage best practices in research software
Jiménez RC, Kuzak M, Alhamdoosh M, ..., Watson-Haigh NS, Crouch S
F1000Res 6 (-) 876 [2017-06-13; online 2017-06-13]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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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]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.
Videvall E, Cornwallis CK, Ahrén D, ..., Valkiūnas G, Hellgren O
Mol. Ecol. 26 (11) 2939-2958 [2017-06-00; online 2017-04-08]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Lower inflammatory markers in women with antenatal depression brings the M1/M2 balance into focus from a new direction
Edvinsson Å, Bränn E, Hellgren C, ..., Cunningham JL, Sundström-Poromaa I
Psychoneuroendocrinology 80 (-) 15-25 [2017-06-00; online 2017-06-00]
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PubMed DOI Crossref
Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).
Grenville-Briggs LJ, Kushwaha SK, Cleary MR, ..., Chawade A, Vetukuri RR
Genom Data 12 (-) 155-156 [2017-06-00; online 2017-05-12]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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]
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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ProQ3D: improved model quality assessments using deep learning.
Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A
Bioinformatics 33 (10) 1578-1580 [2017-05-15; online 2017-01-06]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.
Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB
J Transl Med 15 (1) 102 [2017-05-11; online 2017-05-11]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K
Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Three-dimensional functional human neuronal networks in uncompressed low-density electrospun fiber scaffolds.
Jakobsson A, Ottosson M, Zalis MC, ..., Johansson UE, Johansson F
Nanomedicine 13 (4) 1563-1573 [2017-05-00; online 2017-01-05]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.
Rineau F, Lmalem H, Ahren D, ..., Martin F, Colpaert JV
Mycorrhiza 27 (4) 383-396 [2017-05-00; online 2017-01-09]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast
Lahtvee PJ, Sánchez BJ, Smialowska A, ..., Gatto F, Nielsen J
Cell Syst 4 (5) 495-504.e5 [2017-05-00; online 2017-05-00]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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
Oncotarget 8 (17) 28812-28825 [2017-04-25; online 2017-04-22]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
Porseryd T, Volkova K, Reyhanian Caspillo N, ..., Dinnetz P, Porsh Hällström I
Front. Behav. Neurosci. 11 (-) - [2017-04-20; online 2017-04-20]
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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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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PubMed DOI Crossref
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
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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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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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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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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 Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] 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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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. 66 (2) 152-166 [2017-03-01; online 2016-09-13]
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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. 66 (2) 145-151 [2017-03-01; online 2016-08-04]
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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]
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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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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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Antibody-encoding repertoires of bone marrow and peripheral blood—a focus on IgE
Levin M, Levander F, Palmason R, Greiff L, Ohlin M
Journal of Allergy and Clinical Immunology 139 (3) 1026-1030 [2017-03-00; online 2017-03-00]
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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]
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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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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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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Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.
Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T
Proc. Natl. Acad. Sci. U.S.A. 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]
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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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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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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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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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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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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 [2016-11-29; online 2016-11-29]
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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]
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WhatsHap: fast and accurate read-based phasing
Martin M, Patterson M, Garg S, ..., Schöenhuth 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]
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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]
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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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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]
Advanced FISH Technologies Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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]
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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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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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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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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) 32137 [2016-08-26; online 2016-08-26]
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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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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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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]
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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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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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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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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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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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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]
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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]
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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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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]
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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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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]
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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]
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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]
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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
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MycoKeys 13 (-) 21-33 [2016-05-13; online 2016-05-13]
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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.
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EMBO Rep. 17 (5) 753-768 [2016-05-00; online 2016-02-22]
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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]
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Improved topology prediction using the terminal hydrophobic helices rule.
Peters C, Tsirigos KD, Shu N, Elofsson A
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Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.
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J. Biol. Chem. 291 (15) 7915-7925 [2016-04-08; online 2016-02-11]
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Transcriptomics resources of human tissues and organs.
Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J
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Aging Cell 15 (2) 267-278 [2016-04-00; online 2015-12-22]
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Nat Commun 7 (-) 11017 [2016-03-23; online 2016-03-23]
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PLoS ONE 11 (3) e0151577 [2016-03-17; online 2016-03-17]
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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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bioRxiv - (-) - [2016-03-16; online 2016-03-16]
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The FAIR Guiding Principles for scientific data management and stewardship.
Wilkinson MD, Dumontier M, Aalbersberg IJ, ..., Zhao J, Mons B
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BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]
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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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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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Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients.
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Mol Metab 5 (3) 171-183 [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]
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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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Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.
Obudulu O, Bygdell J, Sundberg B, ..., Trygg J, Wingsle G
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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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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.
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Mol. Ecol. 25 (4) 943-958 [2016-02-00; online 2016-01-11]
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PLoS ONE 11 (1) e0147082 [2016-01-28; online 2016-01-28]
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Thureborn P, Franzetti A, Lundin D, Sjöling S
PeerJ 4 (-) e1593 [2016-01-19; online 2016-01-19]
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Gréen 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 WO, 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.
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Nucleic Acids Res. 44 (D1) D1141-D1147 [2016-01-04; online 2015-11-04]
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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]
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Year 2015

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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]
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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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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]
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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]
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Zubair S, Fischer A, Liljander A, ..., Bongcam-Rudloff E, Jores J
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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.
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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]
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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]
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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.
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J. Nutr. 145 (11) 2456-2463 [2015-11-00; online 2015-09-25]
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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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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]
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Plant Genome 8 (3) eplantgenome2015.06.0045 [2015-11-00; online 2015-11-01]
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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.
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Nucleic Acids Res. 43 (18) 9017-9027 [2015-10-15; online 2015-08-16]
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The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.
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Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.
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Mol. Biol. Evol. 32 (10) 2501-2514 [2015-10-00; online 2015-08-28]
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PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]
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Dis. Markers 2015 (-) 241301 [2015-09-28; online 2015-09-28]
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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.
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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]
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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]
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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.
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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
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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.
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Nucleic Acids Res. 43 (W1) W401-W407 [2015-07-01; online 2015-05-15]
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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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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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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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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 2015-04-02]
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PubMed DOI Crossref
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 2015-06-17]
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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
Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls.
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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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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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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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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The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.
Lindqvist CM, Nordlund J, Ekman D, ..., Syvänen AC, Berglund EC
Hum. Mutat. 36 (1) 118-128 [2015-01-00; online 2014-10-31]
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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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Year 2014

PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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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
FASEB J. 28 (10) 4571-4581 [2014-10-00; 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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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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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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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 2014-02-06]
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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 2013-11-17]
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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

PubMed DOI Crossref
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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PubMed DOI Crossref
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 2013-09-27]
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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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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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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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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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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]
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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]
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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]
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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]
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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]
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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]
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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
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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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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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
PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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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
PubMed DOI Crossref
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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Publications 9.5.1