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

PubMed DOI Crossref
Spatiotemporal single-cell roadmap of human skin wound healing.
Liu Z, Bian X, Luo L, ..., Li D, Landén NX
Cell Stem Cell - (-) - [2024-12-18; online 2024-12-18]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
DOI Crossref
Preanalytical (Mis)Handling of Plasma Investigated by 1H NMR Metabolomics
Malmodin D, Bay Nord A, Zafar H, ..., Karlsson BG, Naluai ÅT
ACS Omega - (-) - [2024-11-27; online 2024-11-27]
Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish NMR Centre (SNC) [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 MdlP, ..., 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] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [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]
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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]
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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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DOI Crossref
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]
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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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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]
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PVT1 interacts with polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma.
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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.
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Lipids Health Dis 22 (1) 97 [2023-07-07; online 2023-07-07]
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Nat Commun 14 (1) 3713 [2023-06-22; online 2023-06-22]
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Elife 12 (-) - [2023-06-21; online 2023-06-21]
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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.
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PLoS Genet. 19 (6) e1010801 [2023-06-00; online 2023-06-30]
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J Transl Med 21 (1) 342 [2023-05-23; online 2023-05-23]
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Vats S, Sundquist K, Li Y, ..., Gottsäter A, Memon AA
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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
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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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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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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.
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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
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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
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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
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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.
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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
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Li F, Chen Y, Anton M, Nielsen J
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ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.
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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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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.
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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.
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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.
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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.
De Loma J, Vicente M, Tirado N, ..., Schlebusch CM, Broberg K
Chemosphere 301 (-) 134764 [2022-08-00; online 2022-04-28]
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Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.
Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR
Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]
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High-throughput muscle fiber typing from RNA sequencing data.
Oskolkov N, Santel M, Parikh HM, ..., Pääbo S, Hansson O
Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]
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Regulatory networks and 5' partner usage of miRNA host gene fusions in breast cancer.
Hafstað V, Søkilde R, Häkkinen J, ..., Rovira C, Persson H
Int. J. Cancer 151 (1) 95-106 [2022-07-01; online 2022-02-26]
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Mercury–Selenium Accumulation Patterns in Muscle Tissue of Two Freshwater Fish Species, Eurasian Perch (Perca fluviatilis) and Vendace (Coregonus albula)
Regnell O, Tesson SVM, Oskolkov N, Nerentorp M
Water Air Soil Pollut 233 (7) - [2022-07-00; online 2022-06-20]
Bioinformatics Support, Infrastructure and Training [Collaborative]
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Genomic dynamics of brown trout populations released to a novel environment.
Kurland S, Rafati N, Ryman N, Laikre L
Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]
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Evidence for further non-coding RNA genes in the fungal rDNA region.
Rosenblad MA, Larsson E, Walker A, ..., Wurzbacher C, Nilsson RH
MycoKeys 90 (-) 203-213 [2022-06-30; online 2022-06-30]
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Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.
Domenzain I, Sánchez B, Anton M, ..., Sonnenschein N, Nielsen J
Nat Commun 13 (1) 3766 [2022-06-30; online 2022-06-30]
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Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.
Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V
Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]
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The immune cell atlas of human neuroblastoma.
Verhoeven BM, Mei S, Olsen TK, ..., Johnsen JI, Baryawno N
Cell Reports Medicine 3 (6) 100657 [2022-06-21; online 2022-06-09]
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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.
Blixt MKE, Hellsand M, Konjusha D, ..., Ring H, Hallböök F
Oncogenesis 11 (1) 34 [2022-06-21; online 2022-06-21]
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GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.
Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D
BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]
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FOXO1 and FOXO3 Cooperatively Regulate Innate Lymphoid Cell Development.
Luu TT, Søndergaard JN, Peña-Pérez L, ..., Månsson R, Kadri N
Front Immunol 13 (-) 854312 [2022-06-09; online 2022-06-09]
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Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.
Srigyan M, Bolívar H, Ureña I, ..., Günther T, Valdiosera C
Commun Biol 5 (1) 554 [2022-06-07; online 2022-06-07]
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Reply to Carlos G. Wambier and Gerard J. Nau's Letter to the Editor re: Karin Welén, Ebba Rosendal, Magnus Gisslén, et al. 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. Eur Urol. 2022;81:285-93. Positive Effects of Enzalutamide for Hospitalized COVID-19 Patients: Still No Positive Effect of Enzalutamide for Hospitalized COVID-19 Patients.
Welén K, Rosendal E, Freyhult E, ..., Överby AK, Josefsson A
Eur. Urol. 81 (6) e143-e144 [2022-06-00; online 2022-02-23]
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Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells
Saghaleyni R, Malm M, Moruzzi N, ..., Robinson JL, Rockberg J
Cell Rep 39 (11) 110936 [2022-06-00; online 2022-06-00]
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Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.
Fineschi S, Klar J, Gustafsson KA, ..., Karlsson B, Dahl N
Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]
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Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.
Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T
iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]
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The impact of digital media on children's intelligence while controlling for genetic differences in cognition and socioeconomic background.
Sauce B, Liebherr M, Judd N, Klingberg T
Sci Rep 12 (1) 7720 [2022-05-11; online 2022-05-11]
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Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.
Kierczak M, Rafati N, Höglund J, ..., Karlsson T, Johansson Å
Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]
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FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.
Peña-Pérez L, Kharazi S, Frengen N, ..., Luc S, Månsson R
Front Immunol 13 (-) 880668 [2022-05-04; online 2022-05-04]
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Combined Transcriptomic and Protein Array Cytokine Profiling of Human Stem Cells from Dental Apical Papilla Modulated by Oral Bacteria.
Zymovets V, Razghonova Y, Rakhimova O, ..., Landström M, Romani Vestman N
Int J Mol Sci 23 (9) 5098 [2022-05-03; online 2022-05-03]
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Re: Chen Dong, Sung-Lang Chen, and Wen-Wei Sung's Letter to the Editor re: Karin Welén, Ebba Rosendal, Magnus Gisslén, et al. 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. Eur Urol. 2022;81:285-93.
Welen K, Rosendal E, Freyhult E, ..., Överby AK, Josefsson A
Eur. Urol. 81 (5) e124-e125 [2022-05-00; online 2022-02-12]
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Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate.
Bradley F, Franzén Boger M, Kaldhusdal V, ..., Tjernlund A, Broliden K
PLoS Pathog. 18 (5) e1010494 [2022-05-00; online 2022-05-09]
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Microbial functional genes influenced by short-term experimental drought across European agricultural fields
Kozjek K, Manoharan L, Ahrén D, Hedlund K
Soil Biology and Biochemistry 168 (-) 108650 [2022-05-00; online 2022-05-00]
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A starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels.
Nilholm C, Manoharan L, Roth B, D'Amato M, Ohlsson B
United European Gastroenterol J 10 (4) 363-375 [2022-05-00; online 2022-04-28]
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Satellite DNA evolution in Corvoidea inferred from short and long reads.
Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A
Mol. Ecol. - (-) - [2022-04-30; online 2022-04-30]
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Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.
Sigeman H, Sinclair B, Hansson B
BMC Genomics 23 (1) 328 [2022-04-27; online 2022-04-27]
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The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies.
Moškrič A, Marinč A, Ferk P, ..., Soler L, Prešern J
Insects 13 (5) 403 [2022-04-22; online 2022-04-22]
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App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden.
Kennedy B, Fitipaldi H, Hammar U, ..., Franks PW, Fall T
Nat Commun 13 (1) 2110 [2022-04-21; online 2022-04-21]
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Silencing of STE20-type kinase STK25 in human aortic endothelial and smooth muscle cells is atheroprotective.
Cansby E, Kumari S, Caputo M, ..., Goncalves I, Mahlapuu M
Commun Biol 5 (1) 379 [2022-04-19; online 2022-04-19]
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Evaluation of polarity switching for untargeted lipidomics using liquid chromatography coupled to high resolution mass spectrometry.
Carlsson H, Vaivade A, Emami Khoonsari P, Burman J, Kultima K
Journal of Chromatography B 1195 (-) 123200 [2022-04-15; online 2022-02-28]
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PubMed DOI Crossref
Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity
Omokanye A, Ong LC, Lebrero-Fernandez C, ..., Czarnewski P, Lycke N
Mucosal Immunol 15 (4) 717-729 [2022-04-00; online 2022-04-00]
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PubMed DOI Crossref
Acute sleep loss alters circulating fibroblast growth factor 21 levels in humans: A randomised crossover trial.
Mateus Brandão LE, Espes D, Westholm JO, ..., Benedict C, Cedernaes J
J Sleep Res 31 (2) e13472 [2022-04-00; online 2021-09-02]
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Weakened resilience of benthic microbial communities in the face of climate change
Seidel L, Ketzer M, Broman E, ..., Hylander S, Dopson M
ISME COMMUN. 2 (1) - [2022-03-08; online 2022-03-08]
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Hypoxia induces radioresistance, epithelial‑mesenchymal transition, cancer stem cell‑like phenotype and changes in genes possessing multiple biological functions in head and neck squamous cell carcinoma.
Wiechec E, Matic N, Ali A, Roberg K
Oncol. Rep. 47 (3) - [2022-03-00; online 2022-01-21]
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Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.
Eshghi Sahraei S, Furneaux B, Kluting K, ..., Hytteborn H, Rosling A
Ecol Evol 12 (3) e8676 [2022-03-00; online 2022-03-08]
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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
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Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies
Nguyen D, Peona V, Unneberg P, ..., Jern P, Johannesson H
Fungal Genetics Reports 66 (1) - [2022-02-18; online 2022-02-18]
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Similar risk of cancer in patients younger than 55 years with or without a total hip arthroplasty (THA): a population- based cohort study on 18,771 exposed to THA and 87,683 controls.
Hailer YD, Kärrholm J, Eriksson N, Holmberg L, Hailer NP
Acta Orthop 93 (-) 317-326 [2022-02-08; online 2022-02-08]
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Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation
Sparreman Mikus M, Kolmert J, Andersson LI, ..., Dahlén SE, James A
Eur Respir J 59 (2) 2100142 [2022-02-00; online 2021-11-04]
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Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C.
Thysell E, Köhn L, Semenas J, ..., Bergh A, Wikström P
Mol Oncol 16 (4) 846-859 [2022-02-00; online 2021-12-27]
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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
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Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
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Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L
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Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]
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Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.
Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L
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.
Yang M, Johnsson P, Bräutigam L, ..., Cao Y, Höiom V
Genet Med 24 (1) 157-169 [2022-01-00; online 2021-11-30]
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Year 2021

PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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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
Cancers (Basel) 14 (1) 9 [2021-12-21; online 2021-12-21]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
Waterhouse RM, Adam-Blondon AF, Agosti D, ..., Willassen NP, Lanfear J
F1000Res 10 (-) 1238 [2021-12-03; online 2021-12-03]
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PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought
Kozjek K, Kundel D, Kushwaha SK, ..., Birkhofer K, Hedlund K
Applied Soil Ecology 168 (-) 104140 [2021-12-00; online 2021-12-00]
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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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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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.
Abreha KB, Alexandersson E, Resjö S, ..., Levander F, Andreasson E
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.
Paulsson JO, Rafati N, DiLorenzo S, ..., Zedenius J, Juhlin CC
J. Clin. Endocrinol. Metab. 106 (11) 3265-3282 [2021-10-21; online 2021-06-26]
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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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Int. J. Cancer 148 (4) 884-894 [2021-02-15; online 2020-09-05]
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Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.
Stratmann S, Yones SA, Mayrhofer M, ..., Cavelier L, Holmfeldt L
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Plasma proteome profiling of cardiotoxicity in patients with diffuse large B-cell lymphoma.
Mörth C, Sabaa AA, Freyhult E, ..., Eriksson A, Enblad G
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Sallinen RJ, Dethlefsen O, Ruotsalainen S, ..., Kaunisto MA, Kallioniemi O
J. Nutr. 151 (2) 281-292 [2021-02-01; online 2021-01-01]
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Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Lund [Service]
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Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.
Rengefors K, Gollnisch R, Sassenhagen I, ..., Bassham S, Ahrén D
Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer
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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.
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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.
Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L
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]
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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]
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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]
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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]
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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]
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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]
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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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Willforss J, Leonova S, Tillander J, ..., Chawade A, Levander F
J Proteomics 218 (-) 103688 [2020-04-30; online 2020-02-14]
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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]
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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]
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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]
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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]
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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]
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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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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]
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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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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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]
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
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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]
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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
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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]
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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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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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]
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] National Genomics Infrastructure [Service]
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The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Abramova A, Lind U, Blomberg A, Rosenblad MA
Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]
Bioinformatics 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]
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Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.
Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A
Sci Rep 9 (1) 2379 [2019-02-20; online 2019-02-20]
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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]
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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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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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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PubMed DOI Crossref
Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.
Nilsson E, Benrick A, Kokosar M, ..., Ling C, Stener-Victorin E
J. Clin. Endocrinol. Metab. 103 (12) 4465-4477 [2018-12-01; online 2018-08-17]
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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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PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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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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PubMed DOI Crossref
Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.
Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B
Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]
Bioinformatics 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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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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PubMed DOI Crossref
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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PubMed DOI Crossref
Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation
Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O
Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions
Franzén B, Kamali-Moghaddam M, Alexeyenko A, ..., Landegren U, Lewensohn R
Mol Oncol 12 (9) 1415-1428 [2018-09-00; online 2018-08-09]
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PubMed DOI Crossref
Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression
Klum S, Zaouter C, Alekseenko Z, ..., Muhr J, Bergsland M
EMBO Rep. - (-) e46635 [2018-08-30; online 2018-08-30]
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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]
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
Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes
Salami F, Lee HS, Freyhult E, ..., Lernmark Å, Törn C
Diabetes - (-) db180355 [2018-08-13; online 2018-08-13]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]
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PubMed DOI Crossref
Clonal relatedness in tumour pairs of breast cancer patients.
Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K
Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]
Bioinformatics 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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PubMed DOI Crossref
Delineating closely related dinoflagellate lineages using phylotranscriptomics.
Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K
J. Phycol. 54 (4) 571-576 [2018-08-00; online 2018-06-13]
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PubMed DOI Crossref
Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy
Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC
Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]
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PubMed DOI Crossref
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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PubMed DOI Crossref
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.
Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A
Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]
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PubMed DOI Crossref
Bioconda: sustainable and comprehensive software distribution for the life sciences
Grüning B, Dale R, Sjödin A, ..., Valieris R, Köster J
Nat Methods 15 (7) 475-476 [2018-07-00; online 2018-07-02]
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Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.
Garcia SL, Buck M, Hamilton JJ, ..., McMahon KD, Eiler A
mSphere 3 (3) - [2018-06-27; online 2018-05-30]
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PubMed DOI Crossref
Topology of membrane proteins — predictions, limitations and variations
Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A
Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]
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PubMed DOI Crossref
Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol
Porseryd T, Reyhanian Caspillo N, Volkova K, ..., Olsson PE, Porsch-Hällström I
General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]
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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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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]
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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]
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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]
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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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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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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]
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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]
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RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG
BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]
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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]
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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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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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PubMed DOI Crossref
Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.
Celauro E, Mukaj A, Fierro-González JC, Wittung-Stafshede P
Biochem. Biophys. Res. Commun. 491 (1) 147-153 [2017-09-09; online 2017-07-12]
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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]
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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]
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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]
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Cerium oxide nanoparticles inhibit differentiation of neural stem cells.
Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B
Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]
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]
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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]
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Protein expression in tension wood formation monitored at high tissue resolution in Populus
Bygdell J, Srivastava V, Obudulu O, ..., Mellerowicz EJ, Wingsle G
- 68 (13) 3405-3417 [2017-06-15; online 2017-06-13]
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Four simple recommendations to encourage best practices in research software
Jiménez RC, Kuzak M, Alhamdoosh M, ..., Watson-Haigh NS, Crouch S
F1000Res 6 (-) 876 [2017-06-13; online 2017-06-13]
Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
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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]
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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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Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).
Grenville-Briggs LJ, Kushwaha SK, Cleary MR, ..., Chawade A, Vetukuri RR
Genom Data 12 (-) 155-156 [2017-06-00; online 2017-05-12]
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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]
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Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.
Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB
J Transl Med 15 (1) 102 [2017-05-11; online 2017-05-11]
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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]
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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]
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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]
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Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.
Rineau F, Lmalem H, Ahren D, ..., Martin F, Colpaert JV
Mycorrhiza 27 (4) 383-396 [2017-05-00; online 2017-01-09]
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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]
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Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.
Tobiasson M, Abdulkadir H, Lennartsson A, ..., Hellström-Lindberg E, Ungerstedt J
Oncotarget 8 (17) 28812-28825 [2017-04-25; online 2017-04-22]
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Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
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Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
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Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.
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Frequent low-level mutations of protein kinase D2 in angiolipoma
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Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology
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Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]
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NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.
Jeggari A, Alexeyenko A
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Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.
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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.
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Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
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SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.
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Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays
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Mol Cell Proteomics 16 (3) 502-511 [2017-03-00; online 2017-01-22]
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Towards a whole-genome sequence for rye (Secale cereale L.).
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Antibody-encoding repertoires of bone marrow and peripheral blood—a focus on IgE
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Defining the human copper proteome and analysis of its expression variation in cancers.
Blockhuys S, Celauro E, Hildesjö C, ..., Fierro-González JC, Wittung-Stafshede P
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RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.
Alkasalias T, Alexeyenko A, Hennig K, ..., Gad AK, Pavlova T
Proc. Natl. Acad. Sci. U.S.A. 114 (8) E1413-E1421 [2017-02-21; online 2017-02-07]
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