Systems Biology

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SciLifeLab Infrastructure Unit 2016–2020.

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

Started: 2016

Ended: 2020

Year 2023

PubMed DOI Crossref
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data.
Gustafsson J, Anton M, Roshanzamir F, ..., Robinson JL, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 120 (6) e2217868120 [2023-02-07; online 2023-01-31]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
GotEnzymes: an extensive database of enzyme parameter predictions.
Li F, Chen Y, Anton M, Nielsen J
Nucleic Acids Res. 51 (D1) D583-D586 [2023-01-06; online 2022-09-29]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Year 2022

PubMed DOI Crossref
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]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
DOI Crossref
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]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Glycoproteomics [Service] Systems Biology [Collaborative]

Year 2021

PubMed DOI Crossref
Genome-scale metabolic network reconstruction of model animals as a platform for translational research.
Wang H, Robinson JL, Kocabas P, ..., Zetterberg H, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 118 (30) e2102344118 [2021-07-27; online 2021-07-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Technology development]
PubMed DOI Crossref
BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.
Gustafsson J, Robinson J, Nielsen J, Pachter L
Genome Biol. 22 (1) 174 [2021-06-08; online 2021-06-08]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology
PubMed DOI Crossref
Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells
Mathew NR, Jayanthan JK, Smirnov IV, ..., Bemark M, Angeletti D
Cell Rep 35 (12) 109286 [2021-06-00; online 2021-06-00]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.
Morgell A, Reisz JA, Ateeb Z, ..., Chen MS, D'Alessandro A
J. Proteome Res. 20 (5) 2725-2738 [2021-05-07; online 2021-03-15]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.
Olsson Lindvall M, Angerfors A, Andersson B, ..., Stanne TM, Jern C
Thromb. Haemost. 121 (5) 573-583 [2021-05-00; online 2020-11-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Machine learning-based investigation of the cancer protein secretory pathway.
Saghaleyni R, Sheikh Muhammad A, Bangalore P, Nielsen J, Robinson JL
PLoS Comput. Biol. 17 (4) e1008898 [2021-04-00; online 2021-04-05]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Year 2020

PubMed DOI Crossref
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]
PubMed DOI Crossref
Sources of variation in cell-type RNA-Seq profiles.
Gustafsson J, Held F, Robinson JL, ..., Jörnsten R, Nielsen J
PLoS ONE 15 (9) e0239495 [2020-09-21; online 2020-09-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.
Halvorsen M, Huh R, Oskolkov N, ..., Sullivan PF, Szatkiewicz JP
Nat Commun 11 (1) 1842 [2020-04-15; online 2020-04-15]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Building blocks are synthesized on demand during the yeast cell cycle.
Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
An atlas of human metabolism.
Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J
Sci Signal 13 (624) - [2020-03-24; online 2020-03-24]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Year 2019

PubMed DOI Crossref
A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver
Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C
Thromb. Haemost. 120 (02) 229-242 [2019-12-30; online 2019-12-30]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
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]
PubMed DOI Crossref
ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C
Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media.
Raethong N, Wang H, Nielsen J, Vongsangnak W
Computational and Structural Biotechnology Journal 18 (-) 1-8 [2019-11-26; online 2019-11-26]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.
Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM
Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes.
Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C
Sci Rep 9 (1) 8169 [2019-06-03; online 2019-06-03]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E
PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]

Year 2018

PubMed DOI Crossref
Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease.
Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M
Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2018-12-19; online 2018-12-19]
Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
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]
Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Service]
PubMed DOI Crossref
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]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G
Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Year 2017

PubMed DOI Crossref
Genome scale metabolic modeling of cancer.
Nilsson A, Nielsen J
Metab. Eng. 43 (Pt B) 103-112 [2017-09-00; online 2016-11-04]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
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]

Year 2016

PubMed DOI Crossref
Integrative analysis of human omics data using biomolecular networks.
Robinson JL, Nielsen J
Mol Biosyst 12 (10) 2953-2964 [2016-10-20; online 2016-08-12]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.
Gatto F, Schulze A, Nielsen J
Cell Rep 16 (3) 878-895 [2016-07-19; online 2016-07-12]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.
Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J
Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.
Gatto F, Volpi N, Nilsson H, ..., Basso U, Nielsen J
Cell Rep 15 (8) 1822-1836 [2016-05-24; online 2016-05-18]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
PubMed DOI Crossref
Transcriptomics resources of human tissues and organs.
Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J
Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]
Bioinformatics Support, Infrastructure and Training [Technology development] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Technology development] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.
Gatto F, Nielsen J
J Hematol Oncol 9 (-) 15 [2016-03-02; online 2016-03-02]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Year 2015

PubMed DOI Crossref
In search for symmetries in the metabolism of cancer.
Gatto F, Nielsen J
Wiley Interdiscip Rev Syst Biol Med 8 (1) 23-35 [2015-11-05; online 2015-11-05]
Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]
SciLifeLab Data Centre
Publications 9.5.0