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2018 (651)
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2015 (429)
2014 (376)
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2012 (245)
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SciLifeLab Infrastructure Unit 2016–2020.
Primary
: Shown in the list of current labels.
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 and MS Proteomics [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 Support for Computational Resources [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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
Bioinformatics Support, Infrastructure and Training [Collaborative]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
NGI Uppsala (Uppsala Genome Center) [Collaborative]
National Genomics Infrastructure [Service]
Systems Biology [Collaborative]
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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
Bioinformatics Support, Infrastructure and Training [Collaborative]
NGI Stockholm (Genomics Applications) [Service]
NGI Stockholm (Genomics Production) [Service]
National Genomics Infrastructure [Service]
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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
Bioinformatics Support, Infrastructure and Training [Collaborative]
NGI Stockholm (Genomics Applications) [Service]
NGI Stockholm (Genomics Production) [Service]
National Genomics Infrastructure [Service]
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 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]
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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
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]
Publications
9.5.0