Nielsen J

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Family name Nielsen
Given name Jens
Initials J
ORCID

ORCID 0000-0002-9955-6003
Affiliations Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

48 publications

PubMed DOI Crossref
Longitudinal big biological data in the AI era.
Mardinoglu A, Turkez H, Shong M, ..., Hood L, Uhlen M
Mol Syst Biol 21 (9) 1147-1165 [2025-09-00; online 2025-08-05]
PubMed DOI Crossref
Multi-omics characterization of improved cognitive functions in Parkinson's disease patients after the combined metabolic activator treatment: a randomized, double-blinded, placebo-controlled phase II trial.
Yulug B, Altay O, Li X, ..., Uhlén M, Mardinoglu A
Brain Commun 7 (1) fcae478 [2025-01-06; online 2025-01-06]
PubMed DOI Crossref
The acute effect of different NAD+ precursors included in the combined metabolic activators.
Li X, Yang H, Jin H, ..., Borén J, Mardinoglu A
Free Radic. Biol. Med. 205 (-) 77-89 [2023-08-20; online 2023-06-02]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
standard-GEM: standardization of open-source genome-scale metabolic models
Anton M, Almaas E, Benfeitas R, ..., Zeidan AA, Kerkhoven EJ
- - (-) - [2023-03-23; online 2023-03-23]
PubMed DOI Crossref
Integrative functional analysis uncovers metabolic differences between Candida species.
Begum N, Lee S, Portlock TJ, ..., Moyes DL, Shoaie S
Commun Biol 5 (1) 1013 [2022-09-26; online 2022-09-26]
Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Metastatic triple negative breast cancer adapts its metabolism to destination tissues while retaining key metabolic signatures.
Roshanzamir F, Robinson JL, Cook D, Karimi-Jafari MH, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 119 (35) e2205456119 [2022-08-30; online 2022-08-22]
DOI Crossref
Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
Zhang C, Shi M, Kim W, ..., Boren J, Mardinoglu A
- - (-) - [2022-02-17; online 2022-02-17]
PubMed DOI Crossref
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection.
Lu H, Li F, Yuan L, ..., Kerkhoven EJ, Nielsen J
Mol Syst Biol 17 (10) e10427 [2021-10-00; online 2021-10-23]
PubMed DOI Crossref
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.
Zeybel M, Altay O, Arif M, ..., Borén J, Mardinoglu A
Mol Syst Biol 17 (10) e10459 [2021-10-00; online 2021-10-26]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
iNetModels 2.0: an interactive visualization and database of multi-omics data.
Arif M, Zhang C, Li X, ..., Uhlen M, Mardinoglu A
Nucleic Acids Res. 49 (W1) W271-W276 [2021-07-02; online 2021-04-14]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Global and temporal state of the human gut microbiome in health and disease
Shoaie S, Lee S, Almeida M, ..., Ehrlich S, Uhlen M
- - (-) - [2021-04-01; online 2021-04-01]
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
- - (-) - [2021-03-05; online 2021-03-05]
PubMed DOI Crossref
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism.
Li G, Hu Y, Luo H, ..., Ji B, Nielsen J
Nat Commun 12 (1) 190 [2021-01-08; online 2021-01-08]
DOI Crossref
A Network-Based Approach Reveals the Dysregulated Transcriptional Regulation in Non- Alcohol Fatty Liver Disease
Yang H, Arif M, Yuan M, ..., Zhang C, Mardinoglu A
- - (-) - [2021-00-00; online 2021-00-00]
DOI Crossref
Drug Repositioning for Clear Cell Renal Cell Carcinoma Based on Stratification of Patients
Li X, Kim W, Juszczak K, ..., Zhang C, Mardinoglu A
- - (-) - [2021-00-00; online 2021-00-00]
PubMed DOI Crossref
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.
Zrimec J, Börlin CS, Buric F, ..., Töpel M, Zelezniak A
Nat Commun 11 (1) 6141 [2020-12-01; online 2020-12-01]
PubMed DOI Crossref
Current Status of COVID-19 Therapies and Drug Repositioning Applications.
Altay O, Mohammadi E, Lam S, ..., Uhlen M, Mardinoglu A
iScience 23 (7) 101303 [2020-07-24; online 2020-06-20]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.
Nilsson A, Haanstra JR, Engqvist M, ..., Teusink B, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 117 (19) 10294-10304 [2020-05-12; online 2020-04-27]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
Lieven C, Beber ME, Olivier BG, ..., Zakhartsev M, Zhang C
Nat. Biotechnol. 38 (4) 504 [2020-04-00; online 2020-04-09]
PubMed DOI Crossref
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.
Zhang C, Bjornson E, Arif M, ..., Borén J, Mardinoglu A
Mol Syst Biol 16 (4) e9495 [2020-04-00; online 2020-04-28]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
An atlas of human metabolism.
Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J
Sci Signal 13 (624) eaaz1482 [2020-03-24; online 2020-03-24]
Adil Mardinoglu Avlant Nilsson SciLifeLab Fellow
PubMed DOI Crossref
MEMOTE for standardized genome-scale metabolic model testing.
Lieven C, Beber ME, Olivier BG, ..., Zakhartsev M, Zhang C
Nat. Biotechnol. 38 (3) 272-276 [2020-03-00; online 2020-03-04]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
DOI Crossref
Evolution from adherent to suspension – systems biology of HEK293 cell line development
Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J
- - (-) - [2020-01-30; online 2020-01-30]
DOI Crossref
Discovery of Functional Alternatively Spliced <i>PKM</i> Transcripts in Human Cancers
Li X, Zhang C, Kim W, ..., Uhlen M, Mardinoglu A
- - (-) - [2020-00-00; online 2020-00-00]
PubMed DOI Crossref
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs).
Othoum G, Prigent S, Derouiche A, ..., Mijakovic I, Essack M
Sci Rep 9 (1) 19254 [2019-12-17; online 2019-12-17]
PubMed DOI Crossref
The human secretome.
Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å
Sci Signal 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Complex I is bypassed during high intensity exercise.
Nilsson A, Björnson E, Flockhart M, Larsen FJ, Nielsen J
Nat Commun 10 (1) 5072 [2019-11-07; online 2019-11-07]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function.
Liu Z, Zhang C, Lee S, ..., Boren J, Mardinoglu A
Metab. Eng. 52 (-) 263-272 [2019-03-00; online 2019-01-04]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Metabolite Depletion Affects Flux Profiling of Cell Lines.
Nilsson A, Haanstra JR, Teusink B, Nielsen J
Trends Biochem. Sci. 43 (6) 395-397 [2018-06-00; online 2018-04-12]
Avlant Nilsson DDLS Fellow
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
- - (-) - [2018-05-13; online 2018-05-13]
PubMed DOI Crossref
An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans
Mardinoglu A, Wu H, Bjornson E, ..., Taskinen MR, Borén J
Cell Metabolism 27 (3) 559-571.e5 [2018-03-00; online 2018-03-00]
Adil Mardinoglu Affiliated researcher SciLifeLab Fellow
PubMed DOI Crossref
Recon3D enables a three-dimensional view of gene variation in human metabolism.
Brunk E, Sahoo S, Zielinski DC, ..., Thiele I, Palsson BO
Nat. Biotechnol. 36 (3) 272-281 [2018-03-00; online 2018-02-19]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Metabolic Models of Protein Allocation Call for the Kinetome.
Nilsson A, Nielsen J, Palsson BO
Cell Systems 5 (6) 538-541 [2017-12-27; online 2017-12-29]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis.
Thorell K, Bengtsson-Palme J, Liu OH, ..., Lundin SB, Sjöling Å
Infect. Immun. 85 (10) - [2017-10-00; online 2017-09-20]
DDLS Fellow Johan Bengtsson-Palme
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]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Network analyses identify liver-specific targets for treating liver diseases.
Lee S, Zhang C, Liu Z, ..., Boren J, Mardinoglu A
Mol Syst Biol 13 (8) 938 [2017-08-21; online 2017-08-21]
Adil Mardinoglu Affiliated researcher SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Human protein secretory pathway genes are expressed in a tissue-specific pattern to match processing demands of the secretome.
Feizi A, Gatto F, Uhlen M, Nielsen J
NPJ Syst Biol Appl 3 (-) 22 [2017-08-18; online 2017-08-18]
PubMed DOI Crossref
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.
Sánchez BJ, Zhang C, Nilsson A, ..., Kerkhoven EJ, Nielsen J
Mol Syst Biol 13 (8) 935 [2017-08-03; online 2017-08-03]
Affiliated researcher Avlant Nilsson
PubMed DOI Crossref
Selection of complementary foods based on optimal nutritional values.
Sen P, Mardinogulu A, Nielsen J
Sci Rep 7 (1) 5413 [2017-07-14; online 2017-07-14]
Adil Mardinoglu Affiliated researcher SciLifeLab Fellow
PubMed DOI Crossref
Personal model-assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD.
Mardinoglu A, Bjornson E, Zhang C, ..., Taskinen MR, Boren J
Mol Syst Biol 13 (3) 916 [2017-03-02; online 2017-03-02]
Adil Mardinoglu Affiliated researcher SciLifeLab Fellow
PubMed DOI Crossref
Predicting growth of the healthy infant using a genome scale metabolic model.
Nilsson A, Mardinoglu A, Nielsen J
NPJ Syst Biol Appl 3 (1) 3 [2017-01-31; online 2017-01-31]
Adil Mardinoglu Avlant Nilsson SciLifeLab Fellow
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]
Adil Mardinoglu Affiliated researcher SciLifeLab Fellow
PubMed DOI Crossref
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase.
Nilsson A, Nielsen J
Sci Rep 6 (-) 22264 [2016-03-01; online 2016-03-01]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
The gut microbiota modulates host amino acid and glutathione metabolism in mice
Mardinoglu A, Shoaie S, Bergentall M, ..., Bäckhed F, Nielsen J
Mol Syst Biol 11 (10) 834 [2015-10-00; online 2015-10-16]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome.
Shoaie S, Ghaffari P, Kovatcheva-Datchary P, ..., Bäckhed F, Nielsen J
Cell Metab. 22 (2) 320-331 [2015-08-04; online 2015-08-06]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
New paradigms for metabolic modeling of human cells.
Mardinoglu A, Nielsen J
Curr. Opin. Biotechnol. 34 (-) 91-97 [2015-08-00; online 2015-01-02]
PubMed DOI Crossref
A dedicated database system for handling multi-level data in systems biology.
Pornputtapong N, Wanichthanarak K, Nilsson A, Nookaew I, Nielsen J
Source Code Biol Med 9 (-) 17 [2014-07-10; online 2014-07-10]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, ..., Nookaew I, Nielsen J
Nucleic Acids Res. 42 (Web Server issue) W175-W181 [2014-07-00; online 2014-05-03]
Avlant Nilsson DDLS Fellow
SciLifeLab Data Centre
Publications 9.5.1