Nielsen J

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.

63 publications

AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with Deep-learning-based Dark Metabolism Mining

Lu H, Han W, Xiao L, ..., Kerkhoven EJ, Nielsen J

- - (-) - [2025-11-14; online 2025-11-14]

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]

Adil Mardinoglu SciLifeLab Fellow

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]

Adil Mardinoglu DDLS Fellow Muhammad Arif Saeed Shoaie SciLifeLab Fellow

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

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]

Adil Mardinoglu SciLifeLab Fellow

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]

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]

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]

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]

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]

Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow

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 DDLS Fellow Muhammad Arif Saeed Shoaie SciLifeLab Fellow

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) - [2021-07-27; online 2021-07-21]

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 DDLS Fellow Muhammad Arif SciLifeLab Fellow

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]

Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow

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]

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]

Aleksej Zelezniak SciLifeLab Fellow

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]

Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow

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]

Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow

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]

Machine learning-based investigation of the cancer protein secretory pathway

Saghaleyni R, Muhammad AS, Bangalore P, Nielsen J, Robinson JL

- - (-) - [2020-09-10; online 2020-09-10]

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

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Gustafsson J, Robinson J, Nielsen J, Pachter L

- - (-) - [2020-07-06; online 2020-07-06]

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

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]

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]

Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow

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 DDLS Fellow Muhammad Arif 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 DDLS Fellow 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

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]

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]

Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow

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 DDLS Fellow Fredrik Edfors 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 DDLS Fellow Muhammad Arif SciLifeLab Fellow

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]

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

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 Metab. 27 (3) 559-571.e5 [2018-03-06; online 2018-02-15]

Adil Mardinoglu Affiliated researcher SciLifeLab Fellow

PubMed DOI Crossref

Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors.

Azimi A, Caramuta S, Seashore-Ludlow B, ..., Uhlen M, Maddalo G

Mol Syst Biol 14 (3) e7858 [2018-03-05; online 2018-03-05]

DDLS Fellow Fredrik Edfors

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

Efficient protein production by yeast requires global tuning of metabolism.

Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J

Nat Commun 8 (1) 1131 [2017-10-25; online 2017-10-25]

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]

Avlant Nilsson DDLS Fellow

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]

Affiliated researcher

PubMed DOI Crossref

Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals.

Yu T, Zhou YJ, Wenning L, ..., Nielsen J, David F

Nat Commun 8 (-) 15587 [2017-05-26; online 2017-05-26]

PubMed DOI Crossref

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.

Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J

Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]

PubMed DOI Crossref

Expanding the product portfolio of fungal type I fatty acid synthases.

Zhu Z, Zhou YJ, Krivoruchko A, ..., Zhao ZK, Nielsen J

Nat. Chem. Biol. 13 (4) 360-362 [2017-04-00; online 2017-02-20]

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

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories.

Zhou YJ, Buijs NA, Zhu Z, ..., Siewers V, Nielsen J

Nat Commun 7 (-) 11709 [2016-05-25; online 2016-05-25]

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