Nielsen Lab


Recent publications

Research papers in international journals with peer review


Z. Zhu; Y.J. Zhou; A. Krivoruchko; M. Grininger; Z.K. Zhao; J. Nielsen (2016) Expanding the product portfolio of fungal type I fatty acid synthases. Nature Chem. Biol., in press

L. Wenning; T. Yu; F. David; J. Nielsen; V. Siewers (2016) Establishing very long-chain fatty alcohol and wax ester biosynthesis. Biotechnol. Bioeng., in press

Y. Wei; V. Siewers; J. Nielsen (2017) Cocoa butter-like lipid production ability of non-oleaginous and oleaginous yeasts under nitrogen limited culture conditions. Appl. Microbiol. Biotechnol., in press

A. Nilsson; A. Mardinoglu; J. Nielsen (2017) Predicting growth of the healthy infant using a genome-scale metabolic model. Systems Biol. Appl., in press


Z.A. Irani; E. Kerkhoven; S.A. Shojaosadati; J. Nielsen (2015) Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins. Biotechnol. Bioeng. 113:961-969

E. Kerkhoven; K. Pmoraning; S. Baker; J. Nielsen (2015) Regulation of amino acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. Systems Biol. Appl. 2:16005

S. Shi; J. Haichuan; V. Siewers; J. Nielsen (2015) Improved production of fatty acids by Saccharomyces cerevisiae through screening a cDNA library from the oleaginous yeast Yarrowia lipolytica. FEMS Yeast Res. 16:fv108

B. de Jong; V. Siewers; J. Nielsen (2016) Physiological and transcriptional characterization of Saccharomyces cerevisiae engineered for production of fatty acid ethyl esters. FEMS Yeast Res. Fov105:1-9

S. Tippmann; G. Scalcinati; V. Siewers; J. Nielsen (2015) Production of farnesene and santalane by Saccharomyces cerevisiae using fed-batch cultivations with RQ-controlled feed. Biotechnol. Bioeng. 113:72-81

S. Tippmann; J. Nielsen; S. Khoomrung (2016) Improved quantification of farnesene during microbial production from Saccharomyces cerevisiae in two-liquid-phase fermentations. Talanta 146:100-106

F. David; J. Nielsen; V. Siewers (2016) Flux control at the malonyl-CoA node through hierarchical dynamic pathway regulation in Saccharomyces cerevisiae. ACS Syn. Biol. 5:224-233

L. Pedersen; M. Idorn; G.H. Olofsson; B. Lauenborg; I. Nookaew; R.H. Hansen; H.H. Johannesen; J.C. Becker; K.S. Pedersen; C. Dethlefsen; J. Nielsen; J. Gehl; B.K. Pedersen; P.T. Straten; P. Hojman (2016) Voluntary running suppresses tumor growth through epinephrine- and IL-6-dependent NK cell mobilization and redistribution. Cell Met. 23:1-9

J, Maury; S.M. Germann; S.A.B. Jacobsen; N.B. Jensen; K.R. Kildegaard; M.J. Heergård; K. Schneider; A. Koza; J. Förster; J. Nielsen; I. Borodina (2016) EasyCloneMulti: A set of vectors for simultaneous and multiple genomic integrations in Saccharomyces cerevisiae. PLOS One 0150394:1-22

F. Gatto; J. Nielsen (2016) Systematic analysis of overall survival and interactions between tumor metabolism and drug treatment. J. Hematology Oncology 9:15

A. Nilsson; J. Nielsen (2016) Metabolic trade-offs in yeast are caused by F1F0-ATP synthase. Sci. Rep. 6:22264
K. Kildegaard; N.B. Jensen; K. Schneider; E. Czarnotta; E. Özdemir; T. Klein; J. Maury; B.E. Ebert; H.B. Christensen; Y. Chen; I.-K. Kim; M.J. Herrgård; L.M. Blank; J. Forster; J. Nielsen; I. Borodina (2016) Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway. Microb. Cell Fac. 15:53

Y. Zhou; N. A. Buijs; Z. Zhu; J. Qin; V. Siewers; J. Nielsen (2016) Production of fatty acid derived oleochemicals and biofuels by synthetic yeast cell factories. Nature Com. 7:11709

I. E. Elsemman; A. Mardinoglu; S. Shoaie; T.H. Soliman; J. Nielsen (2016) Systems biology analysis of metabolism reveals the role of copy number increase in parts of chromosome 1q in hepatitis C virus associated hepatocellular carcinoma. Mol. Biosystems 12:1496-1506

G. Liu; D. Bergenholm; J. Nielsen (2016) Genome-wide mapping of binding sites reveals multiple biological functions of the transcription factor Cst6p in Saccharomyces cerevisiae. mBio 7:e00559-16

F. Gatto; N. Volpi; H. Nilsson; I. Nookaew; M. Maruzzo; A. Roma; M. E. Johansson; U. Steiner; S. Lundstam; U. Basso; J. Nielsen (2016) Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma. Cell Rep. 15:1-15

S.L. Svahn; L. Väremo; B. Gabrielsson; E. Peris; I. Nookaew; L. Grahnemo; A.-S. Sandberg; I.W. Asterholm; J.-O. Jansson; J. Nielsen; M.E. Johansson (2016) Dietary fat composition regulates the transcriptome, especially of immune genes, in the spleen. PLOS One 11:e0155099

R. Pereira; J. Nielsen; I. Rocha (2016) Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae, Met. Eng. Com. 3:153-163

S. Lee; M. Kilicarslan; C. Zhang; E. Björnson; B.M. Hallström; A.K. Groen; E. Ferrannini; M. Laakso; M. Blüher; M. Uhlen; J. Nielsen; U. Smith; J. Boren; M. Serlie; A. Mardinoglu (2016) Integrated network analysis reveals an association between increased plasma mannose levels and insulin resistance and secretion. Cell Met. 24:172-184

L. Caspeta; Y. Chen; J. Nielsen (2016) Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30C. Sci. Rep. 6:27003

S. Lee; A. Marginoglu; C. Zhang; D. Lee; J. Nielsen (2016) Dysregulated signaling hubs of liver metabolism reveal hepatocellular carcinoma pathogenesis. Nuc. Acid Res. 44:5529-5539

S. Busti; V. Mapelli; F. Tripodi; R. Sanvito; F. Magni; M.C. Jewett; J. Nielsen; L. Alberghina; M. Vanoni (2016) Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast. Sci. Rep. 6:27942

F. Gatto; A. Schultze; J. Nielsen (2016) Systematic analysis reveals that cancer mutations converge on deregulated metabolism of arachinodate and xenobiotics. Cell Rep. 16:878-895

P.-J. Lahtvee; R. Kumar; B.M. Hallström; J. Nielsen (2016) Adaption to different types of stress converge on mitochondrial metabolism. Mol. Biol. Cell 27:2505-2514

A.S. Rajkumar; G. Liu; D. Bergenholm; D. Arsovska; M. Kristensen; J. Nielsen; M.K. Jensen; J.D. Keasling (2016) Engineering of synthetic, stress sensitive yeast promoters. Nuc. Acid Res. 44:e136

J.L. Martinez; E. Meza; D. Petranovic; J. Nielsen (2016) The impact of respiration and oxidative stress response on recombinant a-amylase production by Saccharomyces cerevisiae. Metab. Eng. Com. 3:205-210

S. Grijseels; J.C. Nielsen; M. Randelovic; J. Nielsen; K.F. Nielsen; M. Workman; J.C. Frisvad (2015) Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites. Sci. Rep. 6:35112

J. Casey; A. Mardinoglu; J. Nielsen; D. Kari (2016) Adaptive evolution of phosphorous metabolism in Prochlorococcus. mSystems 1:e00065-16

Y. Zhou; N.A.. Buijs; Z. Zhu; D.O. Gomez; A. Boonsombuti; V. Siewers; J. Nielsen (2016) Harnessing peroxisomes for production of fatty acid-derived biofuels and chemicals in yeast. J. Am. Chem. Soc. 138:15368-15377

M. Li; K.R. Kildegaard; Y. Chen; A. Rodriguez; I. Borodina; J. Nielsen (2016) Engineering yeast for high-level production of stilbenoid antioxidants. Sci. Rep. 6:36827

E. Fletcher; A. Feizi; B. Hallström, M. Bisschops; S. Koomrung; V. Siewers; J. Nielsen (2016) Evolutionary engineering revewals divergent paths when yeast is adapted to different acidic environments. Met. Eng. 113:1164-1170

F. Gatto; M. Maruzzo; C. Magro; U. Basso; J. Nielsen (2016) Prognostic value of plasma and urine glycosaminoglycan scores in clear cell renal cell carcinoma. Front. Oncol. 6:253

Bergman; V. Siewers; J. Nielsen; Y. Chen (2016) Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae. AMB Express 6:115


M. Uhlén, L. Fagerberg, B.M. Hallström, C. Lindskog, P. Oksvold, A. Mardinoglu, Å. Sivertsson, C. Kampf, E. Sjöstedt, A. Asplund, I. Olsson, K. Edlund, E. Lundberg, S. Navani, C.A.-K. Szigyarto, J. Odeberg, D. Djureinovic, J.O. Takanen,  S. Hober, T. Alm, H. Berling, H. Tegel, J. Mulder, J. Rockberg, P. Nilsson, J.M. Schwenk, M. Hamsten, K. von Feilitzen, M. Forsberg, L. Persson, F. Johansson, M. Zwahlen, G. von Heijne, J. Nielsen; F. Ponten (2015) Tissue based map of the humane proteome. Science 347:1260419,1-9

N.A. Buijs; Y.J. Zhou; V. Siewers; J. Nielsen (2015) Long-chain alkane production by the yeast Saccharomyces cerevisiae. Biotechnol. Bioeng. 112:1275-1279

P. Ghaffari; A. Mardinoglu; A. Asplund; S. Shoaie; C. Kampf; M. Uhlen; J. Nielsen (2015) Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. Sci. Rep. 5:8183

I. Borodina; K. Kildegaard; N.B. Jensen; T.H. Blicher; J. Maury; S. Sherstyk; K. Schneider; P. Lamosa; M.J. Herrgård; I. Rosenstand; F. Öberg; J. Förster; J. Nielsen (2015) Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine. Met. Eng. 27:57-64

C. Zhang; B. Ji; A. Mardinoglu; J. Nielsen; Q. Hua (2015) Logical transformation of genome scale metabolic models for genetic applications and analysis. Bioinfor. 31:2324-2331

B. de Jong; S. Shi; J.O. Valle-Rodriguez; V. Siewers; J. Nielsen (2015) Metabolic pathway engineering for fatty acid ethyl ester production in Saccharomyces cerevisiae using stable chromosomal integration. J. Ind. Microbiol. Biotechnol. 42:477-486

Y. Chen; Y. Zhang; V. Siewers; J. Nielsen (2015) Ach1 is involved in shutting mitochondrial acetyl units for cytosolic C2 provision in Saccharomyces cerevisiae lacking pyruvate carboxylase. FEMS Yeast Res. 15:fov015

R. Nicastro; F. Tripodi; C. Guzzi; V. Reghellin; S. Khoomrung; C. Airoldi; J. Nielsen; L. Alberghina; P. Cocetti (2015) Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK. BBA Mol. Cell Res. 1853:1615-1625

K.V.Y. Gossens; F.S. Ielasi; I. Nookaew; I. Stals; L. Alonso-Sarduy; L. Daenen; S.E. Van Mulders; R.G.E. van Eijsden; C. Stassen; V. Siewers; F.R. Delvaux; S. Kasas; J. Nielsen; B. Devreese; R.G. Willaert (2015) Molecular mechanisms of flocculation self-recognition in yeast and its role in mating and survival. MBio 6:e00427-15

T. Österlund; S. Bordel; J. Nielsen (2015) Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors. Integr. Biol. 7:560-568

S. Tymoshenko; R.D. Oppenheim; R. Agren; J. Nielsen; D. Soldati-Favre; V. Hatzimanikatis (2015) Metabolic needs and capabilities of Toxoplasma gondii through combined computational and experimental analysis. PLOS Comp. Biol. 11:e1004261

L. Väremo; C. Scheele; C. Broholm; A. Mardinoglu; C. Kampf; A. Asplund; I. Nookaew; M. Uhlen; B.K. Pedersen; J. Nielsen (2015) Transcriptome and proteome driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes. Cell Rep. 11:1-13

M. Engqvist; J. Nielsen (2015) ANT: Software for generating and evaluationg degenerate codons for natural and expandic genetic codes. ACS Synthetic Biol. 4:935-938

A. Feizi; A. Banaei-Esfahani; J. Nielsen (2015) HCSD: the human cancer secretome database. Database bav051:1-8

J. Lopez; K. Essus; I.-K. Kim; R. Pereira; J. Herzog; V. Siewers; J. Nielsen; E. Agosin (2015) Production of b-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae. Mic. Cell Fac. 14:84

Y. Zhang; Z. Dai; A. Krivoruchko; Y. Chen; V. Siewers; J. Nielsen (2015) Functional pyruvate formate lyase pathway expressed in different electron donors in Saccharomyces cerevisiae at aerobic growth. FEMS Yeast Res. 15:fov024

F. Gatto; H. Miess; A. Schulze; J. Nielsen (2015) Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Sci. Rep. 5:10738

C. Lindskog; J. Linne; L. Fagerberg; B.M. Hallström; C.-J. Sundberg; M. Lindholm; M. Huus; C. Kampf; H. Choi; A. Liem; P. Ping; L. Väremo; A. Mardinoglu; J. Nielsen; E. Larsson; F. Ponten; M. Uhlen (2015) The human cardiac and skeletal muscle proteome defined by transcriptomics and antibody-based profiling. BMC Genom. 16:475

S. Shoaie; P. Ghaffari; P. Kovatcheva-Datchary; A. Mardinoglu; P. Sen; E. Pujos-Guillot; T. de Wouters; C. Juste; S. Rizkalla; J. Chilloux; L. Hoyles; J.K. Nicholson; ANR MicroObese Consortium; J. Dore; M.E. Dumas; K. Clement; F. Bäckhed; J. Nielsen (2015) Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metabolism 22:320-331

L. Caspeta; J. Nielsen (2015) Thermotolerant yeast strains adapted by laboratory evolution show trade-off at ancestral temperatures to other stresses. MBio 6:e00431-15

V. Tremaroli; F. Karlsson; M. Weling; M. Ståhlman; P. Kovatcheva-Datchary; T. Olbers; L. Fändriks; C. W. le Roux; J. Nielsen; F. Bäckhed (2015) Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation. Cell Metabolism 22:228-238

N. Pornputtaporn; I. Nookaew; J. Nielsen (2015) Human metabolic atlas: An online resource for human metabolism. Database bav068:1-9

M. Garcia-Albornoz; J. Nielsen (2015) Finding directionality and gene-disease predictions in disease associations. BMC Systems Biol. 9:35

M.H. Medema; R. Kottmann; P. Yilmaz; M. Cummings; J.B. Biggins; K. Blin: I. de Bruijn; Y.H. Chooi; J. Claesen; R.C. Coates; P. Cruz-Morales; S. Duddela; S. Düsterhus; D.J. Edwards; D.P. Fewer; N. Garg; C. Geiger; J.P. Gomez-Escribano; A. Greule; M. Hadjithomas; A.S. Haines; E.J.N. Helfrich; M.L. Hillwig; K. Ishida; A.C. Jones; C.S. Jones; K. Jungmann; C. Kegler; H.U. Kim; P. Kötter; D. Krug; J. Masschelein; A.V. Melnik; S.M. Mantovani; E.A. Monroe; M. Moore; N. Moss; H.-W. Nützmann; G. Pan; A. Pati; D. Petras; J. Reen; F. Rosconi; Z. Rui; Z. Tian; N.J. Tobias; Y. Tsunematsu; P. Wiemann; E. Wyckoff; X. Yan; G. Yim; F. Yu; Y. Xie; B. Aigle; A.K. Apel; C.J. Balibar; E.P. Balskus; F. Barona-Gómez; A. Bechthold; H.B. Bode; R. Borriss; S.F. Brady; A.A. Brakhage; P. Caffrey; Y.-Q. Cheng; J. Clardy; R.J. Cox; R. De Mot; S. Donadio; M.S. Donia; W.A. van der Donk; P.C. Dorrestein; S. Doyle; A.J.M. Driessen; M. Ehling-Schulz; K.-D. Entian; M.A. Fischbach; L. Gerwick; W.H. Gerwick; H. Gross; B. Gust; C. Hertweck; M. Höfte; S.E. Jensen; J. Ju; L. Katz; L. Kaysser; J.L. Klassen; N.P. Keller; J. Kormanec; O.P. Kuipers; T. Kuzuyama; N.C. Kyrpides; H.-J. Kwon; S. Lautru; R. Lavigne; C. Lee; B. Linquan; X. Liu; W. Liu; A. Luzhetskyy; T. Mahmud; Y. Mast; C. Méndez; M. Metsä-Ketelä; J. Micklefield; D.A. Mitchell; B.S. Moore; L.M. Moreira; R. Müller; B.A. Neilan; M. Nett; J. Nielsen; F. O’Gara; H. Oikawa; A. Osbourn; M.S. Osburne; B. Ostash; S.M. Payne; J.-L. Pernodet; M. Petricek; J. Piel; O. Ploux; J.M. Raaijmakers; J.A. Salas; E.K. Schmitt; B. Scott; R.F. Seipke; B. Shen; D.H. Sherman; K. Sivonen; M.J. Smanski; M. Sosio; R.D. Süssmuth; K. Tahlan; C.M. Thomas; Y. Tang; A.W. Truman; M. Viaud; J.D. Walton; C.T. Walsh; T. Weber; G.P. van Wezel; B. Wilkinson; J.M. Willey; W. Wohlleben; G.D. Wright; N. Ziemert; C. Zhang; S.B. Zotchev; R. Breitling; E. Takano; F.O. Glöckner (2015) The Minimum Information about a Biosynthetic Gene cluster (MIBiG) specification. Nature Chem. Biol. 11:625-631

L. Liu; Y. Zhang; Z. Liu; D. Petranovic; J. Nielsen (2015) Improving heterologous protein secretion at aerobic conditions by activating hypoxia induced genes in Saccharomyces cerevisiae. FEMS Yeast Research 15:fov070

Y. Zhang; G. Liu; M.K.M. Engqvist; A. Krivoruchko; B.M. Hallström; Y. Chen; V. Siewers; J. Nielsen (2015) Adaptive mutations in sugar metabolism restores growth on glucose in a pyruvate decarboxylase negative yeast strain. Microb. Cell Fac. 14:116

J.C. Qin; Y.J. Zhou; A. Krivoruchko; M. Huang; L. Liu; S. Khoomrung; V. Siewers; B. Jiang; J. Nielsen (2015) Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornitine. Nature Com. 6:8224

A. Rodriguez; K.R. Kildegaard; M. Li; I. Borodina; J. Nielsen (2015) Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis. Met. Eng. 31:181-188

M. Huang; Y. Bai; S.L. Sjostrom; B.M. Hallström; Z. Liu; D. Petranovic; M. Uhlen; H.N. Joensson; H. Andersson-Svahn; J. Nielsen (2015) Microfluidic screening and whole genome sequencing identifies mutations associated with improved protein secretion by yeast. Proc. Nat. Acad. Sci. USA 112:E4689-96

M. Li; K.R. Kildegaard; Y. Chen; A. Rodriguez; I. Borodina; J. Nielsen (2015) De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae. Met. Eng. 32:1-11

E. Fletcher; A. Feizi; S. Kim; V. Siewers; J. Nielsen (2015) RNAseq analysis of Pichia anomaia reveals important mechansisms required for survival at low pH. Mic. Cell Fac. 14:143

A. Mardinoglu; J. Helker; D. Gärtner; E. Bjornson; M.R. Schön; G. Flehmig; N. Klöting; M. Fasshauer; M. Stumvoll; J. Nielsen; M. Blüher (2015) Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue. Sci. Rep. 5:14841

A. Mardinoglu; S. Shoaie; M. Bergentall; P. Ghaffari; C. Zhang; E. Larsson; F. Bäckhed; J. Nielsen (2015) The gut microbiome modulates host amino acid and glutathione metabolism in mice. Mol. Systems Biol. 11:834

E. Björnson; B. Mukhopadhyay; A. Asplund; N. Pristovsek; R. Cinar; S. Romeo; M. Uhlen; G. Kunos; J. Nielsen; A. Mardinoglu (2015) Stratification of Hepatocellular Carcinoma Patients based on Acetate Utilization. Cell Rep. 13:2014-2026

S. Khoomrung; J.L. Martinez; S. Tippmann; S. Jansa-Ard; M. Buffing; R. Nicastro; J. Nielsen (2015) Expanded metabolite coverage of Saccharomyces cerevisiae extract through improved chemical derivatization. Anal. Chem. Res. 6:9-16

K.R. Kildegaard; Y. Chen; Z. Wang; J. Nielsen; I. Borodina (2015) Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae. Met. Eng. Com. 2:132-136

J. Anfelt; D. Kaczmarzyk; K. Shabestary; B. Renberg; J. Rockberg; J. Nielsen; M. Uhlen; E.P. Hudson (2015) Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production. Mic. Cell Fac. 14:167


Reviews in international journals with peer review


L.J. Sweetlove; J. Nielsen; A.R. Fernie (2017) Engineering central metabolism – a grand challenge for plant biologists. Plant J., in press

J. Geng; J. Nielsen (2017) In silico analysis of human metabolism: Reconstruction, contextualization and application. Curr. Op. Systems Biol., in press


E. Fletcher; A. Krivoruchko; J. Nielsen (2016) Industrial systems biology and its impact on synthetic biology of yeast cell factories. Biotechnol. Bioeng. 113:1164-1170

J.L. Martinez; D. Petranovic; J. Nielsen (2016) Heme metabolism in stress regulation and protein production: From cinderalla to key player. BioEngineered, in press

F. Gatto; J. Nielsen (2016) In search for symmetries in the metabolism of cancer. WIREs Systems Biol. Med. 8:23-35

J. Nielsen; J. Keasling (2016) Engineering Cellular Metabolism. Cell 164:1185-1197

M. Uhlen; B.M. Hallström; C. Lindskog; A. Mardinoglu; F. Ponten; J. Nielsen (2016) The human-tissue-based proteome defined by transcriptomics and metabolic modeling. Mol. Sys. Biol. 12:862

M. Kumar; P. Babaei; B. Ji; J. Nielsen (2016) Human gut microbiota and healthy ageing: Recent developments and future perspective. Nutr. Healthy Ageing, in press

M.-K. Kang; J. Nielsen (2016) Biobased production of alkanes and alkenes through metabolic engineering of microorganisms. J. Ind. Microbiol. Biotechnol., in press

J. Robinson; J. Nielsen (2016) Integrative analysis of human omics data using biomolecular networks. Mol. BioSystems 12:2953-2964

Y. Chen; J. Nielsen (2016) Biobased organic acid production by metabolically engineered microorganisms. Curr. Op. Biotechnol. 37:165-172

Y. Chen; J. Nielsen (2016) Flux control through protein phosphorylation in yeast. FEMS Yeast Res., in press

A. Nilsson; J. Nielsen (2016) Genome-scale metabolic modeling of cancer. Met. Eng., in press


B. Ji; J. Nielsen (2015) New insight into the gut microbiome through metagenomcs. Adv. Genom. Genet. 5:77-91

A. Krivoruchko; Y. Zhang; V. Siewers; J. Nielsen (2015) Microbial acetyl-CoA metabolism and metabolic engineering. Met. Eng. 28:28-42

A. Krivoruchko; J. Nielsen (2015) Production of natural products through metabolic engineering of Saccharomyces cerevisiae. Curr. Op. Biotechnol. 35:7-15

A. Mardinoglu; J. Nielsen (2015) New paradigms for metabolic modeling of human cells. Curr. Op. Biotechnol. 34:91-97

B. Pfleger; M. Gossing; J. Nielsen (2015) Metabolic engineering strategies for microbial production of oleochemicals. Met. Eng. 29:1-11

D. Jullesson; F. David; B. Pfleger; J. Nielsen (2015) Impact of Synthetic Biology and Metabolic Engineering on Industrial Production of Fine Chemicals. Biotechnol. Adv. 33:1395-1402

B. J. Sanchez; J. Nielsen (2015) Genome-scale models of yeast: Towards standardized evaluation and consistent omic integration. Integrative Biol. 7:846-858

O. Kayikci; J. Nielsen (2015) Glucose repression in Saccharomyces cerevisiae. FEMS Yeast Res. 15:fov068

Z. Dai; J. Nielsen (2015) Advancing metabolic engineering through systems biology of industrial microorganisms. Curr. Op. Biotechnol. 36:8-15

P.N. Ghaffari; A. Mardinoglu; J. Nielsen (2015) Cancer metabolism: A modeling perspective. Front. Physiol. 6:Article 382

L. Caspeta; T. Castilio; J. Nielsen (2015) Modifying yeast tolerance to inhibitory conditions of ethanol production. Fron. Bioeng. Biotechnol. 3:Article 184

B. Ji; J. Nielsen (2015) From next-generation sequencing to systematic modeling of the gut microbiome. Front. Genet. 6:219


Commentaries and Short Papers


D. Fraenkel; J. Nielsen (2016) Trehalose-6-phosphate synthase and stabilization of yeast glycolysis. FEMS Yeast Res., in press

A. Mardinoglu; J. Nielsen (2016) The impact of systems medicine on human health and disease. Fron. Physiol., in press


J. Pronk; S.Y. Lee; J. Lievense; J. Pierce; B. Palsson; M. Uhlen; J. Nielsen (2015) How to set up collaborations between academia and industrial biotech companies. Nature Biotechnol. 33:237-240

L. Väremo; J. Nielsen (2015) Networking in metabolism and human disease. Oncotarget 6:18

A. Ebrahim; E. Almaas; E. Bauer; A. Bordbar; A.P. Burgard; R.L. Chang; A. Dräger; I. Famili; A.M. Feist; R.M.T. Fleming; S.S. Fong; V. Hatzimanikatis; M.J. Herrgård; A. Holder; M. Hucka; D. Hyduke; N. Jamshidi; S.Y. Lee; N. Le Novère; J.A. Lerman; N.E. Lewis; D. Ma; R. Mahadevan; C. Maranas; H. Nagarajan; A. Navid; J. Nielsen; L.K. Nielsen; J. Nogales; A. Noronha; C. Pal; B.O. Palsson; J.A. Papin; K.R. Patil; N.D. Price; J.L. Reed; M. Saunders; R.S. Senger; N. Sonnenschein; Y. Sun; I. Thiele (2015) Do genome-scale models need exact solvers or clearer standards? Mol. Sys. Biol. In press

J. Nielsen (2015) Yeast cell factories on the horizon. Science 349:1050-1051




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