Nielsen Lab


Recent publications

Research papers in international journals with peer review


E.L. Bredesweg; K.R. Pomraning; Z. Dai; J. Nielsen; E. Kerkhoven; S. Baker (2016) A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol. Biofuels 10:2

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. 13:360-362

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. npj Systems Biol. Appl. 3:3

A. Mardinoglu; E. Bjornson; C. Zhang; M. Klevstig; S. Söderlund; M. Ståhlman; M. Adiels; A. Hakkarainen; N. Lundbom; M. Kilicarslan; B.M. Hallström; J. Lundbom; B. Verges; P.H.R. Barret; G.F. Watts; M. Serlie; J. Nielsen; M. Uhlen; U. Smith; H.-U. Marschall; M.-R. Taskine; J. Boren (2017) Personalized genome-scale modeling identifies NAD+ and glutathione metabolism as a target for treatment of NAFLD. Mol. Sys. Biol. 13:916

Y. Wei; M. Gossing; D. Bergenholm; V. Siewers; J. Nielsen (2017) Increasing cocoa butter-like lipid production of Saccharomyces cerevisiae by expression of selected cocoa genes. AMB Express, in press

S. Tippmann; R. Ferreira; V. Siewers; J. Nielsen; Y. Chen (2017) Effects of acetoacetyl-CoA synthase expression on production of farnesene in Saccharomyces cerevisiae. J. Ind. Biotechnol. Microbiol. 7:34

S. Tippmann; J. Anfelt; F. David; J.M. Rand; V. Siewers; M. Uhlen; J. Nielsen; E.P. Hudson (2017) Affibody scaffold improve sesquiterpene production in Saccharomyces cerevisiae. ACS Syn. Biol. 6:19-28

E.L. Bredeweg; K.R. Pomraning; Z. Dai; J. Nielsen; E. Kerkhoven; S.E. Baker (2017) A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol. Biofuels 10:2

Y. Chen; Y. Wang; J. Nielsen (2017) Systematic inference of functional phosphorylation events in yeast metabolism. Bioinformatics, in press

P.-J. Lahtvee; B.J. Sanchez; A. Smialowska; S. Kasvandik; I. Elsemman; F. Gatto; J. Nielsen (2017) Absolute quantification of protein and mRNA abundances demonstrate variability in gene-specific translation efficiency in yeast. Cell Systems, in press

Y. Hu; J. Zhou; J. Bao; L. Huang; J. Nielsen; A. Krivoruchko (2017) Metabolic engineering of Saccharomyces cerevisiae for production of germacreme A, a precursor of beta-elemene. J. Ind. Biotechnol. Microbiol., in press

T. Yu; Y.J. Zhou; L. Wenning; Q. Liu; A. Krivoruchko; V. Siewers; J. Nielsen; F. David (2017) Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nature Com., in press

P.G. Teixeira; R. Ferreira; Y.J. Zhou; V. Siewers; J. Nielsen (2017) Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae. Microb. Cell Fac. 16:45

E.D. Jensen; R. Ferreira; T. Jakociunas; D. Arsovska; L. Ding; J.D. Smith; F. David; J. Nielsen; M.K. Jensen; J.D. Keasling (2017) Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies. Microb. Cell Fac., in press

R. Babazadeh; P.-J. Lahtvee; C. Beck; M. Goksör; J. Nielsen; S. Hohmann (2017) The yeast osmostress response is carbon source dependent. Sci. Rep. 7:990

M.-K. Kang; Y. Zhou; N.A. Buijs; J. Nielsen (2017) Functional screening of aldehyde decarboxylases for long-chain alkane production by Saccharomyces cerevisiae. Microb. Cell Fac., in press

L. Väremo; T.I. Henriksen; C. Scheele; C. Broholm; M. Pedersen; M. Uhlen; B.K. Pedersen; J. Nielsen (2017) Type 2 diabetes and obesity are independently associated with similar inherent transcriptional reprogramming in human myocytes. Genome Med., in press

J.C. Nielsen; S. Grijseels; S. Prigent; B. Ji; J. Dainat; K.F. Nielsen; J.C. Frisvad; M. Workman; J. Nielsen (2017) Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nature Microbiol. 2:17044


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) Six tissue transcriptomics reveals specific immune suppression in spleen by dietary polyunsaturated fatty acids. 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

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

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. 2:28-37

J. Nielsen (2017) Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine. Cell Met. 25:572-579

J.C. Nielsen; J. Nielsen (2017) Development of fungal cell factories for the production of secondary metabolites: linking genomics and metabolism. Synth. Systems Biotechnol. 2:5-12

G. Wang; M. Huang; J. Nielsen (2017) Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production. Curr. Opion. Biotechnol. 48:77-84

J. Nielsen (2017) Systems Biology of Metabolism. Ann. Rev. Biochem., in press

J.L. Robinson; J. Nielsen (2017) Anticancer drug discovery through genome-scale metabolic modeling. Curr. Opion. Syst. 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


Commentaries and Short Papers


D. Fraenkel; J. Nielsen (2016) Trehalose-6-phosphate synthase and stabilization of yeast glycolysis. FEMS Yeast Res. 16:fov100

J. Nielsen (2016) All you need is mentorship: A journey of equals. Cell 164:1093

A. Mardinoglu; J. Nielsen (2016) The impact of systems medicine on human health and disease. Fron. Physiol. 7:552

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