Nielsen Lab


Recent publications

Research papers in international journals with peer review


E. Brunk; S. Sahoo; D.C. Zielinski; A. Altunkaya; A. Dräger; N. Mih; F. Gatto; A. Nilsson; G.A.P. Gonzalez; M.K. Aurich; A. Prlic; A. Sastry; A.D. Danielsdottir; A. Heinken; A. Noronha; P.W. Rose; S.K. Burley; R.M.T. Fleming; J. Nielsen; I. Thiele; B.O. Palsson (2018) A resource enabling a three-dimensional view of gene variation in human metabolism. Nature Biotechnol., in press

R. Ferreira; C. Skrekas; J. Nielsen; F. David (2018) Multiplexed CRISPR/Cas9 genome editing and gene regulation using Csy9 in Saccharomyces cerevisiae. ACS Syn. Biol., in press

Y. Hu; Z. Zhu; J. Nielsen; V. Siewers (2018) Transporter engineering for improved fatty alcohol secretion in yeast. Meg. Eng. 45:51-58

D. Bergenholm; M. Gossing; Y. Wei; V. Siewers; J. Nielsen (2018) Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids. Biotechnol. Bioeng., in press

A. Mardinoglu; H. Wu; E. Bjornson; C. Zhang; A. Hakkarainen; S.M. Räsänen; S. Lee; R.M. Mancina; M. Bergentall; K.H. Pietiläinen; S. Söderlund; N. Matikainen; M. Ståhlman; P.-O. Bergh; M. Adiels; B.D. Piening; M. Graner; N. Lundbom; K.J. Williams; S. Romeo; J. Nielsen; M. Snyder; M. Uhlen; G. Bergström; R. Perkins; H.-U. Marschall; F. Bäckhed; M.-R. Taskinen; J. Boren (2018) An integrated understanding of the rapid metabolic benefits of a carbohydrate restricted diet on hepatic steatosis in humans. Cell Metab., in press

Y. Zhou; Y. Hu; Z. Zhu; V. Siewers; J. Nielsen (2018) Engineering of 1-alkene biosynthesis and secretion by dynamic regulation in yeast. ACS Syn. Biol., in press

R. Ferreira; P.G. Teixeira; V. Siewers; J. Nielsen (2018) Redirection of lipid flux towards phospholipids in yeast increases fatty acid turnover and secretion. Proc. Nat. Acad. Sci. USA, in press

P. Jenjaroenpun; T. Wongsurawat; R. Pereira; P. Patumcharoenpol; D.W. Ussery; J. Nielsen; I. Nookaew (2018) Complete genomic and transcriptional landscape analysis using third generation sequencing: A case study of Saccharomyces cerevisiae CEN.PK113-7D. Nuc. Acid Res., in press

A. Azimi; S. Caramuta; R. Jafari; B.S. Ludlow; J. Boström; J. Robinson; F. Edfors; R. Tuominen; J. Nielsen; J. Hansson; S.E. Brage; M. Altun; J. Lehtiö; M. Uhlen; G. Maddalo (2018) Targeting CDK2 overcomes melanoma reistance against BRAF and Hsp90 inhibitors. Mol. Systems Biol., in press

Y. Wei; D. Bergenholm; M. Gossing; V. Siewers; J. Nielsen (2018) Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production. Microb. Cell Fac., in press


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

J. Bao; M. Huang; D. Petranovic; J. Nielsen (2017) Moderate expression of SEC16 increases protein secretion by Saccharomyces cerevisiae. Appl. Environ. Microbiol., in press

E.J. Kerkhoven; Y.-M. Kim; S. Wei; C.D. Nicora; T.L. Filllmore; S.O. Purvine; B.-J. Webb-Robertson; R.D. Smith; S.E. Baker; T.O. Metz; J. Nielsen (2017) Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica. mBio 6:e00857-17

P. Sen; A. Mardinoglu; J. Nielsen (2017) Selection of complementary foods based on optimal nutrition values. Sci. Rep. 7:5413

A. Rodriguez; T. Strucko; S.G. Stahlhut; M. Kristensen; D.K. Svenssen; J. Forster; J. Nielsen; I. Borodina (2017) Metabolic engineering of yeast for fermentative production of flavonoids. Biores. Technol. 245:1645-1654

A. Feizi; F. Gatto; M. Uhlen; J. Nielsen (2017) Human protein secretory pathway genes are expressed in a tissue-specific pattern to match secretion demand. Systems Biol. Appl. 3:22

B.J. Sanchez; C. Zhang; A- Nilsson; P.-J. Lahtvee; E. Kerkhoven; J. Nielsen (2017) Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. Mol. Systems Biol. 13:935

K. Thorell; J. Bengtsson-Palme; O. Liu; R.V. Gonzales; I. Nookaew; L. Rabeneck; L. Paszat; D. Graham; J. Nielsen; S, Lundin; Å. Sjöling (2017) In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastic infection and early stages of carcinogenesis. Infect. Immun. 85:e00031-17

S. Lee; C. Zhang; Z. Liu; M. Klevstig; B. Mukhopadhyay; M. Bergentall; R. Cinar; M. Ståhlman; N. Sikanic; J.K. Park; S. Deshmukh; A.M. Pour; T. Kuijpers; M. Grøtli; S.J. Elsässer; B.D. Piening; M. Snyder; J. Nielsen; F. Bäckhed; G. Kunos; M. Uhlen; J. Boren; A. Mardinoglu (2017) Network analysis identify liver-specific targets for treating liver diseases. Mol. Sys. Biol. 13:938

M. Huang; J. Bao; B.M. Hallström; D. Petranovic; J. Nielsen (2017) Efficient protein production by yeast requires global tuning of metabolism. Nature Com. 8:1131

G. Liu; Y. Chen; N. Færgeman; J. Nielsen (2017) Elimination of the last reactions in ergosterol biosynthesis alters the reistance of Saccharomyces cerevisiae to multiple stress. FEMS Yeast Res. 17:fox063

R. Ferreira; F. Gatto; J. Nielsen (2017) Exploiting off-targeting in guide-RNAs for CRISPR systems for editing of multiple genes. FEBS Let. 591:3288-3295

Z. Zhu; Y.J. Zhou; M.-K. Kang; A. Krivoruchko; N.A. Buijs; J. Nielsen (2017) Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast. Met. Eng. 44:81-88

S. Grijseels; J.C. Nielsen; J. Nielsen; T.O. Larsen; J.C. Frisvad; K.F. Nielsen; R. Frandsen; M. Workman (2017) Physiological characterization of secondary metabolite producing Penicillium cell factories. Fungal Biol. Biotechnol. 4:8

S. Lee; C. Zhang; A. Muhammad; L. Zhengtao; R. Benfeitas; G. Bidkhor; S. Deshmukh; M.A. Shobky; A. Lovric; J. Boren; J. Nielsen; M. Uhlen; A Mardinoglu (2017) TCSBN: a database of tissue and cancer specific biological networks. Nucl. Acid. Res., in press

A. Rodriguez; Y. Chen; S. Khoomrung; E. Özdemir; I. Borodina; J. Nielsen (2017) Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains. Met. Eng. 44:265-272

Reviews in international journals with peer review


R. Ferreira; F. David; J. Nielsen (2018) Advancing biotechnology with CRISPR/Cas9: Recent applications and patent landscape. J. Ind. Microbiol. Biotechnol., in press


A. Nilsson; J. Nielsen (2017) Genome-scale metabolic modeling of cancer. Met. Eng. 43:103-112

L.J. Sweetlove; J. Nielsen; A.R. Fernie (2017) Engineering central metabolism – a grand challenge for plant biologists. Plant J. 90:749-763

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. 86:245-275

J.L. Robinson; J. Nielsen (2017) Anticancer drug discovery through genome-scale metabolic modeling. Curr. Opion. Syst. Biol. 4:1-8

J. Nielsen; J. Archer; V. Bajic; T. Gojobori; I. Mijakovic (2017) Building a biobased industry in the Middle East through harnessing the potential of the Red See biodiversity. Appl. Microbiol. Biotechnol., in press

D. Cook; J. Nielsen (2017) Genome-scale metabolic models applied to human health and disease. WIRE Systems Biol. Med. 9:e1393

X. Chen; C. Gao; L. Guo; G. Hu; Q. Luo; J. Liu; J. Nielsen; J. Chen; L. Liu (2017) DCEO Biotechnology: Tools to Design, Construct, Evaluate and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem. Rev., in press

A. Mardinoglu; J. Boren; U. Smith; M. Uhlen; J. Nielsen (2017) The employment of systems biology in gastroenterology and hepatology. Nature Rev. Gastro. Hep., in press

R. Benfeitas; M. Uhlen; J. Nielsen; A. Mardinoglu (2017) New challenges to study heterogeneity in cancer redox metabolism. Fron. Cell Develop. Biol. 5:65

J. Bosley; C. Boren; S. Lee; M. Grøtli; J. Nielsen; M. Uhlen; J. Boren; A. Mardinoglu (2017) Improving economics of NASH/NAFLD treatment through the use of systems biology. Drug Discov. Today 22:1532-1538

Z. Gong; J. Nielsen; Y. Zhou (2017) Engineering robustness of microbial cell factories. Biotechnol. J. 12:1700014

K. Campbell; J. Xia; J. Nielsen (2017) The impact of systems biology on bioprocessing. Trends Biotechnol. 35:1156-1168

Y. Zhang; J. Nielsen; Z. Liu (2017) Engineering yeast metabolism for production of terpenoids for use a perfume ingredients, pharmaceuticals, and biofuels. FEMS Yeast Res., in press


Commentaries and Short Papers


J. Nielsen (2017) Built on stable catalysts. Nature Microbiol. 2:17085

A. Nilsson; J. Nielsen; B. Palsson (2017) Metabolic models of protein allocation call for the Kinetome. Cell Systems 5:538-541


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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