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Jens Nielsen

Jens Nielsen
Professor, Part-time Principal Investigator
Chair, Soft Matter in Life Science and Technology, Division, BAIC-SM
Dr.techn, 1995,  Danmarks Tekniske Universitet, Denmark 
Ph.D., Biotechnology, 1989,  Danmarks Tekniske Universitet, Denmark 
M.S., Chemical Engineering, 1986, Danmarks Tekniske Universitet, Denmark

Specializations: Systems Biology and Synthetic Biology, Bioenergy and Biofuels, Metabolic Engineering

Research focuses:
Genome-scale modeling of human metabolism
  ●  Metabolic modeling of microbial ecosystems
  ●  Systems Biology of yeast
  ●  Biofuel and biochemical production by metabolic engineering of yeast
Selected recent Publications:
  ●  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
  ●  J. Nielsen (2015) Yeast cell factories on the horizon. Science 349:1050-1051
  ●  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
  ●  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
  ●  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
  ●  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
  ●  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
  ●  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
  ●  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
  ●  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
  ●  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. 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
  ●  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
  ●  Z. Dai; J. Nielsen (2015) Advancing metabolic engineering through systems biology of industrial microorganisms. Curr. Op. Biotechnol. 36:8-15
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
  ●  A. Nilsson; J. Nielsen (2016) Metabolic trade-offs in yeast are caused by F1F0-ATP synthase. Sci. Rep. 6:22264
  ●  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
  ●  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; I. Nookaew; H. Nilsson; M. Maruzzo; A. Roma; M. E. Johansson; U. Steiner; S. Lundstam; N. Volpi; U. Basso; J. Nielsen (2016) Measurements of glycosaminoglycans in plasma and urine for diagnosis of clear cell renal cell carcinoma. Cell Rep. 15:1-15
  ●  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
  ●  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
  ●  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
  ●  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., in press



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