Jens Nielsen

Jens Nielsen has an MSc degree in Chemical Engineering and a PhD degree (1989) in Biochemical Engineering from the Danish Technical University (DTU), and after that established his independent research group and was appointed full Professor there in 1998. He was Fulbright visiting professor at MIT in 1995-1996. At DTU he founded and directed Center for Microbial Biotechnology. In 2008 he was recruited as Professor and Director to Chalmers University of Technology, Sweden, where he is directing a research group of more than 50 people. At Chalmers he established the Area of Advance Life Science Engineering, a cross departmental strategic research initiative and was founding Head of the Department of Biology and Biological Engineering, which now encompass more than 200 people. Jens Nielsen is also a co-founder of the Novo Nordisk Foundation Center for Biosustainability that now have more than 300 people affiliated, for which he served as Chief Science Officer in the period 2013-2018 In 2019 Jens Nielsen was appointed as CEO of the BioInnovation Institute in Denmark, which is a new institute that will foster translational research and support new spin-out companies in life sciences. Jens Nielsen has supervised more than 100 PhD students and more than 75 post doctoral researchers. He has published so far more than 700 papers that have been cited more than 65,000 times (current H-factor 118), and co-authored more than 40 books. He was identified as a highly cited researcher in 2015-2018. He is inventor of more than 50 patents and he has founded several biotech companies. He has received numerous Danish and international awards including the Nature Mentor Award, the ENI Award, the Eric and Sheila Samson Prime Minister Prize, the Novozymes Prize, and the Gold Medal from the Royal Swedish Academy of Engineering Sciences. He is member of several academies, including the National Academy of Engineering and National Academy of Science in USA, the Royal Swedish Academy of Science, the Royal Danish Academy of Science and Letters, the Royal Swedish Academy of Engineering Sciences and the American Academy of Microbiology. He is a founding president of the International Metabolic Engineering Society

Awards

• 1989 Direktør Gorm Petersen’s Mindelegat, Denmark
• 1994 Ulrik Brinch og Hustru Marie Brinch’s legat, Denmark
• 1996 STVFs Jubilæumspris, Statens Teknisk Videnskabelige Forskningsråd, Denmark
• 2001 Aksel Tovborg Jensens Legat, Bjerrum-Brøndsted-Lang Lecture, Carlsberg Foundation, Denmark
• 2002 Villum Kann Rasmussen’s Årslegat, Villum Kann Rasmussen Fonden, Denmark
• 2004 Merck Award for Metabolic Engineering, USA
• 2011 Amgen Biochemical Engineering Award, USA
• 2012 Charles D. Scott Award 2012, Symposium on Biotechnology for Fuels and Chemicals, USA
• 2012 Nature Award for Mentoring, Nature Publishing Group, UK
• 2013 Norblad-Exstrand Medalj, The Swedish Chemical Society, Sweden
• 2016 Gaden Award, American Chemical Society, USA
• 2016 Novozymes Prize, Novo Nordisk Foundation, Denmark
• 2017 ENI Award, ENI, Italy
• 2017 Gold Medal, Royal Swedish Academy of Engineering Sciences, Sweden
• 2017 Eric and Sheila Samson Prime Ministers Prize for Innovation in Alternative Fuels for
• Transportation, Fuels and Smart Mobility Initiative, Israel
• 2019 Emil Chr. Hansen’s Gold Medal for Microbiological Research, Denmark
• 2019 Arvid Carlsson Award, Sahlgrenska Science Park, Sweden
• 2019 James E. Bailey Award, American Institute for Chemical Engineering, USA
• 2020 Gregory Stephanopoulos Award for Metabolic Engineering, IMES, USA

Other Honors

• 1995 Fulbright Fellow, USA
• 2002 Sunner Memorial Lecture, Lund University, Sweden
• 2004 Hough Memorial Lecture, Birmingham University, UK
• 2010 Appointed as Wallenberg Scholar, Sweden
• 2014 William Chalmers Lecture, Chalmers University of Technology, Sweden
• 2014 Honorary Professor, Beijing University of Chemical Technology, Beijing, China
• 2015 Zhang Dayu Lectureship, Dalian Institute for Chemical Physics, Chinese Academy of Science, China
• 2015 Honorary Professor, Dalian Institute for Chemical Physics, Chinese Academy of Science, China
• 2015, 2016 Highly Cited Researcher, Thomson Reuter
• 2017 Honorary Professor, East China University of Science and Technology, Shanghai, China
• 2017 Adjunct Professor, Jiangnan University, Wuxi, China
• 2017, 2018 Highly Cited Researcher, Clarivate
• 2019 Honorary Professor, Jiangnan University, Wuxi, China
• 2019 Ridder af Dannebrog (Knight of the order of Dannebrog), Queen Margrethe II, Denmark
• 2019 Honorary Professor, Tianjin University, Tianjin, China
• 2019 Peiyang Lectureship, Tianjin University, Tianjin, China
• 2019 Honorary Professor, Nankai University, Tianjin, China
• 2019 Highly Cited Researcher, Web-of-Science

Key Publications

Metabolic Engineering

1. S. Ostergaard; L. Olsson; M. Johnston; J. Nielsen (2000) Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nature Biotechnol. 18:1283-1286
2. K.-K. Hong; W. Vongsangnak; G.N. Vemuri; J. Nielsen (2011) Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc. Nat. Acad. Sci. USA 108:12179-12184
3. L. Caspeta; J. Nielsen (2013) Economic and environmental impacts of microbial biodiesel. Nature Biotechnol. 31:789- 793
4. 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
5. M. Huang; Y. Bai; S.L. Sjostrom; B.M. Hallström; Z. Liu; D. Petranovic; M. Uhlen; H.N. Joensson; H. AnderssonSvahn; 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
6. 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
7. 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
8. Z. Zhu; Y.J. Zhou; A. Krivoruchko; M. Grininger; Z.K. Zhao; J. Nielsen (2017) Expanding the product portfolio of fungal type I fatty acid synthases. Nature Chem. Biol. 13:360-362
9. 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
10. 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 115:1262-1267
11. Z. Dai; M. Huang; Y. Chen; V. Siewers; J. Nielsen (2018) Global rewiring of cellular metabolism renders Saccharomyces cerevisiae Crabtree-negative. Nature Com. 9:3059
12. T. Yu; Y. Zhou; M. Huang; Q. Liu; R. Pereira; F. David; J. Nielsen (2018) Reprogramming yeast metabolism from alcoholic fermentation to lipogenesis. Cell 174:1-10
13. M. Huang; G. Wang; J. Qin; D. Petranovic; J. Nielsen (2018) Engineering the protein secretory pathway of Saccharomyces cerevisiae enables improved protein production. Proc. Nat. Acad. Sci. USA 115:E11025-E11032
14. Z. Zhu; Y. Hu; P.G. Teixeira; R. Pereira; Y. Chen; V. Siewers; J. Nielsen (2019) Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids. Nature Cat. 3:64-74
15. Y. Liu; Q. Liu; A. Krivoruchko; S. Khoomrung; J. Nielsen (2019) Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production. Nature Chem. Biol. 16:197-205

Systems Biology

1. J. Förster; I. Famili; P. Fu; B. Ø. Palsson; J. Nielsen (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13:244-253
2. I. Borodina; P. Krabben; J. Nielsen (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res.15:820-829
3. K. R. Patil, J. Nielsen (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Nat. Acad. Sci. 102:2685-2689¨
4. M. R. Andersen; M. L. Nielsen; J. Nielsen (2008) Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol. Systems Biol. 4:178
5. M. R. Andersen; W. Vongsangnak; G. Panagiotou; M. P. Salazar; L. Lehmann; J. Nielsen (2008) A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species. Proc. Nat. Acad. Sci. 105:4387-4392
6. R. Agren; L. Liu; S. Shoaie; W. Vongsangnak; I. Nookaew; J. Nielsen (2013) The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comp. Biol. 9:e1002980
7. L. Caspeta; Y. Chen; P. Ghiaci; A. Feizi; S. Buskov; B.M. Hallström; D. Petranovic; J. Nielsen (2014) Altered sterol composition renders yeast thermotolerant. Science 346:75-78
8. 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
9. 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 4:495-504
10. 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
11. Y. Chen; J. Nielsen (2019) Energy metabolism controls phenotypes by protein efficiency and allocation. Proc. Nat. Acad. Sci. USA 116:17592-17597
12. H. Lu; F. Li; B.J. Sanchez; Z. Zhu; G. Li; I. Domenzain; S. Marcisauskas; P.M. Anton; D. Lappa; C. Lieven; M.E. Beber; N. Sonnenschein; E.J. Kerkhoven; J. Nielsen (2019) A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Com. 10:3586 Page 3 of 52

Human Metabolism

1. F. H. Karlsson; F. Fåk; I. Nookaew; V. Tremaroli; B. Fagerberg; D. Petranovic; F. Bäckhed*; J. Nielsen* (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature Comm. 3:1245
2. F. Karlsson; V. Tremaroli; I. Nookaew; G. Bergström; C.J. Behre; B. Fagerberg; J. Nielsen*; F. Bäckhed* (2013) Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498:99-103
3. A. Mardinoglu; R. Agren; C. Kampf; A. Asplund; I. Nookaew; P. Jacobsen; A.J. Walley; P. Froguel; L.M. Carlsson; M. Uhlen; J. Nielsen (2013) Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol. Systems Biol. 9:649
4. F. Gatto; I. Nookaew; J. Nielsen (2014) Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma. Proc. Nat. Acad. Sci. 111:E866-E875
5. A. Mardinoglu; R. Agren; K. Kampf; A. Asplund; M. Uhlen; J. Nielsen (2014) Genome-scale metabolic modeling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nature Comm. 5:3083
6. R. Agren; A. Mardinoglu; C. Kampf; A. Asplund; M. Uhlen; J. Nielsen (2014) Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol. Systems Biol. 10:721
7. 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 347:1260419,1-9S
8. 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
9. 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
10. 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
11. P. Babaei; S. Shoaei; B. Ji; J. Nielsen (2018) Challenges in modeling the human gut microbiome. Nature Biotechnol. 16:682-686
12. J.L. Robinson; A. Feizi; M. Uhlen; J. Nielsen (2019) A systematic investigation of the malignant functions and diagnostic potential of the cancer secretome. Cell Rep. 10:2622-2635 Reviews
13. S. Ostergaard; L. Olsson; J. Nielsen (2000) Metabolic engineering of Saccharomyces cerevisiae. Microb. Mol. Biol. Rev. 64:34-50
14. J. Nielsen (2001) Metabolic engineering. Appl. Microbiol. Biotechnol. 55:263-283
15. K.-K. Hong; J. Nielsen (2012) Metabolic engineering of Saccharomyces cerevisiae: A key cell factory platform for future biorefineries. Cell. Mol. Life Sci. 16:2671-2690
16. M. Uhlen; B.M. Hallström; C. Lindskog; A. Mardinoglu; F. Ponten; J. Nielsen (2016) Transcriptomics resources of human tissues and organs. Mol. Sys. Biol. 12:862
17. J. Nielsen; J. Keasling (2016) Engineering Cellular Metabolism. Cell 164:1185-1197
18. J. Nielsen (2017) Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine. Cell Met. 25:572-579
19. J. Nielsen (2017) Systems Biology of Metabolism. Ann. Rev. Biochem. 86:245-275
20. K. Campbell; J. Xia; J. Nielsen (2017) The impact of systems biology on bioprocessing. Trends Biotechnol. 35:1156- 1168
21. A. Mardinoglu; J. Boren; U. Smith; M. Uhlen; J. Nielsen (2018) The employment of systems biology in gastroenterology and hepatology. Nature Rev. Gastro. Hep., in press
22. Y. Zhou; E. Kerkhoven; J. Nielsen (2018) Barriers and opportunities in bio-based production of hydrocarbons. Nature Energy 3:925-935
23. M. Kumar; B. Ji; K. Zengler; J. Nielsen (2019) Modeling approaches for studying the gut microbiota. Nature Microbiol. 4:1253-1267 Commentaries and Perspectives
24. J. Nielsen (2007) Principles of optimal metabolic network operation. Mol. Sys. Biol. 3:126
25. J. Nielsen (2011) Transcriptional control of metabolic fluxes. Mol. Systems Biol. 7:478
26. J. Nielsen (2011) Chimeric Synthetic Pathways. Nature Chem. Biol. 7:195-196
27. J. Nielsen; J. Keasling (2011) Synergies between synthetic biology and metabolic engineering. Nature Biotechnol. 29:693-695
28. J. Nielsen; M. Fussenegger; J. Keasling; S.Y. Lee; J.C. Liao; K. Prather; B. Palsson (2014) Engineering synergy in biotechnology. Nature Chem. Biol. 10:319-322
29. J. Nielsen (2014) Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast. mBio 5:e02153-14
30. 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
31. J. Nielsen (2015) Yeast cell factories on the horizon. Science 349:1050-1051
32. J. Nielsen (2017) Built on stable catalysts. Nature Microbiol. 2:17085 Page 4 of 52
33. J. Nielsen (2019) Designer Microbes Serving Society. Cell Met. 29:50
34. J. Nielsen (2019) Cell factory engineering for improved production of natural products. Nat. Prod. Rep. 36;1233
35. J. Nielsen (2019) Antibiotic lethality is impacted by nutrient availabilities: New insights from machine learning. Cell 177:1373-1374
36. J. Nielsen (2019) A stress-coping strategy for yeast cells. Nature 572:184-185