Jens Nielsen, R., PhD, dr. techn.

Jens Nielsen, R., PhD, dr. techn.

Professor, Quantitative Systems Biology
Nielsenj [at] chalmers.se
dk Denmark


Education and degrees

1986 M.Sc. in Chemical Engineering, Dept. of Biotechnology, DTU, Denmark
1989 Ph.D. in Biochemical Engineering, DTU, Denmark
1995 dr.techn., DTU, Denmark


Positions

1986 Research Assistant, School of Engineering, University of Western Ontario, Canada
1987-1989 PhD student, Department of Biotechnology, DTU, Denmark
1989 Post doc, Institut für Technische Chemie, Universität Hannover, Germany
1990-1995 Associate Research Professor, Department of Biotechnology, DTU, Denmark
1995-1996 Visiting Professor, Department of Chemical Engineering, MIT, USA
1996-1998 Associate Professor, Department of Biotechnology, DTU, Denmark
1998-2008 Professor, BioCentrum, DTU, Denmark
2005-2011 Adjunct Professor, Department of Biotechnology, NTNU, Norway
2008- Professor, Department of Chemical and Biological Engineering, Chalmers
2011-2019 Professor, Novo Nordisk Foundation Center for Biosustainability, DTU, Denmark
2012-2017 Adjunct Professor, Department of Biotechnology, Royal Institute of Technology (KTH), Sweden
2013-2019 Chief Science Officer, Novo Nordisk Foundation Center for Biosustainability, DTU, Denmark
2015 Founding Head of Department, Department of Biology and Biological Engineering, Chalmers, Sweden (served 9 months as Head of Department and structured a department of 150 people)
2016- Adjunct Professor, Beijing University of Chemical Technology (BUCT), China
2019- CEO, BioInnovation Institute, Copenhagen, Denmark


Academic Appointments and Merits

1994-1999 Founding Chairman, Danish Biotechnological Forum, Denmark
1995-2000 Deputy Director, Center for Process Biotechnology, DTU, Denmark
1995-1998 Co-ordinator, Physiological Engineering, Nordic Industrial Fund
1998-2002 Co-ordinator, NordPhys, Nordic Industrial Fund
2001-2003 Director, Center for Process Biotechnology, DTU, Denmark
2001-2003 Board Member, Center for BioProcess Technology, KTH, Sweden
2002 Evaluation Panel, Dutch genomics initiative (50 million EUR)
2002-2007 SAB Member, Kluywer Center for Genomics of Industrial Fermentations, TU Delft, The Netherlands
2002-2008 SAB Member, Max-Planck Institute for Dynamic of Complex Technical Systems, Germany
2003 Guest Professor, Tianjin University, China
2004-2007 Founding Director, Center for Microbial Biotechnology, DTU, Denmark
2004-2007 Member of Integrative and Systems Biology Panel, BBSRC, UK (50 million GPD)
2004- Advisory Board, Society for Biological Engineering, USA
2005 Chairman of Evaluation Committee, HepatoSys, Germany
2005-2008 Co-ordinator, Yeast Systems Biology Network, EU Framework VI
2006-2007 Founder and Board Member, Danish Biotechnological Society, Denmark
2008-2011 Member of Review Panel of SystemsX.ch, Switzerland (100 million CHF)
2008-2011 Co-ordinator, Systems Biology as a Driver for Industrial Biotechnology, EU Framework VII
2009- SAB Member, Netherlands Institute for Systems Biology, The Netherlands
2010-2016 Director Area of Advance Life Science, Chalmers University of Technology, Sweden
2010- Member of World Council for Industrial Biotechnology, World Economic Forum
2011-2012 Member of Industrial Biotechnology and Bioenergy Strategy Advisory Panel, BBSRC, UK
2011 Presidential appointed evaluator of Humbolt University, Germany
2011 Member of DoE Evaluation Panel for Joint Bioenergy Institute, USA
2011- Swedish Delegate in International Commission of Yeast (ICY)
2011- National Reference Committee, Science for Life Laboratory, Stockholm, Sweden
2012-2014 Scientific Advisory Board Universeum Science Museum, Gothenburg, Sweden
2012- Founding president of International Metabolic Engineering Society, USA
2012 4th Most cited European researcher in the field of Mycology
2012-2013 Evaluation panel of Academy of Finland, Finland
2012-2014 International Advisory Board, Thailands National Center for Genetic Engineering and Biotechnology, Bangkok, Thailand
2014 Scientific Advisory Board, Energy Biosciences Institute, UC Berkeley, Berkeley, USA
2015- Advisory Board, Gothia Forum, Sahlgrenska University Hospital, Gothenburg, Sweden
2016- Director of Life Science, Beijing Advanced Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, China
2016- Advisory Committee, Joint Bioenergy Institute, Lawrence Berkeley Laboratory, USA
2016- Committee chairma for Novozymes Award for Excellence in Biochemical and Chemical Engineering, Novozymes, Denmark
2016- Novozymes Prize award committee, Novo Nordisk Foundation, Denmark (chairman since 2018)
2018- F1000 Faculty, F1000Prime


Awards

1989 Direktør Gorm Petersen’s Mindelegat, Denmark
1994 Ulrik Brinch og Hustru Marie Brinch’s legat, Denmark
1996 STVFs Jubilæumspris, Denmark
2001 Aksel Tovborg Jensens Legat/Bjerrum-Brøndsted-Lang Lecture, Denmark
2002 Villum Kann Rasmussen’s Årslegat, 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


Academies

1997 Member of the Academy of Technical Sciences, Denmark
2010 Foreign Associate of the National Academy of Engineering, USA
2010 Member of the Royal Danish Academy of Science and Letters, Denmark
2010 Member of the Royal Swedish Academy of Engineering Sciences, Sweden
2011 College of Fellows of American Institute for Medical and Biological Engineering, USA
2012 Member of Royal Society of Arts and Sciences in Gothenburg, Sweden
2012 Fellow of the American Academy of Microbiology, USA
2014 Member of the Royal Swedish Academy of Sciences, Sweden
2019 National Academy of Sciences, USA
2019 Royal Physiographic Society of Lund, Sweden
2019 Chinese Academy of Engineering, China


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, 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


Memberships in Societies

1986- The Danish Society for Engineers, Denmark
1996- Member of American Association for the Advancement of Science, USA
2001- Society for Industrial Microbiology, USA
2004- American Chemical Society, USA
2004- Society for Biological Engineering, USA
2006- American Society for Microbiology, USA
2012- International Metabolic Engineering Society, USA


Publications, Patents & Presentations

Google Scholar: H-factor of 124; >74,000 citations and >38,000 citations since 2015
Web of Science Highly Cited Researcher in 2015-2019

609 Original Papers in Peer Reviewed Journals
120 Review Papers in Peer Reviewed Journals
31 Commentaries in Peer Reviewed Journals
46 Book Contributions
3 Text books: Bioreaction Engineering (1994,2003) (English & Chineese), Metabolic Engineering (1998) (English, Chineese & Japaneese), Metabolome Analysis (2007)
1 Monograph
4 Edited books
38 Issue patents (12 patent families)
36 Patent applications
221 Invited oral presentations at international conferences
134 Invited seminars at universities and companies


Key Grants

1993-1996 Nordic Project on Physiological Engineering, Nordic Industrial Fund (>20 million DKK)
1995-2002 4 Projects, EU Framework VI (about 8 million DKK)
1996-1999 Center for Process Biotechnology, Danish Technical Research Council (20 million DKK)
1997-2000 Nordic network NordPhys, Nordic Industrial Fund (>4 million DKK)
1999-2003 DABIC, Danish Technical Research Council (18MDKK)
2000-2007 6 Projects, EU Framework V (about 15 million DKK)
2003-2007 Heterologous production of polyketides, Danish Technical Research Council (2.8 million DKK)
2004-2008 Center for Microbial Biotechnology, Danish Technical Research Council (36 million DKK)
2005-2009 3 Projects, EU Framework VI (about 8.5 million DKK)
2005-2008 Genome sequencing of A. balhamycina, Lundbech Foundation (1.2 million DKK)
2005-2008 Yeast Systems Biology Network, EU Framework VI (1.3 million €)
2006-2008 Yeast in No Gravity, European Space Agency (2.7 million DKK)
2007-2009 Systems Biology: From model organisms to application, NORDFORSK (0.8 million €)
2008-2011 Systems Biology as a Driver for Industrial Biotechnology, EU Framework VII (1 million €)
2008-2013 UNICELLSYS, EU Framework VII (5.4 million SEK)
2009-2011 Regulation of lipid metabolism in eukaryotic cells, Vetenskapsrådet (3 million SEK)
2010-2014 Industrial Systems Biology, European Research Council (2.5 million €)
2010-2013 Systems Biology of Metabolism, NORDFORSK (0.6 million NOK)
2011-2015 Wallenberg Scholar, Knut and Alice Wallenberg Foundation (15 million SEK)
2011-2020 NNF Center for Biosustainability, Novo Nordisk Foundation (700 MDKK)
2012-2015 Engineering of Acetyl-CoA Metabolism in Yeast, Vetenskapsrådet (6.4 MSEK)
2012-2014 Platform for studying metagenomes and metabolic diseases, Torsten Söderbergs Stiftelse (5 MSEK)
2012-2017 BioVacSafe, Innovative Medicines Initiative, EU (5.5 MSEK)
2012-2016 Excellence Center for Metabolic Engineering, FORMAS (25 MSEK)
2012-2017 MetaCardis, EU Framework VII (7.5 MSEK)
2012-2017 Advanced Biofuel Production by Oleagenous Yeast, Department of Energy, USA (2 MUSD)
2013-2016 Biobased production of diesel and jetfuel, Vetenskapsrådet (17 MSEK)
2014-2016 Mathematical modelling of tissue metabolism in response to malnutrition, Bill & Melinda Gates Foundation (200 KUSD)
2014-2017 YeastCell, ITN Marie Curie, EU Framework VII( 3 MSEK)
2014-2017 QuantFung, ITN Marie Curie, EU Framework VII (5 MSEK)
2015-2018 3 Projects, ERA-SysApp and ERA-Pathogen, EU Framework VII (9 MSEK)
2015-2019 Biotechnological Production of High-Value Added Ingredients, Stiftelsen for Strategisk Forskning (32 MSEK)
2016-2019 Genome-scale transcriptional regulatiuon in yeast, Vetenskapsrådet (4.4 MSEK)
2016-2021 Gut-microbiome effect on CVD, Novo Nordisk Foundation (9 MDKK)
2016-2019 Wallenberg Center for Protein Research, Knut and Alice Wallenberg Foundation (20 MSEK)
2016-2020 CHASSY, Horizon2020 (7 MSEK)
2016-2020 DD-DeCaF, Horizon2020 (8.5 MSEK)
2016-2020 PacMEN, ITN Marie Curie, Horizon2020 (6 MSEK)
2017-2020 Biobased production of diesel and jetfuels, Energimyndigheten (4 MSEK)
2017-2023 Systems biology of the eukaryal protein secretion pathway, Stiftelsen for Strategisk Forskning (34 MSEK)
2018-2019 Proof-of-Concept of cancer biomarkers, Knut and Alice Wallenberg Foundation (5 MSEK)
2018-2023 CellNova, Vinnova (9 MSEK) (co-PI together)


Editorial Activities

1999 Chemical Engineering Science, Guest editor of special volume
1999- Metabolic Engineering, Editorial Board (1999-2002), Associate Editor (2003-)
1999- Applied Microbiology and Biotechnology, Editorial Board
2000- Bioprocess and Biosystems Engineering, Associate Editor (2000-2007), Editorial Board(2007-)
2001- Biotechnology and Bioengineering, Associate Editor
2001- FEMS Yeast Research, Editorial Board (2001-2007), Associate Editor (2007-2010), Editor-in-Chief (2011-)
2004- Journal of Industrial Microbiology and Biotechnology, Editorial Board (2004-2010), Senior Editor (2010-)
2004- Advances in Biochemical Engineering/Biotechnology, Editorial Board
2008- Microbial Cell Factories, Advisory Board
2009- Microbial Biotechnology, Editorial Board
2010- Biotechnology Journal, Editorial Board
2012- ACS Synthetic Biology, Editorial Board
2013- Wiley-Blackwell Biotechnology Book series (3. Edition), Editor-in-Chief
2015- Cell Systems, Editorial Board
2015- Scientific Reports, Editorial Board
2016- Current Opinion of Systems Biology, Editorial Board
2016- Applied and Environmental Microbiology, Editorial Board
2017- Cell Stress, Editorial Board
2017- Biotechnology and Bioprocess Engineering, Editorial Board
2019- Frontiers in Chemical Science and Engineering, Editorial Board


Teaching Experience

Jens Nielsen has organized more than 15 advanced courses on metabolic engineering and systems biology in Denmark, Sweden, Thailand, China and Chile, and he has been teaching in several different courses at all levels in the areas of biotechnology, fermentation technology, bioreaction engineering, metabolic engineering and systems biology. Currently examiner of the MSc courses KMG060 Systems Biology and KKR063 Metabolic Engineering at Chalmers.
Prof Nielsen has extensive experience with developing, organizing and running new courses and he has been actively involved in the design of new teaching programs at both the BSc and MSc level in the field of biotechnology and systems biology.


Mentoring

Main supervisor of graduated PhD students 85
Main supervisor of current PhD students 17
Examiner of current PhD students 7
Co-supervisor of graduated PhD students (including visiting PhD students and as Examiner) 49 Former affiliated post docs 96
Current affiliated post docs and senior researchers 13


Business Experience

1992- Collaboration with industry; collaborated with more than 15 different companies in Austria, Denmark, France, Germany, The Netherlands, Sweden, Switzerland and USA. Cumulative funding from industry to my research group exceeds 30 MSEK.
1996- Consultant for several internationally leading biotech and pharmaceutical companies
1997-2001 N&N Biotechn ApS, Denmark, Founder and CEO (acquired by Fluxome A/S)
2001-2004 Symbion Venture Capital, Denmark, Member of Scientific Advisory Board
2002-2012 Fluxome Sciences A/S, Denmark (acquired by Evolva SA in 2012); Founder (raised more than 25 MEUR in capital), CEO (2002-2004), CSO (2002-2008), Member of BoD (2008-2012), Chairman of SAB (2008-2012)
2002-2007 Gothia Yeast Solutions, Sweden, Member of SAB
2006-2011 MycoTeQ A/S, Denmark, Founder and Chairman of BOD (has raised about 1 million € in capital, one novel antibiotics identified)
2008-2010 GlycoFi, Inc., USA, Member of SAB
2008- Genomatica, Inc., USA, Member of SAB
2011- MetaboGen AB, Sweden, Founder and Member of BoD
2013- Evolva SA, Switzerland, Member of SAB
2014- Biopetrolia AB, Sweden, Founder and Chairman of BoD
2014- Novogy, Inc., USA, Member of SAB
2017- Elypta AB, Sweden. A cancer diagnostic company. Founder, Chairman of BoD (2017-2018) and member of BoD (2018-). Raised >13 MEUR in VC capital and soft funding.
2019- Chrysea Labs Inc., Ireland. A yeast synthetic biology company. Raised >9 MEUR in VC capital.


Organization of Conferences

1990- Member of organizing and scientific committee of more than 35 conferences
2000 ESBES3, Denmark, Chairman (~300 delegates)
2002 Analysis of Microbial Cells at the Single Cell Level, Denmark, Co-Chair (~100 delegates)
2002 Metabolic Engineering IV, Italy, Chairman (~250 delegates)
2004 European Conference on Fungal Genetics VI, Denmark, Co-Chair (~800 delegates)
2005 ECB12, Denmark, Chairman of Scientific Committee (~1200 delegates)
2008 ICSB2008, Sweden, Member of Organizing Committee (~2000 delegates)
2010 FEBS2010, Sweden, Member of Organizing Committee (~2000 delegates)
2010 Industrial Systems Biology 2010, Sweden, Chairman (~200 delegates)
2011 Key Symposium on Systems Medicine, Sweden, Chairman (~100 delegates)
2013 Copenhagen Bioscience Conference, Denmark, Co-Chairman (~150 delegates)
2015 Copenhagen Bioscience Conference, Denmark, Chairman (~150 delegates)
2017 Metabolic Engineering Summit, Beijing, China (~600 delegates)
2019 Copenhagen Bioscience Conference, Denmark, Chairman (~150 delegates)


Publications

Recent publications


Research papers in international journals with peer review


2020

N. Raethong; H. Wang; J. Nielsen; W. Vongsangnak (2020) Optimizing cultivation of Cordyceps militaris for fast growth and cordyceptin overproduction using rational design of synthetic media. Comp. Struc. Biotechnol. J. 18:1-8

J. Gutierrez; A. Feizi; S. Li; T. Kallehauge; G.M. Lee; B. Palsson; J. Nielsen; N. Lewis (2020) Genome-scale reconstruction of the mammalian secretory pathway predicts metabolic costs and limitations of protein secretion. Nature Com. 11:68

F. Gatto; R. Ferreira; J. Nielsen (2020) Pan-cancer analysis of the metabolic reaction network. Met. Eng. 57:51-62

Y. Liu; Q. Liu; A. Krivoruchko; S. Khoomrung; J. Nielsen (2020) Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production. Nature Chem. Biol. 16:197-205

S. Khoomrung; I. Nookaew; P. Sen; T. Olafsdottir; J. Persson; T. Moritz; P. Andersen; A. Harandi; J. Nielsen (2019) Metabolic profiling and compound-class identification reveal alterations in serum triglyceride levels in mice immunized with human vaccine adjuvant Alum. J. Prot. Res. 19:269-278

C. Lieven; M.E. Beber; B.G. Olivier; F.T. Bergmann; M. Ataman; P. Babaei; J.A. Bartell; L.M. Blank; S. Chauhan; K. Correia; C. Diener; A. Dräger; B.E. Ebert; J.N. Edirisinghe; J.P. Faria; A.Feist; G. Fengos; R.M.T. Fleming; B. García-Jiménez; V. Hatzimanikatis; W. van Helvoirt; C.S. Henry; H. Hermjakob; M.J. Herrgård; A. Kaafarani; H.U. Kim; Z. King; J.J. Koehorst; M. König; S. Klamt; E. Klipp; M. Lakshmanan; D.-Y. Lee; S.Y. Lee; S. Lee; N.E. Lewis; F. Liu; H. Ma; D. Machado; R. Mahadevan; P. Maia; A. Mardinoglu; G.L. Medlock; J.M. Monk; J. Nielsen; L.K. Nielsen; J. Nogales; I. Nookaew; O. Resendis-Antonio; B.O. Palsson; J.A. Papin; K.R. Patil; M. Poolman; N.D. Price; A. Richelle; I. Rocha; B.J. Sánchez; P.J. Schaap; R.S.M. Sheriff; S. Shoaie; N. Sonnenschein; B. Teusink; P. Vilaça; J.O. Vik; J.A.H. Wodke; J.C. Xavier; Q. Yuan; M. Zakhartsev; C. Zhang (2019) Memote for standardized genome-scale metabolic model testing. Nature Biotechnol. 38:272-276

Z. Zhu; Y. Hu; P.G. Teixeira; R. Pereira; Y. Chen; V. Siewers; J. Nielsen (2020) Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids. Nature Cat. 3:64-74

S. Lam; S. Doran; H. Yuksel; O. Altay; H. Turkez; J. Nielsen; J. Boren; M. Uhlen; A. Mardinoglu (2020) Addressing the heterogeneity in liver diseases using biological networks. Brief. Bioinform., in press

X. Li; B. Turanli; K. Juszczak; W. Kim; M. Arif; Y. Sato; S. Ogawa; H. Turkez; J. Nielsen; J. Boren; M. Uhlen; C. Zhang; A. Mardinoglu (2020) Heliyon 6:e03440

K. Campbell; J. Westholm; S. Kasvendik; F. Di Bartolomei; M. Mormino; J. Nielsen (2020) Building blocks are synthesized on demand during the yeast cell cycle. Proc. Nat. Acad. Sci. USA, in press

F. Di Bartolomeo; C. Malina; K. Campbell; M. Mormini; J. Fuchs; E. Vorontsov; C.M. Gustafsson; J. Nielsen (2020) Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. Proc. Nat. Acad. Sci. USA, in press

C. Zhang; E. Björnson; M. Arif; A. Tebani; A. Lovric; R. Benfeitas; M. Ozcan; K. Juszczak; W. Kim; J.T. Kim; G. Bidkhori; M. Ståhlman; P.-O. Bergh; M. Adiels; H. Turkez; M.-R. Taskinen; J. Bosley; H.-U. Marschall; J. Nielsen; M. Uhlen; J. Boren; A. Mardinoglu (2020) The acute effect of naturally occurring metabolic cofactor supplementation. Mol. Systems Biol., in press

D.J. Cook; J. Kallus; R. Jörnsten; J. Nielsen (2020) Molecular natural history of breast cancer: leveraging transcriptomics to predict breast cancer diagnosis and aggressiveness. (2020) Cancer Med. 9:3551-3562

K.S. Pedersen; F. Gatto; B. Zerahn; J. Nielsen; B.K. Pedersen; P. Hojman; J. Gehl (2020) Exercise-mediated lowering of glutamine availability suppresses tumor growth and attenuates muscle wasting. iScience, in press

J.L. Robinson; P. Kocabas; H. Wang; P.-E. Cholly; D. Cook; A. Nilsson; M. Anton; R. Ferreira; I. Domenzain; V. Billa; A. Limeta; A. Hedin; J. Gustafsson; E.J. Kerkhoven; L.T. Svensson; B.O. Palsson; A. Mardinoglu; L. Hansson; M. Uhlen; J. Nielsen (2020) An Atlas of Human Metabolism. Science Signal. 13:eaaz1482

A. Nilsson; J.R. Haanstra; M. Engqvist; A. Gerding; B.M. Bakker; U. Klingmüller; B. Teusink; J. Nielsen (2020) Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. Proc. Nat. Acad. Sci. USA 117:10294-10304

R. Yu; K. Campbell; R. Pereira; J. Björkeroth; Q. Qi; E. Vorontsov; C. Sihlbom; J. Nielsen (2020) Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast. Nature Com. 11:1881

T.W. Doughty; I. Domenzain; A. Millan-Oropeza; N. Montini; P.A. de Groot; R. Pereira; J. Nielsen; C. Henry; J.-M.G. Daran; V. Siewers; J.P. Morriseey (2020) Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts. Nature Com. 11:2144

C. Zhang; E. Bjornson; M. Arif; A. Tebani; A. Lovric; R. Benfeitas; M. Ozcan; K. Juszczak; E. Kim; J.T. Kim; G. Bidkhori; M. Ståhlman; P.-O. Bergh; M. Adiels; M.-R. Taskinen; J. Bosley; H.-U. Marschall; J. Nielsen; M. Uhlen; J. Boren; A. Mardinoglu (2020) The acute effect of naturally occurring metabolic cofactors supplementation. Mol. Systems Biol. 16:e9495

L. Dzanaeva; B. Kruk; J. Ruchala; J. Nielsen; A. Sibirny; K. Dmytruk (2020) The role of peroxisomes in xylose alcoholic fermentation in the engineered Saccharomyces cerevisiae. Cell Biol. Int. 44:1606-1615

S. Vieira-Silva; G. Falony; E. Belda; T. Nielsen; J. Aron-Wisnewsky; R. Chakaroun; S.K. Forslund; K. Assmann; M. Valles-Colomer; T.T.D. Nguyen; S. Proost; E. Prifti; V. Tremaroli; N. Pons: E. Le Chatelier; F. Andreelli; J.-P. Bastard; L.P. Coelho; N. Galleron; T.H. Hansen; J.-S. Hulot1; C. Lewinter; H.K. Pedersen; B. Quinquis; C. Rouault; H. Roume; J.-E. Salem; N.B. Søndertoft; S. Touch; MetaCardis Consortium*, M.-E. Dumas; S.D. Ehrlich; P. Galan; J.P. Gøtze; T. Hansen; J.J. Holst; L. Køber; I. Letunic; J. Nielsen; J.-M. Oppert; M. Stumvoll; H. Vestergaard; J.-D. Zucker; P. Bork; O. Pedersen; F. Bäckhed; K. Clément; J. Raes (2020) Statin therapy is associated with a lower prevalence of gut microbiota dysbiosis. Nature 581:310-315

J. Hou; C. Gao; L. Guo; J. Nielsen; Q. Ding; W. Tang; G. Hu; X. Chen; L. Liu (2020) Rewiring carbon flux in Escherichia coli using a bifunctional molecular switch. Met. Eng., in press

C. Börlin; J. Nielsen; V. Siewers (2020) The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability. FEMS Microbiol. Lett., in press

M. Babaei; G.B. Zamfir; X. Chen; H.B. Christensen; M. Kristensen; J. Nielsen; I. Borodina (2020) Metabolic engineering of Saccharomyces cerevisiae. ACS Syn. Biol., in press

C.C. van Olden; A.W. van de Laar; A.S. Meijnikman; O. Aydin; N. van Olst; J. Hoozemans; L.M. de Brauw; S.C. Bruin; Y.I.Z. Acherman; J. Verheij; M. Hoogendoorn; J. Nielsen; T. Schwartz; A.K. Groen; V.E.A. Gerdes; F. Bäckhed; M. Nieuwdorp (2020) Systems Biology and Gut Microbiota in understanding the metabolic effects of Bariatric Surgery: The BARIA Longitudinal Cohort Study. J. Int. Med., in press

J. Björkeroth; K. Campbell; C. Malina; R. Yu; F. Di Bartolomeo; J. Nielsen (2020) Proteome re-allocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media. Proc. Nat. Acad. Sci. USA 117:21804-21812 A.A.-Haleem; V. Ravikumar; B. Ji; K. Mineta; X. Gao; J. Nielsen; T. Gojobori; I. Mijakovic (2020) Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC. mSystems, in press J. Zhang; S. Petersen; T. Radivojevic; A. Ramirez; A. Perez-Manriquez; E. Abeliuk; B. Sanchez; Z. Costello; Y. Chen; M. Fero; M.G. Martin; J. Nielsen; J. Keasling; M. Jensen (2020) Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism. Nature Com., in press

Y. Hu; Z. Zhu; D. Gradischnig; M. Winkler; J. Nielsen; V. Siewers (2020) Engineering carboxylic acid reductase for selective synthesis of medium-chain fatty alcohols in yeast. Proc. Nat. Acad. Sci. USA, in press

S. Vaga; S. Lee; B. Ji: A. Andreasson; N.J. Talley; L. Agreus; G. Bidkhori; P. Kovatcheva-Datchary; J. Park; D. Lee; G. Proctor; D. Eherlich: J. Nielsen; L. Engstrand; S. Shoaie (2020) Composition and functional differences of the mucosal microbiota along the intestine of healthy individuals. Sci. Rep., in press

J. Hellgren; A. Godina; O. Vidalin; J. Nielsen; V. Siewers (2020) Promiscuous phosphoketolase and metabolic rewiring enables non-oxidative glycolysis in yeast for high yield production of acetyl-CoA products. Met. Eng., in press

J. Gustafsson; F. Held; J. Robinson; E. Björnson; R. Jörnsten; J. Nielsen (2020) Sources of variation in cell-type RNA-seq profiles. PLOS One, in press


2019

T. Ma; B. Shi; Z. Ye; X. Li; M. Liu; Y. Chen; J. Xia; J. Nielsen; Z. Deng; T. Liu (2018) Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene. Met. Eng. 52:134-142

P. Holland; J. Nielsen; T.D.G.A. Mondeel; M. Barberis (2019) Coupling cell division to metabolic pathways through transcription. Encyclopedia Bioinf. Comp. Biol. 3:74-92

B.J. Sanchez; F. Li; E. Kerkhoven; J. Nielsen (2019) SLIMEr: Probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. BMC Systems Biol. 13:4

C. Börlin; N. Cvetesic; P. Holland; D. Bergenholm; V. Siewers; B. Lenhard; J. Nielsen (2019) Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. FEMS Yeast Res. 19:foy128

R. Benfeitas; G. Bidkhori; B. Mukhopadhyay; M. Klevstig; M. Arif; C. Zhang; S. Lee; R. Cinar; J. Nielsen; M. Uhlen; J. Boren; G. Kunos; A. Mardinoglu (2019) Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis. E Biomed. 40:471-487

Z. Liu; C. Zhang; S. Lee; W. Kim; M. Klevstig; A.M. Harzandi; N. Sikanic; M. Arif; M. Stählman; J. Nielsen; M. Uhlen; J. Boren; A. Mardinoglu (2019) Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function. Met. Eng. 52:263-272

D. Bergenholm; G. Liu; D. Hansson; J. Nielsen (2019) Construction of mini-chemostats for high-throughput strain characterization. Biotechnol. Bioeng. 116:1029-1038

A. Bergman; J. Hellgren; T. Moritz; V. Siewers; J. Nielsen; Y. Chen (2019) Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae. Microb. Cell Fac. 18:25

P. Kovatcheva-Datchary; S. Shoaie; S. Lee; A. Wahlström; I. Nookaew; A. Hallen; R. Perkins; J. Nielsen; F. Bäckhed (2019) Simplified intestinal microbiota to study microbe-diet-host interactions in a mouse model. Cell Rep. 26:3772-3783

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

Y. Wei; B. Ji; V. Siewers; D. Xu; B.A. Halkier; J. Nielsen (2019) Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression. Appl. Mic. Biotechnol. 103:3727-3736

L. Wenning; C.S. Ejsing; F. David; R.R. Sprenger; J. Nielsen; V. Siewers (2019) Increasing jojoba-like wax ester production in Saccharomyces cerevisiae by enhancing very long-chain, monosaturated fatty acid synthesis. Microb. Cell Factories 18:49

P. Das; P. Babaei; J. Nielsen (2019) Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. BMC Genom. 20:208

J.C. Nielsen; S. Prigent; S. Grijseels; M. Workman; B. Ji; J. Nielsen (2019) Comparative transcriptome analysis shows conserved metabolic regulations during production of secondary metabolites in filamentous fungi. mSystems 4:e00012-19

G. Wang; G. S.M. Björk; M. Huang; Q. Liu; K. Campbell; J. Nielsen; H.N. Jönsson; D. Petranovic (2019) RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in Saccharomyces cerevisiae. Proc. Nat. Acad. Sci. USA 116:9324-9332

A. Bergman; D. Vitay; J. Hellgren; Y. Chen; J. Nielsen; V. Siewers (2019) Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome. FEMS Yeast Res. 19:foz027

P. Holland; D. Bergenholm; C. Börlin; G. Liu; J. Nielsen (2019) Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions. Nuc. Acid Res. 47:4986-5000

R. Pereira; P. Vilaca; P. Maia; J. Nielsen; I. Rocha (2019) TDPS – Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies. ACS Syn. Biol. 8:976-988

I.A. Tiukova; M.E. Pettersson; M.P. Hoeppner; R.-A. Olsen; M. Käller; J. Nielsen; J. Dainat; H. Lantz; J. Söderberg; V. Passoth (2019) Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Bretanomyces bruxellensis. PLOS One 14:e0215077

I.A. Tiukova; J. Brandenburg; J. Blomqvist; S. Samples; N. Mikkelsen; M. Skaugen; M.Ø. Arntzen; J. Nielsen; M. Sandgren; E.J. Kerkhoven (2019) Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production. Biotechnol. Bioeng. 12:137

T.I. Henriksen; L.V. Wigge; J. Nielsen; B.K. Pedersen; M. Sandri; C. Scheele (2019) Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes. Sci. Rep. 9:8169

P. Das; S. Marcisauskas; B. Ji; J. Nielsen (2019) Metagenomic analysis of bile salt biotransformation in the human gut microbiome. BMC Genom. 20:517

T.D.G.A. Mondeel; P. Holland; J. Nielsen; M. Barberis (2019) ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast. Nuc. Acid Res. 47:7825-7841

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

Y. Dabirian; P.G. Teixeira; J. Nielsen; V. Siewers; F. David (2019) FadR-based biosensor assisted screening for genes enhancing fatty acyl-CoA pools in Saccharomyces cerevisiae. ACS Syn. Biol. 8:1788-1800

Y. Chen; J. Nielsen (2019) Energy metabolism controls phenotypes by protein efficiency and allocation. Proc. Nat. Acad. Sci. USA 116:17592-17597

C. Börlin; D. Bergenholm; P. Holland; J. Nielsen (2019) A bioinformatics pipeline to analyze ChIP-exo datasets. Biol. Meth. Protoc. 4:bpz011

Y. Dabirian; X. Li; Y. Chen; F. David; J. Nielsen; V. Siewers (2019) Expanding the dynamic range of a transcription factor-based biosensor in Saccharomyces cerevisiae. ACS Syn. Biol. 8:1968-1975

I. Tiukova; S. Prigent; J. Nielsen; M. Sandgren; E.J. Kerkhoven (2019) Genome-scale model of Rhodotorula toruloides metabolism. Biotechnol. Bioeng. 116:3396-3408

R. Pereira; Y. Wei; E. Mohamed; M. Radi; C. Malina; M.J. Herrgård; A.M. Feist; J. Nielsen; Y. Chen (2019) Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae. Met. Eng. 56:130-141

G. Li; B. Ji; J. Nielsen (2019) The pan-genome of Saccharomyces cerevisiae. FEMS Yeast Res. 19:foz064

R. Ferreira; C. Skrekas; A. Hedin; B. Sanchez; V. Siewers; J. Nielsen; F. David (2019) Model-assisted fine-tuning of central carbon metabolism in yeast through dCas9-based regulation. ACS Syn. Biol. 8:2457-2463

G. Li; K.S. Rabe; J. Nielsen; M.K.M. Engqvist (2019) Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima. ACS Syn. Biol. 8:1411-1420

Q. Liu; T. Yu; X. Li; Y. Chen; K. Campbell; J. Nielsen; Y. Chen (2019) Rewiring carbon metabolism in yeast for high level production of aromatic chemicals. Nature Com. 10:4976

S. Marcisauskas; B. Ji; J. Nielsen (2019) Reconstruction and analysis of a Klyveromyces marxianus genome-scale metabolic model. BMC Bioinfor. 20:551

I. Tiukova; I Møller-Hansen; Z.M. Belew; D. Darbani: E. Boles; E. Nour; H. Hussam; T. Linder; J. Nielsen; I. Borodina (2019) Identification and characterization of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis. FEMS Lett. 366:fnz222

I.A. Tiukova; H. Jiang; J. Dainat; M.P. Hoeppner; H. Lantz; J. Piskur; M. Sandgren; J. Nielsen; Z. Gu; V. Passoth (2019) Assembly and analysis of the genome sequence of the yeast Brettanomyces naardenensis CBS7540. Microorganisms 7:489

G.M. Borja; A. Rodriguez; K. Campbell; I. Borodina; Y. Chen; J. Nielsen (2019) Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose. Microb. Cell Fac. 18:191

M. Uhlen; H. Tegel; Å. Sivertsson; C.-C. Kuo; J.M. Gutierrez; N. Lewis; B. Forsström; M. Dannemeyer; L. Fagerberg; J. Rockberg; M. Malm; H. Vunk; F. Edfors; A. Hober; E. Sjöstedt; J. Mulder; A. Mardinoglu; J. Schwenk; P. Nilsson; M. Zwahlen; K. von Feilitzen; C. Lindskog; F. Ponten; J. Nielsen; B.G. Voldborg; B.O. Palsson; A.-L.R. Volk; M. Lundqvist; A. Berling; A.-S. Svensson; S. Kanje; H. Enstedt; D. Afshari; S. Ekblad; J. Scheffel; L. Xu; R. Mihai; L. Bremer; M. Westin; M. Muse; L. Mayr; S. Knight; S. Göpel; R. Davies; P. Varley; D. Hatton; J.O. Takanen; L.H. Schiavone; S. Hober (2019) The human secretome. Science Signaling 12:eaaz0274

L. Ye; P. Das; P. Li; B. Ji; J. Nielsen (2019) Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota. FEMS Microb. Eco. 95:fiz159

G. Othoum; S. Prigent; A. Derouiche; L. Shi; A. Bokhari; S. Alamoudi; S. Bougouffa; X. Gao; R. Hoehndorf; S.T. Aroid; T. Gojobori; H. Hirt; F.F. Lafi; J. Nielsen; V.B. Bajic; I. Mijakovic; M. Essack (2019) Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs). Sci. Rep. 9:19254

A. Nilsson; E. Björnson; M. Flockhart; F.J. Larsen; J. Nielsen (2019) Complex I is bypassed during high intensity exercise. Nature Com. 10:5072


Reviews in international journals with peer review


2020

Z. Liu; K. Wang; Y. Chen; T. Tan; J. Nielsen (2020) Third-generation biorefineries as a mean to produce fuels and chemicals from CO2. Nature Cat. 3:274-288

Q. Liu; Y. Liu; Y. Chen; J. Nielsen (2020) Current state of aromatics production using yeast: Achievements and challenges. Curr. Opion. Biotechnol., in press

Z. Lin; J. Nielsen; Z. Liu (2020) Bioprospecting through cloning of whole natural product biosynthetic gene clusters. Fron. Bioeng. Biotechnol., in press


2019

R. Ferreira; A. Limeta; J. Nielsen (2019) Tackling cancer with yeast based technologies. Trends Biotechnol. 37:592-603

L. Zihe; Y. Zhang; J. Nielsen (2019) Synthetic biology of yeast. Biochem. 58:1511-1520

X. Li; Y. Chen; J. Nielsen (2019) Harnessing xylose pathways for biofuels production. Curr. Opion. Biotechnol. 57:56-65

J. Nielsen (2019) Yeast Cell Factory: Model Organism and Cell Factory. Biotechnol. J. 14:1800421

T. Yu; Y. Dabirian; Q. Liu; V. Siewers; J. Nielsen (2019) Challenges and strategies for metabolic rewiring. Curr. Op. Systems Biol. 15:30-38

Y. Hu; Z. Zhu; J. Nielsen; V. Siewers (2019) Engineering Saccharomyces cerevisiae cells for production of fatty acid derived biofuels and chemicals. Open Biol. 9:190049

M. Kumar; B. Ji; K. Zengler; J. Nielsen (2019) Modeling approaches for studying the gut microbiota. Nature Microbiol. 4:1253-1267

Y. Liu; J. Nielsen (2019) Recent trends in metabolic engineering of microbial chemical factories. Curr. Op. Biotechnol. 60:188-197

B. Turanli; O. Altay; J. Boren; H. Turkez; J. Nielsen; M. Uhlen; K.Y. Arga; A. Mardinoglu (2019) Systems biology based drug repositioning for development of cancer therapy. Sem. Cancer Biol., in press

R. Yu; J. Nielsen (2019) Big data in yeast systems biology. FEMS Yeast Res. 19:foz070

M. Palmnäs; C. Brunius; L. Shi; A. Rostgaard-Hansen; N.E. Torres; R. Gonzalez-Dominguez; R. Zamra-Ros; Y. Lingqun; J. Halkjær; A. Tjønneland; G. Riccardi; T. Giacco; G. Costabile; C. Vetrani; J. Nielsen; C. Andres-Lacueva; R. Landberg (2019) Metabotyping: A potential personalized nutrition strategy for precision prevention of cardiometabolic disease. Adv. Nutrition 11:524-532

S. Bratulic; F. Gatto; J. Nielsen (2019) The translational status of cancer liquid biopsies. Reg. Eng. Transl. Med., in press

R. Yu; J. Nielsen (2019) Yeast systems biology in understanding principles of physiology underlying complex human diseases. Curr. Op. Biotechnol. 121:1-9


Commentaries and Short Papers


2019

J. Nielsen (2019) Designer Microbes Serving Society. Cell Met. 29:509

J. Nielsen (2019) Cell factory engineering for improved production of natural products. Nat. Prod. Rep. 36:1233-1236

J. Nielsen (2019) Antibiotic lethality is impacted by nutrient availabilities: New insights from machine learning. Cell 177:1373-1374

J. Nielsen (2019) A stress-coping strategy for yeast cells. Nature 572:184-185


2018

A. Nilsson; J.R. Haanstra; B. Teusink; J. Nielsen (2018) Metabolite depletion affects flux profiling of cell lines. Trends Biochem. Sci. 43:395-397