Nielsen Lab

Professor
Jens Nielsen

Phone: +46 (0)31 772 3804
E-mail: nielsenj [at] chalmers.se
Office: Room 2060B

Nielsen Lab

Research Projects      |      CV      |      Publications      |      Videos      |      Theses      |      Alumni


Our research focus is on systems biology of metabolism. The yeast Saccharomyces cerevisiae is our key organism for experimental research, but we also have experimental research on Aspergilli oryzae. Interview about some of our work

Our research activities fall in three areas:

  • Studying regulatory pathways that are conserved in the Eukaryal kingdom such as the Snf1/AMPK pathway, the Tor1/mTOR pathway, protein folding, secretion and degradation and regulation of lipid biosynthesis and degradation.
  • Developing efficient cell factories (yeast and Aspergilli) for sustainable production of fuels and chemicals. We are looking into both the production of high-value chemicals such as isoprenoids that can be used as fine chemicals, commodity chemicals that can be used as feedstocks in the chemical industry for polymer production, and novel advanced biofuels.
  • Developing metabolic models for Eukaryal cells, including rodent and human cells, and using these models as scaffolds for analysis of omics data with the objective to understand global responses to nutrient and disease. Experimental work is carried out in collaboration with other research groups.

Several of our research activities are part of the Novo Nordisk Foundation Center for Biosustainability. See www.biosustain.dtu.dk and video for more information

Research Projects

Human Metabolic Atlas
We are building genome-scale metabolic models for different human cell types and using these models for identification of novel prognostic biomarkers for human diseases like type 2 diabetes, cardiovascular disease and cancer (see www.metabolicatlas.com). We have many national and international collaborators on this project.

Gut Metagenomics
We are analyzing the gut metagenome in different cohort studies and aim to identify biomarkers and novel treatment strategies for human diseases. Much of our work in this field is in close collaboration with Prof. Fredrik Båckhed at Sahlgrenska Academy, Gothenburg University.

Microbial models
Genome-scale metabolic models are developed for different microorganisms and we are in particular advancing genome-scale modeling of the yeast Saccharomyces cerevisiae. All our models are available through www.sysbio.se/BioMet.

Stress and Regulation
Key signal transduction pathways in S. cerevisiae are analyzed using systems biology approaches. Our focus is on energy and lipid metabolism.

Protein production
Using systems biology and metabolic engineering we are advancing the use of S. cerevisiae for recombinant protein production. Through a combination of advanced modeling and engineering of the secretory pathway we are developing yeasts that can be used for production of human therapeutic proteins and for consolidated bioprocesses.

Advanced Biofuel Production
We have a large and focuses effort on developing yeast cell factories for production of advanced biofuels that can be used as diesel and jet fuels.

Biochemical Production
We are developing yeast cell factories for production of chemical building blocks and fine chemicals, e.g. 3-OH-propionic acid that can be used for sustainable production of super-adsorbent materials and isoprenoids used as perfumes and fine fragrances.

Synthetic Biology
We are developing novel synthetic biology tools for metabolic engineering of yeast. These research activities are mainly carried out at the DTU site of Center for Biosustainability.

Infrastructures

We provide a number of infrastructures that are part of either Chalmers infrastructures or National infrastructures.

Databases, BioMet Toolbox, Bioinformatics
We are developing a number of repositories and databases that are combined with advanced systems biology tools and bioinformatics tools. All tools and database are available through www.sysbio.se

Fermentation
We host an extensive fermentation infrastructure consisting of 32 DASGIB bioreactors and more than 10 other highly instrumented bioreactors.

Metabolomics
We are part of the Swedish Universities Metabolomics Infrastructure (hosted by Umeå University) and is also part of Chalmers infrastructure for metabolomics. Our infrastructure involves 2 GC-MS systems and 5 HPLC systems.

Publications

Full list of publications (PDF)

Videos

  • Samson Prize Winners - Fuel Choices and Smart Mobility Summit
  • ENI Award, 2017
  • Presentation at Molecular Frontiers Symposium, Stockholm: From yeast to human, 2017
  • Talk “Impact of systems biology on metabolic engineering” in Kitano, H. (ed.), Systems Biology: , The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London, 2014
  • Interview in connection with Science paper on thermotolerant yeast, 2014
  • Presentation at the Metabolic Engineering X conference, Vancouver, Canada, 2014
  • Presentation at Molecular Frontiers Symposium: Meet Science Superheroes, Singapore, 2012
  • Interview about mentoring at Molecular Frontiers Symposium: Meet Science Superheroes, Singapore, 2012
  • Fungal Cell Factories at Center for Biosustainability, 2011
  • The Novo Nordisk Foundation Center for Biosustainability, 2011
Webinars:
  • Advancing the Design-Build-Test Cycle for
  • Metabolic Engineering of Yeast, 2016
  • Society of Biological Engineering, 2009

Theses

2009

Wanwipa Vongsangnak:
SYSBIOMICS of Aspergilli: SYStems Biology, BIoinformatics and OMICS analysis of Aspergilli cell factories (ISBN 978-91-7385-330-9)

José Manuel Otero Romero:
Industrial Systems Biology and Metabolic Engineering of Saccharomyces cerevisiae (ISBN 978-91-7385-346-0)

2010

Margarita Salazar:
Systems Biology of Glucose Sensing and Repression in Aspergillus niger: Lessons from Genomics and Transcriptomics (ISBN 978-91-7385-439-9)

2011

Jie Zhang:
Global Regulation of Snf1 in Saccharomyces cerevisiae: A case study of experimental systems biology (ISBN 978-91-7385-558-7)

Roberto Olivares Hernandez:
Systems Biology in Saccharomyces cerevisiae. Statistical data analysis and mathematical methods (ISBN 978-91-7385-624-9)

2012

Pramote Chumnanpuen:
Systems Biology of Yeast Lipid Metabolism (ISBN 978-91-7385-661-4)

Marta Papini:
Metabolic Engineering of Central Carbon Metabolism in Saccharomyces cerevisiae
The contribution of systems biology to physiological studies Metabolic Engineering of Saccharomyces cerevisiae for Sesquiterpene Production
(ISBN 978-91-7385-698-0)

Gionata Scalcinati:
Metabolic Engineering of Saccharomyces cerevisiae for Sesquiterpene Production (ISBN 978-91-7385-720-8)

Siavash Partow:
Novel Synthetic Biology Tools for Metabolic Engineering of Saccharomyces cerevisiae (ISBN 978-91-7385-727-7)

Kuk-ki Hong:
Advancing Metabolic Engineering through Combination of Systems Biology and Adaptive Evolution (ISBN 978-91-7385-735-2)

Zihe Liu:
Metabolic Engineering of Recombinant Protein Production by Saccharomyces cerevisiae (ISBN 978-91-7385-741-3)

2013

Kanokarn Kocharin:
Metabolic Engineering of Saccharomyces cerevisiae for Polyhydroxybutyrate Production (ISBN 978-91-7385-819-9)

Rasmus Ågren:
On metabolic networks and multi-omics integration (ISBN 978-91-7385-839-7)

2014

Tobias Österlund:
Reconstruction of Biological Networks for Integrative analysis
Reconstruction and Analysis of the Metabolic, Protein Secretion and Regulatory Network in Yeast
(ISBN 978-91-7385-960-8)

Fredrik Karlsson:
Systems Biology of the Gut Microbiome in Metabolic Diseases (ISBN 978-91-7385-965-3)

Christoph Knuf:
Malic acid production by Aspergillus oryzae (ISBN 978-91-7385-984-4)

Natapol Pornputtapong:
Database and Visualization for Advanced Systems Biology (ISBN 978-91-7385-983-7)

Lifang Liu:
Systems Biology of Recombinant Protein Production by Fungi (ISBN 978-91-7597-038-7)

2015

Bouke Wim de Jong:
A study on fatty acid ethyl ester production in a Saccharomyces cerevisiae cell factory (ISBN 978-91-7597-132-2)

Yiming Zhang:
Engineering Cytosolic Acetyl-CoA Metabolism in Saccharomyces cerevisiae (ISBN: 978-91-7597-147-6)

Francesco Gatto:
The Origin of Symmetry in the Matabolism of Cancer (ISBN: 978-91-7597-225-1)

Saeed Shoaie:
Metabolic Modeling of the Gut Microbiome-Host Interactions and Meta’omics Integration (ISBN 978-91-7597-256-5)

2016

Amir Feizi:
Systems Analysis of the Protein Secretory Pathway in Yeast and Human Cells (ISBN: 978-91-7597-313-5)

Leif Väremo:
Systems Biology of Type 2 Diabetes in Skeletal Muscle (ISBN: 978-91-7597-322-7)

Nicolaas A. A. (Klaas) Buijs:
Metabolic engineering of the yeast Saccharomyces cerevisiae to enable biosynthesis of long-chain alkanes and olefins (ISBN: 978-91-7597-402-6)

Stefan Tippmann:
Engineering Yeast Metabolism for Production of Sesquiterpenes (ISBN: 978-91-7597-459-0)

2017

Pouyan Ghaffari Nouran:
Heterogeneity of human metabolism in health and disease: a modelling perspective (ISBN: 978-91-7597-586-3)

Joachim Almquist:
Kinetic Models in Life Science - Contributions to Methods and Applications (ISBN 978-91-7597-653-2)

2018

Jens Christian Nielsen:
Systems Biology of the Secondary Metabolism in Filamentous Fungi (ISBN 978-91-7597-671-6)

Paulo Gonçalves Teixeira:
Engineering Lipid Metabolism for Production of Oleochemicals in Saccharomyces cerevisiae (ISBN 978-91-7597-686-0)

Jichen Bao:
Engineering the Secretory Pathway for Recombinant Protein Secretion in Saccharomyces cerevisiae (ISBN 978-91-7597-598-6)



Alumni

Post Doctoral Researchers

  1. Lars Højlund Christensen, DTU (1992-1994)
  2. Gunnar Liden, DTU (1993-1994)
  3. Lisbeth OIsson, DTU (1994-1996)
  4. Morten Carlsen, DTU (1995-1997)
  5. Anne Santerre Henriksen, DTU (1995-1999)
  6. Aradhana Srivastava, DTU (1996-1998)
  7. Hans Peter Smits, DTU (1996-1999; 2000-2001)
  8. Alexei Aleksenko, DTU (1997-2001)
  9. Philippe Duboc, DTU (1997-1999)
  10. Fernando Bautista, DTU (1998-1999)
  11. Uffe Mortensen, DTU (1999-2002)
  12. Ana Borges, DTU (1999-2001)
  13. Bjarke Christensen, DTU (1999-2001)
  14. Mhairi Workman, DTU (1999-2004)
  15. Birgitte Regenberg, DTU (1999-2005)
  16. Anna Eliasson Lantz, DTU (2000-2002)
  17. Christian Müller, DTU (2001-2002)
  18. Vsevolod Serebrianyi, DTU (2001-2002)
  19. Mats Åkesson, DTU (2001-2003)
  20. Kasper Møller, DTU (2001-2003)
  21. Per Bruheim, DTU (2002)
  22. Vasimon Ruanglek, DTU (2002)
  23. Tamay Seker, DTU (2002-2003)
  24. Sandrine Mas, DTU (2002-2005)
  25. Gerald Hofmann, DTU (2004-2006)
  26. Roberta Mustachi, DTU (2004-2007)
  27. Jerome Maury, DTU (2004-2008)
  28. Isabel Rocha, DTU (2004)
  29. Jette Thykær, DTU (2005-2007)
  30. Dongmei Bai, DTU (2005-2007)
  31. Michael Jewett, DTU (2005-2008)
  32. Goutham Vemuri, DTU (2006-2007)
  33. Manuel Quiros Asensio, DTU (2006-2008)
  34. Prashant Bapat, DTU (2006-2008)
  35. Sven Even Borgos, DTU (2007)
  36. Dina Petranovic, DTU (2007-2008)
  37. Subir Kumar Nandy, Chalmers (2008-2010)
  38. Keith Tyo, Chalmers (2008-2010)
  39. Marija Cvijovic, Chalmers (2008-2010)
  40. Andrea Neiss, Chalmers (2009-2010)
  41. Wanwipa Vongsangnak, Chalmers (2010)
  42. Liming Liu, Chalmers (2009-2010)
  43. Sergio Bordel Velasco (2008-2010)
  44. Intawat Nookaew (2008-2012)
  45. Jin Hou, Chalmers (2010-2012)
  46. Fredrik Öberg, DTU (2011-2012)
  47. Shuobo Shi (2009-2012)
  48. Luis Caspeta (2009-2013)
  49. Il-Kwon Kim (2010-2013)
  50. Rahul Kumar (2010-2013)
  51. Antonio Roldao (2010-2013)
  52. Adil Mardinoglu, Chalmers (2010-2015)
  53. Marina Sanchez Martinez (2011-2013)
  54. Manuel Garcia, Chalmers (2012-2014)
  55. Clara Navarrete, Chalmers (2013-2014)
  56. Zheng Wang, Chalmers (2013-2014)
  57. Subazini Thankaswarmy, Chalmers (2013-2014)
  58. Martin Engqvist, Chalmers (2014-2015)
  59. Anastasia Krivoruchko, Post doc, Chalmers (2010-2016)
  60. Jose L. Martinez, Chalmers (2011-2015)
  61. Agata Smialowska, Chalmers (2014-2015)
  62. Sunjae Lee, Chalmers (2014-2015)
  63. Petri-Jaan Lahtvee, Chalmers (2013-2015)
  64. Eugene Fletcher, Chalmers (2014-2015)
  65. Hülya Karaca Gencer, Chalmers (2014-2015)
  66. Silveira Wendel, Chalmers (2015-2016)
  67. Min-Kyoung Kang, Chalmers (2014-2016)
  68. Guodong Liu, Chalmers (2013-2016)
  69. Mark Bisschops, Chalmers (2014-2016)
  70. Ömür Kayikci, Chalmers (2014-2016)
  71. Tatiana Moreira, Chalmers (2015-2016)
  72. Yongjin Zhou, Chalmers (2012-2016)
  73. Yongjun Wei, Chalmers (2014-2016)
  74. Amir Feizi, Chalmers (2016)
  75. Mingtao Huang, Chalmers (2012-2017)
  76. Zongjie Dai, Chalmers (2013-2017)
  77. Partho Sarathi Sen, Chalmers (2014-2017)
  78. Sakda Khoomrung, Chalmers (2011-2017)
  79. Michael Gossing, Chalmers (2014-2017)
  80. JinHo Kim, Chalmers (2016-2018)

Graduated PhD Students (main supervisor)

  1. Henrik Jørgensen, DTU (1991-1993)
  2. Claus Lindvad Johansen, DTU (1991-1993)
  3. Morten Carlsen, DTU (1992-1995)
  4. Rong Wei Min, DTU (1992-1995)
  5. Anders Spohr, DTU (1993-1996)
  6. Preben Krabben, DTU (1993-1997)
  7. Claus Maxel Henriksen, DTU (1993-1996)
  8. Christoffer Klein, DTU (1995-1998)
  9. Karsten Schmidt, DTU (1995-1998)
  10. Torben Nissen, DTU (1995-1998)
  11. Henrik Pedersen, DTU (1996-1999)
  12. Bjarke Christensen, DTU (1996-1999)
  13. Teit Agger, DTU (1996-1999)
  14. Hanne Theilgaard, DTU (1996-1999)
  15. Simon Østergaard, DTU (1997-2000)
  16. Wai Prathumpai, DTU (1998-2001)
  17. Tina Lübbehüsen, DTU (1998-2001)
  18. Jens Dynesen, DTU (1998-2001)
  19. Torben Christiansen (1998-2001)
  20. Christian Müller, DTU (1998-2001)
  21. Jarno Robin, DTU (1998-2002)
  22. Jochen Förster, DTU (1999-2002)
  23. Michael Lynge Nielsen, DTU (1999-2003)
  24. Jette Thykær, DTU (2000-2005)
  25. Nina Gunnarsson, DTU (2000-2003)
  26. Margarida Moreira dos Santos, DTU (1999-2003)
  27. Christoffer Bro, DTU (2000-2003)
  28. Gerald Hofmann, DTU (2001-2004)
  29. Helga David, DTU (2001-2005)
  30. Thomas Grotkjær, DTU (2001-2004)
  31. Nadine Eckert-Boulet, DTU (2001-2004)
  32. Vijay Raghavendran, DTU (2001-2005)
  33. Steen Lund Westergaard, DTU (2002-2005)
  34. Wian de Jongh, DTU (2002-2005)
  35. Silas Granato Villas-Boas, DTU (2002-2005)
  36. Kiran Patil, DTU (2003-2006)
  37. Songsak Wattanachaisaereekul, DTU (2003-2007)
  38. Audrey Diano, DTU (2003-2007)
  39. Torsten Bak Reguira, DTU (2003-2007)
  40. Irina Borodina, DTU (2004-2008)
  41. Susan Meijer, DTU (2004-2007)
  42. Ana Paula Oliveira, DTU (2004-2008)
  43. Mohammad Asahollahi, DTU (2004-2008)
  44. Mikael Rørdam Andersen, DTU (2004-2008)
  45. Jesper Højer Pedersen, DTU (2004-2008)
  46. Kjeld Kjeldsen, DTU (2005-2008)
  47. Wanwipa Vongsangnak, Chalmers (2005-2009)
  48. Jose Manuel Otero, Chalmers (2005-2009)
  49. Margarita Salazar Peña (2006-2010)
  50. Jie Zhang, Chalmers (2007-2011)
  51. Roberto Olivares-Hernández (2005-2012)
  52. Pramote Chumnanpuen (2007-2012)
  53. Marta Papini (2007-2012)
  54. Gionata Scalcinati (2008-2012)
  55. Siavash Partow (2008-2012)
  56. Kuk-ki Hong (2008-2012)
  57. Zihe Liu, Chalmers (2008-2012)
  58. Kanokarn Kocharin (2009-2013)
  59. Rasmus Ågren (2008-2013)
  60. Tobias Österlund (2009-2014)
  61. Fredrik Karlsson (2009-2014)
  62. Christoph Knuf (2009-2014)
  63. Natapol Pornputtapong (2010-2014)
  64. Lifang Liu (2010-2014)
  65. Bouke de Jong (2010-2015)
  66. Yiming Zhang, Chalmers (2010-2015)
  67. Francesco Gatto, Chalmers (2012-2015)
  68. Saeed Shoaie, Chalmers (2011-2015)
  69. Amir Feizi, Chalmers (2012-2016)
  70. Leif Väremo, Chalmers (2012-2016)
  71. Nicolaas Buijs, Chalmers (2011-2016)
  72. Mingji Li, DTU (2013-2016)
  73. Edith Angelica Rodriguez Prado, DTU (2013-2016)
  74. Stefan Tippmann, Chalmers (2012-2016)
  75. Pouyan Ghaffari Nouran (2013-2017)
  76. Jens Christian F. Nielsen, Chalmers (2014-2018)
  77. Paulo Teixeira, Chalmers (2013-2018)
  78. Jichen Bao, Chalmers (2013-2018)

Graduated PhD Students (co-supervisor)

  1. Lars Højlund Christensen, DTU (1989-1992)
  2. Stig Benthin, DTU (1989-1992)
  3. Annemarie Gade Pedersen, DTU (1990-1992)
  4. Simone de Jong Frandsen, DTU (1991-1993)
  5. Ulrik Schultze, DTU (1992-1995)
  6. Teresa Zangorilami, DTU (1994-1998)
  7. Kasper Møller, DTU (1998-2001)
  8. Mikkel Nordkvist, DTU (2001-2005)
  9. Renata Usaite, DTU (2004-2008)
  10. Lasse Pedersen, DTU (2007-2010)
  11. Kanchana Rueksomtawin Kildegaard, DTU (2004-2011)
  12. Xiao Chen, DTU (2007-2011)
  13. Kwanjeera Wanichthanarak, Chalmers (2010-2014)
  14. Kaisa Thorell, Gothenburg University, Sweden (2010-2014)

Visiting PhD Students (co-supervisor)

  1. Robert Lejeune, Free University of Brussels (1994-1995)
  2. Pedro N. Pissarra, DTU (visiting PhD student) (1994-1995)
  3. Einar Jonsbu, DTU (visiting PhD student) (1999-2000)
  4. Andreas Karoly Gomberg, DTU (visiting PhD student) (1998-2000)
  5. Joel Forest Moxley, DTU (visiting PhD student) (2003-2005)
  6. Tunahan Cakir, DTU (visiting PhD student) (2004-2005)
  7. Kazim Yalcin Arga, DTU (visiting PhD student) (2004-2005)
  8. Intawat Nookaew, KMUTT (2005-2006)
  9. Goutham Vemuri, University of Georgia (2005-2006)
  10. Donatella Cimini, DTU (visiting PhD student) (2006)
  11. Valeria Mapelli, DTU (visiting PhD student) (2006-2007)
  12. Paula Jouhten, Chalmers (visiting PhD student) (2008-2009)
  13. Raphael Aggio, University of Auckland (2009)
  14. William Alfonso Rodriguez Limas, National University of Mexico (2009-2010)
  15. Kantida Kusonmano, UMIT (2011)
  16. Akarin Boonsombuti, Mahasarakham University (2011-2012)
  17. Jorge Alberto Vasquez Castillo, Antioquia University (2011-2012)
  18. Josh Michener, Caltech/Stanford (2011)
  19. Ibrahim E. El-Semman, Assiut University (2012-2014)
  20. Jiufu Qin, Jiangnan University, China (2011-)
  21. Rui Pereira, University of Minho, Portugal (2012-2014)
  22. Cheng Zhang, East China Univesity of Science and Technology, China (2013-2015)
  23. John Casey, University of Hawaii, USA (2014)
  24. Jacqueline Rand, University of Wisconsin, USA (2014)
  25. Zahra Azim Zadeh Irani, Tarbiat Modares University, Iran (2014-2015)
  26. Yu Chen, East China University of Science and Technology, China (2015-2017)

Other affiliated researchers and staff

  1. Tina Johansen, Research Engineer, DTU (1990-2008)
  2. Lene Christiansen, Research Engineer, DTU (1992-2008)
  3. Martin Hjortso, Visiting Professor, DTU (1992-1993, 2002-2003)
  4. Susanne Sloth Larsen, Head of Administration, DTU (1995-1999)
  5. Jette Mortensen, Laboratory Technician, DTU (1996-2008)
  6. Birgitte Karsbøl, Secretary, DTU (1996-2008)
  7. Kirsten Nielsen, Secretary, DTU (1998-2005)
  8. Trine Bro, Head of Administration, DTU (1999-2008)
  9. Lars K. Nielsen, Visiting Professor, DTU (2004)
  10. Stefan Rokem, Visiting Professor, DTU (2004-2005)
  11. Eduardo Agosin, Visiting Professor, DTU (2005)
  12. Stefan Rokem, Visiting Professor, Chalmers (2010)
  13. Pegah Khorramzadeh, Research Engineering, Chalmers (2010-2011)
  14. Sergio Bordel Velasco, Assistant Professor (2010-2014)
  15. Suwanee Jansa-Ard, Research Engineer, Chalmers (2011-2014)
  16. Danilo Porro, Visiting Professor, Chalmers (2012)
  17. Martin Markström, Co-Director AoA, Chalmers (2011-2014)
  18. Brian Pfleger, Visitng Professor, Chalmers (2014)
  19. Malin Nordvall, Research Engineer, Chalmers (2009-2014)
  20. Emma Ribbenhed, Research Engineer, Chalmers (2013-2015)
  21. Antonio Marras, Research Assistant, Chalmers (2013-2015)
  22. Ximena Rozo Sevilla, Chalmers (2011-2015)
  23. Julia Karlsson, Research Engineer, Chalmers (2014-2016)
  24. Matthias Nilsson, Chalmers (2015-2016)
  25. Daniel Hermansson, Chalmers (2016)
  26. Jianye Xia, Visiting Professor, Chalmers (2016-2017)
  27. Marie Nordqvist, Research Engineering and Lab Manager (2008-2017)