Nielsen Lab

Professor
Jens Nielsen

Phone: +46 (0)31 772 3804
E-mail: nielsenj [at] chalmers.se
Office: Room 2060B (Fysik Origo, Kemigården 1)

CV | Publications | Videos | Theses | Alumni

Our research focused on systems biology of metabolism. Over the years we have used the yeast Saccharomyces cerevisiae as both a model organism and as a cell factory, but the group do not have any active research on yeast anymore. In recent years focus has been on systems biology of human metabolism, including the human gut microbiome. Interview about some of our work

All research activities are now carried out in collaboration with former students and post docs of the group.

There are no current research projects

Publications

Full list of publications (PDF)

Videos

Webinars:

Systems Biology of Yeast Metabolism. CHASSY Webinar, University of Cork, Ireland
Advancing the Design-Build-Test Cycle for Metabolic Engineering of Yeast, 2016
Impact of systems biology on metabolic engineering, in H. Kitano (Ed), Systems Biology: The Biomedical and Life Science Collection, Henry Stewart Talks Ltd., London, 2014.
Industrial Systems Biology, Society of Biological Engineering, 2009

Theses

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)

2019

Avlant Nilsson:
Constraint-based modeling of metabolism - interpreting predictions of growth and ATP synthesis in human and yeast (ISBN 978-91-7597-853-6)

Parizad Babaei:
In silico analysis of microbial communities through constraint-based metabolic modelling (ISBN 978-91-7597-876-5)

Benjamín José Sánchez Barja:
Computing abundance constraints in Saccharomyces cerevisiae’s metabolism (ISBN 978-91-7597-863-5)

Promi Das:
Systems and Synthetic Biology: “Mining human gut microbial metabolism through in vitro and in silico approaches” (ISBN 978-91-7597-875-8)

Alexandra Bergman:
Evaluation of precursor and cofactor engineering strategies influencing fatty acid metabolism in Saccharomyces cerevisiae (ISBN 978-91-7597-868-0)

Raphael Ferreira:
Advancing CRISPR technologies to engineer yeast metabolism (ISBN 978-91-7905-148-8)

2020

David Bergenholm:
A holistic view on transcriptional regulatory networks in S. cerevisiae: Implications and utilization (ISBN 978-91-7905-211-9)

Gang Li:
Application of machine learning in systems biology (ISBN 978-91-7905-290-4)

Simonas Marcisauskas:
An insight towards food-related microbial sets through metabolic modelling and functional analysis (ISBN 978-91-7905-276-8)

Christoph Börlin:
An analytical framework for studying transcriptional regulation (ISBN 978-91-7905-332-1)

2021

Rasool Saghaleyni:
Systems Biology of Protein Secretion in Human Cells: Multi-omics Analysis and Modeling of the Protein Secretion Process in Human Cells and its Application. (978-91-7905-517-2)

Carl Malina:
Systems biology of yeast metabolism - Understanding metabolism through proteomics and constraint-based modeling (978-91-7905-520-2)

Qi Qi:
Systems biology of protein synthesis and secretion in yeast (978-91-7905-556-1)

Feiran Li:
Constraint-based modeling of yeast metabolism and protein secretion (978-91-7905-557-8)

Alumni

Post Doctoral Researchers

Lars Højlund Christensen, DTU (1992-1994)
Gunnar Liden, DTU (1993-1994)
Lisbeth OIsson, DTU (1994-1996)
Morten Carlsen, DTU (1995-1997)
Anne Santerre Henriksen, DTU (1995-1999)
Aradhana Srivastava, DTU (1996-1998)
Hans Peter Smits, DTU (1996-1999; 2000-2001)
Alexei Aleksenko, DTU (1997-2001)
Philippe Duboc, DTU (1997-1999)
Fernando Bautista, DTU (1998-1999)
Uffe Mortensen, DTU (1999-2002)
Ana Borges, DTU (1999-2001)
Bjarke Christensen, DTU (1999-2001)
Mhairi Workman, DTU (1999-2004)
Birgitte Regenberg, DTU (1999-2005)
Anna Eliasson Lantz, DTU (2000-2002)
Christian Müller, DTU (2001-2002)
Vsevolod Serebrianyi, DTU (2001-2002)
Mats Åkesson, DTU (2001-2003)
Kasper Møller, DTU (2001-2003)
Per Bruheim, DTU (2002)
Vasimon Ruanglek, DTU (2002)
Tamay Seker, DTU (2002-2003)
Sandrine Mas, DTU (2002-2005)
Gerald Hofmann, DTU (2004-2006)
Roberta Mustachi, DTU (2004-2007)
Jerome Maury, DTU (2004-2008)
Isabel Rocha, DTU (2004)
Jette Thykær, DTU (2005-2007)
Dongmei Bai, DTU (2005-2007)
Michael Jewett, DTU (2005-2008)
Goutham Vemuri, DTU (2006-2007)
Manuel Quiros Asensio, DTU (2006-2008)
Prashant Bapat, DTU (2006-2008)
Sven Even Borgos, DTU (2007)
Dina Petranovic, DTU (2007-2008)
Subir Kumar Nandy, Chalmers (2008-2010)
Keith Tyo, Chalmers (2008-2010)
Marija Cvijovic, Chalmers (2008-2010)
Andrea Neiss, Chalmers (2009-2010)
Wanwipa Vongsangnak, Chalmers (2010)
Liming Liu, Chalmers (2009-2010)
Sergio Bordel Velasco (2008-2010)
Intawat Nookaew (2008-2012)
Jin Hou, Chalmers (2010-2012)
Fredrik Öberg, DTU (2011-2012)
Shuobo Shi (2009-2012)
Luis Caspeta (2009-2013)
Il-Kwon Kim (2010-2013)
Rahul Kumar (2010-2013)
Antonio Roldao (2010-2013)
Adil Mardinoglu, Chalmers (2010-2015)
Marina Sanchez Martinez (2011-2013)
Manuel Garcia, Chalmers (2012-2014)
Clara Navarrete, Chalmers (2013-2014)
Zheng Wang, Chalmers (2013-2014)
Subazini Thankaswarmy, Chalmers (2013-2014)
Martin Engqvist, Chalmers (2014-2015)
Anastasia Krivoruchko, Post doc, Chalmers (2010-2016)
Jose L. Martinez, Chalmers (2011-2015)
Agata Smialowska, Chalmers (2014-2015)
Sunjae Lee, Chalmers (2014-2015)
Petri-Jaan Lahtvee, Chalmers (2013-2015)
Eugene Fletcher, Chalmers (2014-2015)
Hülya Karaca Gencer, Chalmers (2014-2015)
Silveira Wendel, Chalmers (2015-2016)
Min-Kyoung Kang, Chalmers (2014-2016)
Guodong Liu, Chalmers (2013-2016)
Mark Bisschops, Chalmers (2014-2016)
Ömür Kayikci, Chalmers (2014-2016)
Tatiana Moreira, Chalmers (2015-2016)
Yongjin Zhou, Chalmers (2012-2016)
Yongjun Wei, Chalmers (2014-2016)
Amir Feizi, Chalmers (2016)
Mingtao Huang, Chalmers (2012-2017)
Zongjie Dai, Chalmers (2013-2017)
Partho Sarathi Sen, Chalmers (2014-2017)
Sakda Khoomrung, Chalmers (2011-2017)
Michael Gossing, Chalmers (2014-2017)
Francesco Gatto, Chalmers (2015-2017)
Yi Liu, Chalmers (2015-2020)
JinHo Kim, Chalmers (2016-2018)
Manish Kumar, Chalmers (2015-2018)
Petter Holland, Chalmers (2016-2018)
Sylvain Prigent, Chalmers (2015-2018)
Ibrahim El-Semman, DTU (2015-2018)
Francesca Di Bartolomeo, Chalmers (2017-2019)
Lucy Fang-I Chao, Chalmers (2017-2019)
Zhiwei Zhu, Chalmers (2014-2019)
Tao Yu, Chalmers (2014-2019)
Tyler Doughty, Chalmers (2017-2019)
Ling-Qun Ye, Chalmers (2017-2019)
Yeping Zhang, BUCT (2017-2019)
Kate Campbell, Chalmers (2016-2020)
Jonathan Robinson, Chalmers (2016-2020)
Rui Pereira, Chalmers (2016-2020)
Xiaowei Li, Chalmers (2016-2020)
Quanli Liu, Chalmers (2016-2020)
Daniel Cook, Chalmers (2017-2020)
Ievgeniia Tiukova, Chalmers (2018-2020)
Hongzhong Lu, Chalmers (2017-2020)
Pinar Kocabas, Chalmers (2017-2020)
Jun Geng, Chalmers (2015-2020)
Jiufu Qin, Chalmers & DTU (2015-2020)
Boyang Ji, Chalmers (2013-2020)
Yiming Zhang, BUCT (2016-2021)
Rosemary Yu, Chalmers (2017-2021)
Hao Wang, Chalmers (2017-2021)

Graduated PhD Students (main supervisor)

Henrik Jørgensen, DTU (1991-1993)
Claus Lindvad Johansen, DTU (1991-1993)
Morten Carlsen, DTU (1992-1995)
Rong Wei Min, DTU (1992-1995)
Anders Spohr, DTU (1993-1996)
Preben Krabben, DTU (1993-1997)
Claus Maxel Henriksen, DTU (1993-1996)
Christoffer Klein, DTU (1995-1998)
Karsten Schmidt, DTU (1995-1998)
Torben Nissen, DTU (1995-1998)
Henrik Pedersen, DTU (1996-1999)
Bjarke Christensen, DTU (1996-1999)
Teit Agger, DTU (1996-1999)
Hanne Theilgaard, DTU (1996-1999)
Simon Østergaard, DTU (1997-2000)
Wai Prathumpai, DTU (1998-2001)
Tina Lübbehüsen, DTU (1998-2001)
Jens Dynesen, DTU (1998-2001)
Torben Christiansen (1998-2001)
Christian Müller, DTU (1998-2001)
Jarno Robin, DTU (1998-2002)
Jochen Förster, DTU (1999-2002)
Michael Lynge Nielsen, DTU (1999-2003)
Jette Thykær, DTU (2000-2005)
Nina Gunnarsson, DTU (2000-2003)
Margarida Moreira dos Santos, DTU (1999-2003)
Christoffer Bro, DTU (2000-2003)
Gerald Hofmann, DTU (2001-2004)
Helga David, DTU (2001-2005)
Thomas Grotkjær, DTU (2001-2004)
Nadine Eckert-Boulet, DTU (2001-2004)
Vijay Raghavendran, DTU (2001-2005)
Steen Lund Westergaard, DTU (2002-2005)
Wian de Jongh, DTU (2002-2005)
Silas Granato Villas-Boas, DTU (2002-2005)
Kiran Patil, DTU (2003-2006)
Songsak Wattanachaisaereekul, DTU (2003-2007)
Audrey Diano, DTU (2003-2007)
Torsten Bak Reguira, DTU (2003-2007)
Irina Borodina, DTU (2004-2008)
Susan Meijer, DTU (2004-2007)
Ana Paula Oliveira, DTU (2004-2008)
Mohammad Asahollahi, DTU (2004-2008)
Mikael Rørdam Andersen, DTU (2004-2008)
Jesper Højer Pedersen, DTU (2004-2008)
Kjeld Kjeldsen, DTU (2005-2008)
Wanwipa Vongsangnak, Chalmers (2005-2009)
Jose Manuel Otero, Chalmers (2005-2009)
Margarita Salazar Peña (2006-2010)
Jie Zhang, Chalmers (2007-2011)
Roberto Olivares-Hernández (2005-2012)
Pramote Chumnanpuen (2007-2012)
Marta Papini (2007-2012)
Gionata Scalcinati (2008-2012)
Siavash Partow (2008-2012)
Kuk-ki Hong (2008-2012)
Zihe Liu, Chalmers (2008-2012)
Kanokarn Kocharin (2009-2013)
Rasmus Ågren (2008-2013)
Tobias Österlund (2009-2014)
Fredrik Karlsson (2009-2014)
Christoph Knuf (2009-2014)
Natapol Pornputtapong (2010-2014)
Lifang Liu (2010-2014)
Bouke de Jong (2010-2015)
Yiming Zhang, Chalmers (2010-2015)
Francesco Gatto, Chalmers (2012-2015)
Saeed Shoaie, Chalmers (2011-2015)
Amir Feizi, Chalmers (2012-2016)
Leif Väremo, Chalmers (2012-2016)
Nicolaas Buijs, Chalmers (2011-2016)
Mingji Li, DTU (2013-2016)
Edith Angelica Rodriguez Prado, DTU (2013-2016)
Stefan Tippmann, Chalmers (2012-2016)
Pouyan Ghaffari Nouran (2013-2017)
Jens Christian F. Nielsen, Chalmers (2014-2018)
Paulo Teixeira, Chalmers (2013-2018)
Jichen Bao, Chalmers (2013-2018)
Alexandra Bergman, Chalmers (2013-2019)
Avlant Nilsson, Chalmers (2014-2019)
Benjamín José Sánchez Barja, Chalmers (2014-2019)
David Bergenholm, Chalmers (2014-2020)
Parizad Babaei, Chalmers (2015-2019)
Promi Das, Chalmers (2015-2019)
Raphael Ferreira, Chalmers (2015-2019)
Gang Li, Chalmers (2016-2020)
Simonas Marcišauskas, Chalmers (2015-2020)
Christoph Börlin, Chalmers (2016-2020)
Rasool Saghaleyni, Chalmers (2016-2021)
Carl Melina, Chalmers (2016-2021)
Ning Qin, BUCT (2016-2021)
Qi Qi, Chalmers (2017-2021)
Feiran Li, Chalmers (2017-2021)
Yijin Zhao, BUCT (2017-2021)

Graduated PhD Students (examiner)

Joachim Almquist, FCC, Sweden (2010-2017)
Yasaman Dabirian, Chalmers (2016-2021)

Graduated PhD Students (co-supervisor)

Lars Højlund Christensen, DTU (1989-1992)
Stig Benthin, DTU (1989-1992)
Annemarie Gade Pedersen, DTU (1990-1992)
Simone de Jong Frandsen, DTU (1991-1993)
Ulrik Schultze, DTU (1992-1995)
Teresa Zangorilami, DTU (1994-1998)
Kasper Møller, DTU (1998-2001)
Mikkel Nordkvist, DTU (2001-2005)
Renata Usaite, DTU (2004-2008)
Lasse Pedersen, DTU (2007-2010)
Kanchana Rueksomtawin Kildegaard, DTU (2004-2011)
Xiao Chen, DTU (2007-2011)
Kwanjeera Wanichthanarak, Chalmers (2010-2014)
Kaisa Thorell, Gothenburg University, Sweden (2010-2014)
Leonie Wenning, Chalmers (2014-2018)
Yating Hu, Chalmers (2015-2019)
Elias Björnson, Gothenburg University (2014-2021)
John Hellgren (2017-2022)

Visiting PhD Students (co-supervisor)

Robert Lejeune, Free University of Brussels (1994-1995)
Pedro N. Pissarra, DTU (visiting PhD student) (1994-1995)
Einar Jonsbu, DTU (visiting PhD student) (1999-2000)
Andreas Karoly Gomberg, DTU (visiting PhD student) (1998-2000)
Joel Forest Moxley, DTU (visiting PhD student) (2003-2005)
Tunahan Cakir, DTU (visiting PhD student) (2004-2005)
Kazim Yalcin Arga, DTU (visiting PhD student) (2004-2005)
Intawat Nookaew, KMUTT (2005-2006)
Goutham Vemuri, University of Georgia (2005-2006)
Donatella Cimini, DTU (visiting PhD student) (2006)
Valeria Mapelli, DTU (visiting PhD student) (2006-2007)
Paula Jouhten, Chalmers (visiting PhD student) (2008-2009)
Raphael Aggio, University of Auckland (2009)
William Alfonso Rodriguez Limas, National University of Mexico (2009-2010)
Kantida Kusonmano, UMIT (2011)
Akarin Boonsombuti, Mahasarakham University (2011-2012)
Jorge Alberto Vasquez Castillo, Antioquia University (2011-2012)
Josh Michener, Caltech/Stanford (2011)
Ibrahim E. El-Semman, Assiut University (2012-2014)
Jiufu Qin, Jiangnan University, China (2011-)
Rui Pereira, University of Minho, Portugal (2012-2014)
Cheng Zhang, East China Univesity of Science and Technology, China (2013-2015)
John Casey, University of Hawaii, USA (2014)
Jacqueline Rand, University of Wisconsin, USA (2014)
Zahra Azim Zadeh Irani, Tarbiat Modares University, Iran (2014-2015)
Yu Chen, East China University of Science and Technology, China (2015-2017)
Chinh Bkrong Nguyen, Oslo University, Norway (2017-2018)
Zhengming Zhu, Jiangnan University, China (2017-2018)
Chunjun Zhan, Jiangnan University, China (2017-2018)
Zeinab Hefny, Katholiek University of Leuven, Belgium (2017-2019)

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. Verena Siewers, Senior Researcher & Docent, DTU & Chalmers (2006-2020) 13. Yun Chen, Resarcher & Docent, Chalmers (2008-2020) 14. Marie Nordqvist, Research Engineering and Lab Manager (2008-2017) 15. Marie-Louise Wennerhag, Financial Officer, Chalmers (2008-2018) 16. Martina Butorac (2008-2020) 17. Malin Nordvall, Research Engineer, Chalmers (2009-2014) 18. Stefan Rokem, Visiting Professor, Chalmers (2010) 19. Pegah Khorramzadeh, Research Engineering, Chalmers (2010-2011) 20. Sergio Bordel Velasco, Assistant Professor (2010-2014) 21. Suwanee Jansa-Ard, Research Engineer, Chalmers (2011-2014) 22. Martin Markström, Co-Director AoA, Chalmers (2011-2014) 23. Ximena Rozo Sevilla, Research Engineer, Chalmers (2011-2015) 24. Danilo Porro, Visiting Professor, Chalmers (2012) 25. Emma Ribbenhed, Research Engineer, Chalmers (2013-2015) 26. Antonio Marras, Research Assistant, Chalmers (2013-2015) 27. Eduard Kerkhoven, Researcher, Chalmers (2013-2020) 28. Shaghayegh Hosseini, Data Manager, Chalmers (2013-2019) 29. Gheorge Manuel Borja Zamfir, PhD student, DTU (2013-2019) 30. Brian Pfleger, Visiting Professor, Chalmers (2014) 31. Julia Karlsson, Research Engineer, Chalmers (2014-2016) 32. Matthias Nilsson, Research Engineer, Chalmers (2015-2016) 33. Daniel Hermansson, Research Engineer, Chalmers (2016) 34. Jianye Xia, Visiting Professor, Chalmers (2016-2017) 35. Xiaojun Ji, Visiting Professor, Chalmers (2016-2017) 36. Liming Quyang, Visiting Professor, Chalmers (2016-2017) 37. Takayoshi Fujii, Visiting Researcher, Chalmers (2016-2018) 38. Fredrik Schubert, Chalmers (2016-2019) 39. Joakim Norbeck, Researcher & Docent, Chalmers (2015-2020) 40. Johan Björkeroth, PhD student, Chalmers (2016-2020) 41. Erica Dahlin, Chalmers (2008-2020) 42. Angelica Ardehed (Lab Manager), Chalmers (2016-2020) 43. Emilie Lindquist, Chalmers (2017-2020) 44. Pierre-Etienne Cholley, Chalmers (2017-2020) 45. Virinchi Billa, Chalmers (2017-2019) 46. Mihail Anton, Chalmers (2017-2020) 47. Felipe Lopez-Isunza, Visiting Professor, Chalmers (2019)