Project Scientist

Until Feb 2008 I was a project scientist in the Systems Biology Research Group at UCSD. I got my Ph.D. from UCSD in 2004 in Bioengineering/Bioinformatics. While at UCSD I worked on the following projects:

• Reconstruction and modeling of genome-scale metabolic networks focusing on yeast and human metabolism
• Reconstruction of regulatory networks based on high-throughput datasets and the integrated modeling of regulatory and metabolic networks.
• Development of the Cobra Toolbox - a suite of in silico tools for constraint-based modeling of biochemical networks. Please note that I don't maintain the Toolbox anymore. Direct your questions about the toolbox to Jan Schellenberger.

Synthetic biology with emphasis on metabolic engineering.

Education

2004 Ph.D. in Bioengineering with Specialization in Bioinformatics University of California, San Diego GPA: 4.0/4.0 Coursework in bioinformatics, statistics, bioengineering, and biology

1998-1999 Ph.D. program in Physics University of Illinois at Urbana-Champaign GPA: 4.0/4.0 Coursework in biochemistry, biophysics, and statistical physics

1998 M.Sc. in Engineering Physics and Mathematics 1997 B.Sc. in Engineering Physics and Mathematics Helsinki University of Technology, Finland GPA: 4.7/5.0 Major: Applied Physics
Minor: Theoretical and Computational Physics Graduated with honors

1996-1997 Exchange Student in the Physics M.Phys. program University of York, UK

Research Experience

Bioinformatics and Computational Biology and the Genetic Circuits Research Groups UCSD Bioengineering 1999- Graduate research assistant/Computer system administrator Functional genomics and biochemical pathway bioinformatics Supervisor: Profs. Shankar Subramaniam and Bernhard Palsson

Laboratory of Physics, Helsinki University of Technology 1997-1998 Implementing and applying the Berry phase method for polarization calculations in semiconductors using parallel computers (M.Sc. thesis) Supervisor: Prof. Risto Nieminen

Department of Physics, University of York 1996-1997 Computational investigation of exact density functional theory (B.Sc. thesis) Supervisor: Prof. Rex Godby

Low Temperature Laboratory, Helsinki University of Technology 1995-1996 Computer simulations of arrays of nanoscale tunnel junctions Supervisor: Prof. Mikko Paalanen

Department of Neurophysiology, Kuopio University Hospital 1994 Statistical analysis of neurophysiological data

Teaching Experience

University of California, San Diego 2000 and 2001 Teaching assistant for BENG 130 Molecular Physical Chemistry

University of Illinois at Urbana-Champaign 1998-1999 Teaching assistant for Physics 113 (Thermodynamics) and Physics 114 (Quantum Mechanics)

Helsinki University of Technology 1995-1998 Teaching assistant for Physics I (Classical mechanics), Mathematics II, and Numerical Analysis A

Honors and Awards

Sun Microsystems fellowship 2000-2002 Fulbright scholarship 1998-1999 Helsinki University of Technology scholarship 1997 Honkanen Foundation scholarship 1996 European Union exchange student fellowship 1996

Computer Skills

Programming languages: Python, Perl, Java, PHP, C/C++, Fortran 90 Operating systems: Unix (Linux, Solaris, IRIX, AIX) as system administrator, Windows

Other technologies: Matlab, XML, Apache, MySQL

Professional Societies

Member of the International Society for Computational Biology (ISCB) Member of the Genetics Society of America

Publications

Articles

Becker SA, Feist AM, Mo MM, Hannum G, Palsson BO, Herrgard MJ. Quantitative Prediction of Cellular Metabolism with Constraint-based Models: The COBRA Toolbox, Nature Protocols (accepted).

Herrgard MJ, Fong SS, Palsson BO. Systematic identification of genome-scale metabolic models using experimentally measured flux profiles, PLoS Computational Biology, 2(7): e72 (2006).

Herrgard MJ, Lee B-S, Portnoy V, Palsson BO. "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae, Genome Research, 16(5):627-35 (2006).

Herrgard MJ,Palsson BO. Untangling the web of functional and physical interactions in yeast, Journal of Biology, 4:5 (2005).*

Duarte NC, Herrgard MJ, Palsson BO. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model, Genome Research, 14:1289-1309 (2004).

Herrgard MJ, Palsson BO. Flagellar biosynthesis in silico: building quantitative models of regulatory networks00537-9), Cell, 117:689-690 (2004).*

Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks, Nature, 429:92-96 (2004).

Herrgard MJ, Covert MW, Palsson BO. Reconstruction of Microbial Transcriptional Regulatory Networks, Current Opinion in Biotechnology, 15:70-77 (2004).

Herrgard MJ, Covert MW, Palsson BO. Reconciling Gene Expression Data with Known Genome-scale Regulatory Network Structures, Genome Research, 13: 2423-2434 (2003).

Allen TE, Herrgard MJ., Mingzhu L, Qiu Y, Glasner JD, Blattner FR, Palsson BO. Genome-scale analysis of the uses of the Escherichia coli genome: a model-driven analysis of heterogeneous datasets, Journal of Bacteriology, 185(21):6392-6399 (2003).

*Commentaries

Book Chapters

Herrgard MJ, Palsson BO. Genome Scale Models of Metabolic and Regulatory Networks, In: Systems Biology - Volume 2: Networks and Models, Oxford University Press, 2006.

Conferences

Herrgard, M.J., Covert, M.W., and Palsson, B.O. Reconciling bottom-up and top-down reconstruction of regulatory networks. 3rd International Conference in Systems Biology, Stockholm, Sweden, 2002.

Herrgard, M.J, and Palsson, B.O. Iterative constraint-based model building. 4th International Conference in Systems Biology, St. Louis, MO, 2003.

Allen, T.E., Herrgard, M.J., Liu, M., Qiu, Y., Glasner, J.D., Blattner, F.R., and Palsson, B.O. Genome-scale Analysis of the Uses of the Escherichia coli Genome: A Model-Driven Analysis of Heterogeneous Datasets. The 11th International Conference on Microbial Genomes. Durham, NC 2003

Duarte, N.C., Herrgard, M.J., and Palsson, B.O. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. 4th International Conference in Systems Biology, St. Louis, MO, 2003.

Herrgard, M.J., Lee, B.-S., and Palsson, B.O. Carbon source and oxygen regulation in Saccharomyces cerevisiae – Insights from a transcriptionally regulated metabolic model. Yeast Genetics and Molecular Biology Meeting, Seattle, WA, 2004.

Duarte, N.C., Herrgard, M.J., and Palsson, B.O. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Yeast Genetics and Molecular Biology Meeting, Seattle, WA, 2004.

Contact Information

Email Address: markus.herrgard_at_gmail.com Phone: 24 92 17 80 Current Address: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm