Markus Herrgard

Markus Herrgard

Senior researcher

Kogle Alle 6

Building: Thuja House, 2.L.01a

2970 Hørsholm


Mobile: 24 92 17 80

iLoop Core


I'm the director of the iLoop Core unit at the NNF Center for Biosustainability. The iLoop (Iterative Cell Factory Development Loop) Core works on translational projects related to microbial cell factory engineering. The core consists of five platforms led by independent group leaders with a total staff of ~30 researchers, engineers and technicians: 

  1. Genome engineering - Dr. Jerome Maury
  2. Screening and fermentation - Dr. Konstantin Schneider
  3. Automation - Mr. Olivier Bitterlin
  4. Analytics - Dr. Scott Harrison
  5. Sequencing, informatics and modeling - Drs. Niko Sonnenschein and Markus Herrgard

Sequencing, Informatics and Modeling (SIM) Group


I'm also the group leader for Sequencing, Informatics and Modeling Group at the NNF Center for Biosustainability. Our group works on:

  1. Genome-scale modeling of biochemical networks
  2. Data-driven computational approaches to cell factory design
  3. Systems biology of microbial platform cell factories
  4. Next generation sequencing applied to cell factory development
  5. Software development to support cell factory development workflows

We collaborate extensively with other groups at the CFB DTU site as well as CFB satellite sections at University of California San Diego and Chalmers University.


My publications:  Complete list of publications in Google Scholar

My CV: LinkedIn profile


SIM staff:


Modeling team:

  • Niko Sonnenschein, research scientist, subgroup leader
  • Emre Özdemir, postdoc, metabolic modeling
  • Joao Cardoso, Ph.D. student
  • Marta Matos, Ph.D. student
  • Chistian Lieven, Ph.D. student

Sequencing and informatics team:

  • Ida Bonde, postdoc, microbial bioinformatics
  • Anna Koza, postdoc, next generation sequencing
  • Lasse Ebdrup Pedersen, bioinformatics scientist, CHO bioinformatics

Software development team:

  • Lars Schöning, lead software engineer
  • Ju Goncalves, software engineer

Other affliated staff at CFB:

  • Rebecca Lennen, research scientist, project leader for platform strain development
  • Hao Luo, strain development scientist, project leader for production strain development
  • Kai Zhuang, research scientist, multi-scale techno-economic modeling
  • Sumesh Sukumara, postdoc, multi-scale techno-economic modeling
  • Miguel Campodonico, postdoc, multi-scale techno-economic modeling



1993 - 1998 M.Sc. - Aalto University, Finland
1999 - 2004 Ph.D. - University of California, San Diego

Academic grades


Professional experience

2004 - 2006 Post-doctoral researcher - University of California, San Diego, Bioengineering
2006 - 2008 Project Scientist - University of California, San Diego, Bioengineering
2008 - 2012 Senior Scientist - Synthetic Genomics, Inc.
2012 - Group leader - DTU, Biosustain
2014 - iLoop Core Manager - DTU, Biosustain
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  • Frontiers in Microbiology

    ISSNs: 1664-302X

    Frontiers Research Foundation, Switzerland

    BFI (2015): BFI-level 1, ISI indexed (2013): ISI indexed no

    Central database


  • B M C Systems Biology

    ISSNs: 1752-0509, 17520509

    BioMed Central Ltd., United Kingdom

    BFI (2015): BFI-level 1, ISI indexed (2013): ISI indexed yes

    Central database


  • P L o S One

    ISSNs: 1932-6203, 19326203

    Public Library of Science, United States

    BFI (2015): BFI-level 1, ISI indexed (2013): ISI indexed yes

    Central database


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