Markus Herrgard

Markus Herrgard

Professor

DTU BIOSUSTAIN
Novo Nordisk Foundation Center for Biosustainability

Technical University of Denmark

Kemitorvet

Building 220, room 227F

2800 Kgs. Lyngby

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2019
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Building a global alliance of biofoundries

Hillson, Nathan ; Caddick, Mark ; Cai, Yizhi ; Carrasco, Jose A. ; Chang, Matthew Wook ; Curach, Natalie C. ; Bell, David J. ; Le Feuvre, Rosalind ; Friedman, Douglas C. ; Fu, Xiongfei ; Gold, Nicholas D. ; Herrgård, Markus J. ; Holowko, Maciej B. ; Johnson, James R. ; Johnson, Richard A. ; Keasling, Jay D. ; Kitney, Richard I. ; Kondo, Akihiko ; Liu, Chenli ; Martin, Vincent J.J. ; Menolascina, Filippo ; Ogino, Chiaki ; Patron, Nicola J. ; Pavan, Marilene ; Poh, Chueh Loo ; Pretorius, Isak S. ; Rosser, Susan J. ; Scrutton, Nigel S. ; Storch, Marko ; Tekotte, Hille ; Travnik, Evelyn ; Vickers, Claudia E. ; Yew, Wen Shan ; Yuan, Yingjin ; Zhao, Huimin ; Freemont, Paul S.
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-10079-2

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Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Mohamed, Elsayed Tharwat Tolba ; Mundhada, Hemanshu ; Landberg, Jenny Marie ; Cann, Isaac ; Mackie, Roderick I. ; Nielsen, Alex Toftgaard ; Herrgard, Markus J. ; Feist, Adam M.
in: Microbial Cell Factories, vol: 18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-019-1165-2

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Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Massaiu, Ilaria ; Pasotti, Lorenzo ; Sonnenschein, Nikolaus ; Rama, Erlinda ; Cavaletti, Matteo ; Magni, Paolo ; Calvio, Cinzia ; Herrgård, Markus J.
in: Microbial Cell Factories, vol: 18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-018-1052-2

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OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Jensen, Kristian ; Broeken, Valentijn ; Hansen, Anne Sofie Lærke ; Sonnenschein, Nikolaus ; Herrgård, Markus J.
in: Metabolic Engineering Communications, vol: 8

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.mec.2019.e00087

2018
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Bacterial cells with improved tolerance to diacids

Lennen, Rebecca ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander ; Feist, Adam ; Tharwat Tolba Mohamed, Elsayed
Patent no.: WO2018091525 , Date: 2018-05-24

Type: Patent

Status: Published     |    Year: 2018

 

Computational Methods to Assess the Production Potential of Bio-Based Chemicals

Campodonico, Miguel A ; Sukumara, Sumesh ; Feist, Adam M. ; Herrgård, Markus J.
part of: Synthetic Metabolic Pathways, pages: 97-116, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_7

 

Enhancing Metabolic Models with Genome-Scale Experimental Data

Jensen, Kristian ; Gudmundsson, Steinn ; Herrgård, Markus
part of: Systems Biology, pages: 337-350, 2018, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-3-319-92967-5_17

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Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology

Lieven, Christian ; Herrgård, Markus J. ; Sonnenschein, Nikolaus
in: Biotechnology Journal, vol: 13, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/biot.201800011

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RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli

McCloskey, Douglas ; Xu, Julia ; Schrübbers, Lars ; Christensen, Hanne B. ; Herrgård, Markus J.
in: Metabolic Engineering, vol: 47, pages: 383-392

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.04.009

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Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

Shepelin, Denis ; Hansen, Anne Sofie Lærke ; Lennen, Rebecca ; Luo, Hao ; Herrgård, Markus J.
in: Genes, vol: 9, issue: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3390/genes9050249

2017
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Bacterial cells with improved tolerance to polyols

Lennen, Rebecca ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander ; Feist, Adam ; Tharwat Tolba Mohamed, Elsayed
Patent no.: WO2017211883, Date: 2017-12-14

Type: Patent

Status: Published     |    Year: 2017

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DD-DeCaF: Data-Driven Design of Cell Factories and Communities

Beber, Moritz Emanuel ; Dannaher, Danny ; Fodor, Matyas ; Galkina, Svetlana ; Redestig, Nils Henning ; Sonnenschein, Nikolaus ; Herrgard, Markus
part of: Book of Abstracts, Sustain 2017, 2017, Technical University of Denmark (DTU)
Presented at:
Sustain 2017

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2017

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Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution

Mohamed, Elsayed T. ; Wang, Shizeng ; Lennen, Rebecca M. ; Herrgård, Markus J. ; Simmons, Blake A. ; Singer, Steven W. ; Feist, Adam M.
in: Microbial Cell Factories, vol: 16, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1186/s12934-017-0819-1

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Isolation and characterization of the E. coli membrane protein production strain Mutant56(DE3)

Baumgarten, Thomas ; Schlegel, Susan ; Wagner, Samuel ; Löw, Mirjam ; Eriksson, Jonas ; Bonde, Ida ; Herrgard, Markus ; Heipieper, Hermann J. ; Nørholm, Morten ; Slotboom, Dirk Jan ; de Gier, Jan-Willem
in: Scientific Reports, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1038/srep45089

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Systems biology solutions for biochemical production challenges

Hansen, Anne Sofie Lærke ; Lennen, Rebecca M ; Sonnenschein, Nikolaus ; Herrgard, Markus
in: Current Opinion in Biotechnology, vol: 45, pages: 85-91

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.copbio.2016.11.018

2016
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Bio-based chemicals - green, but also sustainable?

Ögmundarson, Ólafur ; Herrgard, Markus ; Förster, Jochen ; Fantke, Peter
Presented at:
ATV Sustain conference

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2016

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Engineering and systems level analysis of Saccharomyces cerevisiae for production of 3 hydroxypropionic acid via malonyl CoA reductase dependent pathway

Kildegaard, Kanchana Rueksomtawin ; Jensen, Niels Bjerg ; Schneider, Konstantin ; Czarnotta, Eik ; Özdemir, Emre ; Klein, Tobias ; Maury, Jerome ; E. Eber, Birgitta ; Christensen, Hanne Bjerre ; Chen, Yun ; Kim, Il-Kwon ; Herrgard, Markus ; Blank, Lars Mathias ; Förster, Jochen ; Nielsen, Jens ; Borodina, Irina
in: Microbial Cell Factories, vol: 15, issue: 53

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016

 

Genome-Scale Models

Bergdahl, Basti ; Sonnenschein, Nikolaus ; Machado, Daniel ; Herrgard, Markus ; Förster, Jochen
part of: Fundamental Bioengineering, pages: 143-182, 2015, Wiley-VCH, Weinheim, Germany

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1002/9783527697441.ch06

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Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Monk, Jonathan M ; Koza, Anna ; Campodonico, Miguel A ; Machado, Daniel ; Seoane, Jose Miguel ; Palsson, Bernhard ; Herrgard, Markus ; Feist, Adam
in: Cell Systems, vol: 3, issue: 3, pages: 238-251

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.08.013

 

Predictable tuning of protein expression in bacteria

Bonde, Mads ; Pedersen, Margit ; Klausen, Michael Schantz ; Ingemann Jensen, Sheila ; Wulff, Tune ; Harrison, Scott James ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander
in: Nature Methods, vol: 13, pages: 233-236

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2016     |    DOI: https://doi.org/10.1038/nmeth.3727

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Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Machado, Daniel ; Herrgard, Markus ; Rocha, Isabel
in: P L o S Computational Biology (Online), vol: 12, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1371/journal.pcbi.1005140

2015
 

A Multi-scale, Multi-disciplinary Approach for Assessing the Technological, Economic, and Environmental Performance of Bio-based Chemicals

Herrgard, Markus ; Sukumara, Sumesh ; Campodonico Alt, Miguel Angel ; Zhuang, Kai
in: Biochemical Society. Transactions, vol: 43, issue: 6, pages: 1151-1156

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1042/BST20150144

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A Multi-Scale, Multi-Disciplinary Approach for Assessing the Technological, Economic, and Environmental Performance of Bio-Based Chemicals

Campodonico, Miguel ; Herrgard, Markus ; Sukumara, Sumesh ; Zhuang, Kai
part of: Book of Abstracts. DTU's Sustain Conference 2015, 2015, Technical University of Denmark (DTU)
Presented at:
DTU Sustain Conference 2015

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2015

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Analysis of gene essentiality in Escherichia coli across strains and growth conditions

Bonde, Ida ; Lennen, Rebecca ; Cardoso, Joao ; Koza, Anna ; Herrgard, Markus
Presented at:
First Annual Danish Bioinformatics Conference

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2015

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Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Cardoso, Joao ; Andersen, Mikael Rørdam ; Herrgard, Markus ; Sonnenschein, Nikolaus
in: Frontiers in Bioengineering and Biotechnology, vol: 3, issue: 13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.3389/fbioe.2015.00013

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Co-evolution of strain design methods based on flux balance and elementary mode analysis

Machado, Daniel ; Herrgard, Markus
in: Metabolic Engineering Communications, vol: 2, pages: 85-92

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.meteno.2015.04.001

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Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A. ; Almaas, E. ; Bauer, E. ; Bordbar, A. ; Burgard, A. P. ; Chang, R. L. ; Drager, A. ; Famili, I. ; Feist, A. M. ; Fleming, R. M. ; Fong, S. S. ; Hatzimanikatis, V. ; Herrgard, M. J. ; Holder, A. ; Hucka, M. ; Hyduke, D. ; Jamshidi, N. ; Lee, Sang Yup ; Le Novere, N. ; Lerman, J. A. ; Lewis, Nathan ; Ma, D. ; Mahadevan, R. ; Maranas, C. ; Nagarajan, H. ; Navid, A. ; Nielsen, Jens ; Nielsen, L. K. ; Nogales, J. ; Noronha, A. ; Pal, C. ; Palsson, Bernhard ; Papin, J. A. ; Patil, Kiran R. ; Price, N. D. ; Reed, J. L. ; Saunders, M. ; Senger, R. S. ; Sonnenschein, Nikolaus ; Sun, Yuekai ; Thiele, I.
in: Molecular Systems Biology, vol: 11, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.15252/msb.20156157

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Editorial: Current Challenges in Modeling Cellular Metabolism

Machado, Daniel ; Zhuang, Kai ; Sonnenschein, Nikolaus ; Herrgard, Markus
in: Frontiers in Bioengineering and Biotechnology, vol: 3

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.3389/fbioe.2015.00193

 

Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

Mirzadeh, Kiavash ; Martinez, Virginia ; Toddo, Stephen ; Guntur, Suchithra ; Herrgard, Markus ; Elofsson, Arne ; Nørholm, Morten ; Daley, Daniel O.
in: A C S Synthetic Biology, vol: 4, issue: 9, pages: 959-965

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1021/acssynbio.5b00033

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Methods for modeling chinese hamster ovary (cho) cell metabolism.

Herrgard, Markus ; Pedersen, Lasse Ebdrup ; Lewis, Nathan E. (Inventor) ; Bruntse, Anders Bech
Patent no.: WO2015010088, Date: 2015-01-22

Type: Patent

Status: Published     |    Year: 2015

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Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Machado, Daniel ; Herrgard, Markus ; Rocha, Isabel
in: Frontiers in Bioengineering and Biotechnology, vol: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.3389/fbioe.2015.00154

 

Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae

Jakociunas, Tadas ; Bonde, Ida ; Herrgard, Markus ; Harrison, Scott James ; Kristensen, Mette ; Pedersen, Lasse Ebdrup ; Jensen, Michael Krogh ; Keasling, Jay
in: Metabolic Engineering, vol: 28, pages: 213-222

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.ymben.2015.01.008

 

Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production

Zhuang, Kai ; Herrgard, Markus
in: Metabolic Engineering, vol: 31, pages: 1-12

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.ymben.2015.05.007

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Multi-Scale Technoeconomic Framework for Assessing Viability of Emerging Bio-based Processes

Zhuang, Kai ; Sukumara, Sumesh ; Campodonico Alt, Miguel ; Herrgard, Markus
part of: Book of Abstracts. DTU's Sustain Conference 2015, 2015, Technical University of Denmark (DTU), Lyngby
Presented at:
DTU Sustain Conference 2015

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2015

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Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

Zielinski, Daniel C. ; Filipp, F. V. ; Bordbar, A. ; Jensen, K. ; Smith, J. W. ; Herrgard, Markus ; Mo, Monica L. ; Palsson, B. O.
in: Nature Communications, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/ncomms8101

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Seven gene deletions in seven days

Ingemann Jensen, Sheila ; Lennen, Rebecca ; Herrgard, Markus ; Nielsen, Alex Toftgaard
in: Scientific Reports, vol: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/srep17874

2014
 

A compendium of genetic variant data

Cardoso, Joao ; Schöning, Lars Yannik ; Herrgard, Markus ; Sonnenschein, Nikolaus
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Technical University of Denmark (DTU), Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

 

A kinetic model of thiamine biosynthesis in Escherichia coli

Matos, Marta ; Herrgard, Markus ; Andersen, Mikael Rørdam ; Sonnenschein, Nikolaus
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Technical University of Denmark (DTU), Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

 

Biotechnology for renewable chemicals

Borodina, Irina ; Kildegaard, Kanchana Rueksomtawin ; Jensen, Niels Bjerg ; Sherstyk, Svetlana ; Maury, Jerome ; Forster, Jochen ; Herrgard, Markus ; Nielsen, Jens
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Technical University of Denmark (DTU), Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

 

Combinatorial Strategies for Improving Multiple-Stress Resistance in Industrially Relevant Escherichia coli Strains.

Lennen, Rebecca ; Herrgard, Markus
in: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol: 80, issue: 19, pages: 6223-6242

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1128/AEM.01542-14

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Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.

Sandberg, Troy E. ; Pedersen, Margit ; LaCroix, Ryan A. ; Ebrahim, Ali ; Bonde, Mads ; Herrgard, Markus ; Palsson, Bernhard ; Sommer, Morten ; Feist, Adam
in: Molecular Biology and Evolution, vol: 31, issue: 10, pages: 2647-2662

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1093/molbev/msu209

 

Evolution Reveals A Glutathione-dependent Mechanism Of 3-hydroxypropionic Acid Detoxification

Kildegaard, Kanchana Rueksomtawin ; Hallström, Björn M. ; Blicher, Thomas H. ; Sonnenschein, Nikolaus ; Jensen, Niels Bjerg ; Sherstyk, Svetlana ; Harrison, Scott James ; Maury, Jerome ; Herrgard, Markus ; Juncker, Agnieszka ; Förster, Jochen ; Nielsen, Jens ; Borodina, Irina
Presented at:
Metabolic Engineering X

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2014

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Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

Kildegaard, Kanchana Rueksomtawin ; Hallström, Björn M. ; Blicher, Thomas H. ; Sonnenschein, Nikolaus ; Jensen, Niels Bjerg ; Sherstyk, Svetlana ; Harrison, Scott James ; Maury, Jerome ; Herrgard, Markus ; Juncker, Agnieszka ; Förster, Jochen ; Nielsen, Jens ; Borodina, Irina
in: Metabolic Engineering, vol: 26, pages: 57-66

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.ymben.2014.09.004

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Increased tolerance towards serine obtained by adaptive laboratory evolution

Mundhada, Hemanshu ; Seoane, Jose Miguel ; Koza, Anna ; Herrgard, Markus ; Feist, Adam ; Nielsen, Alex Toftgaard
part of: Proceedings of SIMB Annual meeting 2014, 2015
Presented at:
2014 Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting and Exhibition

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

 

Library sequencing strategies for comparative analysis of stress resistance mechanisms in Escherichia coli strains

Lennen, Rebecca ; Bonde, Ida ; Koza, Anna ; Herrgard, Markus
in: New Biotechnology, vol: 31, pages: S86

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.nbt.2014.05.1811

 

Multi-scale Exploration of the Technical, Economic, and Environmental Dimensions of Bio-based Chemical Production

Zhuang, Kai ; Herrgard, Markus
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Technical University of Denmark (DTU), Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

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Putting computational modeling at the fingertips of bench biologists

Sonnenschein, Nikolaus ; Herrgard, Markus
Presented at:
2nd EMBO Conference on Visualizing Biological Data

Type: Poster (Peer reviewed)

Status: Published     |    Year: 2014

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Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.

Machado, Daniel ; Herrgard, Markus
in: P L o S Computational Biology (Online), vol: 10, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1371/journal.pcbi.1003580

2013
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Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments

Klatt, Christian G. ; Inskeep, William P. ; Herrgard, Markus ; Jay, Zackary J. ; Rusch, Douglas B. ; Tringe, Susannah G. ; Parenteau, M. Niki ; Ward, DavidM. ; Boomer, Sarah M. ; Bryant, Donald A. ; Miller, Scott R.
in: Frontiers in Microbiology, vol: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.3389/fmicb.2013.00106

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Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.

Takacs-Vesbach, Cristina ; Inskeep, William P ; Jay, Zackary J ; Herrgard, Markus ; Rusch, Douglas B ; Tringe, Susannah G ; Kozubal, Mark A ; Hamamura, Natsuko ; Macur, Richard E ; Fouke, Bruce W ; Reysenbach, Anna-Louise ; McDermott, Timothy R ; Jennings, Ryan deM ; Hengartner, Nicolas W ; Xie, Gary
in: Frontiers in Microbiology, vol: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.3389/fmicb.2013.00084

 

Multi-scale modeling for sustainable chemical production

Zhuang, Kai ; Bakshi, Bhavik R. ; Herrgard, Markus
in: Biotechnology Journal, vol: 8, issue: 9, pages: 973-984

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1002/biot.201200272

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Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

Inskeep, William P ; Jay, Zackary J ; Herrgard, Markus ; Kozubal, Mark A ; Rusch, Douglas B ; Tringe, Susannah G ; Macur, Richard E ; Jennings, Ryan deM ; Boyd, Eric S ; Spear, John R ; Roberto, Francisco F
in: Frontiers in Microbiology, vol: 4, pages: 95

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.3389/fmicb.2013.00095

 

The Uses and Future Prospects of Metabolomics and Targeted Metabolite Profiling in Cell Factory Development

Harrison, Scott James ; Herrgard, Markus
in: Industrial Biotechnology, vol: 9, issue: 4, pages: 196-202

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1089/ind.2013.0008

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The YNP metagenome project

Inskeep, William P. ; Jay, Zackary J. ; Tringe, Susannah G. ; Herrgard, Markus ; B. Rusch, Douglas
in: Frontiers in Microbiology, vol: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.3389/fmicb.2013.00067

2012
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Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”

Herrgard, Markus ; Panagiotou, Gianni
in: Computational and Structural Biotechnology Journal, vol: 3, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2012     |    DOI: https://doi.org/10.5936/csbj.201210012

 

Choosing the right platform for the right product: Sustainable production of chemicals in microbial cell factories

Herrgard, Markus
Presented at:
Chemical engineering at the Life science interface conference

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2012

2010
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Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

Inskeep, William P. ; Rusch, Douglas B. ; Jay, Zackary J. ; Herrgard, Markus J. ; Kozubal, Mark A. ; Richardson, Toby H. ; Macur, Richard E. ; Hamamura, Natsuko ; Jennings, Ryan deM. ; Fouke, Bruce W. ; Reysenbach, Anna-Louise ; Roberto, Frank ; Young, Mark ; Schwartz, Ariel ; Boyd, Eric S. ; Badger, Jonathan H. ; Mathur, Eric J. ; Ortmann, Alice C. ; Bateson, Mary ; Geesey, Gill ; Frazier, Marvin
in: P L o S One, vol: 5, issue: 3, pages: Article No.: e9773

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2010     |    DOI: https://doi.org/10.1371/journal.pone.0009773

2009
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Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Mo, Monica L. ; Palsson, Bernhard O. ; Herrgard, Markus J.
in: B M C Systems Biology, vol: 3, pages: Article No.: 37

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2009     |    DOI: https://doi.org/10.1186/1752-0509-3-37

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Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation

Barrett, Christian L ; Herrgard, Markus J ; Palsson, Bernhard
in: B M C Systems Biology, vol: 3, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2009     |    DOI: https://doi.org/10.1186/1752-0509-3-30

 

Reconstruction of biochemical networks in microorganisms.

Feist, Adam ; Herrgard, Markus ; Thiele, Ines ; Reed, Jennie L ; Palsson, Bernhard Ø
in: Nature Reviews. Microbiology, vol: 7, issue: 2, pages: 129-143

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2009     |    DOI: https://doi.org/10.1038/nrmicro1949

2008
 

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgard, Markus ; Swainston, Neil ; Dobson, Paul ; Dunn, Warwick B. ; Arga, K Yalçin ; Arvas, Mikko ; Blüthgen, Nils ; Borger, Simon ; Costenoble, Roeland ; Heinemann, Matthias ; Hucka, Michael ; Le Novère, Nicolas ; Li, Peter ; Liebermeister, Wolfram ; Mo, Minica L. ; Soberano de Oliveira, Ana Paula ; Petranovic, Dina ; Pettifer, Stephen ; Simeonidis, Evangelos ; Smallbone, Kieran ; Spasić, Irena ; Weichart, Dieter ; Brent, Roger ; Broomhead, David S. ; Westerhoff, Hans V. ; Kirdar, Betül ; Penttilä, Merja ; Klipp, Edda ; Palsson, Bernhard Ø. ; Sauer, Uwe ; Oliver, Stephen G. ; Mendes, Pedro ; Nielsen, Jens ; Kell, Douglas B.
in: Nature Biotechnology, vol: 26, issue: 10, pages: 1155-1160

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2008     |    DOI: https://doi.org/10.1038/nbt1492

 

Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain

Portnoy, V. A. ; Herrgard, Markus ; Palsson, B. O.
in: Applied and Environmental Microbiology, vol: 74, issue: 24, pages: 7561-7569

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2008     |    DOI: https://doi.org/10.1128/AEM.00880-08

 

Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli

Applebee, M. Kenyon ; Herrgard, Markus J. ; Palsson, Bernhard Ø.
in: Journal of Bacteriology, vol: 190, issue: 14, pages: 5087-5094

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2008     |    DOI: https://doi.org/10.1128/JB.01976-07

 

Network-based prediction of human tissue-specific metabolism.

Shlomi, Tomer ; Cabili, Moran N ; Herrgard, Markus ; Palsson, Bernhard Ø ; Ruppin, Eytan
in: Nature Biotechnology, vol: 26, issue: 9, pages: 1003-1010

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2008     |    DOI: https://doi.org/10.1038/nbt.1487

2007
 

Microbial regulatory and metabolic networks

Cho, Byung-Kwan ; Charusanti, Pep ; Herrgard, Markus ; Palsson, Bernhard ∅.
in: Current Opinion in Biotechnology, vol: 18, issue: 4, pages: 360-364

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2007     |    DOI: https://doi.org/10.1016/j.copbio.2007.07.002

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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

Beck, Scott A. ; Feist, Adam ; Mo, M. L. ; Hannum, G. ; Palsson, B. O. ; Herrgard, Markus
in: Nature Protocols (Online), vol: 2, issue: 3, pages: 727-738

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2007     |    DOI: https://doi.org/10.1038/nprot.2007.99

 

Systematic condition-dependent annotation of metabolic genes

Shlomi, Tomer ; Herrgard, Markus ; Portnoy, Vasiliy ; Naim, Efrat ; Palsson, Bernhard Ø. ; Sharan, Roded ; Ruppin, Eytan
in: Genome Research, vol: 17, issue: 11, pages: 1626-1633

Type: Journal article

Status: Published     |    Year: 2007     |    DOI: https://doi.org/10.1101/gr.6678707

2006
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Identification of genome-scale metabolic network models using experimentally measured flux profiles

Herrgard, Markus ; Fong, Stephen S. ; Palsson, Bernhard Ø.
in: P L o S One, vol: 2, issue: 7, pages: e72

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2006     |    DOI: https://doi.org/10.1371/journal.pcbi.0020072

 

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

Herrgard, Markus ; Lee, Baek-Seok ; Portnoy, Vasiliy ; Ø. Palsson, Bernhard
in: Genome Research, vol: 16

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2006     |    DOI: https://doi.org/10.1101/gr.4083206