Herrgård, Markus J.: search on Z-Library

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1

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories

Cardoso, Joao, Jensen, Kristian, Lieven, Christian, Hansen, Anne Sofie Lærke, Galkina, Svetlana, Beber, Moritz Emanuel, Özdemir, Emre, Herrgard, Markus, Redestig, Henning, Sonnenschein, Nikolaus

Journal:

ACS Synthetic Biology

Year:

2018

Language:

english

File:

PDF, 2.52 MB

english, 2018

2

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, Thordis, Bosma, Elleke F., Branco dos Santos, Filipe, Özdemir, Emre, Herrgård, Markus J., França, Lucas, Ferreira, Bruno, Nielsen, Alex T., Gudmundsson, Steinn

Journal:

Microbial Cell Factories

Year:

2019

Language:

english

File:

PDF, 1.84 MB

english, 2019

3

Network-based prediction of human tissue-specific metabolism

Shlomi, Tomer, Cabili, Moran N, Herrgård, Markus J, Palsson, Bernhard Ø, Ruppin, Eytan

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 609 KB

english, 2008

4

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, Herrgård, Markus J., Heipieper, Hermann J., Nørholm, Morten H. H., Slotboom, Dirk Jan, de Gier, Jan-Wille

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.62 MB

english, 2017

5

Machine learning framework for assessment of microbial factory performance

Oyetunde, Tolutola, Liu, Di, Martin, Hector Garcia, Tang, Yinjie J., Herrgard, Markus

Journal:

Year:

2019

Language:

english

File:

PDF, 2.62 MB

english, 2019

6

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 O., Herrgård, Markus J., Feist, Adam M.

Journal:

Year:

2016

Language:

english

File:

PDF, 4.54 MB

english, 2016

7

Editorial: Current Challenges in Modeling Cellular Metabolism

Machado, Daniel, Zhuang, Kai H., Sonnenschein, Nikolaus, Herrgård, Markus J.

Journal:

Frontiers in Bioengineering and Biotechnology

Year:

2015

Language:

english

File:

PDF, 81 KB

english, 2015

8

Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

Luo, Hao, Yang, Lei, Kim, Se Hyeuk, Wulff, Tune, Feist, Adam M., Herrgard, Markus, Palsson, Bernhard Ã.

Journal:

ACS Synthetic Biology

Year:

2020

File:

PDF, 1.41 MB

2020

9

Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae

Jakočiūnas, Tadas, Bonde, Ida, Herrgård, Markus, Harrison, Scott J., Kristensen, Mette, Pedersen, Lasse E., Jensen, Michael K., Keasling, Jay D.

Journal:

Metabolic Engineering

Year:

2015

Language:

english

File:

PDF, 767 KB

english, 2015

10

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, Thordis, Bosma, Elleke F., Branco dos Santos, Filipe, Özdemir, Emre, Herrgård, Markus J., França, Lucas, Ferreira, Bruno, Nielsen, Alex T., Gudmundsson, Steinn

Journal:

Microbial Cell Factories

Year:

2019

File:

PDF, 1.84 MB

2019

11

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

Kildegaard, Kanchana R., Hallström, Björn M., Blicher, Thomas H., Sonnenschein, Nikolaus, Jensen, Niels B., Sherstyk, Svetlana, Harrison, Scott J., Maury, Jérôme, Herrgård, Markus J., Juncker, Agniesz

Journal:

Metabolic Engineering

Year:

2014

Language:

english

File:

PDF, 1.35 MB

english, 2014

12

Integrating high-throughput and computational data elucidates bacterial networks

Palsson, Bernhard O., Covert, Markus W., Knight, Eric M., Reed, Jennifer L., Herrgard, Markus J.

Journal:

Year:

2004

Language:

english

File:

PDF, 885 KB

english, 2004

13

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

Lieven, Christian, Herrgård, Markus J., Sonnenschein, Nikolaus

Journal:

Biotechnology Journal

Year:

2018

Language:

english

File:

PDF, 927 KB

english, 2018

14

Flagellar Biosynthesis In Silico: Building Quantitative Models of Regulatory Networks

Markus J Herrgård, Bernhard Ø Palsson

Journal:

Year:

2004

Language:

english

File:

PDF, 38 KB

english, 2004

15

Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects

Lennen, Rebecca M., Nilsson Wallin, Annika I., Pedersen, Margit, Bonde, Mads, Luo, Hao, Herrgård, Markus J., Sommer, Morten O. A.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 3.20 MB

english, 2016

16

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

Mundhada, Hemanshu, Miguel, Jose S., Schneider, Konstantin, Koza, Anna, Christensen, Hanne B., Klein, Tobias, Phaneuf, Patrick V., Herrgard, Markus, Feist, Adam M., Nielsen, Alex T.

Journal:

Metabolic Engineering

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

17

Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress

Jensen, Sheila I., Lennen, Rebecca M., Herrgård, Markus J., Nielsen, Alex T.

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 844 KB

english, 2015

18

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

Machado, Daniel, Herrgård, Markus J., Rocha, Isabel

Journal:

Frontiers in Bioengineering and Biotechnology

Year:

2015

Language:

english

File:

PDF, 11.65 MB

english, 2015

19

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 J., Rusch, Douglas B., Tringe, Susannah G., Kozubal, Mark A., Hamamura, Natsuko, Macur, Richard E., Fouke, Bruce W., Re

Journal:

Frontiers in Microbiology

Year:

2013

Language:

english

File:

PDF, 13.40 MB

english, 2013

20

Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling

D'Arrigo, Isotta, Cardoso, João G. R., Rennig, Maja, Sonnenschein, Nikolaus, Herrgård, Markus J., Long, Katherine S.

Journal:

Environmental Microbiology Reports

Year:

2018

Language:

english

File:

PDF, 1.11 MB

english, 2018

21

Systems biology solutions for biochemical production challenges

Hansen, Anne Sofie Lærke, Lennen, Rebecca M., Sonnenschein, Nikolaus, Herrgård, Markus J

Journal:

Current Opinion in Biotechnology

Year:

2017

Language:

english

File:

PDF, 953 KB

english, 2017

22

MARSI: metabolite analogues for rational strain improvement

Cardoso, João G R, Zeidan, Ahmad A, Jensen, Kristian, Sonnenschein, Nikolaus, Neves, Ana Rute, Herrgård, Markus J, Wren, Jonathan

Journal:

Year:

2018

Language:

english

File:

PDF, 327 KB

english, 2018

23

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.

Journal:

Metabolic Engineering Communications

Year:

2019

File:

PDF, 1.48 MB

2019

24

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

Becker, Scott A, Feist, Adam M, Mo, Monica L, Hannum, Gregory, Palsson, Bernhard Ø, Herrgard, Markus J

Journal:

Nature Protocols

Year:

2007

Language:

english

File:

PDF, 359 KB

english, 2007

25

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

Machado, Daniel, Herrgård, Markus J.

Journal:

Metabolic Engineering Communications

Year:

2015

Language:

english

File:

PDF, 1.25 MB

english, 2015

26

Predictable tuning of protein expression in bacteria

Bonde, Mads T, Pedersen, Margit, Klausen, Michael S, Jensen, Sheila I, Wulff, Tune, Harrison, Scott, Nielsen, Alex T, Herrgård, Markus J, Sommer, Morten O A

Journal:

Year:

2016

Language:

english

File:

PDF, 745 KB

english, 2016

27

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., Reysenb

Journal:

Year:

2010

Language:

english

File:

PDF, 6.53 MB

english, 2010

28

Addressing environmental sustainability of biochemicals

Ögmundarson, Ólafur, Herrgård, Markus J., Forster, Jochen, Hauschild, Michael Z., Fantke, Peter

Journal:

Nature Sustainability

Year:

2020

File:

PDF, 1.03 MB

2020

29

Microbial regulatory and metabolic networks

Byung-Kwan Cho, Pep Charusanti, Markus J. Herrgård, Bernhard ∅. Palsson

Journal:

Current Opinion in Biotechnology

Year:

2007

Language:

english

File:

PDF, 128 KB

english, 2007

30

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

Christian L Barrett, Markus J Herrgard, Bernhard Palsson

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 472 KB

english, 2009

31

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 J., Kozubal, Mark A., Rusch, Douglas B., Tringe, Susannah G., Macur, Richard E., Jennings, Ryan deM., Boyd, Eric S., Spear, John R., Roberto, Fra

Journal:

Frontiers in Microbiology

Year:

2013

Language:

english

File:

PDF, 2.82 MB

english, 2013

32

Dietary Change Enables Robust Growth-Coupling of Heterologous Methyltransferase Activity in Yeast

Hansen, Anne Sofie LÃ¦rke, Dunham, Maitreya J., Arsovska, Dushica, Zhang, Jie, Keasling, Jay D., Herrgard, Markus J., Jensen, Michael K.

Journal:

ACS Synthetic Biology

Year:

2020

File:

PDF, 1.35 MB

2020

33

Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

Borodina, Irina, Kildegaard, Kanchana R., Jensen, Niels B., Blicher, Thomas H., Maury, Jérôme, Sherstyk, Svetlana, Schneider, Konstantin, Lamosa, Pedro, Herrgård, Markus J., Rosenstand, Inger, Öberg,

Journal:

Metabolic Engineering

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

34

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

Mirzadeh, Kiavash, Martínez, Virginia, Toddo, Stephen, Guntur, Suchithra, Herrgård, Markus J., Elofsson, Arne, Nørholm, Morten H. H., Daley, Daniel O.

Journal:

ACS Synthetic Biology

Year:

2015

Language:

english

File:

PDF, 3.19 MB

english, 2015

35

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.

Journal:

Metabolic Engineering Communications

Year:

2019

Language:

english

File:

PDF, 1.48 MB

english, 2019

36

Reconstruction of microbial transcriptional regulatory networks

Markus J Herrgård, Markus W Covert, Bernhard Ø Palsson

Journal:

Current Opinion in Biotechnology

Year:

2004

Language:

english

File:

PDF, 267 KB

english, 2004

37

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

Harrison, Scott J., Herrgård, Markus J.

Journal:

Industrial Biotechnology

Year:

2013

Language:

english

File:

PDF, 375 KB

english, 2013

38

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

Zhuang, Kai H., Herrgård, Markus J.

Journal:

Metabolic Engineering

Year:

2015

Language:

english

File:

PDF, 827 KB

english, 2015

39

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles

Herrgård, Markus J., Fong, Stephen S., Palsson, Bernhard Ø.

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 511 KB

english, 2006

40

EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae

Maury, Jérôme, Germann, Susanne M., Baallal Jacobsen, Simo Abdessamad, Jensen, Niels B., Kildegaard, Kanchana R., Herrgård, Markus J., Schneider, Konstantin, Koza, Anna, Forster, Jochen, Nielsen, Jens

Journal:

Year:

2016

Language:

english

File:

PDF, 2.13 MB

english, 2016

41

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

Adam M. Feist, Daniel C. Zielinski, Jeffrey D. Orth, Jan Schellenberger, Markus J. Herrgard, Bernhard Ø. Palsson

Journal:

Metabolic Engineering

Year:

2010

Language:

english

File:

PDF, 462 KB

english, 2010

42

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

McCloskey, Douglas, Xu, Julia, Schrübbers, Lars, Christensen, Hanne B., Herrgård, Markus J.

Journal:

Metabolic Engineering

Year:

2018

Language:

english

File:

PDF, 804 KB

english, 2018

43

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

Machado, Daniel, Herrgård, Markus J., Rocha, Isabel, Patil, Kiran Raosaheb

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 2.32 MB

english, 2016

44

Untangling the web of functional and physical interactions in yeast

Markus J Herrgård, Bernhard Ø Palsson

Journal:

Journal of Biology

Year:

2005

Language:

english

File:

PDF, 83 KB

english, 2005

45

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

Shepelin, Denis, Hansen, Anne, Lennen, Rebecca, Luo, Hao, Herrgård, Markus

Journal:

Year:

2018

Language:

english

File:

PDF, 2.61 MB

english, 2018

46

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

Mohamed, Elsayed T., Mundhada, Hemanshu, Landberg, Jenny, Cann, Isaac, Mackie, Roderick I., Nielsen, Alex Toftgaard, Herrgård, Markus J., Feist, Adam M.

Journal:

Microbial Cell Factories

Year:

2019

Language:

english

File:

PDF, 2.21 MB

english, 2019

47

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Monica L Mo, Bernhard Ø Palsson, Markus J Herrgård

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 1.53 MB

english, 2009

48

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

Lennen, Rebecca, Bonde, Ida, Koza, Anna, Herrgård, Markus

Journal:

New Biotechnology

Year:

2014

Language:

english

File:

PDF, 71 KB

english, 2014

49

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

Zielinski, Daniel C., Filipp, Fabian V., Bordbar, Aarash, Jensen, Kasper, Smith, Jeffrey W., Herrgard, Markus J., Mo, Monica L., Palsson, Bernhard O.

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 5.44 MB

english, 2015

50

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.

Journal:

Microbial Cell Factories

Year:

2017

Language:

english

File:

PDF, 2.67 MB

english, 2017

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