Markus Juhana Herrgard - Publications

Affiliations: 
2004 University of California, San Diego, La Jolla, CA 

44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Lieven C, Petersen LAH, Jørgensen SB, Gernaey KV, Herrgard MJ, Sonnenschein N. A Genome-Scale Metabolic Model for (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. Frontiers in Microbiology. 9: 2947. PMID 30564208 DOI: 10.3389/fmicb.2018.02947  0.6
2018 Cardoso J, Jensen K, Lieven C, Hansen ASL, Galkina S, Beber ME, Özdemir E, Herrgard M, Redestig H, Sonnenschein N. Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories. Acs Synthetic Biology. PMID 29558112 DOI: 10.1021/acssynbio.7b00423  0.64
2016 Bonde MT, Pedersen M, Klausen MS, Jensen SI, Wulff T, Harrison S, Nielsen AT, Herrgård MJ, Sommer MO. Predictable tuning of protein expression in bacteria. Nature Methods. PMID 26752768 DOI: 10.1038/nmeth.3727  0.96
2015 Jensen SI, Lennen RM, Herrgård MJ, Nielsen AT. Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Scientific Reports. 5: 17874. PMID 26643270 DOI: 10.1038/srep17874  0.96
2015 Machado D, Zhuang KH, Sonnenschein N, Herrgård MJ. Editorial: Current Challenges in Modeling Cellular Metabolism. Frontiers in Bioengineering and Biotechnology. 3: 193. PMID 26636080 DOI: 10.3389/fbioe.2015.00193  0.6
2015 Herrgård M, Sukumara S, Campodonico M, Zhuang K. A multi-scale, multi-disciplinary approach for assessing the technological, economic and environmental performance of bio-based chemicals. Biochemical Society Transactions. 43: 1151-6. PMID 26614653 DOI: 10.1042/BST20150144  0.96
2015 Machado D, Herrgård MJ, Rocha I. Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli. Frontiers in Bioengineering and Biotechnology. 3: 154. PMID 26501058 DOI: 10.3389/fbioe.2015.00154  0.4
2015 Lennen RM, Nilsson Wallin AI, Pedersen M, Bonde M, Luo H, Herrgård MJ, Sommer MO. Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects. Nucleic Acids Research. PMID 26496947 DOI: 10.1093/nar/gkv1090  1
2015 Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284  0.96
2015 Zhuang KH, Herrgård MJ. Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production. Metabolic Engineering. 31: 1-12. PMID 26116515 DOI: 10.1016/j.ymben.2015.05.007  0.96
2015 Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nature Communications. 6: 7101. PMID 26055627 DOI: 10.1038/ncomms8101  0.96
2015 Mirzadeh K, Martínez V, Toddo S, Guntur S, Herrgård MJ, Elofsson A, Nørholm MH, Daley DO. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. Acs Synthetic Biology. PMID 25951437 DOI: 10.1021/acssynbio.5b00033  0.96
2015 Cardoso JG, Andersen MR, Herrgård MJ, Sonnenschein N. Analysis of genetic variation and potential applications in genome-scale metabolic modeling. Frontiers in Bioengineering and Biotechnology. 3: 13. PMID 25763369 DOI: 10.3389/fbioe.2015.00013  0.6
2015 Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, Schneider K, Lamosa P, Herrgård MJ, Rosenstand I, Öberg F, Forster J, Nielsen J. Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine. Metabolic Engineering. 27: 57-64. PMID 25447643 DOI: 10.1016/j.ymben.2014.10.003  0.96
2014 Kildegaard KR, Hallström BM, Blicher TH, Sonnenschein N, Jensen NB, Sherstyk S, Harrison SJ, Maury J, Herrgård MJ, Juncker AS, Forster J, Nielsen J, Borodina I. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metabolic Engineering. 26: 57-66. PMID 25263954 DOI: 10.1016/j.ymben.2014.09.004  0.96
2014 Lennen RM, Herrgård MJ. Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. Applied and Environmental Microbiology. 80: 6223-42. PMID 25085490 DOI: 10.1128/AEM.01542-14  1
2014 Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Molecular Biology and Evolution. 31: 2647-62. PMID 25015645 DOI: 10.1093/molbev/msu209  0.96
2013 Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Frontiers in Microbiology. 4: 106. PMID 23761787 DOI: 10.3389/fmicb.2013.00106  0.96
2013 Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings Rd, Hengartner NW, Xie G. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Frontiers in Microbiology. 4: 84. PMID 23755042 DOI: 10.3389/fmicb.2013.00084  0.96
2013 Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Frontiers in Microbiology. 4: 95. PMID 23720654 DOI: 10.3389/fmicb.2013.00095  0.96
2013 Zhuang K, Bakshi BR, Herrgård MJ. Multi-scale modeling for sustainable chemical production. Biotechnology Journal. 8: 973-84. PMID 23520143 DOI: 10.1002/biot.201200272  0.96
2013 Harrison SJ, Herrgard MJ. The uses and future prospects of metabolomics and targeted metabolite profiling in cell factory development Industrial Biotechnology. 9: 196-202. DOI: 10.1089/ind.2013.0008  0.96
2012 Herrgard M, Panagiotou G. Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology" Computational and Structural Biotechnology Journal. 3. DOI: 10.5936/csbj.201210012  0.96
2010 Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. Plos One. 5: e9773. PMID 20333304 DOI: 10.1371/journal.pone.0009773  0.96
2010 Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli Metabolic Engineering. 12: 173-186. PMID 19840862 DOI: 10.1016/j.ymben.2009.10.003  0.96
2009 Mo ML, Palsson BO, HerrgÃ¥rd MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. Bmc Systems Biology. 3: 37. PMID 19321003 DOI: 10.1186/1752-0509-3-37  0.96
2009 Barrett CL, Herrgard MJ, Palsson B. Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. Bmc Systems Biology. 3: 30. PMID 19267928 DOI: 10.1186/1752-0509-3-30  0.96
2009 Feist AM, HerrgÃ¥rd MJ, Thiele I, Reed JL, Palsson BØ. Reconstruction of biochemical networks in microorganisms. Nature Reviews. Microbiology. 7: 129-43. PMID 19116616 DOI: 10.1038/nrmicro1949  0.96
2008 Portnoy VA, Herrgård MJ, Palsson BØ. Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. Applied and Environmental Microbiology. 74: 7561-9. PMID 18952873 DOI: 10.1128/AEM.00880-08  0.96
2008 HerrgÃ¥rd MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 26: 1155-60. PMID 18846089 DOI: 10.1038/nbt1492  0.96
2008 Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nature Biotechnology. 26: 1003-10. PMID 18711341 DOI: 10.1038/nbt.1487  0.96
2008 Applebee MK, Herrgård MJ, Palsson BØ. Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. Journal of Bacteriology. 190: 5087-94. PMID 18487343 DOI: 10.1128/JB.01976-07  0.96
2007 Shlomi T, Herrgard M, Portnoy V, Naim E, Palsson BØ, Sharan R, Ruppin E. Systematic condition-dependent annotation of metabolic genes. Genome Research. 17: 1626-33. PMID 17895423 DOI: 10.1101/gr.6678707  0.96
2007 Cho BK, Charusanti P, Herrgård MJ, Palsson BO. Microbial regulatory and metabolic networks. Current Opinion in Biotechnology. 18: 360-4. PMID 17719767 DOI: 10.1016/j.copbio.2007.07.002  0.96
2007 Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocols. 2: 727-38. PMID 17406635 DOI: 10.1038/nprot.2007.99  0.96
2006 Herrgård MJ, Fong SS, Palsson BØ. Identification of genome-scale metabolic network models using experimentally measured flux profiles. Plos Computational Biology. 2: e72. PMID 16839195 DOI: 10.1371/journal.pcbi.0020072  0.96
2006 Herrgård MJ, Lee BS, Portnoy V, Palsson BØ. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Research. 16: 627-35. PMID 16606697 DOI: 10.1101/gr.4083206  0.96
2005 Herrgård MJ, Palsson BØ. Untangling the web of functional and physical interactions in yeast. Journal of Biology. 4: 5. PMID 15982410 DOI: 10.1186/jbiol26  0.88
2004 Duarte NC, Herrgård MJ, Palsson BØ. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research. 14: 1298-309. PMID 15197165 DOI: 10.1101/gr.2250904  0.88
2004 Herrgård MJ, Palsson BØ. Flagellar biosynthesis in silico: building quantitative models of regulatory networks. Cell. 117: 689-90. PMID 15186769 DOI: 10.1016/j.cell.2004.05.020  0.88
2004 Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 429: 92-6. PMID 15129285 DOI: 10.1038/nature02456  0.96
2004 Herrgård MJ, Covert MW, Palsson BØ. Reconstruction of microbial transcriptional regulatory networks. Current Opinion in Biotechnology. 15: 70-7. PMID 15102470 DOI: 10.1016/j.copbio.2003.11.002  0.96
2003 Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. Journal of Bacteriology. 185: 6392-9. PMID 14563874 DOI: 10.1128/JB.185.21.6392-6399.2003  0.96
2003 Herrgård MJ, Covert MW, Palsson BØ. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Research. 13: 2423-34. PMID 14559784 DOI: 10.1101/gr.1330003  0.96
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