Sort by
Items per page

Send to

Choose Destination

Search results

Items: 47


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

Campodonico MA, Sukumara S, Feist AM, Herrgård MJ.

Methods Mol Biol. 2018;1671:97-116. doi: 10.1007/978-1-4939-7295-1_7.


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

Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM.

Microb Cell Fact. 2017 Nov 16;16(1):204. doi: 10.1186/s12934-017-0819-1.


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

Baumgarten T, Schlegel S, Wagner S, Löw M, Eriksson J, Bonde I, Herrgård MJ, Heipieper HJ, Nørholm MH, Slotboom DJ, de Gier JW.

Sci Rep. 2017 Mar 24;7:45089. doi: 10.1038/srep45089.


Systems biology solutions for biochemical production challenges.

Hansen ASL, Lennen RM, Sonnenschein N, Herrgård MJ.

Curr Opin Biotechnol. 2017 Jun;45:85-91. doi: 10.1016/j.copbio.2016.11.018. Epub 2017 Mar 16. Review.


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

Machado D, Herrgård MJ, Rocha I.

PLoS Comput Biol. 2016 Oct 6;12(10):e1005140. doi: 10.1371/journal.pcbi.1005140. eCollection 2016 Oct.


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

Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM.

Cell Syst. 2016 Sep 28;3(3):238-251.e12. doi: 10.1016/j.cels.2016.08.013. Epub 2016 Sep 22.


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

Kildegaard KR, Jensen NB, Schneider K, Czarnotta E, Özdemir E, Klein T, Maury J, Ebert BE, Christensen HB, Chen Y, Kim IK, Herrgård MJ, Blank LM, Forster J, Nielsen J, Borodina I.

Microb Cell Fact. 2016 Mar 15;15:53. doi: 10.1186/s12934-016-0451-5.


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

Maury J, Germann SM, Baallal Jacobsen SA, Jensen NB, Kildegaard KR, Herrgård MJ, Schneider K, Koza A, Forster J, Nielsen J, Borodina I.

PLoS One. 2016 Mar 2;11(3):e0150394. doi: 10.1371/journal.pone.0150394. eCollection 2016.


Predictable tuning of protein expression in bacteria.

Bonde MT, Pedersen M, Klausen MS, Jensen SI, Wulff T, Harrison S, Nielsen AT, Herrgård MJ, Sommer MO.

Nat Methods. 2016 Mar;13(3):233-6. doi: 10.1038/nmeth.3727. Epub 2016 Jan 11.


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

Jensen SI, Lennen RM, Herrgård MJ, Nielsen AT.

Sci Rep. 2015 Dec 8;5:17874. doi: 10.1038/srep17874.


Editorial: Current Challenges in Modeling Cellular Metabolism.

Machado D, Zhuang KH, Sonnenschein N, Herrgård MJ.

Front Bioeng Biotechnol. 2015 Nov 26;3:193. doi: 10.3389/fbioe.2015.00193. eCollection 2015. No abstract available.


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

Machado D, Herrgård MJ, Rocha I.

Front Bioeng Biotechnol. 2015 Oct 8;3:154. doi: 10.3389/fbioe.2015.00154. eCollection 2015.


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

Lennen RM, Nilsson Wallin AI, Pedersen M, Bonde M, Luo H, Herrgård MJ, Sommer MO.

Nucleic Acids Res. 2016 Feb 29;44(4):e36. doi: 10.1093/nar/gkv1090. Epub 2015 Oct 22.


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

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, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


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

Zhuang KH, Herrgård MJ.

Metab Eng. 2015 Sep;31:1-12. doi: 10.1016/j.ymben.2015.05.007. Epub 2015 Jun 24.


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

Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO.

Nat Commun. 2015 Jun 9;6:7101. doi: 10.1038/ncomms8101.


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

Mirzadeh K, Martínez V, Toddo S, Guntur S, Herrgård MJ, Elofsson A, Nørholm MH, Daley DO.

ACS Synth Biol. 2015 Sep 18;4(9):959-65. doi: 10.1021/acssynbio.5b00033. Epub 2015 May 15.


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

Cardoso JG, Andersen MR, Herrgård MJ, Sonnenschein N.

Front Bioeng Biotechnol. 2015 Feb 16;3:13. doi: 10.3389/fbioe.2015.00013. eCollection 2015. Review.


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

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.

Metab Eng. 2015 Jan;27:57-64. doi: 10.1016/j.ymben.2014.10.003. Epub 2014 Oct 23.


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

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.

Metab Eng. 2014 Nov;26:57-66. doi: 10.1016/j.ymben.2014.09.004. Epub 2014 Sep 28.


Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains.

Lennen RM, Herrgård MJ.

Appl Environ Microbiol. 2014 Oct;80(19):6223-42. doi: 10.1128/AEM.01542-14. Epub 2014 Aug 1.


Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations.

Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM.

Mol Biol Evol. 2014 Oct;31(10):2647-62. doi: 10.1093/molbev/msu209. Epub 2014 Jul 10.


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

Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR.

Front Microbiol. 2013 Jun 3;4:106. doi: 10.3389/fmicb.2013.00106. eCollection 2013.


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

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.

Front Microbiol. 2013 May 29;4:84. doi: 10.3389/fmicb.2013.00084. eCollection 2013.


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

Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF.

Front Microbiol. 2013 May 15;4:95. doi: 10.3389/fmicb.2013.00095. eCollection 2013.


The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem.

Inskeep WP, Jay ZJ, Tringe SG, Herrgård MJ, Rusch DB; YNP Metagenome Project Steering Committee and Working Group Members.

Front Microbiol. 2013 May 6;4:67. doi: 10.3389/fmicb.2013.00067. eCollection 2013.


Multi-scale modeling for sustainable chemical production.

Zhuang K, Bakshi BR, Herrgård MJ.

Biotechnol J. 2013 Sep;8(9):973-84. doi: 10.1002/biot.201200272. Epub 2013 Mar 21. Review.


Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

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, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M.

PLoS One. 2010 Mar 19;5(3):e9773. doi: 10.1371/journal.pone.0009773.


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

Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ.

Metab Eng. 2010 May;12(3):173-86. doi: 10.1016/j.ymben.2009.10.003. Epub 2009 Oct 17.


Connecting extracellular metabolomic measurements to intracellular flux states in yeast.

Mo ML, Palsson BO, Herrgård MJ.

BMC Syst Biol. 2009 Mar 25;3:37. doi: 10.1186/1752-0509-3-37.


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

Barrett CL, Herrgard MJ, Palsson B.

BMC Syst Biol. 2009 Mar 6;3:30. doi: 10.1186/1752-0509-3-30.


Reconstruction of biochemical networks in microorganisms.

Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ.

Nat Rev Microbiol. 2009 Feb;7(2):129-43. doi: 10.1038/nrmicro1949. Epub 2008 Dec 31. Review.


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

Portnoy VA, Herrgård MJ, Palsson BØ.

Appl Environ Microbiol. 2008 Dec;74(24):7561-9. doi: 10.1128/AEM.00880-08. Epub 2008 Oct 24.


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

Herrgård 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, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.

Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.


Network-based prediction of human tissue-specific metabolism.

Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E.

Nat Biotechnol. 2008 Sep;26(9):1003-10. doi: 10.1038/nbt.1487.


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

Applebee MK, Herrgård MJ, Palsson BØ.

J Bacteriol. 2008 Jul;190(14):5087-94. doi: 10.1128/JB.01976-07. Epub 2008 May 16.


Microbial regulatory and metabolic networks.

Cho BK, Charusanti P, Herrgård MJ, Palsson BO.

Curr Opin Biotechnol. 2007 Aug;18(4):360-4. Epub 2007 Aug 24. Review.


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

Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ.

Nat Protoc. 2007;2(3):727-38.


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

Herrgård MJ, Fong SS, Palsson BØ.

PLoS Comput Biol. 2006 Jul 7;2(7):e72. Epub 2006 May 10.


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

Herrgård MJ, Lee BS, Portnoy V, Palsson BØ.

Genome Res. 2006 May;16(5):627-35. Epub 2006 Apr 10.


Untangling the web of functional and physical interactions in yeast.

Herrgård MJ, Palsson BØ.

J Biol. 2005;4(2):5. Epub 2005 Jun 8. Review.


Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.

Duarte NC, Herrgård MJ, Palsson BØ.

Genome Res. 2004 Jul;14(7):1298-309. Epub 2004 Jun 14.


Flagellar biosynthesis in silico: building quantitative models of regulatory networks.

Herrgård MJ, Palsson BØ.

Cell. 2004 Jun 11;117(6):689-90. Review.


Integrating high-throughput and computational data elucidates bacterial networks.

Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO.

Nature. 2004 May 6;429(6987):92-6.


Reconstruction of microbial transcriptional regulatory networks.

Herrgård MJ, Covert MW, Palsson BØ.

Curr Opin Biotechnol. 2004 Feb;15(1):70-7. Review.


Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets.

Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ.

J Bacteriol. 2003 Nov;185(21):6392-9.


Reconciling gene expression data with known genome-scale regulatory network structures.

Herrgård MJ, Covert MW, Palsson BØ.

Genome Res. 2003 Nov;13(11):2423-34. Epub 2003 Oct 14.

Supplemental Content

Loading ...
Support Center