Literature DB >> 21943909

Whole-genome metabolic network reconstruction and constraint-based modeling.

Charles R Haggart1, Jennifer A Bartell, Jeffrey J Saucerman, Jason A Papin.   

Abstract

With the advent of modern high-throughput genomics, there is a significant need for genome-scale analysis techniques that can assist in complex systems analysis. Metabolic genome-scale network reconstructions (GENREs) paired with constraint-based modeling are an efficient method to integrate genomics, transcriptomics, and proteomics to conduct organism-specific analysis. This text explains key steps in the GENRE construction process and several methods of constraint-based modeling that can help elucidate basic life processes and development of disease treatment, bioenergy solutions, and industrial bioproduction applications.
Copyright © 2011 Elsevier Inc. All rights reserved.

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Year:  2011        PMID： 21943909      PMCID： PMC3361743          DOI： 10.1016/B978-0-12-385118-5.00021-9

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


  56 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2003-11-14       Impact factor: 11.205

Review 6.  Genome-scale models of microbial cells: evaluating the consequences of constraints.

Authors:  Nathan D Price; Jennifer L Reed; Bernhard Ø Palsson
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Authors:  Matthew A Oberhardt; Joanna B Goldberg; Michael Hogardt; Jason A Papin
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Review 10.  Metabolic pathways in the post-genome era.

Authors:  Jason A Papin; Nathan D Price; Sharon J Wiback; David A Fell; Bernhard O Palsson
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  9 in total

Review 1.  Multiscale computational models of complex biological systems.

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Authors:  Patricio Godoy; Nicola J Hewitt; Ute Albrecht; Melvin E Andersen; Nariman Ansari; Sudin Bhattacharya; Johannes Georg Bode; Jennifer Bolleyn; Christoph Borner; Jan Böttger; Albert Braeuning; Robert A Budinsky; Britta Burkhardt; Neil R Cameron; Giovanni Camussi; Chong-Su Cho; Yun-Jaie Choi; J Craig Rowlands; Uta Dahmen; Georg Damm; Olaf Dirsch; María Teresa Donato; Jian Dong; Steven Dooley; Dirk Drasdo; Rowena Eakins; Karine Sá Ferreira; Valentina Fonsato; Joanna Fraczek; Rolf Gebhardt; Andrew Gibson; Matthias Glanemann; Chris E P Goldring; María José Gómez-Lechón; Geny M M Groothuis; Lena Gustavsson; Christelle Guyot; David Hallifax; Seddik Hammad; Adam Hayward; Dieter Häussinger; Claus Hellerbrand; Philip Hewitt; Stefan Hoehme; Hermann-Georg Holzhütter; J Brian Houston; Jens Hrach; Kiyomi Ito; Hartmut Jaeschke; Verena Keitel; Jens M Kelm; B Kevin Park; Claus Kordes; Gerd A Kullak-Ublick; Edward L LeCluyse; Peng Lu; Jennifer Luebke-Wheeler; Anna Lutz; Daniel J Maltman; Madlen Matz-Soja; Patrick McMullen; Irmgard Merfort; Simon Messner; Christoph Meyer; Jessica Mwinyi; Dean J Naisbitt; Andreas K Nussler; Peter Olinga; Francesco Pampaloni; Jingbo Pi; Linda Pluta; Stefan A Przyborski; Anup Ramachandran; Vera Rogiers; Cliff Rowe; Celine Schelcher; Kathrin Schmich; Michael Schwarz; Bijay Singh; Ernst H K Stelzer; Bruno Stieger; Regina Stöber; Yuichi Sugiyama; Ciro Tetta; Wolfgang E Thasler; Tamara Vanhaecke; Mathieu Vinken; Thomas S Weiss; Agata Widera; Courtney G Woods; Jinghai James Xu; Kathy M Yarborough; Jan G Hengstler
Journal:  Arch Toxicol       Date:  2013-08-23       Impact factor: 5.153

3.  Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti.

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4.  Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach.

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5.  Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism.

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6.  Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.

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7.  Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig.

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8.  In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products.

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  9 in total

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