Literature DB >> 24811519

Optimizing genome-scale network reconstructions.

Jonathan Monk1, Juan Nogales2, Bernhard O Palsson3.   

Abstract

Mesh：

Year:  2014        PMID： 24811519     DOI： 10.1038/nbt.2870

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  53 in total

1.  Integrating high-throughput and computational data elucidates bacterial networks.

Authors:  Markus W Covert; Eric M Knight; Jennifer L Reed; Markus J Herrgard; Bernhard O Palsson
Journal:  Nature       Date:  2004-05-06       Impact factor: 49.962

Review 2.  Recent advances in reconstruction and applications of genome-scale metabolic models.

Authors:  Tae Yong Kim; Seung Bum Sohn; Yu Bin Kim; Won Jun Kim; Sang Yup Lee
Journal:  Curr Opin Biotechnol       Date:  2011-11-04       Impact factor: 9.740

3.  Teaching the design principles of metabolism.

Authors:  Joshua D Rabinowitz; Livia Vastag
Journal:  Nat Chem Biol       Date:  2012-05-17       Impact factor: 15.040

4.  Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses.

Authors:  Xiyan Li; Tara A Gianoulis; Kevin Y Yip; Mark Gerstein; Michael Snyder
Journal:  Cell       Date:  2010-10-28       Impact factor: 41.582

5.  Orphan enzymes?

Authors:  Olivier Lespinet; Bernard Labedan
Journal:  Science       Date:  2005-01-07       Impact factor: 47.728

6.  Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications.

Authors:  Paul Janssen; Leon Goldovsky; Victor Kunin; Nikos Darzentas; Christos A Ouzounis
Journal:  EMBO Rep       Date:  2005-05       Impact factor: 8.807

Review 7.  Fifteen years of large scale metabolic modeling of yeast: developments and impacts.

Authors:  Tobias Osterlund; Intawat Nookaew; Jens Nielsen
Journal:  Biotechnol Adv       Date:  2011-08-06       Impact factor: 14.227

8.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

Authors:  Jeffrey D Orth; Tom M Conrad; Jessica Na; Joshua A Lerman; Hojung Nam; Adam M Feist; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2011-10-11       Impact factor: 11.429

9.  Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.

Authors:  Kenji Nakahigashi; Yoshihiro Toya; Nobuyoshi Ishii; Tomoyoshi Soga; Miki Hasegawa; Hisami Watanabe; Yuki Takai; Masayuki Honma; Hirotada Mori; Masaru Tomita
Journal:  Mol Syst Biol       Date:  2009-09-15       Impact factor: 11.429

10.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).

Authors:  Jennifer L Reed; Thuy D Vo; Christophe H Schilling; Bernhard O Palsson
Journal:  Genome Biol       Date:  2003-08-28       Impact factor: 13.583
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  81 in total

Review 1.  In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories.

Authors:  Paulo Maia; Miguel Rocha; Isabel Rocha
Journal:  Microbiol Mol Biol Rev       Date:  2015-11-25       Impact factor: 11.056

Review 2.  Using Genome-scale Models to Predict Biological Capabilities.

Authors:  Edward J O'Brien; Jonathan M Monk; Bernhard O Palsson
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

3.  Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells.

Authors:  H Fouladiha; S-A Marashi; M A Shokrgozar
Journal:  Cell Prolif       Date:  2015-07-01       Impact factor: 6.831

4.  Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.

Authors:  Jared T Broddrick; Benjamin E Rubin; David G Welkie; Niu Du; Nathan Mih; Spencer Diamond; Jenny J Lee; Susan S Golden; Bernhard O Palsson
Journal:  Proc Natl Acad Sci U S A       Date:  2016-12-01       Impact factor: 11.205

5.  Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice.

Authors:  Bin Du; Daniel C Zielinski; Jonathan M Monk; Bernhard O Palsson
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-11       Impact factor: 11.205

6.  Reply to "Challenges in modeling the human gut microbiome".

Authors:  Stefanía Magnúsdóttir; Almut Heinken; Ronan M T Fleming; Ines Thiele
Journal:  Nat Biotechnol       Date:  2018-08-06       Impact factor: 54.908

Review 7.  Transparency in metabolic network reconstruction enables scalable biological discovery.

Authors:  Benjamin D Heavner; Nathan D Price
Journal:  Curr Opin Biotechnol       Date:  2015-01-03       Impact factor: 9.740

Review 8.  The Need for Integrated Approaches in Metabolic Engineering.

Authors:  Anna Lechner; Elizabeth Brunk; Jay D Keasling
Journal:  Cold Spring Harb Perspect Biol       Date:  2016-11-01       Impact factor: 10.005

9.  What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

Authors:  Derrick E Fouts; Michael A Matthias; Haritha Adhikarla; Ben Adler; Luciane Amorim-Santos; Douglas E Berg; Dieter Bulach; Alejandro Buschiazzo; Yung-Fu Chang; Renee L Galloway; David A Haake; Daniel H Haft; Rudy Hartskeerl; Albert I Ko; Paul N Levett; James Matsunaga; Ariel E Mechaly; Jonathan M Monk; Ana L T Nascimento; Karen E Nelson; Bernhard Palsson; Sharon J Peacock; Mathieu Picardeau; Jessica N Ricaldi; Janjira Thaipandungpanit; Elsio A Wunder; X Frank Yang; Jun-Jie Zhang; Joseph M Vinetz
Journal:  PLoS Negl Trop Dis       Date:  2016-02-18

10.  In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories.

Authors:  Meiyappan Lakshmanan; Kai Yu; Lokanand Koduru; Dong-Yup Lee
Journal:  J Ind Microbiol Biotechnol       Date:  2015-08-08       Impact factor: 3.346
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