Literature DB >> 19040774

Network-based approaches for linking metabolism with environment.

Sarath Chandra Janga1, M Madan Babu.   

Abstract

Progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat.

Entities:  

Mesh：

Year:  2008        PMID： 19040774      PMCID： PMC2614483          DOI： 10.1186/gb-2008-9-11-239

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  27 in total

1.  Small-molecule metabolism: an enzyme mosaic.

Authors:  S A Teichmann; S C Rison; J M Thornton; M Riley; J Gough; C Chothia
Journal:  Trends Biotechnol       Date:  2001-12       Impact factor: 19.536

2.  Genome evolution reveals biochemical networks and functional modules.

Authors:  Christian von Mering; Evgeny M Zdobnov; Sophia Tsoka; Francesca D Ciccarelli; Jose B Pereira-Leal; Christos A Ouzounis; Peer Bork
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-12       Impact factor: 11.205

3.  Hierarchical organization of modularity in metabolic networks.

Authors:  E Ravasz; A L Somera; D A Mongru; Z N Oltvai; A L Barabási
Journal:  Science       Date:  2002-08-30       Impact factor: 47.728

4.  Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.

Authors:  Agustino Martínez-Antonio; Sarath Chandra Janga; Heladia Salgado; Julio Collado-Vides
Journal:  Trends Microbiol       Date:  2005-11-28       Impact factor: 17.079

5.  On the Evolution of Biochemical Syntheses.

Authors:  N H Horowitz
Journal:  Proc Natl Acad Sci U S A       Date:  1945-06       Impact factor: 11.205

6.  Functional metagenomic profiling of nine biomes.

Authors:  Elizabeth A Dinsdale; Robert A Edwards; Dana Hall; Florent Angly; Mya Breitbart; Jennifer M Brulc; Mike Furlan; Christelle Desnues; Matthew Haynes; Linlin Li; Lauren McDaniel; Mary Ann Moran; Karen E Nelson; Christina Nilsson; Robert Olson; John Paul; Beltran Rodriguez Brito; Yijun Ruan; Brandon K Swan; Rick Stevens; David L Valentine; Rebecca Vega Thurber; Linda Wegley; Bryan A White; Forest Rohwer
Journal:  Nature       Date:  2008-03-12       Impact factor: 49.962

Review 7.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.

Authors:  Adam M Feist; Bernhard Ø Palsson
Journal:  Nat Biotechnol       Date:  2008-06       Impact factor: 54.908

8.  Large-scale reconstruction and phylogenetic analysis of metabolic environments.

Authors:  Elhanan Borenstein; Martin Kupiec; Marcus W Feldman; Eytan Ruppin
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-11       Impact factor: 11.205

Review 9.  Enzyme recruitment in evolution of new function.

Authors:  R A Jensen
Journal:  Annu Rev Microbiol       Date:  1976       Impact factor: 15.500

10.  KEGG Atlas mapping for global analysis of metabolic pathways.

Authors:  Shujiro Okuda; Takuji Yamada; Masami Hamajima; Masumi Itoh; Toshiaki Katayama; Peer Bork; Susumu Goto; Minoru Kanehisa
Journal:  Nucleic Acids Res       Date:  2008-05-13       Impact factor: 16.971
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  20 in total

1.  Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.

Authors:  Roie Levy; Elhanan Borenstein
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-15       Impact factor: 11.205

Review 2.  Evolution of biomolecular networks: lessons from metabolic and protein interactions.

Authors:  Takuji Yamada; Peer Bork
Journal:  Nat Rev Mol Cell Biol       Date:  2009-11       Impact factor: 94.444

3.  Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

Authors:  Roie Levy; Elhanan Borenstein
Journal:  Gut Microbes       Date:  2014-02-20

Review 4.  Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities.

Authors:  Sharon Greenblum; Hsuan-Chao Chiu; Roie Levy; Rogan Carr; Elhanan Borenstein
Journal:  Curr Opin Biotechnol       Date:  2013-04-23       Impact factor: 9.740

5.  The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.

Authors:  Tasia M Taxis; Sara Wolff; Sarah J Gregg; Nicholas O Minton; Chiqian Zhang; Jingjing Dai; Robert D Schnabel; Jeremy F Taylor; Monty S Kerley; J Chris Pires; William R Lamberson; Gavin C Conant
Journal:  Nucleic Acids Res       Date:  2015-09-29       Impact factor: 16.971

6.  Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species.

Authors:  Shiri Freilich; Anat Kreimer; Elhanan Borenstein; Uri Gophna; Roded Sharan; Eytan Ruppin
Journal:  PLoS Comput Biol       Date:  2010-02-26       Impact factor: 4.475

7.  The large-scale organization of the bacterial network of ecological co-occurrence interactions.

Authors:  Shiri Freilich; Anat Kreimer; Isacc Meilijson; Uri Gophna; Roded Sharan; Eytan Ruppin
Journal:  Nucleic Acids Res       Date:  2010-03-01       Impact factor: 16.971

8.  PINT: Pathways INtegration Tool.

Authors:  Y-T Wang; Y-H Huang; Y-C Chen; C-L Hsu; U-C Yang
Journal:  Nucleic Acids Res       Date:  2010-06-10       Impact factor: 16.971

9.  In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study.

Authors:  Reed Taffs; John E Aston; Kristen Brileya; Zackary Jay; Christian G Klatt; Shawn McGlynn; Natasha Mallette; Scott Montross; Robin Gerlach; William P Inskeep; David M Ward; Ross P Carlson
Journal:  BMC Syst Biol       Date:  2009-12-10

10.  Metabolic-network-driven analysis of bacterial ecological strategies.

Authors:  Shiri Freilich; Anat Kreimer; Elhanan Borenstein; Nir Yosef; Roded Sharan; Uri Gophna; Eytan Ruppin
Journal:  Genome Biol       Date:  2009-06-05       Impact factor: 13.583
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