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Results: 1 to 20 of 179

1.

Metabolic-network-driven analysis of bacterial ecological strategies.

Freilich S, Kreimer A, Borenstein E, Yosef N, Sharan R, Gophna U, Ruppin E.

Genome Biol. 2009;10(6):R61. doi: 10.1186/gb-2009-10-6-r61. Epub 2009 Jun 5.

PMID:
19500338
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth.

Morine MJ, Gu H, Myers RA, Bielawski JP.

J Mol Evol. 2009 May;68(5):506-15. doi: 10.1007/s00239-009-9226-5. Epub 2009 Apr 14.

PMID:
19365645
[PubMed - indexed for MEDLINE]
3.

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

Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E.

Nucleic Acids Res. 2010 Jul;38(12):3857-68. doi: 10.1093/nar/gkq118. Epub 2010 Mar 1.

PMID:
20194113
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Toward the automated generation of genome-scale metabolic networks in the SEED.

DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A.

BMC Bioinformatics. 2007 Apr 26;8:139.

PMID:
17462086
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Diversity, dilemmas, and monopolies of niche construction.

Krakauer DC, Page KM, Erwin DH.

Am Nat. 2009 Jan;173(1):26-40. doi: 10.1086/593707.

PMID:
19061421
[PubMed - indexed for MEDLINE]
6.

Convergent evolution of modularity in metabolic networks through different community structures.

Zhou W, Nakhleh L.

BMC Evol Biol. 2012 Sep 14;12:181. doi: 10.1186/1471-2148-12-181.

PMID:
22974099
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A phylogenomic analysis of bacterial helix-turn-helix transcription factors.

Santos CL, Tavares F, Thioulouse J, Normand P.

FEMS Microbiol Rev. 2009 Mar;33(2):411-29. doi: 10.1111/j.1574-6976.2008.00154.x. Epub 2008 Dec 9. Review.

PMID:
19076237
[PubMed - indexed for MEDLINE]
8.

Elucidation of multifaceted evolutionary processes of microorganisms by comparative genome-based analysis.

Nguyen TV, Hong SH, Lee SY.

J Microbiol Biotechnol. 2009 Nov;19(11):1301-5.

PMID:
19996680
[PubMed - indexed for MEDLINE]
Free Article
9.

An environmental perspective on metabolism.

Handorf T, Christian N, Ebenhöh O, Kahn D.

J Theor Biol. 2008 Jun 7;252(3):530-7. Epub 2007 Nov 4.

PMID:
18086477
[PubMed - indexed for MEDLINE]
10.

Environmental variability and modularity of bacterial metabolic networks.

Parter M, Kashtan N, Alon U.

BMC Evol Biol. 2007 Sep 23;7:169.

PMID:
17888177
[PubMed]
Free PMC Article
11.

When can we distinguish between neutral and non-neutral processes in community dynamics under ecological drift?

Ruokolainen L, Ranta E, Kaitala V, Fowler MS.

Ecol Lett. 2009 Sep;12(9):909-19. doi: 10.1111/j.1461-0248.2009.01346.x. Epub 2009 Jun 30.

PMID:
19570103
[PubMed - indexed for MEDLINE]
12.

Compensatory ability to null mutation in metabolic networks.

Jiang D, Zhou S, Chen YP.

Biotechnol Bioeng. 2009 Jun 1;103(2):361-9. doi: 10.1002/bit.22237.

PMID:
19160379
[PubMed - indexed for MEDLINE]
13.

Competitive and cooperative metabolic interactions in bacterial communities.

Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, Gophna U, Sharan R, Ruppin E.

Nat Commun. 2011 Dec 13;2:589. doi: 10.1038/ncomms1597.

PMID:
22158444
[PubMed - indexed for MEDLINE]
14.

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.

Lee J, Yun H, Feist AM, Palsson BØ, Lee SY.

Appl Microbiol Biotechnol. 2008 Oct;80(5):849-62. doi: 10.1007/s00253-008-1654-4. Epub 2008 Aug 29.

PMID:
18758767
[PubMed - indexed for MEDLINE]
15.

Reconstructing the metabolic network of a bacterium from its genome.

Francke C, Siezen RJ, Teusink B.

Trends Microbiol. 2005 Nov;13(11):550-8. Epub 2005 Sep 19. Review.

PMID:
16169729
[PubMed - indexed for MEDLINE]
16.

Large-scale reconstruction and phylogenetic analysis of metabolic environments.

Borenstein E, Kupiec M, Feldman MW, Ruppin E.

Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14482-7. doi: 10.1073/pnas.0806162105. Epub 2008 Sep 11.

PMID:
18787117
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Species' traits predict the effects of disturbance and productivity on diversity.

Haddad NM, Holyoak M, Mata TM, Davies KF, Melbourne BA, Preston K.

Ecol Lett. 2008 Apr;11(4):348-56. doi: 10.1111/j.1461-0248.2007.01149.x. Epub 2008 Jan 14.

PMID:
18201199
[PubMed - indexed for MEDLINE]
18.

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

Freilich S, Kreimer A, Borenstein E, Gophna U, Sharan R, Ruppin E.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000690. doi: 10.1371/journal.pcbi.1000690.

PMID:
20195496
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Ecological fitting by phenotypically flexible genotypes: implications for species associations, community assembly and evolution.

Agosta SJ, Klemens JA.

Ecol Lett. 2008 Nov;11(11):1123-34. doi: 10.1111/j.1461-0248.2008.01237.x. Epub 2008 Sep 4.

PMID:
18778274
[PubMed - indexed for MEDLINE]
20.

Topological signatures of species interactions in metabolic networks.

Borenstein E, Feldman MW.

J Comput Biol. 2009 Feb;16(2):191-200. doi: 10.1089/cmb.2008.06TT.

PMID:
19178139
[PubMed - indexed for MEDLINE]
Free PMC Article

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