Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.

Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS.

Genome Biol. 2004;5(11):R90. Epub 2004 Oct 22.

PMID: 15535866 [PubMed - indexed for MEDLINE]

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Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS.

Nucleic Acids Res. 2003 Dec 1;31(23):6748-57.

PMID: 14627808 [PubMed - indexed for MEDLINE]

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Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS.

Nucleic Acids Res. 2004 Jun 23;32(11):3340-53. Print 2004.

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Comparative genomic analysis of T-box regulatory systems in bacteria.

Vitreschak AG, Mironov AA, Lyubetsky VA, Gelfand MS.

RNA. 2008 Apr;14(4):717-35.

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Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis.

Zhang W, Culley DE, Hogan M, Vitiritti L, Brockman FJ.

Antonie Van Leeuwenhoek. 2006 Jul;90(1):41-55. Epub 2006 May 6.

PMID: 16680520 [PubMed - indexed for MEDLINE]

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Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS.

PLoS Comput Biol. 2005 Oct;1(5):e55. Epub 2005 Oct 28.

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Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis.

Wan XF, Verberkmoes NC, McCue LA, Stanek D, Connelly H, Hauser LJ, Wu L, Liu X, Yan T, Leaphart A, Hettich RL, Zhou J, Thompson DK.

J Bacteriol. 2004 Dec;186(24):8385-400.

PMID: 15576789 [PubMed - indexed for MEDLINE]

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Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough.

Bender KS, Yen HC, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD.

Appl Environ Microbiol. 2007 Sep;73(17):5389-400. Epub 2007 Jul 13.

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Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.

Rodionov DA, Gelfand MS, Todd JD, Curson AR, Johnston AW.

PLoS Comput Biol. 2006 Dec 15;2(12):e163. Epub 2006 Oct 18.

PMID: 17173478 [PubMed - indexed for MEDLINE]

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Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms.

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS.

J Biol Chem. 2002 Dec 13;277(50):48949-59. Epub 2002 Oct 9.

PMID: 12376536 [PubMed - indexed for MEDLINE]

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Genome-assisted analysis of dissimilatory metal-reducing bacteria.

Fredrickson JK, Romine MF.

Curr Opin Biotechnol. 2005 Jun;16(3):269-74. Review.

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Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.

Gelfand MS, Koonin EV, Mironov AA.

Nucleic Acids Res. 2000 Feb 1;28(3):695-705.

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Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis.

Valdés J, Veloso F, Jedlicki E, Holmes D.

BMC Genomics. 2003 Dec 15;4(1):51.

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NssR, a member of the Crp-Fnr superfamily from Campylobacter jejuni, regulates a nitrosative stress-responsive regulon that includes both a single-domain and a truncated haemoglobin.

Elvers KT, Turner SM, Wainwright LM, Marsden G, Hinds J, Cole JA, Poole RK, Penn CW, Park SF.

Mol Microbiol. 2005 Aug;57(3):735-50.

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Cell envelope stress response in Bacillus licheniformis: integrating comparative genomics, transcriptional profiling, and regulon mining to decipher a complex regulatory network.

Wecke T, Veith B, Ehrenreich A, Mascher T.

J Bacteriol. 2006 Nov;188(21):7500-11. Epub 2006 Aug 25.

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Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element.

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RNA. 2003 Sep;9(9):1084-97.

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Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria.

Sun J, van den Heuvel J, Soucaille P, Qu Y, Zeng AP.

Biotechnol Prog. 2003 Mar-Apr;19(2):263-72.

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Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.

Yan B, Lovley DR, Krushkal J.

Biosystems. 2007 Sep-Oct;90(2):421-41. Epub 2006 Oct 26.

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Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion.

Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan XF, Hazen TC, Arkin AP, Wall JD, Zhou JZ, Fields MW.

Appl Environ Microbiol. 2006 Aug;72(8):5578-88.

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Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.

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Nucleic Acids Res. 2002 Jul 15;30(14):3141-51.

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