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Items: 1 to 20 of 81


Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR.

Microb Biotechnol. 2009 Mar;2(2):274-86. doi: 10.1111/j.1751-7915.2009.00087.x.


Prodigal: prokaryotic gene recognition and translation initiation site identification.

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.

BMC Bioinformatics. 2010 Mar 8;11:119. doi: 10.1186/1471-2105-11-119.


Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer.

N'Guessan AL, Elifantz H, Nevin KP, Mouser PJ, Methé B, Woodard TL, Manley K, Williams KH, Wilkins MJ, Larsen JT, Long PE, Lovley DR.

ISME J. 2010 Feb;4(2):253-66. doi: 10.1038/ismej.2009.115. Epub 2009 Dec 10.


Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments.

Zhao J, Fang Y, Scheibe TD, Lovley DR, Mahadevan R.

J Contam Hydrol. 2010 Mar 1;112(1-4):30-44. doi: 10.1016/j.jconhyd.2009.10.002. Epub 2009 Nov 5.


Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases.

Kung JW, Löffler C, Dörner K, Heintz D, Gallien S, Van Dorsselaer A, Friedrich T, Boll M.

Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17687-92. doi: 10.1073/pnas.0905073106. Epub 2009 Oct 6.


Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens.

Risso C, Sun J, Zhuang K, Mahadevan R, DeBoy R, Ismail W, Shrivastava S, Huot H, Kothari S, Daugherty S, Bui O, Schilling CH, Lovley DR, Methé BA.

BMC Genomics. 2009 Sep 22;10:447. doi: 10.1186/1471-2164-10-447.


CcpA from Geobacter sulfurreducens is a basic di-heme cytochrome c peroxidase.

Hoffmann M, Seidel J, Einsle O.

J Mol Biol. 2009 Nov 6;393(4):951-65. doi: 10.1016/j.jmb.2009.09.001. Epub 2009 Sep 6.


Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.

Wilkins MJ, Verberkmoes NC, Williams KH, Callister SJ, Mouser PJ, Elifantz H, N'guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovley DR, Hettich RL, Long PE, Banfield JF.

Appl Environ Microbiol. 2009 Oct;75(20):6591-9. doi: 10.1128/AEM.01064-09. Epub 2009 Aug 28.


Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis.

Lei J, Zhou YF, Li LF, Su XD.

Protein Sci. 2009 Aug;18(8):1792-800. doi: 10.1002/pro.178.


The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens.

Aklujkar M, Krushkal J, DiBartolo G, Lapidus A, Land ML, Lovley DR.

BMC Microbiol. 2009 May 27;9:109. doi: 10.1186/1471-2180-9-109.


Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells.

Nevin KP, Kim BC, Glaven RH, Johnson JP, Woodard TL, Methé BA, Didonato RJ, Covalla SF, Franks AE, Liu A, Lovley DR.

PLoS One. 2009 May 20;4(5):e5628. doi: 10.1371/journal.pone.0005628.


Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria.

Wischgoll S, Taubert M, Peters F, Jehmlich N, von Bergen M, Boll M.

J Bacteriol. 2009 Jul;191(13):4401-9. doi: 10.1128/JB.00205-09. Epub 2009 Apr 24.


Genome-scale constraint-based modeling of Geobacter metallireducens.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.

BMC Syst Biol. 2009 Jan 28;3:15. doi: 10.1186/1752-0509-3-15.


Riboswitches in eubacteria sense the second messenger cyclic di-GMP.

Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR.

Science. 2008 Jul 18;321(5887):411-3. doi: 10.1126/science.1159519.


Investigation of direct vs. indirect involvement of the c-type cytochrome MacA in Fe(III) reduction by Geobacter sulfurreducens.

Kim BC, Lovley DR.

FEMS Microbiol Lett. 2008 Sep;286(1):39-44. doi: 10.1111/j.1574-6968.2008.01252.x.


Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens.

Segura D, Mahadevan R, Juárez K, Lovley DR.

PLoS Comput Biol. 2008 Feb;4(2):e36. doi: 10.1371/journal.pcbi.0040036. Erratum in: PLoS Comput Biol. 2008 Mar;4(3). doi: 10.1371/annotation/67743d4d-2993-4d0c-951b-3f11ce65a8b4. PLoS Comput Biol. 2008 Feb;4(2):e36.


Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments.

Holmes DE, O'Neil RA, Vrionis HA, N'guessan LA, Ortiz-Bernad I, Larrahondo MJ, Adams LA, Ward JA, Nicoll JS, Nevin KP, Chavan MA, Johnson JP, Long PE, Lovley DR.

ISME J. 2007 Dec;1(8):663-77. Epub 2007 Oct 18.


The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD.

Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31. Epub 2007 Oct 27.


Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid.

Tang YJ, Chakraborty R, Martín HG, Chu J, Hazen TC, Keasling JD.

Appl Environ Microbiol. 2007 Jun;73(12):3859-64. Epub 2007 Apr 27.

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