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Feist AM, Nagarajan H, Rotaru A-E, Tremblay P-L, Zhang T, Nevin KP, Lovley DR, Zengler K.\'a0 2014.\'a0\'a0Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.. PLoS Comput Biol. 10(4):e1003575.\par \par Nagarajan H, Embree M, Rotaru A-E, Shrestha PM, Feist AM, Palsson B\'d8, Lovley DR, Zengler K.\'a0 2013.\'a0\'a0Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.. Nat Commun. 4:2809.\par \par Butler JE, Young ND, Aklujkar M, Lovley DR.\'a0 2012.\'a0\'a0Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production.. BMC Genomics. 13:471.\par \par Jung J-H, Holden JF, Seo D-H, Park K-H, Shin H, Ryu S, Lee J-H, Park C-S.\'a0 2012.\'a0\'a0Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain CL1, isolated from a Paralvinella sp. polychaete worm collected from a hydrothermal vent.. J Bacteriol. 194(17):4769-70.\par \par Aklujkar M, Haveman SA, DiDonato R, Chertkov O, Han CS, Land ML, Brown P, Lovley DR.\'a0 2012.\'a0\'a0The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.. BMC Genomics. 13:690.\par \par Tremblay P-L, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR.\'a0 2011.\'a0\'a0A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.. Environ Microbiol. 13(1):13-23.\par \par Fang Y, Scheibe TD, Mahadevan R, Garg S, Long PE, Lovley DR.\'a0 2011.\'a0\'a0Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.. J Contam Hydrol. 122(1-4):96-103.\par \par Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, Lovley DR.\'a0 2011.\'a0\'a0Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.. ISME J. 5(2):305-16.\par \par Mahadevan R, Palsson B\'d8, Lovley DR.\'a0 2011.\'a0\'a0In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.. Nat Rev Microbiol. 9(1):39-50.\par \par Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Meth\'e9 BA, Palsson B\'d8, Lovley DR et al..\'a0 2010.\'a0\'a0De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.. PLoS One. 5(6):e10922.\par \par Butler JE, Young ND, Lovley DR.\'a0 2010.\'a0\'a0Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes.. BMC Genomics. 11:40.\par \par Aklujkar M, Young ND, Holmes D, Chavan M, Risso C, Kiss HE, Han CS, Land ML, Lovley DR.\'a0 2010.\'a0\'a0The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.. BMC Genomics. 11:490.\par \par Ueki T, Lovley DR.\'a0 2010.\'a0\'a0Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species.. Nucleic Acids Res. 38(3):810-21.\par \par Krushkal J, Ju\'e1rez K, Barbe JF, Qu Y, Andrade A, Puljic M, Adkins RM, Lovley DR, Ueki T.\'a0 2010.\'a0\'a0Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens.. Gene. 469(1-2):31-44.\par \par Aklujkar M, Lovley DR.\'a0 2010.\'a0\'a0Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.. BMC Evol Biol. 10:230.\par \par Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR.\'a0 2009.\'a0\'a0Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.. Microb Biotechnol. 2(2):274-86.\par \par Butler JE, Young ND, Lovley DR.\'a0 2009.\'a0\'a0Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.. BMC Genomics. 10:103.\par \par Aklujkar M, Krushkal J, DiBartolo G, Lapidus A, Land ML, Lovley DR.\'a0 2009.\'a0\'a0The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens.. BMC Microbiol. 9:109.\par \par Risso C, Sun J, Zhuang K, Mahadevan R, DeBoy R, Ismail W, Shrivastava S, Huot H, Kothari S, Daugherty S et al..\'a0 2009.\'a0\'a0Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens.. BMC Genomics. 10:447.\par \par Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.\'a0 2009.\'a0\'a0Genome-scale constraint-based modeling of Geobacter metallireducens.. BMC Syst Biol. 3:15.\par \par Qu Y, Brown P, Barbe JF, Puljic M, Merino E, Adkins RM, Lovley DR, Krushkal J.\'a0 2009.\'a0\'a0GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.. OMICS. 13(5):439-49.\par \par M Siegrist S, Unnikrishnan M, McConnell MJ, Borowsky M, Cheng T-Y, Siddiqi N, Fortune SM, D Moody B, Rubin EJ.\'a0 2009.\'a0\'a0Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition.. Proc Natl Acad Sci U S A. 106(44):18792-7.\par \par Mahadevan R, Yan B, Postier B, Nevin KP, Woodard TL, O'Neil R, Coppi MV, Meth\'e9 BA, Krushkal J.\'a0 2008.\'a0\'a0Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis.. OMICS. 12(1):33-59.\par \par Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM.\'a0 2008.\'a0\'a0Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.. BMC Genomics. 9:471.\par \par Haveman SA, Didonato RJ, Villanueva L, Shelobolina ES, Postier BL, Xu B, Liu A, Lovley DR.\'a0 2008.\'a0\'a0Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production.. Appl Environ Microbiol. 74(14):4277-84.\par \par Risso C, Meth\'e9 BA, Elifantz H, Holmes DE, Lovley DR.\'a0 2008.\'a0\'a0Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.. Microbiology. 154(Pt 9):2589-99.\par \par Kim B-C, Postier BL, Didonato RJ, Chaudhuri SK, Nevin KP, Lovley DR.\'a0 2008.\'a0\'a0Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.. Bioelectrochemistry. 73(1):70-5.\par \par Krushkal J, Yan B, DiDonato LN, Puljic M, Nevin KP, Woodard TL, Adkins RM, Meth\'e9 BA, Lovley DR.\'a0 2007.\'a0\'a0Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.. Funct Integr Genomics. 7(3):229-55.\par \par Yan B, Lovley DR, Krushkal J.\'a0 2007.\'a0\'a0Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.. Biosystems. 90(2):421-41.\par \par Lopper M, Boonsombat R, Sandler SJ, Keck JL.\'a0 2007.\'a0\'a0A hand-off mechanism for primosome assembly in replication restart.. Mol Cell. 26(6):781-93.\par \par Ueki T, Lovley DR.\'a0 2007.\'a0\'a0Heat-shock sigma factor RpoH from Geobacter sulfurreducens.. Microbiology. 153(Pt 3):838-46.\par \par Yan B, N\'fa\'f1ez C, Ueki T, Esteve-N\'fa\'f1ez A, Puljic M, Adkins RM, Meth\'e9 BA, Lovley DR, Krushkal J.\'a0 2006.\'a0\'a0Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.. Gene. 384:73-95.\par \par Morita YS, Sena CBC, Waller RF, Kurokawa K, Sernee FM, Nakatani F, Haites RE, Billman-Jacobe H, McConville MJ, Maeda Y et al..\'a0 2006.\'a0\'a0PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of phosphatidylinositol mannoside in mycobacteria.. J Biol Chem. 281(35):25143-55.\par \par Afkar E, Reguera G, Schiffer M, Lovley DR.\'a0 2005.\'a0\'a0A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens.. BMC Microbiol. 5:41.\par \par Sandler SJ.\'a0 2005.\'a0\'a0Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12.. Genetics. 169(4):1799-806.\par \par Yan B, Meth\'e9 BA, Lovley DR, Krushkal J.\'a0 2004.\'a0\'a0Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae.. J Theor Biol. 230(1):133-44.\par \par de la Salmoni\'e8re Y-OLuc Goguet, Kim CC, Tsolaki AG, Pym AS, Siegrist MS, Small PM.\'a0 2004.\'a0\'a0High-throughput method for detecting genomic-deletion polymorphisms.. J Clin Microbiol. 42(7):2913-8.\par \par Lovley DR.\'a0 2003.\'a0\'a0Cleaning up with genomics: applying molecular biology to bioremediation.. Nat Rev Microbiol. 1(1):35-44.\par \par Meth\'e9 BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ et al..\'a0 2003.\'a0\'a0Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.. Science. 302(5652):1967-9.\par \par Lovley DR.\'a0 2002.\'a0\'a0Analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter.. OMICS. 6(4):331-9.\par \par Griffith KL, Shah IM, Myers TE, O'Neill MC, Wolf RE.\'a0 2002.\'a0\'a0Evidence for "pre-recruitment" as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell.. Biochem Biophys Res Commun. 291(4):979-86.\par \par Lovley DR.\'a0 2001.\'a0\'a0Bioremediation. Anaerobes to the rescue.. Science. 293(5534):1444-6.\par \par }