Feist AM, Nagarajan H, Rotaru A-E, Tremblay P-L, Zhang T, Nevin KP, Lovley DR, Zengler K.  2014.  Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.. PLoS Comput Biol. 10(4):e1003575.

Nagarajan H, Embree M, Rotaru A-E, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.  2013.  Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.. Nat Commun. 4:2809.

Butler JE, Young ND, Aklujkar M, Lovley DR.  2012.  Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production.. BMC Genomics. 13:471.

Aklujkar M, Haveman SA, DiDonato R, Chertkov O, Han CS, Land ML, Brown P, Lovley DR.  2012.  The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.. BMC Genomics. 13:690.

Tremblay P-L, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR.  2011.  A 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.

Fang Y, Scheibe TD, Mahadevan R, Garg S, Long PE, Lovley DR.  2011.  Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.. J Contam Hydrol. 122(1-4):96-103.

Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, Lovley DR.  2011.  Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.. ISME J. 5(2):305-16.

Mahadevan R, Palsson BØ, Lovley DR.  2011.  In 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.

Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR et al..  2010.  De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.. PLoS One. 5(6):e10922.

Butler JE, Young ND, Lovley DR.  2010.  Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes.. BMC Genomics. 11:40.

Aklujkar M, Young ND, Holmes D, Chavan M, Risso C, Kiss HE, Han CS, Land ML, Lovley DR.  2010.  The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.. BMC Genomics. 11:490.

Ueki T, Lovley DR.  2010.  Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species.. Nucleic Acids Res. 38(3):810-21.

Krushkal J, Juárez K, Barbe JF, Qu Y, Andrade A, Puljic M, Adkins RM, Lovley DR, Ueki T.  2010.  Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens.. Gene. 469(1-2):31-44.

Aklujkar M, Lovley DR.  2010.  Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.. BMC Evol Biol. 10:230.

Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR.  2009.  Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.. Microb Biotechnol. 2(2):274-86.

Butler JE, Young ND, Lovley DR.  2009.  Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.. BMC Genomics. 10:103.

Aklujkar M, Krushkal J, DiBartolo G, Lapidus A, Land ML, Lovley DR.  2009.  The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens.. BMC Microbiol. 9:109.

Risso C, Sun J, Zhuang K, Mahadevan R, DeBoy R, Ismail W, Shrivastava S, Huot H, Kothari S, Daugherty S et al..  2009.  Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens.. BMC Genomics. 10:447.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.  2009.  Genome-scale constraint-based modeling of Geobacter metallireducens.. BMC Syst Biol. 3:15.

Qu Y, Brown P, Barbe JF, Puljic M, Merino E, Adkins RM, Lovley DR, Krushkal J.  2009.  GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.. OMICS. 13(5):439-49.

Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM.  2008.  Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.. BMC Genomics. 9:471.

Haveman SA, Didonato RJ, Villanueva L, Shelobolina ES, Postier BL, Xu B, Liu A, Lovley DR.  2008.  Genome-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.

Risso C, Methé BA, Elifantz H, Holmes DE, Lovley DR.  2008.  Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.. Microbiology. 154(Pt 9):2589-99.

Kim B-C, Postier BL, Didonato RJ, Chaudhuri SK, Nevin KP, Lovley DR.  2008.  Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.. Bioelectrochemistry. 73(1):70-5.

Krushkal J, Yan B, DiDonato LN, Puljic M, Nevin KP, Woodard TL, Adkins RM, Methé BA, Lovley DR.  2007.  Genome-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.

Yan B, Lovley DR, Krushkal J.  2007.  Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.. Biosystems. 90(2):421-41.

Ueki T, Lovley DR.  2007.  Heat-shock sigma factor RpoH from Geobacter sulfurreducens.. Microbiology. 153(Pt 3):838-46.

Yan B, Núñez C, Ueki T, Esteve-Núñez A, Puljic M, Adkins RM, Methé BA, Lovley DR, Krushkal J.  2006.  Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.. Gene. 384:73-95.

Afkar E, Reguera G, Schiffer M, Lovley DR.  2005.  A 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.

Yan B, Methé BA, Lovley DR, Krushkal J.  2004.  Computational 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.

Lovley DR.  2003.  Cleaning up with genomics: applying molecular biology to bioremediation.. Nat Rev Microbiol. 1(1):35-44.

Lovley DR.  2002.  Analysis 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.