Publications

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C
Griffith KL, Becker SM, Wolf RE.  2005.  Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon.. Mol Microbiol. 56(4):1103-17.
Mahadevan R, Yan B, Postier B, Nevin KP, Woodard TL, O'Neil R, Coppi MV, Methé BA, Krushkal J.  2008.  Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis.. OMICS. 12(1):33-59.
Elkhaimi M, Kaadige MR, Kamath D, Jackson JC, Biliran H, Lopes JM.  2000.  Combinatorial regulation of phospholipid biosynthetic gene expression by the UME6, SIN3 and RPD3 genes.. Nucleic Acids Res. 28(16):3160-7.
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.
D
Griffith KL, Grossman AD.  2008.  A degenerate tripartite DNA-binding site required for activation of ComA-dependent quorum response gene expression in Bacillus subtilis.. J Mol Biol. 381(2):261-75.
Shetty A, Lopes JM.  2010.  Derepression of INO1 transcription requires cooperation between the Ino2p-Ino4p heterodimer and Cbf1p and recruitment of the ISW2 chromatin-remodeling complex.. Eukaryot Cell. 9(12):1845-55.
E
Gardocki M E, Lopes JM.  2003.  Expression of the yeast PIS1 gene requires multiple regulatory elements including a Rox1p binding site.. J Biol Chem. 278(40):38646-52.
F
Sandler SJ, Clark AJ.  1990.  Factors affecting expression of the recF gene of Escherichia coli K-12.. Gene. 86(1):35-43.
G
O'Neil RA, Holmes DE, Coppi MV, Adams LA, Larrahondo JM, Ward JE, Nevin KP, Woodard TL, Vrionis HA, N'guessan LA et al..  2008.  Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation.. Environ Microbiol. 10(5):1218-30.
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.
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.
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.
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.
Jara M, Núñez C, Campoy S, Fernández de Henestrosa AR, Lovley DR, Barbé J.  2003.  Geobacter sulfurreducens has two autoregulated lexA genes whose products do not bind the recA promoter: differing responses of lexA and recA to DNA damage.. J Bacteriol. 185(8):2493-502.
H
Ueki T, Lovley DR.  2007.  Heat-shock sigma factor RpoH from Geobacter sulfurreducens.. Microbiology. 153(Pt 3):838-46.
I
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.
Wood TI, Griffith KL, Fawcett WP, Jair KW, Schneider TD, Wolf RE.  1999.  Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters.. Mol Microbiol. 34(3):414-30.
M
M Siegrist S, Unnikrishnan M, McConnell MJ, Borowsky M, Cheng T-Y, Siddiqi N, Fortune SM, D Moody B, Rubin EJ.  2009.  Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition.. Proc Natl Acad Sci U S A. 106(44):18792-7.
N
Ueki T, Lovley DR.  2010.  Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens.. Nucleic Acids Res. 38(21):7485-99.
P
Juárez K, Kim B-C, Nevin K, Olvera L, Reguera G, Lovley DR, Methé BA.  2009.  PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens.. J Mol Microbiol Biotechnol. 16(3-4):146-58.
Griffith KL, Shah IM, Wolf RE.  2004.  Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons.. Mol Microbiol. 51(6):1801-16.
R
Sha K, Choi S-H, Im J, Lee GG, Loeffler F, Park JH.  2014.  Regulation of ethanol-related behavior and ethanol metabolism by the Corazonin neurons and Corazonin receptor in Drosophila melanogaster.. PLoS One. 9(1):e87062.
Leang C, Lovley DR.  2005.  Regulation of two highly similar genes, omcB and omcC, in a 10 kb chromosomal duplication in Geobacter sulfurreducens.. Microbiology. 151(Pt 6):1761-7.
T
Shetty A, Swaminathan A, Lopes JM.  2013.  Transcription regulation of a yeast gene from a downstream location.. J Mol Biol. 425(3):457-65.
He Y, Swaminathan A, Lopes JM.  2012.  Transcription regulation of the Saccharomyces cerevisiae PHO5 gene by the Ino2p and Ino4p basic helix-loop-helix proteins.. Mol Microbiol. 83(2):395-407.

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