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He Y, Swaminathan A, Lopes JM.\'a0 2012.\'a0\'a0Transcription regulation of the Saccharomyces cerevisiae PHO5 gene by the Ino2p and Ino4p basic helix-loop-helix proteins.. Mol Microbiol. 83(2):395-407.\par \par Shetty A, Lopes JM.\'a0 2010.\'a0\'a0Derepression 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.\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, 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 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 Chen M, Hancock LC, Lopes JM.\'a0 2007.\'a0\'a0Transcriptional regulation of yeast phospholipid biosynthetic genes.. Biochim Biophys Acta. 1771(3):310-21.\par \par Kaadige MR, Lopes JM.\'a0 2006.\'a0\'a0Analysis of Opi1p repressor mutants.. Curr Genet. 49(1):30-8.\par \par Griffith KL, Becker SM, Wolf RE.\'a0 2005.\'a0\'a0Characterization 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.\par \par Gardenour KR, Levy J, Lopes JM.\'a0 2004.\'a0\'a0Identification of novel dominant INO2c mutants with an Opi- phenotype.. Mol Microbiol. 52(5):1271-80.\par \par Kaadige MR, Lopes JM.\'a0 2003.\'a0\'a0Opi1p, Ume6p and Sin3p control expression from the promoter of the INO2 regulatory gene via a novel regulatory cascade.. Mol Microbiol. 48(3):823-32.\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 Griffith KL, Wolf RE.\'a0 2001.\'a0\'a0Systematic mutagenesis of the DNA binding sites for SoxS in the Escherichia coli zwf and fpr promoters: identifying nucleotides required for DNA binding and transcription activation.. Mol Microbiol. 40(5):1141-54.\par \par Elkhaimi M, Kaadige MR, Kamath D, Jackson JC, Biliran H, Lopes JM.\'a0 2000.\'a0\'a0Combinatorial regulation of phospholipid biosynthetic gene expression by the UME6, SIN3 and RPD3 genes.. Nucleic Acids Res. 28(16):3160-7.\par \par Robinson KA, Koepke JI, Kharodawala M, Lopes JM.\'a0 2000.\'a0\'a0A network of yeast basic helix-loop-helix interactions.. Nucleic Acids Res. 28(22):4460-6.\par \par Robinson KA, Lopes JM.\'a0 2000.\'a0\'a0The promoter of the yeast INO4 regulatory gene: a model of the simplest yeast promoter.. J Bacteriol. 182(10):2746-52.\par \par Wood TI, Griffith KL, Fawcett WP, Jair KW, Schneider TD, Wolf RE.\'a0 1999.\'a0\'a0Interdependence 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.\par \par }