Publications

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Chen M, Lopes JM.  2007.  Multiple basic helix-loop-helix proteins regulate expression of the ENO1 gene of Saccharomyces cerevisiae.. Eukaryot Cell. 6(5):786-96.
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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.
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.
G
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.
Griffith KL, Fitzpatrick MM, Keen EF, Wolf RE.  2009.  Two functions of the C-terminal domain of Escherichia coli Rob: mediating "sequestration-dispersal" as a novel off-on switch for regulating Rob's activity as a transcription activator and preventing degradation of Rob by Lon protease.. J Mol Biol. 388(3):415-30.
H
Hancock LC, Behta RP, Lopes JM.  2006.  Genomic analysis of the Opi- phenotype.. Genetics. 173(2):621-34.
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.
I
Izallalen M, Mahadevan R, Burgard A, Postier B, DiDonato R, Sun J, Schilling CH, Lovley DR.  2008.  Geobacter sulfurreducens strain engineered for increased rates of respiration.. Metab Eng. 10(5):267-75.
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Long J E, Renzette N, Centore RC, Sandler SJ.  2008.  Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12.. PLoS One. 3(12):e4100.
Lopper M, Boonsombat R, Sandler SJ, Keck JL.  2007.  A hand-off mechanism for primosome assembly in replication restart.. Mol Cell. 26(6):781-93.
Lovley DR.  2003.  Cleaning up with genomics: applying molecular biology to bioremediation.. Nat Rev Microbiol. 1(1):35-44.
Lovley DR.  2005.  Crystal ball. In silico biology meets in situ phenomenology.. Environ Microbiol. 7(4):478-9.
Lovley DR.  2017.  Happy together: microbial communities that hook up to swap electrons.. ISME J. 11(2):327-336.
Lovley DR.  2008.  Extracellular electron transfer: wires, capacitors, iron lungs, and more.. Geobiology. 6(3):225-31.
M
Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR.  2006.  Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.. Appl Environ Microbiol. 72(2):1558-68.
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.
Mahadevan R, Lovley DR.  2008.  The degree of redundancy in metabolic genes is linked to mode of metabolism.. Biophys J. 94(4):1216-20.
Meniche X, Otten R, M Siegrist S, Baer CE, Murphy KC, Bertozzi CR, Sassetti CM.  2014.  Subpolar addition of new cell wall is directed by DivIVA in mycobacteria.. Proc Natl Acad Sci U S A. 111(31):E3243-51.
Morita YS, Velasquez R, Taig E, Waller RF, Patterson JH, Tull D, Williams SJ, Billman-Jacobe H, McConville MJ.  2005.  Compartmentalization of lipid biosynthesis in mycobacteria.. J Biol Chem. 280(22):21645-52.
Morita YS, Fukuda T, Sena CBC, Yamaryo-Botte Y, McConville MJ, Kinoshita T.  2011.  Inositol lipid metabolism in mycobacteria: biosynthesis and regulatory mechanisms.. Biochim Biophys Acta. 1810(6):630-41.
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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.
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Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho B-K, Elkins JG, Nevin KP, Barrett CL et al..  2013.  Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.. Nat Commun. 4:1755.
R
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.
S
Sandler SJ, McCool JD, Do TT, Johansen RU.  2001.  PriA mutations that affect PriA-PriC function during replication restart.. Mol Microbiol. 41(3):697-704.
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.

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