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Items: 1 to 20 of 118


Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y.

Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014.


Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.

Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin AP.

PLoS Genet. 2011 Nov;7(11):e1002385. doi: 10.1371/journal.pgen.1002385. Epub 2011 Nov 17.


A system-level approach for deciphering the transcriptional response to prion infection.

Zampieri M, Legname G, Segrè D, Altafini C.

Bioinformatics. 2011 Dec 15;27(24):3407-14. doi: 10.1093/bioinformatics/btr580. Epub 2011 Oct 20.


The RpoS-mediated general stress response in Escherichia coli.

Battesti A, Majdalani N, Gottesman S.

Annu Rev Microbiol. 2011;65:189-213. doi: 10.1146/annurev-micro-090110-102946. Review.


Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.

Cruz-García C, Murray AE, Rodrigues JL, Gralnick JA, McCue LA, Romine MF, Löffler FE, Tiedje JM.

BMC Microbiol. 2011 Mar 30;11:64. doi: 10.1186/1471-2180-11-64.


Indirect modulation of the intracellular c-Di-GMP level in Shewanella oneidensis MR-1 by MxdA.

Rakshe S, Leff M, Spormann AM.

Appl Environ Microbiol. 2011 Mar;77(6):2196-8. doi: 10.1128/AEM.01985-10. Epub 2011 Jan 28.


Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis.

Gao H, Wang X, Yang ZK, Chen J, Liang Y, Chen H, Palzkill T, Zhou J.

PLoS One. 2010 Dec 28;5(12):e15295. doi: 10.1371/journal.pone.0015295.


EcoCyc: a comprehensive database of Escherichia coli biology.

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD.

Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21.


Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor.

Rosenbaum MA, Bar HY, Beg QK, Segrè D, Booth J, Cotta MA, Angenent LT.

Bioresour Technol. 2011 Feb;102(3):2623-8. doi: 10.1016/j.biortech.2010.10.033. Epub 2010 Oct 12.


Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.

Karpinets TV, Romine MF, Schmoyer DD, Kora GH, Syed MH, Leuze MR, Serres MH, Park BH, Samatova NF, Uberbacher EC.

Database (Oxford). 2010 Jul 6;2010:baq012. doi: 10.1093/database/baq012.


Structural insight into the oxidation-sensing mechanism of the antibiotic resistance of regulator MexR.

Chen H, Yi C, Zhang J, Zhang W, Ge Z, Yang CG, He C.

EMBO Rep. 2010 Sep;11(9):685-90. doi: 10.1038/embor.2010.96. Epub 2010 Jul 9. Erratum in: EMBO Rep. 2010 Sep;11(9):717.


Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation.

Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, Osterman A, Scott JH, Reed SB, Romine MF, Konopka AE, Beliaev AS, Fredrickson JK, Reed JL.

PLoS Comput Biol. 2010 Jun 24;6(6):e1000822. doi: 10.1371/journal.pcbi.1000822.


RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.

Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W299-307. doi: 10.1093/nar/gkq531. Epub 2010 Jun 11.


Spatiotemporal activity of the mshA gene system in Shewanella oneidensis MR-1 biofilms.

Saville RM, Dieckmann N, Spormann AM.

FEMS Microbiol Lett. 2010 Jul 1;308(1):76-83. doi: 10.1111/j.1574-6968.2010.01995.x. Epub 2010 Apr 21.


Light energy to bioelectricity: photosynthetic microbial fuel cells.

Rosenbaum M, He Z, Angenent LT.

Curr Opin Biotechnol. 2010 Jun;21(3):259-64. doi: 10.1016/j.copbio.2010.03.010. Epub 2010 Apr 6. Review.


ArcS, the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1.

Lassak J, Henche AL, Binnenkade L, Thormann KM.

Appl Environ Microbiol. 2010 May;76(10):3263-74. doi: 10.1128/AEM.00512-10. Epub 2010 Mar 26.


Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1.

Syed MH, Karpinets TV, Leuze MR, Kora GH, Romine MR, Uberbacher EC.

Bioinformation. 2009 Oct 15;4(4):169-72.


Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli.

Dörr T, Vulić M, Lewis K.

PLoS Biol. 2010 Feb 23;8(2):e1000317. doi: 10.1371/journal.pbio.1000317.


Growth rate-dependent global effects on gene expression in bacteria.

Klumpp S, Zhang Z, Hwa T.

Cell. 2009 Dec 24;139(7):1366-75. doi: 10.1016/j.cell.2009.12.001.


Metals, minerals and microbes: geomicrobiology and bioremediation.

Gadd GM.

Microbiology. 2010 Mar;156(Pt 3):609-43. doi: 10.1099/mic.0.037143-0. Epub 2009 Dec 17. Review.


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