My NCBISign In
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
Dmitry A Rodionov, Inna Dubchak, Adam Arkin, Eric Alm, Mikhail S Gelfand
Genome Biol. 2004; 5(11): R90. Published online 2004 October 22. doi: 10.1186/gb-2004-5-11-r90
PMCID:
PMC545781
Abstract Full Text PDF–1.7M Supplementary Material

Is Cited by the Following 28 Articles in this Archive:

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough
Aifen Zhou, Yunyu I. Chen, Grant M. Zane, Zhili He, Christopher L. Hemme, Marcin P. Joachimiak, Jason K. Baumohl, Qiang He, Matthew W. Fields, Adam P. Arkin, Judy D. Wall, Terry C. Hazen, Jizhong Zhou
Appl Environ Microbiol. 2012 February; 78(4): 1168–1177. doi: 10.1128/AEM.05666-11
PMCID:
PMC3273024
Free in PMC on 2012/08/01
Contributions of the Peroxisome and β-Oxidation Cycle to Biotin Synthesis in Fungi
Pasqualina Magliano, Michel Flipphi, Bulak A. Arpat, Syndie Delessert, Yves Poirier
J Biol Chem. 2011 December 9; 286(49): 42133–42140. Published online 2011 October 13. doi: 10.1074/jbc.M111.279687
PMCID:
PMC3234907
Free in PMC on 2012/12/09
Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses
Yujie Men, Helene Feil, Nathan C VerBerkmoes, Manesh B Shah, David R Johnson, Patrick K H Lee, Kimberlee A West, Stephen H Zinder, Gary L Andersen, Lisa Alvarez-Cohen
ISME J. 2012 February; 6(2): 410–421. Published online 2011 September 1. doi: 10.1038/ismej.2011.111
PMCID:
PMC3260503
Free in PMC on 2013/02/01
Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough
Swapnil R. Chhabra, Marcin P. Joachimiak, Christopher J. Petzold, Grant M. Zane, Morgan N. Price, Sonia A. Reveco, Veronica Fok, Alyssa R. Johanson, Tanveer S. Batth, Mary Singer, John-Marc Chandonia, Dominique Joyner, Terry C. Hazen, Adam P. Arkin, Judy D. Wall, Anup K. Singh, Jay D. Keasling
PLoS One. 2011; 6(6): e21470. Published online 2011 June 28. doi: 10.1371/journal.pone.0021470
PMCID:
PMC3125180
Abstract Full Text PDF–712K Supplementary Material
Comparative Genomics and Evolution of Molybdenum Utilization
Yan Zhang, Steffen Rump, Vadim N. Gladyshev
Coord Chem Rev. Author manuscript; available in PMC 2012 May 1.
Published in final edited form as: Coord Chem Rev. 2011 May; 255(9-10): 1206–1217. doi: 10.1016/j.ccr.2011.02.016
PMCID:
PMC3311541
Abstract Full Text PDF–1.7M
Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens
Toshiyuki Ueki, Derek R. Lovley
Nucleic Acids Res. 2010 November; 38(21): 7485–7499. Published online 2010 July 24. doi: 10.1093/nar/gkq652
PMCID:
PMC2995071
Abstract Full Text PDF–2.4M Supplementary Material
Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough
Grant M. Zane, Huei-che Bill Yen, Judy D. Wall
Appl Environ Microbiol. 2010 August; 76(16): 5500–5509. Published online 2010 June 25. doi: 10.1128/AEM.00691-10
PMCID:
PMC2918943
Abstract Full Text PDF–1.5M Supplementary Material
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
Pavel S. Novichkov, Dmitry A. Rodionov, Elena D. Stavrovskaya, Elena S. Novichkova, Alexey E. Kazakov, Mikhail S. Gelfand, Adam P. Arkin, Andrey A. Mironov, Inna Dubchak
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W299–W307. Published online 2010 June 11. doi: 10.1093/nar/gkq531
PMCID:
PMC2896116
Abstract Full Text PDF–6.6M
The Zur regulon of Corynebacterium glutamicum ATCC 13032
Jasmin Schröder, Nina Jochmann, Dmitry A Rodionov, Andreas Tauch
BMC Genomics. 2010; 11: 12. Published online 2010 January 7. doi: 10.1186/1471-2164-11-12
PMCID:
PMC2823685
Abstract Full Text PDF–3.3M Supplementary Material
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
Nucleic Acids Res. 2010 January; 38(Database issue): D111–D118. Published online 2010 January. doi: 10.1093/nar/gkp894
PMCID:
PMC2808921
Abstract Full Text PDF–450K
Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation
Zhili He, Aifen Zhou, Edward Baidoo, Qiang He, Marcin P. Joachimiak, Peter Benke, Richard Phan, Aindrila Mukhopadhyay, Christopher L. Hemme, Katherine Huang, Eric J. Alm, Matthew W. Fields, Judy Wall, David Stahl, Terry C. Hazen, Jay D. Keasling, Adam P. Arkin, Jizhong Zhou
Appl Environ Microbiol. 2010 March; 76(5): 1574–1586. Published online 2009 December 28. doi: 10.1128/AEM.02141-09
PMCID:
PMC2832388
Abstract Full Text PDF–1.2M Supplementary Material
The Role of PerR in O2-Affected Gene Expression of Clostridium acetobutylicum
Falk Hillmann, Christina Döring, Oliver Riebe, Armin Ehrenreich, Ralf-Jörg Fischer, Hubert Bahl
J Bacteriol. 2009 October; 191(19): 6082–6093. Published online 2009 July 31. doi: 10.1128/JB.00351-09
PMCID:
PMC2747897
Abstract Full Text PDF–1.0M Supplementary Material
Engineering transcription factors with novel DNA-binding specificity using comparative genomics
Tasha A. Desai, Dmitry A. Rodionov, Mikhail S. Gelfand, Eric J. Alm, Christopher V. Rao
Nucleic Acids Res. 2009 May; 37(8): 2493–2503. Published online 2009 May. doi: 10.1093/nar/gkp079
PMCID:
PMC2677863
Abstract Full Text PDF–2.6M Supplementary Material
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
Yan Zhang, Dmitry A Rodionov, Mikhail S Gelfand, Vadim N Gladyshev
BMC Genomics. 2009; 10: 78. Published online 2009 February 10. doi: 10.1186/1471-2164-10-78
PMCID:
PMC2667541
Abstract Full Text PDF–558K Supplementary Material
On the nature of fur evolution: A phylogenetic approach in Actinobacteria
Catarina L Santos, João Vieira, Fernando Tavares, David R Benson, Louis S Tisa, Alison M Berry, Pedro Moradas-Ferreira, Philippe Normand
BMC Evol Biol. 2008; 8: 185. Published online 2008 June 25. doi: 10.1186/1471-2148-8-185
PMCID:
PMC2464607
Abstract Full Text PDF–504K Supplementary Material
Molybdoproteomes and evolution of molybdenum utilization
Yan Zhang, Vadim N. Gladyshev
J Mol Biol. Author manuscript; available in PMC 2009 June 13.
Published in final edited form as: J Mol Biol. 2008 June 13; 379(4): 881–899. Published online 2008 April 3. doi: 10.1016/j.jmb.2008.03.051
PMCID:
PMC2670968
Abstract Full Text PDF–1.2M Supplementary Material
Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis
Zhili He, Jizhong Zhou
Appl Environ Microbiol. 2008 May; 74(10): 2957–2966. Published online 2008 March 14. doi: 10.1128/AEM.02536-07
PMCID:
PMC2394959
Abstract Full Text PDF–589K Supplementary Material
The distributions, mechanisms, and structures of metabolite-binding riboswitches
Jeffrey E Barrick, Ronald R Breaker
Genome Biol. 2007; 8(11): R239. Published online 2007 November 12. doi: 10.1186/gb-2007-8-11-r239
PMCID:
PMC2258182
Abstract Full Text PDF–814K Supplementary Material
Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria
Dmitry A. Rodionov
Chem Rev. Author manuscript; available in PMC 2009 February 16.
Published in final edited form as: Chem Rev. 2007 August; 107(8): 3467–3497. Published online 2007 July 18. doi: 10.1021/cr068309+
PMCID:
PMC2643304
Full Text PDF–4.6M Supplementary Material
Analysis of a Ferric Uptake Regulator (Fur) Mutant of Desulfovibrio vulgaris Hildenborough
Kelly S. Bender, Huei-Che Bill Yen, Christopher L. Hemme, Zamin Yang, Zhili He, Qiang He, Jizhong Zhou, Katherine H. Huang, Eric J. Alm, Terry C. Hazen, Adam P. Arkin, Judy D. Wall
Appl Environ Microbiol. 2007 September; 73(17): 5389–5400. Published online 2007 July 13. doi: 10.1128/AEM.00276-07
PMCID:
PMC2042090
Abstract Full Text PDF–229K
Cell-Wide Responses to Low-Oxygen Exposure in Desulfovibrio vulgaris Hildenborough
Aindrila Mukhopadhyay, Alyssa M. Redding, Marcin P. Joachimiak, Adam P. Arkin, Sharon E. Borglin, Paramvir S. Dehal, Romy Chakraborty, Jil T. Geller, Terry C. Hazen, Qiang He, Dominique C. Joyner, Vincent J. J. Martin, Judy D. Wall, Zamin Koo Yang, Jizhong Zhou, Jay D. Keasling
J Bacteriol. 2007 August; 189(16): 5996–6010. Published online 2007 June 1. doi: 10.1128/JB.00368-07
PMCID:
PMC1952033
Abstract Full Text PDF–1.2M Supplementary Material
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis
Rüdiger Welz, Ronald R. Breaker
RNA. 2007 April; 13(4): 573–582. doi: 10.1261/rna.407707
PMCID:
PMC1831863
Abstract Full Text PDF–741K
Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans
Raquel Quatrini, Claudia Lefimil, Felipe A. Veloso, Inti Pedroso, David S. Holmes, Eugenia Jedlicki
Nucleic Acids Res. 2007 April; 35(7): 2153–2166. Published online 2007 March 13. doi: 10.1093/nar/gkm068
PMCID:
PMC1874648
Abstract Full Text PDF–1.0M Supplementary Material
Temporal Transcriptomic Analysis as Desulfovibrio vulgaris Hildenborough Transitions into Stationary Phase during Electron Donor Depletion
M. E. Clark, Q. He, Z. He, K. H. Huang, E. J. Alm, X.-F. Wan, T. C. Hazen, A. P. Arkin, J. D. Wall, J.-Z. Zhou, M. W. Fields
Appl Environ Microbiol. 2006 August; 72(8): 5578–5588. doi: 10.1128/AEM.00284-06
PMCID:
PMC1538716
Abstract Full Text PDF–543K Supplementary Material
Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach
Aindrila Mukhopadhyay, Zhili He, Eric J. Alm, Adam P. Arkin, Edward E. Baidoo, Sharon C. Borglin, Wenqiong Chen, Terry C. Hazen, Qiang He, Hoi-Ying Holman, Katherine Huang, Rick Huang, Dominique C. Joyner, Natalie Katz, Martin Keller, Paul Oeller, Alyssa Redding, Jun Sun, Judy Wall, Jing Wei, Zamin Yang, Huei-Che Yen, Jizhong Zhou, Jay D. Keasling
J Bacteriol. 2006 June; 188(11): 4068–4078. doi: 10.1128/JB.01921-05
PMCID:
PMC1482918
Abstract Full Text PDF–4.5M
Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis
Qiang He, Katherine H. Huang, Zhili He, Eric J. Alm, Matthew W. Fields, Terry C. Hazen, Adam P. Arkin, Judy D. Wall, Jizhong Zhou
Appl Environ Microbiol. 2006 June; 72(6): 4370–4381. doi: 10.1128/AEM.02609-05
PMCID:
PMC1489655
Abstract Full Text PDF–882K Supplementary Material
Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough
S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A. P. Arkin, A. K. Singh
J Bacteriol. 2006 March; 188(5): 1817–1828. doi: 10.1128/JB.188.5.1817-1828.2006
PMCID:
PMC1426554
Abstract Full Text PDF–667K Supplementary Material
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
Dmitry A Rodionov, Inna L Dubchak, Adam P Arkin, Eric J Alm, Mikhail S Gelfand
PLoS Comput Biol. 2005 October; 1(5): e55. Prepublished online 2005 September 29. Published online 2005 October 28. doi: 10.1371/journal.pcbi.0010055
PMCID:
PMC1274295
Abstract Full Text PDF–1.7M Supplementary Material
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