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Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
Morgan N Price, Paramvir S Dehal, Adam P Arkin
Genome Biol. 2008; 9(1): R4. Published online 2008 January 7. doi: 10.1186/gb-2008-9-1-r4
PMCID:
PMC2395238
Abstract Full Text PDF–1.5M Supplementary Material
 Is Cited by the Following 21 Articles in this Archive:
Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
Elizabeth Skippington, Mark A Ragan
BMC Genomics. 2011; 12: 532. Published online 2011 October 29. doi: 10.1186/1471-2164-12-532
PMCID:
PMC3212841
Abstract Full Text PDF–5.0M
The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold
Francisco J Fernandez, Fernando Garces, Miguel López-Estepa, Juan Aguilar, Laura Baldomà, Miquel Coll, Josefa Badia, M Cristina Vega
BMC Evol Biol. 2011; 11: 273. Published online 2011 September 26. doi: 10.1186/1471-2148-11-273
PMCID:
PMC3219644
Abstract Full Text PDF–19M Supplementary Material
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
Todd J. Treangen, Eduardo P. C. Rocha
PLoS Genet. 2011 January; 7(1): e1001284. Published online 2011 January 27. doi: 10.1371/journal.pgen.1001284
PMCID:
PMC3029252
Abstract Full Text PDF–713K Supplementary Material
Conditions for the Evolution of Gene Clusters in Bacterial Genomes
Sara Ballouz, Andrew R. Francis, Ruiting Lan, Mark M. Tanaka
PLoS Comput Biol. 2010 February; 6(2): e1000672. Published online 2010 February 12. doi: 10.1371/journal.pcbi.1000672
PMCID:
PMC2820515
Abstract Full Text PDF–596K
Asymmetric cross regulation between the nitrate-responsive NarX-NarL and NarQ-NarP two-component regulatory systems from Escherichia coli K-12
Chris E. Noriega, Hsia-Yin Lin, Li-Ling Chen, Stanly B. Williams, Valley Stewart
Mol Microbiol. Author manuscript; available in PMC 2011 February 6.
Published in final edited form as: Mol Microbiol. 2010 January; 75(2): 394–412. Published online 2009 December 4. doi: 10.1111/j.1365-2958.2009.06987.x
PMCID:
PMC3034140
Abstract Full Text PDF–1.2M
Evolution, ecology and the engineered organism: lessons for synthetic biology
Jeffrey M Skerker, Julius B Lucks, Adam P Arkin
Genome Biol. 2009; 10(11): 114. Published online 2009 November 30. doi: 10.1186/gb-2009-10-11-114
PMCID:
PMC3091310
Abstract Full Text PDF–312K
Horizontal gene transfer in evolution: facts and challenges
Luis Boto
Proc Biol Sci. 2010 March 22; 277(1683): 819–827. Published online 2009 November 28. doi: 10.1098/rspb.2009.1679
PMCID:
PMC2842723
Abstract Full Text PDF–240K
Lateral genetic transfer: open issues
Mark A. Ragan, Robert G. Beiko
Philos Trans R Soc Lond B Biol Sci. 2009 August 12; 364(1527): 2241–2251. doi: 10.1098/rstb.2009.0031
PMCID:
PMC2872999
Abstract Full Text PDF–298K
Does negative auto-regulation increase gene duplicability?
Tobias Warnecke, Guang-Zhong Wang, Martin J Lercher, Laurence D Hurst
BMC Evol Biol. 2009; 9: 193. Published online 2009 August 7. doi: 10.1186/1471-2148-9-193
PMCID:
PMC2739200
Abstract Full Text PDF–302K Supplementary Material
Evolution of transcriptional regulatory circuits in bacteria
J. Christian Perez, Eduardo A. Groisman
Cell. Author manuscript; available in PMC 2010 July 23.
Published in final edited form as: Cell. 2009 July 23; 138(2): 233–244. doi: 10.1016/j.cell.2009.07.002
PMCID:
PMC2726713
Abstract Full Text PDF–2.6M
Toolbox model of evolution of prokaryotic metabolic networks and their regulation
Sergei Maslov, Sandeep Krishna, Tin Yau Pang, Kim Sneppen
Proc Natl Acad Sci U S A. 2009 June 16; 106(24): 9743–9748. Published online 2009 May 29. doi: 10.1073/pnas.0903206106
PMCID:
PMC2701025
Abstract Full Text PDF–547K Supplementary Material
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
BMC Syst Biol. 2009; 3: 49. Published online 2009 May 7. doi: 10.1186/1752-0509-3-49
PMCID:
PMC2684101
Abstract Full Text PDF–426K 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
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
Eugene V. Koonin, Yuri I. Wolf
Nucleic Acids Res. 2008 December; 36(21): 6688–6719. Published online 2008 December. doi: 10.1093/nar/gkn668
PMCID:
PMC2588523
Abstract Full Text PDF–2.6M
Regulation by transcription factors in bacteria: beyond description
Enrique Balleza, Lucia N López-Bojorquez, Agustino Martínez-Antonio, Osbaldo Resendis-Antonio, Irma Lozada-Chávez, Yalbi I Balderas-Martínez, Sergio Encarnación, Julio Collado-Vides
FEMS Microbiol Rev. 2009 January; 33(1): 133–151. Published online 2008 December. doi: 10.1111/j.1574-6976.2008.00145.x
PMCID:
PMC2704942
Abstract Full Text PDF–615K
Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location
Rikard Dryselius, Kaori Izutsu, Takeshi Honda, Tetsuya Iida
BMC Genomics. 2008; 9: 559. Published online 2008 November 26. doi: 10.1186/1471-2164-9-559
PMCID:
PMC2612033
Abstract Full Text PDF–1.4M Supplementary Material
What Determines the Assembly of Transcriptional Network Motifs in Escherichia coli?
Francisco M. Camas, Juan F. Poyatos
PLoS ONE. 2008; 3(11): e3657. Published online 2008 November 6. doi: 10.1371/journal.pone.0003657
PMCID:
PMC2577066
Abstract Full Text PDF–320K Supplementary Material
Bioinformatics Resources for the Study of Gene Regulation in Bacteria
Julio Collado-Vides, Heladia Salgado, Enrique Morett, Socorro Gama-Castro, Verónica Jiménez-Jacinto, Irma Martínez-Flores, Alejandra Medina-Rivera, Luis Muñiz-Rascado, Martín Peralta-Gil, Alberto Santos-Zavaleta
J Bacteriol. 2009 January; 191(1): 23–31. Published online 2008 October 31. doi: 10.1128/JB.01017-08
PMCID:
PMC2612416
Full Text PDF–2.4M
Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio
Robert E Lintner, Pankaj K Mishra, Poonam Srivastava, Betsy M Martinez-Vaz, Arkady B Khodursky, Robert M Blumenthal
BMC Microbiol. 2008; 8: 60. Published online 2008 April 11. doi: 10.1186/1471-2180-8-60
PMCID:
PMC2374795
Abstract Full Text PDF–2.7M Supplementary Material
Linking Fold, Function and Phylogeny: A Comparative Genomics View on Protein (Domain) Evolution
Aartjan J.W te Velthuis, Christoph P Bagowski
Curr Genomics. 2008 April; 9(2): 88–96. doi: 10.2174/138920208784139537
PMCID:
PMC2674803
Abstract Full Text PDF–1.4M
The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment
Wagied Davids, Zhaolei Zhang
BMC Evol Biol. 2008; 8: 23. Published online 2008 January 24. doi: 10.1186/1471-2148-8-23
PMCID:
PMC2259305
Abstract Full Text PDF–436K Supplementary Material
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