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The source of laterally transferred genes in bacterial genomes
Vincent Daubin, Emmanuelle Lerat, Guy Perrière
Genome Biol. 2003; 4(9): R57. Published online 2003 August 21.
PMCID:
PMC193657
Abstract Full Text PDF–681K Supplementary Material
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 Is Cited by the Following 34 Articles in this Archive:
Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome
Katherine A. Karberg, Gary J. Olsen, James J. Davis
Proc Natl Acad Sci U S A. 2011 December 13; 108(50): 20154–20159. Published online 2011 November 29. doi: 10.1073/pnas.1109451108
PMCID:
PMC3250135
Abstract Full Text PDF–617K Supplementary Material
Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study
Ofir Cohen, Tal Pupko
Genome Biol Evol. 2011; 3: 1265–1275. Published online 2011 October 4. doi: 10.1093/gbe/evr101
PMCID:
PMC3215202
Abstract Full Text PDF–142K
Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development
Rohini Garg, Ravi K. Patel, Shalu Jhanwar, Pushp Priya, Annapurna Bhattacharjee, Gitanjali Yadav, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K. Tyagi, Mukesh Jain
Plant Physiol. 2011 August; 156(4): 1661–1678. Published online 2011 June 8. doi: 10.1104/pp.111.178616
PMCID:
PMC3149962
Abstract Full Text PDF–1.6M
Evidence of Selection upon Genomic GC-Content in Bacteria
Falk Hildebrand, Axel Meyer, Adam Eyre-Walker
PLoS Genet. 2010 September; 6(9): e1001107. Published online 2010 September 9. doi: 10.1371/journal.pgen.1001107
PMCID:
PMC2936529
Abstract Full Text PDF–205K Supplementary Material
Inferring Bacterial Genome Flux While Considering Truncated Genes
Weilong Hao, G. Brian Golding
Genetics. 2010 September; 186(1): 411–426. doi: 10.1534/genetics.110.118448
PMCID:
PMC2940306
Abstract Full Text PDF–2.2M
Visualizing the structural changes of bacteriophage epsilon15 and its Salmonella host during infection
Juan T. Chang, Michael F. Schmid, Cameron Haase-Pettingell, Peter R. Weigele, Jonathan A. King, Wah Chiu
J Mol Biol. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: J Mol Biol. 2010 October 1; 402(4): 731–740. Published online 2010 August 13. doi: 10.1016/j.jmb.2010.07.058
PMCID:
PMC3164490
Abstract Full Text PDF–1.8M
Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer
Wolfgang Fischer, Lukas Windhager, Stefanie Rohrer, Matthias Zeiller, Arno Karnholz, Reinhard Hoffmann, Ralf Zimmer, Rainer Haas
Nucleic Acids Res. 2010 October; 38(18): 6089–6101. Published online 2010 May 15. doi: 10.1093/nar/gkq378
PMCID:
PMC2952849
Abstract Full Text PDF–3.3M Supplementary Material
Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana
Haining Lin, Gaurav Moghe, Shu Ouyang, Amy Iezzoni, Shin-Han Shiu, Xun Gu, C Robin Buell
BMC Evol Biol. 2010; 10: 41. Published online 2010 February 12. doi: 10.1186/1471-2148-10-41
PMCID:
PMC2829037
Abstract Full Text PDF–458K Supplementary Material
An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes
Adi Stern, Itay Mayrose, Osnat Penn, Shaul Shaul, Uri Gophna, Tal Pupko
Syst Biol. 2010 March; 59(2): 212–225. Published online 2010 January 15. doi: 10.1093/sysbio/syp104
PMCID:
PMC2826268
Abstract Full Text PDF–613K Supplementary Material
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 Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?
Weilong Hao, G. Brian Golding
Genetics. 2009 August; 182(4): 1365–1375. doi: 10.1534/genetics.109.104216
PMCID:
PMC2728873
Abstract Full Text PDF–1.1M
Codon Usages of Genes on Chromosome, and Surprisingly, Genes in Plasmid are Primarily Affected by Strand-specific Mutational Biases in Lawsonia intracellularis
Feng-Biao Guo, Jian-Bo Yuan
DNA Res. 2009 April; 16(2): 91–104. Published online 2009 February 15. doi: 10.1093/dnares/dsp001
PMCID:
PMC2671203
Abstract Full Text PDF–368K Supplementary Material
Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms
Patrick Forterre, Danièle Gadelle
Nucleic Acids Res. 2009 February; 37(3): 679–692. Published online 2009 February. doi: 10.1093/nar/gkp032
PMCID:
PMC2647321
Abstract Full Text PDF–1.5M
Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes
Burkhard Becker, Kerstin Hoef-Emden, Michael Melkonian
BMC Evol Biol. 2008; 8: 203. Published online 2008 July 15. doi: 10.1186/1471-2148-8-203
PMCID:
PMC2490706
Abstract Full Text PDF–590K Supplementary Material
Uncovering rate variation of lateral gene transfer during bacterial genome evolution
Weilong Hao, G Brian Golding
BMC Genomics. 2008; 9: 235. Published online 2008 May 20. doi: 10.1186/1471-2164-9-235
Correction in:
BMC Genomics. 2008; 9: 556.
PMCID:
PMC2426709
Abstract Full Text PDF–343K Supplementary Material Correction
Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms
Saliou Fall, Anne Mercier, Franck Bertolla, Alexandra Calteau, Laurent Gueguen, Guy Perrière, Timothy M. Vogel, Pascal Simonet
PLoS ONE. 2007; 2(10): e1055. Published online 2007 October 24. doi: 10.1371/journal.pone.0001055
PMCID:
PMC2013936
Abstract Full Text PDF–391K Supplementary Material
Unique genes in giant viruses: Regular substitution pattern and anomalously short size
Hiroyuki Ogata, Jean-Michel Claverie
Genome Res. 2007 September; 17(9): 1353–1361. doi: 10.1101/gr.6358607
PMCID:
PMC1950904
Abstract Full Text PDF–548K
The power of phylogenetic approaches to detect horizontally transferred genes
Maria S Poptsova, J Peter Gogarten
BMC Evol Biol. 2007; 7: 45. Published online 2007 March 21. doi: 10.1186/1471-2148-7-45
PMCID:
PMC1847511
Abstract Full Text PDF–2.6M Supplementary Material
Systematic overestimation of gene gain through false diagnosis of gene absence
Olga Zhaxybayeva, Camilla L Nesbø, W Ford Doolittle
Genome Biol. 2007; 8(2): 402. Published online 2007 February 26. doi: 10.1186/gb-2007-8-2-402
PMCID:
PMC1852405
Abstract Full Text PDF–138K Supplementary Material
The role of laterally transferred genes in adaptive evolution
Pradeep Reddy Marri, Weilong Hao, G Brian Golding
BMC Evol Biol. 2007; 7(Suppl 1): S8. Published online 2007 February 8. doi: 10.1186/1471-2148-7-S1-S8
PMCID:
PMC1796617
Abstract Full Text PDF–404K Supplementary Material
Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa
Harshavardhan Doddapaneni, Jiqiang Yao, Hong Lin, M Andrew Walker, Edwin L Civerolo
BMC Genomics. 2006; 7: 225. Published online 2006 September 1. doi: 10.1186/1471-2164-7-225
PMCID:
PMC1574315
Abstract Full Text PDF–475K Supplementary Material
On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
Yanbin Yin, Daniel Fischer
BMC Evol Biol. 2006; 6: 63. Published online 2006 August 16. doi: 10.1186/1471-2148-6-63
PMCID:
PMC1559721
Abstract Full Text PDF–295K Supplementary Material
The fate of laterally transferred genes: Life in the fast lane to adaptation or death
Weilong Hao, G. Brian Golding
Genome Res. 2006 May; 16(5): 636–643. doi: 10.1101/gr.4746406
PMCID:
PMC1457040
Abstract Full Text PDF–441K
The genome of Rhizobium leguminosarum has recognizable core and accessory components
J Peter W Young, Lisa C Crossman, Andrew WB Johnston, Nicholas R Thomson, Zara F Ghazoui, Katherine H Hull, Margaret Wexler, Andrew RJ Curson, Jonathan D Todd, Philip S Poole, Tim H Mauchline, Alison K East, Michael A Quail, Carol Churcher, Claire Arrowsmith, Inna Cherevach, Tracey Chillingworth, Kay Clarke, Ann Cronin, Paul Davis, Audrey Fraser, Zahra Hance, Heidi Hauser, Kay Jagels, Sharon Moule, Karen Mungall, Halina Norbertczak, Ester Rabbinowitsch, Mandy Sanders, Mark Simmonds, Sally Whitehead, Julian Parkhill
Genome Biol. 2006; 7(4): R34. Published online 2006 April 26. doi: 10.1186/gb-2006-7-4-r34
PMCID:
PMC1557990
Abstract Full Text PDF–1.7M Supplementary Material
BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species
Emma Griffiths, Michael S Ventresca, Radhey S Gupta
BMC Genomics. 2006; 7: 14. Published online 2006 January 25. doi: 10.1186/1471-2164-7-14
PMCID:
PMC1403754
Abstract Full Text PDF–459K
Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands
William W. L Hsiao, Korine Ung, Dana Aeschliman, Jenny Bryan, B. Brett Finlay, Fiona S. L Brinkman
PLoS Genet. 2005 November; 1(5): e62. Prepublished online 2005 October 13. Published online 2005 November 18. doi: 10.1371/journal.pgen.0010062
PMCID:
PMC1285063
Abstract Full Text PDF–482K Supplementary Material
New Findings on Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea
J. M. Coombs, T. Barkay
Appl Environ Microbiol. 2005 November; 71(11): 7083–7091. doi: 10.1128/AEM.71.11.7083-7091.2005
PMCID:
PMC1287752
Abstract Full Text PDF–573K Supplementary Material
Species Numbers in Bacteria
Daniel Dykhuizen
Proc Calif Acad Sci. Author manuscript; available in PMC 2011 August 24.
Published in final edited form as: Proc Calif Acad Sci. 2005 June 3; 56(6 Suppl 1): 62–71.
PMCID:
PMC3160642
Abstract Full Text PDF–254K
Examining bacterial species under the specter of gene transfer and exchange
Howard Ochman, Emmanuelle Lerat, Vincent Daubin
Proc Natl Acad Sci U S A. 2005 May 3; 102(Suppl 1): 6595–6599. Published online 2005 April 25. doi: 10.1073/pnas.0502035102
PMCID:
PMC1131874
Abstract Full Text PDF–327K
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
Dave MacLeod, Robert L Charlebois, Ford Doolittle, Eric Bapteste
BMC Evol Biol. 2005; 5: 27. Published online 2005 April 8. doi: 10.1186/1471-2148-5-27
PMCID:
PMC1087482
Abstract Full Text PDF–710K
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