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Mobile genetic elements: the agents of open source evolution.
Frost LS, Leplae R, Summers AO, Toussaint A. Frost LS, et al. Among authors: leplae r. Nat Rev Microbiol. 2005 Sep;3(9):722-32. doi: 10.1038/nrmicro1235. Nat Rev Microbiol. 2005. PMID: 16138100 Review.
ACLAME: a CLAssification of Mobile genetic Elements, update 2010.
Leplae R, Lima-Mendez G, Toussaint A. Leplae R, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D57-61. doi: 10.1093/nar/gkp938. Epub 2009 Nov 23. Nucleic Acids Res. 2010. PMID: 19933762 Free PMC article.
ACLAME: a CLAssification of Mobile genetic Elements.
Leplae R, Hebrant A, Wodak SJ, Toussaint A. Leplae R, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D45-9. doi: 10.1093/nar/gkh084. Nucleic Acids Res. 2004. PMID: 14681355 Free PMC article.
A first global analysis of plasmid encoded proteins in the ACLAME database.
Leplae R, Lima-Mendez G, Toussaint A. Leplae R, et al. FEMS Microbiol Rev. 2006 Nov;30(6):980-94. doi: 10.1111/j.1574-6976.2006.00044.x. FEMS Microbiol Rev. 2006. PMID: 17064288 Review.
Prophinder: a computational tool for prophage prediction in prokaryotic genomes.
Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. Lima-Mendez G, et al. Among authors: leplae r. Bioinformatics. 2008 Mar 15;24(6):863-5. doi: 10.1093/bioinformatics/btn043. Epub 2008 Jan 30. Bioinformatics. 2008. PMID: 18238785
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.
Méndez R, Leplae R, Lensink MF, Wodak SJ. Méndez R, et al. Among authors: leplae r. Proteins. 2005 Aug 1;60(2):150-69. doi: 10.1002/prot.20551. Proteins. 2005. PMID: 15981261
Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes.
Van Houdt R, Leplae R, Lima-Mendez G, Mergeay M, Toussaint A. Van Houdt R, et al. Among authors: leplae r. Mob DNA. 2012 Apr 13;3(1):6. doi: 10.1186/1759-8753-3-6. Mob DNA. 2012. PMID: 22502997 Free PMC article.
Reticulate representation of evolutionary and functional relationships between phage genomes.
Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. Lima-Mendez G, et al. Among authors: leplae r. Mol Biol Evol. 2008 Apr;25(4):762-77. doi: 10.1093/molbev/msn023. Epub 2008 Jan 29. Mol Biol Evol. 2008. PMID: 18234706
PhiGO, a phage ontology associated with the ACLAME database.
Toussaint A, Lima-Mendez G, Leplae R. Toussaint A, et al. Among authors: leplae r. Res Microbiol. 2007 Sep;158(7):567-71. doi: 10.1016/j.resmic.2007.05.002. Epub 2007 May 21. Res Microbiol. 2007. PMID: 17614261
Analysis of the phage sequence space: the benefit of structured information.
Lima-Mendez G, Toussaint A, Leplae R. Lima-Mendez G, et al. Among authors: leplae r. Virology. 2007 Sep 1;365(2):241-9. doi: 10.1016/j.virol.2007.03.047. Epub 2007 May 7. Virology. 2007. PMID: 17482656 Free article. Review.
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