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Microbial evolutionary genomics
- Eduardo P C Rocha, DR CNRS
- Marie Touchon, CR CNRS
- Julien Guglielmini, postdoc
- Peter Chen, PhD student
- Sophie Abby, postdoc
- Louis-Marie Bobay, PhD student
- Sara Vieira-Silva, left for VIB, Be.
- Leonor Quintais, left for the EBI, UK.
- Todd Treangen, left for John Hopkins, US.
- Anne-Laure Abraham, left for INRA, Fr
- Teresa Nogueira, left for U Lisbon, Pt.
- Chris Smillie, left for MIT, US.
Our scientific activities are centered on the bioinformatics and biostatistics analysis of genomes, at the crossroads of molecular evolution, population genetics, evolutionary ecology and molecular genetics. We focus on three major questions: 1) How and why are genomes organized? 2) How are such organizational features evolving in face of the extensive genome dynamics? 3) What are the roles of mobile elements in the trade-offs between organization and dynamics?
- Swelfe, identification of degenerate repeats in genes, proteins and 3D structures.
- Repseek, identification of degenerate repeats in genomes.
- Repeatoire, ab inito prediction of repeat families.
- GrowthPred, prediction of growth-related traits in microbes from genomic and metagenomic data.
- T3SSscan- FLAGscan, prediction of protein secretion systems in diderms (prokaryotes).
- Cassys, search for relaxases and key components of type IV secretion systems in proteomes using an HMM profiles database
Some recent publications
- Abby SS, Rocha EPC (2012) The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems. PLoS Genet 8:e1002983. [FULL TEXT]
- Guglielmini J, de la Cruz F, Rocha EPC (2012) Evolution of Conjugation and Type IV Secretion Systems. Mol Biol Evol in advanced press. [FULL TEXT]
- Namouchi A, Didelot X, Schock U, Gicquel B, Rocha EPC (2012) After the bottleneck: genome wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination and natural selection. Genome Research 22:721-34.
- Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EPC (2012) Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. Plos Pathogens 8: e1002503. [FULL TEXT]
- Vieira-Silva S, Touchon M, Abby S, Rocha EPC (2011) Investment in rapid growth shapes the evolutionary rates of essential proteins. Proc Natl Acad Sci USA 108:20030-20035. [FULL TEXT]
- Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EPC (2011) The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation. PLoS Genet 7:e1002222. [FULL TEXT]
- WarneckeT, Rocha EPC (2011) Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size. Mol Biol Evol 28:2339-49. [FULL TEXT]
- Treangen TJ & Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7: e1001284. [FULL TEXT]
- Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC, de la Cruz F (2010) The mobility of plasmids. Microbiol Mol Biol Rev. 74:434-52. [FULL TEXT]
- Touchon M, Rocha EPC (2010) The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One 5:e11126. [FULL TEXT]
- Vieira-Silva S, Touchon M, Rocha EPC (2010) No evidence for elemental-based streamlining of prokaryotic genomes. Trends Ecol Evol 25:319-20. [FULL TEXT]
- Vieira-Silva S, Rocha EPC (2010) The Systemic Imprint of Growth Rates and its Uses in Ecological (Meta)genomics. PLoS Genetics 6:e1000808.[FULL TEXT]
- Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EPC (2009) Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence. Curr Biol 19:1683-91. [FULL TEXT]
- Treangen T, Abraham AL, Touchon M, Rocha EPC (2009) Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev, 33:539-71. [FULL TEXT]
- Touchon M et al (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5:e1000344.[FULL TEXT ]
- Treangen T, Ambur OH, Tonjum T, Rocha EPC (2008) The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biology 9:R60.[FULL TEXT]
- Rocha EP (2008) The organization of the bacterial genome. Annu Rev Genet 42:211-33. [FULL TEXT]