Our publications:

Group publications

  • 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 in press.
  • 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 in press.
  • 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.
  • 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 Genetics 7:e1002222.
  • Touchon M, Barbier P, Bernardet JF, Loux V, Vacherie B, Barbe V, Rocha EPC, Duchaud E (2011) Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. App Env Microbiol 77:7656-62.
  • Lynch M, Bobay LM, Catania F, Gout JF, Rho M (2011) The repatterning of eukaryotic genomes by random genetic drift. Annu Rev Genomics Hum Genet 12:347-66.
  • Rankin DJ, Rocha EPC, Brown SP (2011) What Traits Are Carried On Mobile Genetic Elements, And Why? Heredity 106:1-10
  • Treangen, T. J. & Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7: e1001284.
  • Touchon M, Charpentier S, Clermont O, Rocha EPC, Demanur E, Branger C. CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection. J Bacteriology 193: 2460-2467.
  • Warnecke T, Rocha EPC (2011) Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size. Molecular Biology Evolution 28:2339-49.
  • Rocha EPC, Feil EJ (2010) Mutational patterns cannot explain genome composition: are there any neutral sites in the genomes of bacteria? Plos Genetics 6:e1001104. [PDF]
  • 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.
  • Vieira-Silva S, Touchon M, Rocha EPC (2010) No evidence for elemental-based streamlining of prokaryotic genomes. Trends Ecol Evol 25:319-20.
  • Touchon M, Rocha EPC (2010) The small, slow and specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella. Plos One 5:e11126.[PDF]
  • Vieira-Silva S, Rocha EPC (2010) The Systemic Imprint of Growth Rates and its Uses in Ecological (Meta)genomics. Plos Genetics 6:e1000808 [PDF].
  • Mil-Homens D, Rocha EPC, Fialho AM (2010) Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of ET-12 lineage. Microbiology 156:1084-96.
  • 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. Current Biology 19:1683-91 [Full Text].
  • Abraham AL, Pothier J, Rocha EPC (2009) An alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification. J Mol Biol 394:522-34 [PDF].
  • Treangen T, Abraham AL, Touchon M, Rocha EPC (2009) Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev, 33:539-71 [PDF].
  • Lescat M, Calteau A, Hoede C, Barbe V, Touchon M, Rocha E, Tenaillon O, Médigue C, Johnson JR, Denamur E (2009) A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A. Antimicrob Agents Chemother 53:2283-8 [PDF].
  • Touchon M, ... (+37 co-authors) ... Rocha EPC*, Denamur E* (2009) Organised genome dynamics in the Escherichia coli species: the path to adaptation. Plos Genetics 5:e1000344 [PDF].
  • Treangen T, Darlin AE, Achaz G, Messeguer X, Rocha EPC (2009) A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Trans Comput Biol BioInf 6:180-9 [PDF].
  • Holden MTG, ... Rocha EPC (+30 co-authors) ..., Parkhill J (2009) The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of Cystic Fibrosis patients. J Bacteriol 191:261-77[PDF].
  • Balbi KJ, Rocha EPC, Feil1 EJ (2009) The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp. Mol Biol Evol 26:345-55 [PDF].
  • Rocha EPC (2008) Evolutionary patterns in prokaryotic genomes. Curr Opin Microbiol 11:454-60 [PDF].
  • Vieira-Silva S, Rocha EPC (2008) An assessment of the impacts of molecular oxygen on the evolution of proteomes. Mol Biol Evol 25:1931-42 [PDF].
  • Abraham AL, Rocha EPC, Pothier J (2008) Swelfe: a detector of internal repeats in sequences and structures. Bioinformatics 24:1536-7 [PDF].
  • Rocha EPC (2008) The organization of the bacterial genome. Annu Rev Genetics 42:211-33 [PDF].
  • Treangen T, Ambur OH, Tonjum T, Rocha EPC (2008) The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 9:R60 [PDF].
  • Touchon M, Rocha EPC (2008) A gentle guide to the analysis of strand asymmetry in genome sequences. Biochimie 90:648-59 [PDF].
  • Fang G, Rocha EPC, Danchin A (2008) Persistence drives gene clustering in bacterial genomes. BMC Genomics 9:4 [PDF].

Eduardo Rocha previous publications

  • Glaser P, Chandler M, Rocha EPC (2007) Microbial Genomics. Res Microbiol 158:721-3.
  • Bailly-Bechet M, Vergassola M, Rocha EPC (2007) Causes for the intriguing presence of tRNAs in phages. Genome Res 17:1486-1495.
  • Gómez-Valero L, Rocha EPC, Latorre A, Silva FJ (2007) Reconstructing the ancestor of Mycobacterium leprae: Dynamics of gene loss and genome reduction. Genome Res 17:1178–1185.
  • Touchon M, Rocha EPC (2007) Causes of Insertion Sequences abundance in prokaryotic genomes. Mol Biol Evol 24:969–981.
  • Achaz G, Boyer F, Rocha EPC, Viari A, Coissac E (2007) Repseek, a tool to retrieve non-exact repeats from large DNA sequences. BioInformatics 23: 119-121.
  • Ochman H, Liu R, Rocha EPC (2007) Erosion of interaction networks in reduced and degraded genomes. J Exp Zool 308:97-103.
  • Rocha EPC, Touchon M, Feil E (2006) Similar compositional biases are caused by very different mutational effects. Genome Res 16:1537-47.
  • Hurst LD, Feil E, Rocha EPC (2006) Causes of trends of amino acid gain and loss. Nature 442:e11-2.
  • Swidan F, Rocha EPC, Shmoish M, Pinter RY (2006) An Integrative Method for Accurate Comparative Genome Mapping. Plos Comput Biol 2:e75.
  • Rocha EPC (2006) The quest for the universals of protein evolution. Trends Genetics 22:412-6.
  • Iverson-Cabral SL, Astete SG, Cohen CR, Rocha EPC, Totten PA (2006) Heterogeneity of the mgpB gene in Mycoplasma genitalium: a mechanism of immune evasion and disease persistence? Infection Immunity 74:3715–3726.
  • Fischer G, Rocha EPC, Brunet F, Vergassola M, Dujon B (2006) Highly variable rates of genome rearrangements between Hemiascomycetous yeast lineages. Plos Genetics 2:e32.
  • Rocha EPC, Maynard Smith J, Hurst LD, Holden MTG, Cooper JE, Smith NH, Feil EJ (2006) Comparisons of dS / dN are time-dependent for closely related bacterial genomes. J Theoret Biol 239:226-235.
  • Couturier E, Rocha EPC (2006) Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol Microbiol 59:1506–1518.
  • Rocha EPC (2006) Inference and analysis of the relative stability of bacterial chromosomes Mol Biol Evol 23:513–522.
  • Médigue C, ... Rocha EPC ... , Danchin A (21 co-authors) (2005) Universal cold adaptive strategies revealed by the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res 15:1325-35.
  • Fang G, Rocha EPC, Danchin A (2005) How essential are non-essential genes? Mol Biol Evol 22:2147-2156.
  • Rocha EPC, Cornet E, Michel B (2005) Comparative and evolutionary analysis of the bacterial homologous recombination systems Plos Genet 1:e15.
  • Figueiredo LM, Rocha EPC, Mancio-Silva L, Prevost C, Hernandez-Verdun D, Scherf A (2005) The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus. Nucleic Acids Res 33:1111-22.
  • Rocha EPC (2004) Codon usage bias from tRNA’s point of view. Genome Res 14:2279-86.
  • Rocha EPC (2004) Order and disorder in Bacterial genomes Curr Opin Microbiol 7:519-27.
  • Rocha EPC (2004) The replication-related structures of bacterial genomes. Microbiology 150: 1609-1627.
  • Wang, Y, Rocha EPC, Leung FCC, Danchin A (2004) Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes. J Mol Evol 58:692-700.
  • Rocha EPC and Danchin A (2004) An analysis of determinants of protein substitution rates in Bacteria. Mol Biol Evol 21:89-97.
  • Rocha EPC and Danchin A (2003) Gene essentiality is a determinant of chromosome organization in Bacteria. Nucleic Acids Res 31:5202-5211.
  • Rocha EPC (2003) DNA repeats lead to the accelerated loss of gene order in Bacteria. Trends Genetics 19:600-603.
  • Rocha EPC and Danchin A (2003) Essentiality, not expressiveness, drives gene strand bias in bacteria. Nature Genetics 34:377-378.
  • Achaz G, Coissac E, Netter P and Rocha EPC (2003) Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics 164:1279-89.
  • Rocha EPC, Fralick J, Vediyappan G, Danchin A and Norris V (2003) A strand-specific model for chromosome segregation in bacteria. Mol Microbiol 49:895-903.
  • Rocha EPC (2003) An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. Genome Res 13:1123-1132.
  • Rocha EPC, Pradillon O, Bui H, Sayada S, and Denamur E (2002) A new family of highly variable proteins in the Chlamydophila pneumoniae genome. Nucleic Acids Res 30:4351-60.
  • Rocha EPC (2002) Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiology 10:393-396.
  • Achaz G, Rocha EPC, Netter P, Coissac E (2002) Origin and fate of repeats in bacteria. Nucleic Acids Res 30:2987-2994.
  • Rocha EPC, Danchin A (2002) Base composition bias might result from competition for metabolic resources. Trends Genetics 18:291-4.
  • Rocha EPC, Blanchard A (2002) Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res 30:2031-42.
  • Rocha EPC, Matic I, Taddei F (2002) Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions? Nucleic Acids Res 30:1886-94.
  • Rocha, EPC, Danchin A (2001) On-going evolution of strand composition in bacterial genomes. Mol Biol Evol 18:1789-1799.
  • Chambaud I, Heilig R, Ferris S, Barbe V, Samson D, Galisson F,Moszer I, Dybvig K, Wroblenski H, Viari A, Rocha EPC, Blanchard A (2001) The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res 29:2145-2153
  • Rocha EPC, Viari A, Danchin A (2001) The evolutionary role of restriction and modification systems as revealed by comparative genome analysis. Genome Res 11:946-958.
  • Rocha EPC, Sekowska A, Danchin A (2000) Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture? FEBS Letters 476:8-11.
  • Rocha EPC, Danchin A, Viari A (2000) The DB case : pattern matching analysis dismisses signal existence. Mol Microbiol 37:216-218.
  • Rocha EPC, Moszer I, Guerdoux-Jamet P, Viari A, Danchin A (2000) Implication of gene distribution in the bacterial chromosome for the bacterial cell factory. J Biotechnology 78:209-219.
  • Rocha EPC, Danchin A, Viari A (2000) Functional and evolutionary roles of long repeats in prokaryotes. Res Microbiol 150:1-9.
  • Rocha EPC, Danchin A, Viari A (1999) Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis. Nucl Acids Res 27: 3567-3576.
  • Rocha EPC, Danchin A, Viari A (1999) Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes. Mol Biol Evol 16:1219-1230.
  • Moszer I, Rocha EPC, Danchin A (1999) Codon usage in Bacillus subtilis and lateral gene transfer. Curr Op Microbiol 2:524-528.
  • Rocha EPC, Danchin A, Viari A (1999) Universal replication biases in bacteria. Mol Microbiol 32:11-16.
  • Rocha EPC, Danchin A, Viari A (1999) Trends Microbiol 7:308.
  • Rocha EPC, Viari A, Danchin A (1998) Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucl Acids Res 26:2971-2980.
  • Kunst F, ... Rocha EPC ..., Danchin A (151 co-authors) (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256.

Marie Touchon previous publications

  • Audit B, Nicolay S, Huvet M, Touchon M, Thermes C, Arneodo A (2007) DNA replication timing data corroborate in silico human replication origin predictions. Phys Rev Lett 99:248102
  • Huvet M, Nicolay S, Touchon M, Audit B, d’Aubenton-Carafa Y, Arneodo A, Thermes C (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res. 17(9):1278-85.
  • Nicolay S, Brodie Of Brodie EB, Touchon M, Audit B, d’Aubenton-Carafa Y, Thermes C, Arneodo A (2007) Bifractality of human DNA strand-asymmetry profiles results from transcription. Phys Rev E, 75(3 Pt 1):032902.
  • Touchon M, Rocha EP (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol, 24(4):969-81.
  • Arnedo A, Audit B, Brodie of Brodie E.B, Nicolay S, Touchon M, Huvet M, Thermes C. (2007) Fractals and Wavelets: what can we learn on transcription and replication from wavelet-based multifractal analysis of DNA sequences? Encyclopedia of Complexity and System Science in press.
  • Rocha E.P.C, Touchon M, Feil E.J  (2006) Similar compositional biases are caused by very different mutational effects. Genome Res, 16(12):1537-47.
  • Arneodo A, d’Aubenton Carafa Y, Audit B, Brodie of Brodie E.B, Nicolay S, St-Jean P, Thermes C, Touchon M and Vaillant C (2006) DNA in chromatin: from genome wide sequence analysis to the modeling of replication in mammals.  Adv. Chem. Phys, 15 :203-252.
  • Touchon M, Nicolay S, Audit B, Brodie of Brodie EB, d’Aubenton-Carafa Y, Arneodo A, Thermes C (2005) Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci U S A,102(28):9836-41.
  • Brodie of Brodie EB, Nicolay S, Touchon M, Audit B, d’Aubenton-Carafa Y, Thermes C, Arneodo A (2005) From DNA Sequence Analysis to Modeling Replication in the Human Genome. Phys Rev Lett, 94(24):248103.
  • Touchon M, Arneodo A, d’Aubenton-Carafa Y, Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes.  Nucleic Acids Res;32(17):4969-78.
  • Nicolay S, Argoul F, Touchon M, d’Aubenton-Carafa Y, Thermes C, Arneodo A (2004)  Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation? Phys Rev Lett, 93(10):108101.
  • Nicolay S, Brodie of Brodie E, Touchon M, d’Aubenton-Carafa Y, Thermes C, Arneodo A (2004) From scale invariance to deterministic chaos in DNA sequences: towards a deterministic description of gene organization in the human genome. Physica A, 342: 270-280.
  • Touchon M, Nicolay S,  Arneodo A, d’Aubenton-Carafa Y, Thermes C (2003) Transcription-coupled TA and GC strand asymmetries in the human genome. FEBS Lett;555(3) :579-82.