Eduardo Pc Rocha

Summary

Affiliation: Institut Pasteur
Country: France

Publications

  1. pmc Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria
    Teresa Nogueira
    Centro de Biologia Ambiental, Evolutionary Ecology of Microorganisms, Faculdade de Ciencias da Universidade de Lisboa, Lisboa, Portugal
    PLoS ONE 7:e49403. 2012
  2. pmc Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens
    João Alves Gama
    Centro de Biologia Ambiental and Departamento de Biologia Vegetal, Faculdade de Ciencias da Universidade de Lisboa, Lisboa, Portugal
    PLoS Pathog 8:e1002503. 2012
  3. pmc The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation
    Julien Guglielmini
    Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
    PLoS Genet 7:e1002222. 2011
  4. pmc Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence
    Teresa Nogueira
    Institut Pasteur, CNRS, URA, Paris, France
    Curr Biol 19:1683-91. 2009
  5. pmc Persistence drives gene clustering in bacterial genomes
    Gang Fang
    Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr, Roux, 75724 Paris Cedex 15, France
    BMC Genomics 9:4. 2008
  6. doi request reprint The organization of the bacterial genome
    Eduardo P C Rocha
    Institut Pasteur, Microbial Evolutionary Genomics, F 75015 Paris, France
    Annu Rev Genet 42:211-33. 2008
  7. ncbi request reprint Essentiality, not expressiveness, drives gene-strand bias in bacteria
    Eduardo P C Rocha
    Unité GGB, URA 2171, Institut Pasteur, 28 rue Dr Roux, 75015 Paris, France
    Nat Genet 34:377-8. 2003
  8. pmc Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    Genome Res 14:2279-86. 2004
  9. doi request reprint Evolutionary patterns in prokaryotic genomes
    Eduardo Pc Rocha
    UPMC Univ Paris 06, Atelier de BioInformatique, F 75005 Paris, France
    Curr Opin Microbiol 11:454-60. 2008
  10. pmc Similar compositional biases are caused by very different mutational effects
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, URA 2171, Institut Pasteur, 75015 Paris, France
    Genome Res 16:1537-47. 2006

Detail Information

Publications50

  1. pmc Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria
    Teresa Nogueira
    Centro de Biologia Ambiental, Evolutionary Ecology of Microorganisms, Faculdade de Ciencias da Universidade de Lisboa, Lisboa, Portugal
    PLoS ONE 7:e49403. 2012
    ..The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation...
  2. pmc Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens
    João Alves Gama
    Centro de Biologia Ambiental and Departamento de Biologia Vegetal, Faculdade de Ciencias da Universidade de Lisboa, Lisboa, Portugal
    PLoS Pathog 8:e1002503. 2012
    ..Understanding these trade-offs provides guidelines to study the evolution of virulence and in particular the micro-evolutionary paths of emerging pathogens...
  3. pmc The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation
    Julien Guglielmini
    Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
    PLoS Genet 7:e1002222. 2011
    ....
  4. pmc Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence
    Teresa Nogueira
    Institut Pasteur, CNRS, URA, Paris, France
    Curr Biol 19:1683-91. 2009
    ..These proteins are costly, rendering populations of cooperators vulnerable to exploitation by nonproducing cheaters arising by gene loss or migration. In such conditions, how can cooperation persist?..
  5. pmc Persistence drives gene clustering in bacterial genomes
    Gang Fang
    Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr, Roux, 75724 Paris Cedex 15, France
    BMC Genomics 9:4. 2008
    ..However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes...
  6. doi request reprint The organization of the bacterial genome
    Eduardo P C Rocha
    Institut Pasteur, Microbial Evolutionary Genomics, F 75015 Paris, France
    Annu Rev Genet 42:211-33. 2008
    ..Since organization results from cellular processes, a better understanding of chromosome organization will help unravel the underlying cellular processes and their diversity...
  7. ncbi request reprint Essentiality, not expressiveness, drives gene-strand bias in bacteria
    Eduardo P C Rocha
    Unité GGB, URA 2171, Institut Pasteur, 28 rue Dr Roux, 75015 Paris, France
    Nat Genet 34:377-8. 2003
    ..Here we show, however, that in Bacillus subtilis and Escherichia coli, essentiality (the transcript product), not expressiveness (the collision rate), selectively drives the biased gene distribution...
  8. pmc Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    Genome Res 14:2279-86. 2004
    ..It also provides new evidence that a selective force for the optimization of the translation machinery is the maximization of growth...
  9. doi request reprint Evolutionary patterns in prokaryotic genomes
    Eduardo Pc Rocha
    UPMC Univ Paris 06, Atelier de BioInformatique, F 75005 Paris, France
    Curr Opin Microbiol 11:454-60. 2008
    ..Through an increased appreciation of genome dynamics in given ecological contexts, a more detailed picture of the genetic basis of prokaryotic evolution is emerging...
  10. pmc Similar compositional biases are caused by very different mutational effects
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, URA 2171, Institut Pasteur, 75015 Paris, France
    Genome Res 16:1537-47. 2006
    ....
  11. ncbi request reprint Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes
    Etienne Couturier
    Atelier de BioInformatique, Universite Pierre et Marie Curie, 12, rue Cuvier, 75005 Paris, France
    Mol Microbiol 59:1506-18. 2006
    ..Together, these results demonstrate that replication-associated gene dosage is an important determinant of chromosome organisation and dynamics, especially among fast-growing bacteria...
  12. pmc Gene essentiality determines chromosome organisation in bacteria
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex 15, France
    Nucleic Acids Res 31:6570-7. 2003
    ..These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes...
  13. pmc Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Paris VI, 12 rue Cuvier, 75005 Paris, France
    Nucleic Acids Res 30:1886-94. 2002
    ....
  14. ncbi request reprint A strand-specific model for chromosome segregation in bacteria
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris 15, France
    Mol Microbiol 49:895-903. 2003
    ..We show that the model is consistent with the asymmetric distribution of highly expressed genes and of stress response genes in Escherichia coli and Bacillus subtilis. The model offers a framework for interpreting data from genomics...
  15. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
    ..Overall, despite a very high gene flow, genes co-exist in an organised genome...
  16. ncbi request reprint An analysis of determinants of amino acids substitution rates in bacterial proteins
    Eduardo P C Rocha
    Unité GGB, Institut Pasteur, Paris, France
    Mol Biol Evol 21:108-16. 2004
    ..They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes...
  17. pmc The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella
    Marie Touchon
    Département Génomes et Génétique, Institut Pasteur, Microbial Evolutionary Genomics, Paris, France
    PLoS ONE 5:e11126. 2010
    ..Since we observe purifying selection for the maintenance of CRISPR these results suggest that alternative evolutionary roles for CRISPR remain to be uncovered...
  18. pmc The systemic imprint of growth and its uses in ecological (meta)genomics
    Sara Vieira-Silva
    Microbial Evolutionary Genomics, Institut Pasteur, CNRS, URA2171, Paris, France
    PLoS Genet 6:e1000808. 2010
    ..Our predictor allows inferring growth rates in the vast majority of uncultivable prokaryotes and paves the way to the understanding of community dynamics from metagenomic data...
  19. pmc An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    Genome Res 13:1123-32. 2003
    ..The assembly of these results indicates that shortly spaced repeats are key players in the dynamics of genome evolution...
  20. ncbi request reprint Order and disorder in bacterial genomes
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    Curr Opin Microbiol 7:519-27. 2004
    ..As a result, the clash between elements generating rearrangements and chromosome organization is a classic case of evolutionary conflict...
  21. pmc Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
    Todd J Treangen
    Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
    PLoS Genet 7:e1001284. 2011
    ..Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families...
  22. pmc Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages
    Gilles Fischer
    Unité de Génétique Moléculaire des Levures CNRS URA 2171, UFR927 Université Pierre et Marie Curie, Département de Structure et Dynamique des Génomes, Institut Pasteur, Paris, France
    PLoS Genet 2:e32. 2006
    ..This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage...
  23. ncbi request reprint The replication-related organization of bacterial genomes
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Pierre et Marie Curie, 12, rue Cuvier, 75005 Paris, France
    Microbiology 150:1609-27. 2004
    ..Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution...
  24. ncbi request reprint Comparisons of dN/dS are time dependent for closely related bacterial genomes
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Paris VI, 75005 Paris, France
    J Theor Biol 239:226-35. 2006
    ..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...
  25. ncbi request reprint DNA repeats lead to the accelerated loss of gene order in bacteria
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    Trends Genet 19:600-3. 2003
  26. ncbi request reprint Inference and analysis of the relative stability of bacterial chromosomes
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, Paris, France and Atelier de BioInformatique, Universite Pierre et Marie Curie Paris VI, Paris, France
    Mol Biol Evol 23:513-22. 2006
    ..Hence, although this method has allowed uncovering some of mechanisms leading to rearrangements, we still ignore the forces that differentially shape selection upon genome stability in different species...
  27. ncbi request reprint Causes of insertion sequences abundance in prokaryotic genomes
    Marie Touchon
    Génétique des Génomes Bactériens, CNRS URA2171, Institut Pasteur, Paris, France
    Mol Biol Evol 24:969-81. 2007
    ..Indeed, IS abundance increases quickly with genome size, which is the exact inverse trend found for the density of genes under strong selection such as essential genes. Hence, for ISs, the bigger the genome the better...
  28. pmc A new family of highly variable proteins in the Chlamydophila pneumoniae genome
    Eduardo P C Rocha
    Unité GGB, CNRS URA2171, Institut Pasteur, Paris, France
    Nucleic Acids Res 30:4351-60. 2002
    ..pneumoniae and could represent targets for future vaccine development...
  29. pmc Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution
    Eduardo P C Rocha
    Atelier de BioInformatique, 12 rue Cuvier, 75005 Paris, France
    Nucleic Acids Res 30:2031-42. 2002
    ..Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats...
  30. pmc Mobility of plasmids
    Chris Smillie
    Institut Pasteur, Microbial Evolutionary Genomics, CNRS, URA2171, F 75015 Paris, France
    Microbiol Mol Biol Rev 74:434-52. 2010
    ..Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts...
  31. doi request reprint A novel heuristic for local multiple alignment of interspersed DNA repeats
    Todd J Treangen
    Institut Pasteur, CNRS and UPMC University, Paris, France
    IEEE/ACM Trans Comput Biol Bioinform 6:180-9. 2009
    ..The described methods have been implemented in freely available software, Repeatoire, available from: http://wwwabi.snv.jussieu.fr/public/Repeatoire...
  32. ncbi request reprint Genesis, effects and fates of repeats in prokaryotic genomes
    Todd J Treangen
    UPMC Univ Paris, Atelier de BioInformatique, France
    FEMS Microbiol Rev 33:539-71. 2009
    ..We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate...
  33. ncbi request reprint Base composition bias might result from competition for metabolic resources
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Pierre et Marie Curie, 12, rue Cuvier, 75005 Paris, France
    Trends Genet 18:291-4. 2002
    ..We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences...
  34. ncbi request reprint The quest for the universals of protein evolution
    Eduardo P C Rocha
    Unité Génomique des Génomes Bactériens, Institut Pasteur, 28 rue Dr Roux, 75015 Paris, France
    Trends Genet 22:412-6. 2006
    ..A recent report by Drummond et al. suggests that the dominant role of expression levels in slowing the rate of protein evolution stems from selection for translation robustness...
  35. doi request reprint Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification
    Anne Laure Abraham
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 06, Paris, France
    J Mol Biol 394:522-34. 2009
    ..These results suggest that oligomerisation and amplification of internal sequences can interplay in evolutionary terms because they result in functional analogues when the latter exhibit rotational symmetry...
  36. pmc An assessment of the impacts of molecular oxygen on the evolution of proteomes
    Sara Vieira-Silva
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    Mol Biol Evol 25:1931-42. 2008
    ....
  37. pmc Swelfe: a detector of internal repeats in sequences and structures
    Anne Laure Abraham
    UPMC Univ Paris 06, Atelier de BioInformatique, F75005 Paris, France
    Bioinformatics 24:1536-7. 2008
    ..The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results...
  38. ncbi request reprint Repseek, a tool to retrieve approximate repeats from large DNA sequences
    Guillaume Achaz
    Atelier de BioInformatique, Université Pierre et Marie Curie Paris 6 12, rue Cuvier, 75005 Paris, France
    Bioinformatics 23:119-21. 2007
    ..Our method is computationally efficient enough to handle large sequences and is flexible enough to account for influencing factors, such as sequence-composition biases both at the seed detection and alignment levels...
  39. ncbi request reprint From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    Biochimie 90:648-59. 2008
    ..We also refer to programs freely available to analyse strand asymmetry...
  40. pmc The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus
    Luisa M Figueiredo
    Institut Pasteur, Biology of Host Parasite Interaction Unit CNRS URA2581 25 rue du Dr Roux, 75724 Paris, France
    Nucleic Acids Res 33:1111-22. 2005
    ..We further demonstrate that this compartment is associated with the nucleolus, hereby defined for the first time in P.falciparum...
  41. ncbi request reprint Protein evolution: causes of trends in amino-acid gain and loss
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
    Nature 442:E11-2; discussion E12. 2006
    ..This reinforces the need for caution in the interpretation of results derived from closely related taxa...
  42. pmc An integrative method for accurate comparative genome mapping
    Firas Swidan
    Department of Computer Science, Technion, Israel Institute of Technology, Haifa, Israel
    PLoS Comput Biol 2:e75. 2006
    ..We use these results to investigate the breakpoint distribution in several prokaryotic genomes...
  43. ncbi request reprint Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes
    Yong Wang
    Department of Zoology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
    J Mol Evol 58:692-700. 2004
    ..This suggests the existence of alternative mechanisms contributing to CpG deficiency in bacteria...
  44. pmc Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction
    Laura Gomez-Valero
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Valencia, Spain
    Genome Res 17:1178-85. 2007
    ..This suggests a scenario of massive genome reduction through many nearly simultaneous pseudogenization events, leading to a highly specialized pathogen...
  45. pmc Associations between inverted repeats and the structural evolution of bacterial genomes
    Guillaume Achaz
    Structure et Dynamique des Génomes, Institut Jacques Monod, 75251 Paris, France
    Genetics 164:1279-89. 2003
    ..g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats...
  46. pmc The impact of the neisserial DNA uptake sequences on genome evolution and stability
    Todd J Treangen
    Algorithms and Genetics Group, Department of Computer Science, Technical University of Catalonia, Jordi Girona Salgado, 1 3, E 08034 Barcelona, Spain
    Genome Biol 9:R60. 2008
    ..Efficient natural transformation in Neisseria requires the presence of short DNA uptake sequences (DUSs). Doubts remain whether DUSs propagate by pure selfish molecular drive or are selected for 'safe sex' among conspecifics...
  47. pmc Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences
    Stefanie L Iverson-Cabral
    Department of Medicine, Harborview Medical Center, R and T Building, 325 9th Avenue, Box 359779, Seattle, WA 98104, USA
    Infect Immun 74:3715-26. 2006
    ..These observations support the hypothesis that recombination occurs between the mgpB gene and MgPar sequences and that the resulting antigenically distinct MgPa variants may contribute to immune evasion and persistence of infection...
  48. ncbi request reprint Erosion of interaction networks in reduced and degraded genomes
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    J Exp Zool B Mol Dev Evol 308:97-103. 2007
    ....
  49. pmc Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
    Claudine Medigue
    Genoscope, CNRS UMR 8030, Atelier de Génomique Comparative, 91006 Evry Cedex, France
    Genome Res 15:1325-35. 2005
    ..Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome...