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Eduardo Rocha

Research Profile

Genes & Molecular Sequences

Phenomena

Evolution, Molecular

Living Beings

Anatomy

Bacterial Chromosomes

Chemicals & Drugs

Concepts & Ideas

Physiology

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Publications

TOP 3
Louis-Marie Bobay; Eduardo P C Rocha; Marie Touchon
The adaptation of temperate bacteriophages to their host genomes.
Eduardo P C Rocha
Evolution. With a little help from prokaryotes.
Julien Guglielmini; Fernando de la Cruz; Eduardo P C Rocha
Evolution of conjugation and type IV secretion systems.

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All Publications

2013: Louis-Marie Bobay; Eduardo P C Rocha; Marie Touchon
The adaptation of temperate bacteriophages to their host genomes.
Molecular biology and evolution 2013;30(4):737-51.
2013: Eduardo P C Rocha
Evolution. With a little help from prokaryotes.
Science (New York, N.Y.) 2013;339(6124):1154-5.
2013: Julien Guglielmini; Fernando de la Cruz; Eduardo P C Rocha
Evolution of conjugation and type IV secretion systems.
Molecular biology and evolution 2013;30(2):315-31.
2013: Patrícia H Brito; Eduardo P C Rocha; KB Xavier; Isabel Gordo
Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception.
Genome biology and evolution 2013;5(1):16-30.
2012: Marie Touchon; Guillaume Arlet; Sophie Charpentier; Erick Denamur; Bertrand Picard; Dominique Pognard; Eduardo P C Rocha; Catherine Branger
Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements.
Microbiology (Reading, England) 2012;158(Pt 12):2997-3004.
2012: Marie Deghorain; Pierre-Alexandre Drèze; David Perez-Morga; Eduardo P C Rocha; Pierre Robert Smeesters; Marie Touchon; Louis-Marie Bobay; Sabrina Bousbata; Marjorie Vermeersch; Laurence Van Melderen
Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages.
Journal of bacteriology 2012;194(21):5829-39.
2012: Sophie S Abby; Eduardo P C Rocha
The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems.
PLoS genetics 2012;8(9):e1002983.
2012: Nicholas N Nickerson; Sophie S Abby; Mohamed Chami; Eduardo P C Rocha; Anthony P Pugsley
A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin.
Journal of bacteriology 2012;194(18):4951-8.
2012: Amine NAMOUCHI; Xavier Didelot; Brigitte Gicquel; Ulrike Schöck; Eduardo P C Rocha
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection.
Genome research 2012;22(4):721-34.
2012: João Alves Gama; Sophie S Abby; Francisco Dionisio; Sara Vieira-Silva; Eduardo P C Rocha
Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens.
PLoS pathogens 2012;8(2):e1002503.
2012: Teresa Nogueira; Marie Touchon; Eduardo P C Rocha
Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.
PloS one 2012;7(11):e49403.
2011: Marie Touchon; Benoit Vacherie; Valentin Loux; Eduardo P C Rocha; Valérie Barbe; Paul Barbier; Jean-François Bernardet; Eric Duchaud
Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.
Applied and environmental microbiology 2011;77(21):7656-62.
2011: Julien Guglielmini; Leonor Quintais; Fernando de la Cruz; M Pilar Garcillán-Barcia; Eduardo P C Rocha
The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.
PLoS genetics 2011;7(8):e1002222.
2011: Tobias Warnecke; Eduardo P C Rocha
Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size.
Molecular biology and evolution 2011;28(8):2339-49.
2011: Marie Touchon; Sophie Charpentier; Olivier Clermont; Eduardo P C Rocha; Erick Denamur; Catherine Branger
CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection.
Journal of bacteriology 2011;193(10):2460-7.
2011: Todd J Treangen; Eduardo P C Rocha
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.
PLoS genetics 2011;7(1):e1001284.
2010: Eduardo P C Rocha; Edward J Feil
Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?
PLoS genetics 2010;6(9):.
2010: Chris Smillie; M Pilar Garcillán-Barcia; M Victoria Francia; Eduardo P C Rocha; Fernando de la Cruz
Mobility of plasmids.
Microbiology and molecular biology reviews : MMBR 2010;74(3):434-52.
2010: Sara Vieira-Silva; Marie Touchon; Eduardo P C Rocha
No evidence for elemental-based streamlining of prokaryotic genomes.
Trends in ecology & evolution 2010;25(6):319-20; author reply 320-1.
2010: Dalila Mil-Homens; Eduardo P C Rocha; Arsenio M Fialho
Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage.
Microbiology (Reading, England) 2010;156(Pt 4):1084-96.
2010: Marie Touchon; Eduardo P C Rocha
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella.
PloS one 2010;5(6):e11126.
2010: Sara Vieira-Silva; Eduardo P C Rocha
The systemic imprint of growth and its uses in ecological (meta)genomics.
PLoS genetics 2010;6(1):e1000808.
2009: Anne-Laure Abraham; Joel Pothier; Eduardo P C Rocha
Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification.
Journal of molecular biology 2009;394(3):522-34.
2009: Teresa Nogueira; Daniel J Rankin; Marie Touchon; François Taddei; Sam P Brown; Eduardo P C Rocha
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence.
Current biology : CB 2009;19(20):1683-91.
2009: Todd J Treangen; Anne-Laure Abraham; Marie Touchon; Eduardo P C Rocha
Genesis, effects and fates of repeats in prokaryotic genomes.
FEMS microbiology reviews 2009;33(3):539-71.
2009: Todd J Treangen; Aaron E Darling; Guillaume Achaz; Mark A Ragan; Xavier Messeguer; Eduardo P C Rocha
A novel heuristic for local multiple alignment of interspersed DNA repeats.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2009;6(2):180-9.
2009: Kevin J Balbi; Eduardo P C Rocha; Edward J Feil
The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp.
Molecular biology and evolution 2009;26(2):345-55.
2008: Eduardo P C Rocha
Evolutionary patterns in prokaryotic genomes.
Current opinion in microbiology 2008;11(5):454-60.
2008: Sara Vieira-Silva; Eduardo P C Rocha
An assessment of the impacts of molecular oxygen on the evolution of proteomes.
Molecular biology and evolution 2008;25(9):1931-42.
2008: Anne-Laure Abraham; Eduardo P C Rocha; Joel Pothier
Swelfe: a detector of internal repeats in sequences and structures.
Bioinformatics (Oxford, England) 2008;24(13):1536-7.
2008: Marie Touchon; Eduardo P C Rocha
From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data.
Biochimie 2008;90(4):648-59.
2008: Eduardo P C Rocha
The organization of the bacterial genome.
Annual review of genetics 2008;42():211-33.
2008: Todd J Treangen; Ole Herman Ambur; Tone Tonjum; Eduardo P C Rocha
The impact of the neisserial DNA uptake sequences on genome evolution and stability.
Genome biology 2008;9(3):R60.
2008: Gang Fang; Eduardo P C Rocha; Antoine Danchin
Persistence drives gene clustering in bacterial genomes.
BMC genomics 2008;9():4.
2007: Laura Gómez-Valero; Eduardo P C Rocha; Amparo Latorre; Francisco J Silva
Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.
Genome research 2007;17(8):1178-85.
2007: Marie Touchon; Eduardo P C Rocha
Causes of insertion sequences abundance in prokaryotic genomes.
Molecular biology and evolution 2007;24(4):969-81.
2007: Howard Ochman; Renyi Liu; Eduardo P C Rocha
Erosion of interaction networks in reduced and degraded genomes.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2007;308(1):97-103.
2007: Guillaume Achaz; Frédéric Boyer; Eduardo P C Rocha; Alain Viari; Eric Coissac
Repseek, a tool to retrieve approximate repeats from large DNA sequences.
Bioinformatics (Oxford, England) 2007;23(1):119-21.
2006: Eduardo P C Rocha; Marie Touchon; Edward J Feil
Similar compositional biases are caused by very different mutational effects.
Genome research 2006;16(12):1537-47.
2006: Laurence D Hurst; Edward J Feil; Eduardo P C Rocha
Protein evolution: causes of trends in amino-acid gain and loss.
Nature 2006;442(7105):E11-2; discussion E12.
2006: Firas Swidan; Eduardo P C Rocha; Michael Shmoish; Ron Y Pinter
An integrative method for accurate comparative genome mapping.
PLoS computational biology 2006;2(8):e75.
2006: Eduardo P C Rocha
The quest for the universals of protein evolution.
Trends in genetics : TIG 2006;22(8):412-6.
2006: Stefanie L Iverson-Cabral; Sabina G Astete; Craig R Cohen; Eduardo P C Rocha; Patricia A Totten
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.
Infection and immunity 2006;74(7):3715-26.
2006: Eduardo P C Rocha; John Maynard Smith; Laurence D Hurst; Matthew T G Holden; Jessica E Cooper; Noel Smith; Edward J Feil
Comparisons of dN/dS are time dependent for closely related bacterial genomes.
Journal of theoretical biology 2006;239(2):226-35.
2006: Gilles Fischer; Eduardo P C Rocha; Frédéric Brunet; Massimo Vergassola; Bernard Dujon
Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.
PLoS genetics 2006;2(3):e32.
2006: Etienne Couturier; Eduardo P C Rocha
Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes.
Molecular microbiology 2006;59(5):1506-18.
2006: Eduardo P C Rocha
Inference and analysis of the relative stability of bacterial chromosomes.
Molecular biology and evolution 2006;23(3):513-22.
2005: Claudine Médigue; Evelyne Krin; Géraldine Pascal; Valérie Barbe; Andreas Bernsel; Philippe N Bertin; Frankie Cheung; Stéphane Cruveiller; Salvino D'Amico; Angela Duilio; Gang Fang; Georges Feller; Christine Ho; Sophie Mangenot; Gennaro Marino; Johan Nilsson; Ermenegilda Parrilli; Eduardo P C Rocha; Zoé Rouy; Agnieszka Sekowska; Maria Luisa Tutino; David Vallenet; Gunnar von Heijne; Antoine Danchin
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.
Genome research 2005;15(10):1325-35.
2005: Eduardo P C Rocha; Emmanuel Cornet; Bénédicte Michel
Comparative and evolutionary analysis of the bacterial homologous recombination systems.
PLoS genetics 2005;1(2):e15.
2005: Luisa M Figueiredo; Eduardo P C Rocha; Liliana Mancio-Silva; Christine Prevost; Danièle Hernandez-Verdun; Artur Scherf
The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus.
Nucleic acids research 2005;33(3):1111-22.
2004: Eduardo P C Rocha
Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization.
Genome research 2004;14(11):2279-86.
2004: Eduardo P C Rocha
Order and disorder in bacterial genomes.
Current opinion in microbiology 2004;7(5):519-27.
2004: Yong Wang; Eduardo P C Rocha; Frederick C C Leung; Antoine Danchin
Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes.
Journal of molecular evolution 2004;58(6):692-700.
2004: Eduardo P C Rocha
The replication-related organization of bacterial genomes.
Microbiology (Reading, England) 2004;150(Pt 6):1609-27.
2004: Eduardo P C Rocha; Antoine Danchin
An analysis of determinants of amino acids substitution rates in bacterial proteins.
Molecular biology and evolution 2004;21(1):108-16.
2003: Eduardo P C Rocha; Antoine Danchin
Gene essentiality determines chromosome organisation in bacteria.
Nucleic acids research 2003;31(22):6570-7.
2003: Eduardo P C Rocha
DNA repeats lead to the accelerated loss of gene order in bacteria.
Trends in genetics : TIG 2003;19(11):600-3.
2003: Guillaume Achaz; Eric Coissac; Pierre Netter; Eduardo P C Rocha
Associations between inverted repeats and the structural evolution of bacterial genomes.
Genetics 2003;164(4):1279-89.
2003: Eduardo P C Rocha; Joe A Fralick; Govindsamy Vediyappan; Antoine Danchin; Vic Norris
A strand-specific model for chromosome segregation in bacteria.
Molecular microbiology 2003;49(4):895-903.
2003: Eduardo P C Rocha; Antoine Danchin
Essentiality, not expressiveness, drives gene-strand bias in bacteria.
Nature genetics 2003;34(4):377-8.
2003: Eduardo P C Rocha
An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction.
Genome research 2003;13(6A):1123-32.
2002: Eduardo P C Rocha; Olivier Pradillon; Hung Bui; Chalom Sayada; Erick Denamur
A new family of highly variable proteins in the Chlamydophila pneumoniae genome.
Nucleic acids research 2002;30(20):4351-60.
2002: Guillaume Achaz; Eduardo P C Rocha; Pierre Netter; Eric Coissac
Origin and fate of repeats in bacteria.
Nucleic acids research 2002;30(13):2987-94.
2002: Eduardo P C Rocha; Antoine Danchin
Base composition bias might result from competition for metabolic resources.
Trends in genetics : TIG 2002;18(6):291-4.
2002: Eduardo P C Rocha; Alain Blanchard
Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution.
Nucleic acids research 2002;30(9):2031-42.
2002: Eduardo P C Rocha; Ivan Matic; François Taddei
Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?
Nucleic acids research 2002;30(9):1886-94.
2001: Eduardo P C Rocha; Antoine Danchin
Ongoing evolution of strand composition in bacterial genomes.
Molecular biology and evolution 2001;18(9):1789-99.
2001: Eduardo P C Rocha; Antoine Danchin; Alain Viari
Evolutionary role of restriction/modification systems as revealed by comparative genome analysis.
Genome research 2001;11(6):946-58.
2001: Isabelle Chambaud; Roland Heilig; Stéphane Ferris; Valérie Barbe; D Samson; F Galisson; Ivan Moszer; K Dybvig; Henri Wróblewski; Alain Viari; Eduardo P C Rocha; Alain Blanchard
The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis.
Nucleic acids research 2001;29(10):2145-53.
2000: Eduardo P C Rocha; Antoine Danchin; Alain Viari
The DB case: pattern matching evidence is not significant.
Molecular microbiology 2000;37(1):216-8.
2000: Eduardo P C Rocha; Agnieszka Sekowska; Antoine Danchin
Sulphur islands in the Escherichia coli genome: markers of the cell's architecture?
FEBS letters 2000;476(1-2):8-11.
2000: Eduardo P C Rocha; P Guerdoux-Jamet; Ivan Moszer; Alain Viari; Antoine Danchin
Implication of gene distribution in the bacterial chromosome for the bacterial cell factory.
Journal of biotechnology 2000;78(3):209-19.
1999: Eduardo P C Rocha; Antoine Danchin; Alain Viari
Functional and evolutionary roles of long repeats in prokaryotes.
Research in microbiology 1999;150(9-10):725-33.
1999: Ivan Moszer; Eduardo P C Rocha; Antoine Danchin
Codon usage and lateral gene transfer in Bacillus subtilis.
Current opinion in microbiology 1999;2(5):524-8.
1999: Eduardo P C Rocha; Antoine Danchin; Alain Viari
Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes.
Molecular biology and evolution 1999;16(9):1219-30.
1999: Eduardo P C Rocha; Antoine Danchin; Alain Viari
Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis.
Nucleic acids research 1999;27(17):3567-76.
1999: Eduardo P C Rocha; Antoine Danchin; Alain Viari
Bacterial DNA strand compositional asymmetry: response.
Trends in microbiology 1999;7(8):308.
1999: Eduardo P C Rocha; Antoine Danchin; Alain Viari
Universal replication biases in bacteria.
Molecular microbiology 1999;32(1):11-6.
1998: Eduardo P C Rocha; Alain Viari; Antoine Danchin
Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons.
Nucleic acids research 1998;26(12):2971-80.