Jean Michel Claverie

Summary

Affiliation: Centre National de la Recherche Scientifique
Country: France

Publications

  1. pmc Mimivirus relatives in the Sargasso sea
    Elodie Ghedin
    Department of Parasite and Virus Genomics, The Institute for Genomic Research, Rockville, MD 20850, USA
    Virol J 2:62. 2005
  2. pmc Determination of strongly overlapping signaling activity from microarray data
    Ghislain Bidaut
    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    BMC Bioinformatics 7:99. 2006
  3. ncbi request reprint Fewer genes, more noncoding RNA
    Jean Michel Claverie
    Structural and Genomics Information Laboratory, CNRS UPR 2589, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, Marseille 13402, France
    Science 309:1529-30. 2005
  4. pmc Viruses take center stage in cellular evolution
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, Marseille 13288, Cedex 9, France
    Genome Biol 7:110. 2006
  5. doi request reprint Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Parc Scientifique de Luminy, Case 934, Marseille, France
    J Invertebr Pathol 101:172-80. 2009
  6. doi request reprint Mimivirus and its virophage
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Aix Marseille University, Parc Scientifique de Luminy, Case 934, FR 13288 Marseille, France
    Annu Rev Genet 43:49-66. 2009
  7. ncbi request reprint The insertion of palindromic repeats in the evolution of proteins
    Jean Michel Claverie
    Information Genetique et Structurale, CNRS AVENTIS UMR 1889, Institut de Biologie Structurale et Microbiologie, Marseille, France
    Trends Biochem Sci 28:75-80. 2003
  8. ncbi request reprint Recent advances in computational genomics
    J M Claverie
    Structural and Genetic Information Laboratory, UMR 1889 CNRS AVENTIS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Pharmacogenomics 2:361-72. 2001
  9. ncbi request reprint Mimivirus and the emerging concept of "giant" virus
    Jean Michel Claverie
    Information Genomique et Structurale, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virus Res 117:133-44. 2006
  10. pmc Giant viruses in the oceans: the 4th Algal Virus Workshop
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Virol J 2:52. 2005

Detail Information

Publications103 found, 100 shown here

  1. pmc Mimivirus relatives in the Sargasso sea
    Elodie Ghedin
    Department of Parasite and Virus Genomics, The Institute for Genomic Research, Rockville, MD 20850, USA
    Virol J 2:62. 2005
    ..Their isolation and genome sequencing could prove invaluable in understanding the origin and diversity of large DNA viruses, and shed some light on the role they eventually played in the emergence of eukaryotes...
  2. pmc Determination of strongly overlapping signaling activity from microarray data
    Ghislain Bidaut
    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    BMC Bioinformatics 7:99. 2006
    ....
  3. ncbi request reprint Fewer genes, more noncoding RNA
    Jean Michel Claverie
    Structural and Genomics Information Laboratory, CNRS UPR 2589, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, Marseille 13402, France
    Science 309:1529-30. 2005
    ..Exploring the role and diversity of these numerous noncoding RNAs now constitutes a main challenge in transcription research...
  4. pmc Viruses take center stage in cellular evolution
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, Marseille 13288, Cedex 9, France
    Genome Biol 7:110. 2006
    ....
  5. doi request reprint Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Parc Scientifique de Luminy, Case 934, Marseille, France
    J Invertebr Pathol 101:172-80. 2009
    ....
  6. doi request reprint Mimivirus and its virophage
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Aix Marseille University, Parc Scientifique de Luminy, Case 934, FR 13288 Marseille, France
    Annu Rev Genet 43:49-66. 2009
    ..Post-genomic studies are now in progress, slowly shedding some light on the physiology of the most complex virus isolated to date...
  7. ncbi request reprint The insertion of palindromic repeats in the evolution of proteins
    Jean Michel Claverie
    Information Genetique et Structurale, CNRS AVENTIS UMR 1889, Institut de Biologie Structurale et Microbiologie, Marseille, France
    Trends Biochem Sci 28:75-80. 2003
    ..Based on previous results and theories on the coding potential of palindromic elements, we speculate that their insertion and mobility might have played a significant role in the early stages of protein evolution...
  8. ncbi request reprint Recent advances in computational genomics
    J M Claverie
    Structural and Genetic Information Laboratory, UMR 1889 CNRS AVENTIS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Pharmacogenomics 2:361-72. 2001
    ..It is thus increasingly difficult for the biologist to choose the computational approaches that perform best in these various areas. This paper attempts to review the most useful developments of the last 2 years...
  9. ncbi request reprint Mimivirus and the emerging concept of "giant" virus
    Jean Michel Claverie
    Information Genomique et Structurale, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virus Res 117:133-44. 2006
    ..We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses...
  10. pmc Giant viruses in the oceans: the 4th Algal Virus Workshop
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Virol J 2:52. 2005
    ....
  11. pmc The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
    PLoS Biol 3:e248. 2005
    ..Our study demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria...
  12. pmc Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR 2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
    PLoS Genet 2:e76. 2006
    ....
  13. pmc Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes
    François Enault
    Structural and Genomic Information CNRS UPR2589, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille, Cedex 20, France
    Nucleic Acids Res 31:3720-2. 2003
    ..An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/...
  14. ncbi request reprint Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets
    Chantal Abergel
    Structural and Genomic Information Laboratory, UMR 1889 CNRS AVENTIS, 13402 Marseille Cedex 20, France
    J Struct Funct Genomics 4:141-57. 2003
    ....
  15. pmc Reductive genome evolution from the mother of Rickettsia
    Guillaume Blanc
    Structural and Genomic Information Laboratory, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
    PLoS Genet 3:e14. 2007
    ....
  16. ncbi request reprint Heart specific genes revealed by EST sampling
    Karine Megy
    Information Génétique et Structurale CNRS UMR 1889, 31, chemin Joseph Aiguier 13402 Marseille Cedex 20, France
    Genome Biol 3:PREPRINT0008. 2002
    ..Expression profiles were then generated for each of these genes by counting their cognate ESTs in all libraries. Differential expression was assessed by applying to these profiles a previously published statistical procedure...
  17. ncbi request reprint Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity
    Chantal Abergel
    Information Génomique and Structurale, CNRS UPR 2589, IBSM, Marseille Cedex, France
    Mol Biol Evol 23:2112-22. 2006
    ....
  18. pmc mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
    Matthieu Legendre
    Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique, UPR2589, Mediterranean Institute of Microbiology IFR88, Aix Marseille University, Parc Scientifique de Luminy, FR 13288 Marseille, France
    Genome Res 20:664-74. 2010
    ....
  19. pmc The conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold
    Sébastien Santini
    Information Génomique et Structurale CNRS UPR2589, Aix Marseille Universite, Mediterranean Institute of Microbiology, Parc Scientifique de Luminy, Marseille, France
    PLoS ONE 6:e18528. 2011
    ..It was then lost by the Saccharomycetales which include Saccharomyces cerevisiae...
  20. pmc Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes
    Sébastien Santini
    Structural and Genomic Information Laboratory, Unité Mixte de Recherche 7256, Centre National de la Recherche Scientifique, Aix Marseille Universite, 13288 Marseille Cedex 9, France
    Proc Natl Acad Sci U S A 110:10800-5. 2013
    ....
  21. pmc Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis
    François Enault
    Information Génomique and Structurale UPR CNRS 2589, Institut de Biologie Structurale et Microbiologie, 31, Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Nucleic Acids Res 32:W336-9. 2004
    ..The Phydbac2 web server is available at http://igs-server.cnrs-mrs.fr/phydbac/...
  22. ncbi request reprint Genome-based design of a cell-free culture medium for Tropheryma whipplei
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, Faculte de Medecine, 27 Boulevard Jean Moulin, 13385, Marseille, France
    Lancet 362:447-9. 2003
    ..Genomic information can, therefore, provide sufficient clues for designing axenic media for fastidious and uncultured pathogens...
  23. ncbi request reprint Molecular evolution of rickettsia surface antigens: evidence of positive selection
    Guillaume Blanc
    Information Genomique et Structurale, UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Mol Biol Evol 22:2073-83. 2005
    ....
  24. ncbi request reprint Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase
    Sandra Jeudy
    Information Genomique et Structurale, CNRS, Marseille, France
    Proteins 62:302-7. 2006
  25. pmc Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus
    Chantal Abergel
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IBSM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:212-5. 2005
    ..Experimental evidence that Mimivirus tyrosyl tRNA synthetase recombinant gene product does indeed activate tyrosine is also presented...
  26. pmc FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
    Karsten Suhre
    Information Génomique and Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Nucleic Acids Res 32:D273-6. 2004
    ..Together, these servers provide the complete set of information required for in-depth analysis of non-homology-based gene function attribution...
  27. pmc CaspR: a web server for automated molecular replacement using homology modelling
    Jean Baptiste Claude
    Information Génomique and Structurale UPR CNRS 2589, Institut de Biologie Structurale et Microbiologie, 31, Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Nucleic Acids Res 32:W606-9. 2004
    ..We expect this automated procedure to have a significant impact on the throughput of large-scale structural genomics projects. CaspR is freely available at http://igs-server.cnrs-mrs.fr/Caspr/...
  28. pmc Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes
    Karsten Suhre
    Information Genomique et Structurale, Centre National de la Recherche Scientifique, Institut de Biologie Structurale et Microbiologie, 13402 Marseille, France
    Proc Natl Acad Sci U S A 102:14689-93. 2005
    ..This unprecedented conservation of core promoter regions is another exceptional feature of Mimivirus that again raises the question of its evolutionary origin...
  29. pmc Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis
    François Enault
    Structural and Genomic Information, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13009 Marseille, France
    BMC Bioinformatics 6:247. 2005
    ....
  30. pmc Protein coding palindromes are a unique but recurrent feature in Rickettsia
    Hiroyuki Ogata
    Information Génétique and Structurale, CNRS AVENTIS UMR 1889, 13402 Marseille Cedex 20, France
    Genome Res 12:808-16. 2002
    ..This comprehensive study of Rickettsia repeats confirms and extends our previous observations and further indicates a significant role of selfish DNAs in the creation and modification of proteins...
  31. pmc Comparative genomics of multidrug resistance in Acinetobacter baumannii
    Pierre Edouard Fournier
    Information Genomique et Structurale, Institute for Structural Biology and Microbiology, IBSM, Marseille, France
    PLoS Genet 2:e7. 2006
    ..Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance...
  32. pmc The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'
    Deborah Byrne
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Aix Marseille University, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Genome Res 19:1233-42. 2009
    ..The precise molecular mechanisms implementing the hairpin rule into the 3'-end processing of Mimivirus pre-mRNAs remain to be elucidated...
  33. pmc Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome
    Guillaume Blanc
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Institut de Biologie Structurale et Microbiologie, IFR 88, Parc Scientifique de Luminy, 13288 Marseille Cedex 9, France
    Genome Res 17:1657-64. 2007
    ..Further analysis of the genomic sequences identifies additional candidates of LGT between Rickettsia. Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought...
  34. pmc BLAST-EXPLORER helps you building datasets for phylogenetic analysis
    Alexis Dereeper
    Information Génomique and Structurale CNRS UPR2589, Institut de Microbiologie de la Méditerranée IFR 88, Marseille, France
    BMC Evol Biol 10:8. 2010
    ....
  35. pmc Marine mimivirus relatives are probably large algal viruses
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virol J 5:12. 2008
    ..The existence of mimivirus relatives was first suggested by the analysis of the Sargasso Sea metagenomic data...
  36. doi request reprint Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes
    Nadège Philippe
    Structural and Genomic Information Laboratory, UMR 7256 CNRS Aix Marseille Université, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Science 341:281-6. 2013
    ..9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study. ..
  37. pmc Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids
    Takashi Yoshida
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Aix Marseille University, Mediterranean Institute of Microbiology, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virol J 8:427. 2011
    ..Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes...
  38. pmc Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment
    Hiroyuki Ogata
    Information Genomique et Structurale, CNRS UPR2589, Institut de Microbiologie de la Mediterranee, Parc Scientifique de Luminy, Aix Marseille Universite, Marseille Cedex 9, France
    ISME J 5:1143-51. 2011
    ..Giruses thus seem to represent a major source of the underexplored diversity of the MutS family in the microbial world...
  39. pmc Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae
    Defne Arslan
    Information Genomique et Structurale, Centre National de la Recherche Scientifique Unité Propre de Recherche 2589, Aix Marseille University, Institut de Microbiologie de la Mediterranee, Parc Scientifique de Luminy, Case 934, FR 13288 Marseille, France
    Proc Natl Acad Sci U S A 108:17486-91. 2011
    ....
  40. pmc Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, 163 Avenue de Luminy, FR 13288, Marseille Cedex 09, France
    BMC Genomics 8:456. 2007
    ..We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer...
  41. ncbi request reprint The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides
    Sandra Jeudy
    Information Génomique and Structurale, CNRS UPR 2589, IBSM, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France
    J Bioenerg Biomembr 38:247-54. 2006
    ....
  42. pmc A new example of viral intein in Mimivirus
    Hiroyuki Ogata
    Information Genomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Virol J 2:8. 2005
    ..After their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus...
  43. pmc Heart-specific genes revealed by expressed sequence tag (EST) sampling
    Karine Megy
    Information Génétique et Structurale CNRS UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Genome Biol 3:RESEARCH0074. 2002
    ..Expression profiles were then generated for each gene by counting their cognate ESTs in all libraries. Differential expression was assessed by applying a previously published statistical procedure to these profiles...
  44. ncbi request reprint Mechanisms of evolution in Rickettsia conorii and R. prowazekii
    H Ogata
    , CNRS-AVENTIS UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Science 293:2093-8. 2001
    ..A 38-kilobase sequence inversion was dated shortly after the divergence of the genus...
  45. pmc Brucella microti: the genome sequence of an emerging pathogen
    Stephane Audic
    Laboratoire Information Génomique et Structurale, CNRS UPR2589, Aix Marseille University, Institut de Microbiologie de la Méditerranée IM2, IFR 88, Parc Scientifique de Luminy, FR 13288, Marseille Cedex 09, France
    BMC Genomics 10:352. 2009
    ..The atypical phenotype of B. microti prompted us to look for genomic differences compared to other Brucella species and to look for similarities with Ochrobactrum...
  46. pmc Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria
    Stephane Audic
    Structural and Genomic Information Laboratory, Institute for Structural Biology and Microbiology, Marseille, France
    PLoS Genet 3:e138. 2007
    ..The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors...
  47. pmc Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria
    Chantal Abergel
    Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2589, 13288 Marseille, Cedex 9, France
    Proc Natl Acad Sci U S A 104:6394-9. 2007
    ..As such, Ivy acts as a virulence factor for a number of Gram-negative bacteria-infecting vertebrates...
  48. pmc Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS
    Chantal Abergel
    Structural and Genomic Information Laboratory, CNRS UPR2589, IBSM IFR88, 163 Avenue de Luminy, Case 934, 13288, Marseille Cedex 9, France
    J Virol 81:12406-17. 2007
    ....
  49. pmc Taxonomic distribution of large DNA viruses in the sea
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Université de la Méditerranée Parc Scientifique de Luminy, Avenue de Luminy, FR 13288 Marseille, France
    Genome Biol 9:R106. 2008
    ..In this study, we used a new approach--'phylogenetic mapping'--to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set...
  50. pmc Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes
    Sandra Jeudy
    CNRS, Aix Marseille Universite, IGS UMR7256, Marseille, France
    PLoS Genet 8:e1003122. 2012
    ..Lastly, the perplexing occurrence of a bacterial-like regulatory mechanism in a eukaryotic/archaeal homologous gene is yet another oddity brought about by the study of giant viruses...
  51. pmc Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
    Matthieu Legendre
    Structural and genomic Information Laboratory CNRS, UPR2589, Mediterranean Institute of Microbiology, Aix Marseille Universite, 163 Avenue de Luminy, Case 934, FR 13288 Marseille, France
    Virol J 8:99. 2011
    ..Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes...
  52. pmc Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase
    Sandra Jeudy
    Structural and Genomic Information Laboratory, CNRS UPR2589, IFR88, Marseille Cedex 9, France
    J Virol 83:7142-50. 2009
    ..Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment...
  53. pmc Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data
    Per Unneberg
    Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique CNRS UPR 2589, Institut de Biologie Structurale et Microbiologie, Marseille, France
    PLoS ONE 2:e254. 2007
    ..Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology...
  54. doi request reprint Microbiology. How to infect a Mimivirus
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, CNRSUPR 2589, IFR 88, Universite de la Mediterranee, Parc Scientifique de Luminy, FR 13288 Marseille, France
    Science 321:1305-6. 2008
  55. pmc Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
    Hiroyuki Ogata
    Information Genomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Nucleic Acids Res 33:D321-4. 2005
    ..The web interface of Metagrowth helps users to design new axenic culture media eventually suitable for those bacteria. Metagrowth is accessible at http://igs-server.cnrs-mrs.fr/axenic/...
  56. pmc Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses
    Adrien Jeanniard
    Information Génomique and Structurale, IGS UMR7256, CNRS, Aix Marseille Universite, FR 13288, Marseille, France
    BMC Genomics 14:158. 2013
    ..These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses...
  57. pmc The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella
    Stephane Audic
    Laboratoire Information Génomique et Structurale, CNRS UPR2589, Aix Marseille University, Institut de Microbiologie de la Mediterranee, IFR 88, Parc Scientifique de Luminy 163 Avenue de Luminy Case 934 FR 13288, Marseille Cedex 09, France
    BMC Evol Biol 11:200. 2011
    ..pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus...
  58. pmc Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR2589, Mediterranean Institute of Microbiology IFR 88, Universite de la Mediterranee, Parc Scientifique de Luminy, Marseille, France
    Genome Res 19:1441-9. 2009
    ....
  59. pmc Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli K-12 MG1655
    J P Alimi
    Structural and Genetic Information Laboratory, Marseille, France
    Genome Res 10:959-66. 2000
    ..By extension, this implies that randomly occurring "junk" ORFs have been actively counter selected during the evolution of the dense E. coli genome...
  60. pmc Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22
    Karine Megy
    Genomic and Structural Information, UMR 1998 CNRS Aventis, 31, Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Genome Biol 4:P1. 2003
    ..Here we further explore the relationship between co-expression and chromosomal co-localization in the human genome by analyzing the expression status of the genes along the best-annotated chromosomes 20, 21 and 22...
  61. doi request reprint Mimivirus: the emerging paradox of quasi-autonomous viruses
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Aix Marseille University, Mediterranean Institute of Microbiology, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Trends Genet 26:431-7. 2010
    ....
  62. pmc Unique genes in giant viruses: regular substitution pattern and anomalously short size
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory CNRS UPR 2589, IBSM Parc Scientifique de Luminy, Case 934 13288 Marseille Cedex 9, France
    Genome Res 17:1353-61. 2007
    ..We propose that their characteristic features are the consequences of the specific evolutionary forces shaping the viral gene repertoires in the context of their parasitic lifestyles...
  63. pmc The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex
    Guillaume Blanc
    Centre National de la Recherche Scientifique, Laboratoire Information Génomique et Structurale UPR2589, Aix Marseille Universite, Institut de Microbiologie de la Mediterranee, 13009 Marseille, France
    Plant Cell 22:2943-55. 2010
    ..Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes...
  64. ncbi request reprint Computational methods for the identification of differential and coordinated gene expression
    J M Claverie
    Structural and Genetic Information Laboratory, Chemin Joseph Aiguier, Marseille, France
    Hum Mol Genet 8:1821-32. 1999
    ..ii) identify genes expressed in a coordinated manner across a set of conditions; and (iii) delineate clusters of genes sharing coherent expression features, eventually defining global biological pathways...
  65. ncbi request reprint Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers
    C Abergel
    Information Genetique et Structurale, CNRS UMR 1889, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Acta Crystallogr D Biol Crystallogr 55:1487-9. 1999
    ..Flash-frozen crystals diffract to 1. 78 A resolution using synchrotron radiation. A molecular-replacement solution was obtained using the human Reg/lithostathine structure and the AMoRe software...
  66. pmc "Hidden" dUTPase sequence in human immunodeficiency virus type 1 gp120
    C Abergel
    Laboratory of Structural and Genetic Information, CNRS EP 91, Marseille F 13402, France
    J Virol 73:751-3. 1999
    ..W. Sweet, J. Sodroski, and W. A. Hendrickson, Nature 393:648-659, 1998), our results strongly suggest that an ancestral dUTPase gene has evolved into the present primate lentivirus CD4 and cytokine receptor interacting region of gp120...
  67. ncbi request reprint Computational methods for exon detection
    J M Claverie
    Mol Biotechnol 10:27-48. 1998
    ..After reviewing the intrinsic difficulties in interpreting vertebrate genomic sequences, this article presents the state-of-the-art, with an emphasis on similarity search methods and the resources available through Internet...
  68. ncbi request reprint Computational methods for the identification of genes in vertebrate genomic sequences
    J M Claverie
    Structural and Genetic Information Laboratory, CNRS EP 91, Marseille, France
    Hum Mol Genet 6:1735-44. 1997
    ..As the human and mouse genome sequencing projects enter a production mode, the fully automated annotation of megabase-long anonymous genomic sequences is the next big challenge in bioinformatics...
  69. ncbi request reprint Crystallization and preliminary crystallographic study of a component of the Escherichia coli tol system: TolB
    C Abergel
    Information Genetique et Structurale, EP 91, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, Marseille, 13402 cedex 20, France
    Acta Crystallogr D Biol Crystallogr 54:102-4. 1998
    ..In addition, a selenomethionine-substituted protein is being produced in order to use the MAD method for structure determination...
  70. pmc Self-identification of protein-coding regions in microbial genomes
    S Audic
    Structural and Genetic Information Laboratory, Centre National de la Recherche Scientifique EP 91, 31 rue Joseph Aiguier, Marseille F 13402, France
    Proc Natl Acad Sci U S A 95:10026-31. 1998
    ..The results show that protein-coding regions can be identified with an accuracy of up to 90% with a totally automated and objective procedure...
  71. ncbi request reprint Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering
    D Gautheret
    Structural and Genetic Information, Center National de la Recherche Scientifique E P 91, 13 402 Marseille Cedex 20, France
    Genome Res 8:524-30. 1998
    ..This study demonstrates that, besides quantitative aspects of gene expression, the distribution of alternate mRNA forms can be analyzed through EST sampling...
  72. ncbi request reprint The difficulty of identifying genes in anonymous vertebrate sequences
    J M Claverie
    Structural and Genetic Information Laboratory, C N R S E P 91, Institute of Structural Biology and Microbiology, Marseille, France
    Comput Chem 21:203-14. 1997
    ..Thus, it appears that our only hope of turning genome data into genome information must rely on drastic progresses in the way we identify and analyse genes in silico...
  73. pmc Phylogeny.fr: robust phylogenetic analysis for the non-specialist
    A Dereeper
    Information Génomique et Structurale IGS, CNRS UPR2589, IFR 88, Marseille, France
    Nucleic Acids Res 36:W465-9. 2008
    ..A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/..
  74. pmc Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression
    R M Ewing
    Structural and Genetic Information SGI Laboratory, Centre National de la Recherche Scientifique Unité mixte de Recherche 1889, Marseille 13402 cedex 20, France
    Genome Res 9:950-9. 1999
    ..The analysis presented here combines the application of a correlation-based clustering method with a graphical color map allowing intuitive visualization of patterns within a large table of expression measurements...
  75. ncbi request reprint Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets
    R Ewing
    Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
    In Silico Biol 1:197-213. 1999
    ..Our results show that 58% of non-singleton ESTs are derived from genes in gene families common to the two species. These gene families constitute the basis of a core set of higher plant genes...
  76. ncbi request reprint Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution
    C Abergel
    Information Genetique et Structurale, CNRS UMR 1889 Institut de Biologie Structurale et Microbiologie 31 Chemin Joseph Aiguier, Marseille, 13402, Cedex 20, France
    Structure 7:1291-300. 1999
    ..TolB homologues are found in many gram-negative bacteria and the Tol-PAL system is thought to play a role in bacterial envelope integrity. TolB is required for lethal infection by Salmonella typhimurium in mice...
  77. ncbi request reprint Structural and genomic correlates of hyperthermostability
    C Cambillau
    Architecture et Fonction des Macromolecules Biologiques, CNRS UPR9039, France
    J Biol Chem 275:32383-6. 2000
    ..The biophysical requirements for the presence of charged residues at the protein surface, allowing protein stabilization through ion bonds, is therefore clearly imprinted and detectable in all genome sequences available to date...
  78. ncbi request reprint Annotation of bacterial genomes using improved phylogenomic profiles
    F Enault
    Structural and Genomic Information, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13009 Marseille, France
    Bioinformatics 19:i105-7. 2003
    ....
  79. ncbi request reprint Identification of odorant receptors from the Alpine marmot (Marmota marmota)
    V Matarazzo
    CNRS UPR 9024, Laboratoire de Neurobiologie, Groupe des Laboratoires de Marseille, France
    Cell Mol Biol (Noisy-le-grand) 46:1249-58. 2000
    ..Finally, Northern blot analysis revealed specific expression of these sequences in the Alpine Marmot olfactory epithelium tissue...
  80. ncbi request reprint The statistical significance of nucleotide position-weight matrix matches
    J M Claverie
    Structural and Genetic Information Laboratory, CNRS E P 91, Institute of Structural Biology and Microbiology, Marseille, France
    Comput Appl Biosci 12:431-9. 1996
    ..To improve the detection of nucleotide sequence signals (e.g. promoter elements) by position-weight matrices (PWM) using the concept of statistically significant matches...
  81. ncbi request reprint Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli
    C Abergel
    Information Genetique et Structurale, UMR1889 CNRS AVENTIS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Acta Crystallogr D Biol Crystallogr 56:1694-5. 2000
    ..Frozen crystals diffract to 1.6 A resolution using synchrotron radiation. Phasing was performed using multiwavelength anomalous dispersion (MAD) on the selenomethionine-substituted b0220 protein...
  82. ncbi request reprint Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme
    V Monchois
    Information Genetique et Structurale, UMR1889 CNRS AVENTIS and Laboratoire d Ingénierie des Systèmes Macromoléculaires, UPR 9027, 31 Chemin Joseph Aiguier, 13402 Marseille, Cedex 20, France
    J Biol Chem 276:18437-41. 2001
    ..To denote this newly assigned function, ykfE has now been registered under the new gene name Ivy (inhibitor of vertebrate lysozyme) at the E. coli genetic stock center...
  83. ncbi request reprint The structure of Acidithiobacillus ferrooxidans c(4)-cytochrome: a model for complex-induced electron transfer tuning
    Chantal Abergel
    Information Genomique et Structurale, UPR 2589, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 20, Marseille Cedex, France
    Structure 11:547-55. 2003
    ....
  84. pmc The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii
    Magali Lescot
    Structural and Genomic Information Laboratory, CNRS UPR2589, IFR88, Parc Scientifique de Luminy, Marseille, France
    PLoS Genet 4:e1000185. 2008
    ..The correlation between gene loss and increased virulence of B. recurrentis parallels that of Rickettsia prowazekii, with both species being genomic subsets of less-virulent strains...
  85. doi request reprint Open questions about giant viruses
    Jean Michel Claverie
    Aix Marseille Universite, CNRS, IGS UMR 7256, Marseille, France
    Adv Virus Res 85:25-56. 2013
    ....
  86. pmc Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase
    Sébastien Santini
    Information Genomique et Structurale, UPR2589, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
    BMC Struct Biol 8:33. 2008
    ..Since thiamine pyrophosphate is an essential product involved in a variety of metabolic pathways, proteins responsible for its production satisfied these two criteria...
  87. ncbi request reprint Genomic correlates of hyperthermostability, an update
    Karsten Suhre
    Structural and Genomic Information Laboratory, UPR 2589 CNRS, Institute of Structural Biology and Microbiology, CNRS, Marseille, France
    J Biol Chem 278:17198-202. 2003
    ..and Suzuki, M. (2000) Proc. Natl. Acad. Sci. 97, 14257-14262). We show that the CvP-bias is the sole criterion that is able to clearly discriminate hyperthermophile from mesothermophile microorganisms on a global genomic basis...
  88. pmc The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation
    Guillaume Blanc
    Structural and Genomic Information Laboratory, UMR7256 CNRS, Aix Marseille University, Mediterranean Institute of Microbiology FR3479, Marseille, FR 13385, France
    Genome Biol 13:R39. 2012
    ..This is the first eukaryotic microorganism from a polar environment to have its genome sequenced...
  89. pmc Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
    Pascal Hingamp
    CNRS, Aix Marseille Universite, Laboratoire Information Génomique et Structurale UMR 7256, Mediterranean Institute of Microbiology FR 3479, Marseille, France
    ISME J 7:1678-95. 2013
    ....
  90. ncbi request reprint Rickettsia felis, from culture to genome sequencing
    H Ogata
    CNRSIBSM, Information Genomique et Structurale, Marseille, France
    Ann N Y Acad Sci 1063:26-34. 2005
    ..It also contains toxin-antitoxin system encoding genes that are extremely rare in intracellular bacteria and may be linked to plasmid maintenance...
  91. ncbi request reprint [Transcriptome analysis in cancerology: bioinformatics aspects]
    J M Claverie
    , UMR 1889 CNRS-AVENTIS, 31, chemin Joseph-Aiguier, 13402 Marseille Cedex 20
    Bull Cancer 88:269-76. 2001
    ..This is the purpose of the present article...
  92. ncbi request reprint Discovery of protein-coding palindromic repeats in Wolbachia
    Hiroyuki Ogata
    Trends Microbiol 13:253-5. 2005
  93. ncbi request reprint Bayesian decomposition analysis of bacterial phylogenomic profiles
    Ghislain Bidaut
    Division of Population Science, Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Am J Pharmacogenomics 5:63-70. 2005
    ..At the same time, the effectiveness of the existing antibacterials is rapidly decreasing due to the spread of multidrug-resistant pathogens...
  94. ncbi request reprint Some lessons from Rickettsia genomics
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
    FEMS Microbiol Rev 29:99-117. 2005
    ..Environmental adaptation of Rickettsia is also discussed...
  95. ncbi request reprint The 1.2-megabase genome sequence of Mimivirus
    Didier Raoult
    Unite des Rickettsies, Faculte de Medecine, CNRS UMR6020, Universite de la Mediterranee, 13385 Marseille Cedex 05, France
    Science 306:1344-50. 2004
    ..This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes...
  96. pmc Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome
    Didier Raoult
    Unite des Rickettsies, Faculte de Medecine, CNRS UMR6020, Universite de la Mediterranee, 13385 Marseille Cedex 05, France
    Genome Res 13:1800-9. 2003
    ..The analysis of the genome sequence of this previously largely unknown human pathogen is now guiding the development of molecular diagnostic tools and more convenient culture conditions...
  97. pmc Characterization of the naturally occurring oxacillinase of Acinetobacter baumannii
    Claire Héritier
    Service de Bacteriologie Virologie, Hopital de Bicetre, Le Kremlin Bicetre, France
    Antimicrob Agents Chemother 49:4174-9. 2005
    ..By PCR and sequencing bla(OXA-69)-like genes were identified in all A. baumannii strains tested (n = 12), suggesting that this oxacillinase is naturally occurring in that species...
  98. ncbi request reprint A giant virus in amoebae
    Bernard La Scola
    Unite des Rickettsies, Universite de la Mediterranee, CNRS UMR 6020, 13385 Marseille, France
    Science 299:2033. 2003
  99. pmc Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria
    Delphine Benarroch
    Molecular Biology Program, Sloan Kettering Institute, New York, NY 10021, USA
    J Virol 80:314-21. 2006
    ....
  100. pmc Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, IFR 48, Faculte de Medecine, 27 Boulevard Jean Moulin, 13385 Marseille, France
    J Virol 80:11678-85. 2006
    ..Thus, anonymous and unique genes constituting the majority of the mimivirus gene complement encode bona fide proteins that are likely to participate in well-integrated processes...
  101. pmc Comparative analysis of Acinetobacters: three genomes for three lifestyles
    David Vallenet
    Génomique Métabolique, CNRS UMR8030, CEA Institut de Génomique Genoscope, Evry, France
    PLoS ONE 3:e1805. 2008
    ..Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil...