Alessandra Carbone

Summary

Affiliation: Institut des Hautes Etudes Scientifiques
Country: France

Publications

  1. pmc Circuits and programmable self-assembling DNA structures
    Alessandra Carbone
    Institut des Hautes Etudes Scientifiques, 35, route de Chartres, F 91440 Bures sur Yvette, France
    Proc Natl Acad Sci U S A 99:12577-82. 2002
  2. ncbi request reprint Codon adaptation index as a measure of dominating codon bias
    A Carbone
    Institut des Hautes Etudes Scientifiques, 35, route de Chartres, 91440 Bures sur Yvette, France
    Bioinformatics 19:2005-15. 2003
  3. ncbi request reprint Codon bias signatures, organization of microorganisms in codon space, and lifestyle
    A Carbone
    Génomique Analytique, Universite Pierre et Marie Curie, INSERM U511, 91, Bd de l Hopital, 75013 Paris, France
    Mol Biol Evol 22:547-61. 2005
  4. ncbi request reprint Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis
    Alessandra Carbone
    Génomique Analytique, Universite Pierre et Marie Curie, INSERM U511, 91 Bd de l Hopital, 75013 Paris, France
    J Mol Evol 61:456-69. 2005
  5. pmc Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling
    Stefan Engelen
    Génomique Analytique, Universite Pierre et Marie Curie Paris 6, UMR S511, Paris, France
    PLoS Comput Biol 5:e1000267. 2009
  6. pmc Chromosomal periodicity and positional networks of genes in Escherichia coli
    Anthony Mathelier
    UPMC Univ Paris 06, FRE3214, Génomique Analytique, 15 rue de l Ecole de Medecine, Paris, France
    Mol Syst Biol 6:366. 2010
  7. pmc Large scale chromosomal mapping of human microRNA structural clusters
    Anthony Mathelier
    Universite Pierre et Marie Curie, UMR7238, 15, rue de l Ecole de Medecine, 75006 Paris, France and CNRS, UMR7238, Laboratoire de Génomique des Microorganismes, 75006 Paris, France
    Nucleic Acids Res 41:4392-408. 2013
  8. pmc Protein fragments: functional and structural roles of their coevolution networks
    Linda Dib
    Universite Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France
    PLoS ONE 7:e48124. 2012
  9. pmc CLAG: an unsupervised non hierarchical clustering algorithm handling biological data
    Linda Dib
    UPMC, UMR7238, Génomique Analytique, 15 rue de l Ecole de Medecine, F 75006 Paris, France
    BMC Bioinformatics 13:194. 2012
  10. doi request reprint Codon bias is a major factor explaining phage evolution in translationally biased hosts
    Alessandra Carbone
    Génomique Analytique, Universite Pierre et Marie Curie Paris 6, UMR S511, 91 Bd de l Hopital, 75013, Paris, France
    J Mol Evol 66:210-23. 2008

Collaborators

Detail Information

Publications17

  1. pmc Circuits and programmable self-assembling DNA structures
    Alessandra Carbone
    Institut des Hautes Etudes Scientifiques, 35, route de Chartres, F 91440 Bures sur Yvette, France
    Proc Natl Acad Sci U S A 99:12577-82. 2002
    ..The molecular system that we describe is fundamentally a pair of two-dimensional layers, but it seems possible to extend this system to multiple layers...
  2. ncbi request reprint Codon adaptation index as a measure of dominating codon bias
    A Carbone
    Institut des Hautes Etudes Scientifiques, 35, route de Chartres, 91440 Bures sur Yvette, France
    Bioinformatics 19:2005-15. 2003
    ..The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. AVAILABILITY: http://www.ihes.fr/~materials...
  3. ncbi request reprint Codon bias signatures, organization of microorganisms in codon space, and lifestyle
    A Carbone
    Génomique Analytique, Universite Pierre et Marie Curie, INSERM U511, 91, Bd de l Hopital, 75013 Paris, France
    Mol Biol Evol 22:547-61. 2005
    ..quot; Evolutionary perspectives are noted, numerical criteria and distances among organisms are validated on known cases, and various results and predictions are discussed both on methodological and biological grounds...
  4. ncbi request reprint Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis
    Alessandra Carbone
    Génomique Analytique, Universite Pierre et Marie Curie, INSERM U511, 91 Bd de l Hopital, 75013 Paris, France
    J Mol Evol 61:456-69. 2005
    ....
  5. pmc Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling
    Stefan Engelen
    Génomique Analytique, Universite Pierre et Marie Curie Paris 6, UMR S511, Paris, France
    PLoS Comput Biol 5:e1000267. 2009
    ..JET is compared at a large scale to ET and to Consurf, Rate4Site, siteFiNDER|3D, and SCORECONS on specific structures. A significant improvement in performance and computational efficiency is shown...
  6. pmc Chromosomal periodicity and positional networks of genes in Escherichia coli
    Anthony Mathelier
    UPMC Univ Paris 06, FRE3214, Génomique Analytique, 15 rue de l Ecole de Medecine, Paris, France
    Mol Syst Biol 6:366. 2010
    ..The methodology can be applied to any set of genes and can be taken as a footprint for large-scale bacterial and archaeal analysis...
  7. pmc Large scale chromosomal mapping of human microRNA structural clusters
    Anthony Mathelier
    Universite Pierre et Marie Curie, UMR7238, 15, rue de l Ecole de Medecine, 75006 Paris, France and CNRS, UMR7238, Laboratoire de Génomique des Microorganismes, 75006 Paris, France
    Nucleic Acids Res 41:4392-408. 2013
    ..This analysis provides new fundamental insights on the genomic organization of miRNAs in human chromosomes...
  8. pmc Protein fragments: functional and structural roles of their coevolution networks
    Linda Dib
    Universite Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France
    PLoS ONE 7:e48124. 2012
    ....
  9. pmc CLAG: an unsupervised non hierarchical clustering algorithm handling biological data
    Linda Dib
    UPMC, UMR7238, Génomique Analytique, 15 rue de l Ecole de Medecine, F 75006 Paris, France
    BMC Bioinformatics 13:194. 2012
    ..Under these hypotheses, hierarchical agglomerative clustering is not appropriate. Moreover, if the dataset is not known enough, like often is the case, supervised classification is not appropriate either...
  10. doi request reprint Codon bias is a major factor explaining phage evolution in translationally biased hosts
    Alessandra Carbone
    Génomique Analytique, Universite Pierre et Marie Curie Paris 6, UMR S511, 91 Bd de l Hopital, 75013, Paris, France
    J Mol Evol 66:210-23. 2008
    ..The adaptation analysis of the set of Microviridae phages defined around phi MH2K shows that phage classification based on adaptation does not reflect bacterial phylogeny...
  11. pmc A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence
    Julie Baussand
    Génomique Analytique, Universite Pierre et Marie Curie, Paris, France
    PLoS Comput Biol 5:e1000488. 2009
    ..We apply the method to four protein families where we show an accurate detection of functional networks and the possibility to treat sets of protein sequences of variable divergence...
  12. doi request reprint MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data
    Anthony Mathelier
    UPMC Universite Paris 06, FRE3214, Génomique Analytique, Paris, France
    Bioinformatics 26:2226-34. 2010
    ..Several computational methods were developed to detect new miRNAs starting from known ones or from deep sequencing data, and to validate their pre-miRNAs...
  13. pmc New highly divergent rRNA sequence among biodiverse genotypes of Enterocytozoon bieneusi strains isolated from humans in Gabon and Cameroon
    Jacques Breton
    Unité INSERM 511, CHU Pitie Salpetriere, 91 Bd de l Hopital, 75013 Paris, France
    J Clin Microbiol 45:2580-9. 2007
    ..Phylogenetic analysis of the new genotype CAF4, identified in both HIV-negative and HIV-positive subjects, indicates that it represents a highly divergent strain...
  14. ncbi request reprint Computational prediction of genomic functional cores specific to different microbes
    Alessandra Carbone
    Génomique Analytique, Universite Pierre et Marie Curie Paris 6, INSERM U511, 91, Bd de I Hôpital, 75013, Paris, France
    J Mol Evol 63:733-46. 2006
    ..The case of small parasitic genomes is discussed. Data issued by the analysis are compared with previous computational and experimental studies. Results are discussed both on methodological and biological grounds...
  15. ncbi request reprint Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins
    J Baussand
    Génomique Analytique, INSERM UMRS511, Universite Pierre et Marie Curie Paris 6, 91, Bd de l Hopital, 75013 Paris, France
    Proteins 67:695-708. 2007
    ..A new notion, the SAD-coefficient, to assess the difficulty of structural alignment is also introduced. PHYBAL has been compared with Hydrophobic Cluster Analysis and HMMSUM methods...
  16. ncbi request reprint A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes
    Bud Mishra
    Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, New York, USA
    OMICS 7:253-68. 2003
    ....
  17. ncbi request reprint Modelling macromolecular networks: two meetings in Paris, July, 2002
    Francois Kepes
    ATelier de Génomique Cognitive, CNRS ESA8071 genopole, Evry, France
    Bioessays 24:1188-90. 2002