Affiliation: Institut des Hautes Etudes Scientifiques
- Circuits and programmable self-assembling DNA structuresAlessandra 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...
- Codon adaptation index as a measure of dominating codon biasA 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...
- Codon bias signatures, organization of microorganisms in codon space, and lifestyleA 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..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...
- Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysisAlessandra 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....
- Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence samplingStefan 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...
- Chromosomal periodicity and positional networks of genes in Escherichia coliAnthony 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...
- Large scale chromosomal mapping of human microRNA structural clustersAnthony Mathelier
Universite Pierre et Marie Curie, UMR7238, 15, rue de l Ecole de Medecine, 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...
- Protein fragments: functional and structural roles of their coevolution networksLinda Dib
Universite Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France
PLoS ONE 7:e48124. 2012....
- Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary informationAnne Lopes
Universite Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France CNRS, UMR 7238, Laboratoire de Génomique des Microorganismes, Paris, France
PLoS Comput Biol 9:e1003369. 2013..Download site: http://www.lgm.upmc.fr/CCDMintseris/ ..
- CLAG: an unsupervised non hierarchical clustering algorithm handling biological dataLinda 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...
- Codon bias is a major factor explaining phage evolution in translationally biased hostsAlessandra 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...
- A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergenceJulie 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...
- MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing dataAnthony 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...
- New highly divergent rRNA sequence among biodiverse genotypes of Enterocytozoon bieneusi strains isolated from humans in Gabon and CameroonJacques 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...
- Computational prediction of genomic functional cores specific to different microbesAlessandra 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...
- Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteinsJ 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...
- A sense of life: computational and experimental investigations with models of biochemical and evolutionary processesBud 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....
- Modelling macromolecular networks: two meetings in Paris, July, 2002Francois Kepes
ATelier de Génomique Cognitive, CNRS ESA8071 genopole, Evry, France
Bioessays 24:1188-90. 2002