T Schiex

Summary

Affiliation: Institut National de la Recherche Agronomique
Country: France

Publications

  1. pmc Integrating alternative splicing detection into gene prediction
    Sylvain Foissac
    Unité de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan, France
    BMC Bioinformatics 6:25. 2005
  2. ncbi request reprint CARTHAGENE: constructing and joining maximum likelihood genetic maps
    T Schiex
    Institut National de la Recherche Agronomique, Castanet Tolosan, France
    Proc Int Conf Intell Syst Mol Biol 5:258-67. 1997
  3. ncbi request reprint CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping
    Simon de Givry
    INRA, Biométrie et Intelligence Artificielle Génétique Cellulaire, BP 27, 31326 Castanet Tolosan Cedex, France
    Bioinformatics 21:1703-4. 2005
  4. pmc FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
    Thomas Schiex
    Unité de Biométrie et Intelligence Artificielle, INRA, CNRS INRA, 31326, Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:3738-41. 2003
  5. ncbi request reprint A comparative genome approach to marker ordering
    T Faraut
    Laboratoire de génétique cellulaire BP 52627, 31326 Castanet Tolosan, France
    Bioinformatics 23:e50-6. 2007
  6. pmc LeARN: a platform for detecting, clustering and annotating non-coding RNAs
    Celine Noirot
    Laboratoire Interactions Plantes Micro organismes UMR441 2594, INRA CNRS, F 31320 Castanet Tolosan, France
    BMC Bioinformatics 9:21. 2008
  7. pmc Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
    Etienne Pascal Journet
    Laboratoire de Biologie Moleculaire des relations Plantes Microorganismes, CNRS INRA, Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan Cedex, France
    Nucleic Acids Res 30:5579-92. 2002
  8. doi request reprint Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
    Pierre Abad
    INRA, UMR 1301, 400 Route des Chappes, F 06903 Sophia Antipolis, France
    Nat Biotechnol 26:909-15. 2008
  9. pmc Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
    Sébastien Aubourg
    Unité de Recherche en Génomique Végétale URGV, UMR INRA 1165 CNRS 8114 UEVE, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    BMC Genomics 8:401. 2007
  10. pmc EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences
    Sylvain Foissac
    Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326, Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:3742-5. 2003

Detail Information

Publications16

  1. pmc Integrating alternative splicing detection into gene prediction
    Sylvain Foissac
    Unité de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan, France
    BMC Bioinformatics 6:25. 2005
    ..Despite considerable progresses in term of accuracy in computational gene prediction, the ability to reliably predict AS variants when there is local experimental evidence of it remains an open challenge for gene finders...
  2. ncbi request reprint CARTHAGENE: constructing and joining maximum likelihood genetic maps
    T Schiex
    Institut National de la Recherche Agronomique, Castanet Tolosan, France
    Proc Int Conf Intell Syst Mol Biol 5:258-67. 1997
    ..In both cases, it compares quite favorably with existing softwares as far as maximum likelihood is considered as a significant criteria...
  3. ncbi request reprint CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping
    Simon de Givry
    INRA, Biométrie et Intelligence Artificielle Génétique Cellulaire, BP 27, 31326 Castanet Tolosan Cedex, France
    Bioinformatics 21:1703-4. 2005
    ..Dedicated heuristics for framework mapping are also included. CAR(H)(T)A GENE: can be used as a C++ library, through a shell command and a graphical interface. The XML output for companion tools is integrated...
  4. pmc FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
    Thomas Schiex
    Unité de Biométrie et Intelligence Artificielle, INRA, CNRS INRA, 31326, Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:3738-41. 2003
    ..The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms...
  5. ncbi request reprint A comparative genome approach to marker ordering
    T Faraut
    Laboratoire de génétique cellulaire BP 52627, 31326 Castanet Tolosan, France
    Bioinformatics 23:e50-6. 2007
    ..The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering...
  6. pmc LeARN: a platform for detecting, clustering and annotating non-coding RNAs
    Celine Noirot
    Laboratoire Interactions Plantes Micro organismes UMR441 2594, INRA CNRS, F 31320 Castanet Tolosan, France
    BMC Bioinformatics 9:21. 2008
    ....
  7. pmc Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
    Etienne Pascal Journet
    Laboratoire de Biologie Moleculaire des relations Plantes Microorganismes, CNRS INRA, Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan Cedex, France
    Nucleic Acids Res 30:5579-92. 2002
    ..These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface...
  8. doi request reprint Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
    Pierre Abad
    INRA, UMR 1301, 400 Route des Chappes, F 06903 Sophia Antipolis, France
    Nat Biotechnol 26:909-15. 2008
    ..Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies...
  9. pmc Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
    Sébastien Aubourg
    Unité de Recherche en Génomique Végétale URGV, UMR INRA 1165 CNRS 8114 UEVE, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    BMC Genomics 8:401. 2007
    ..We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models...
  10. pmc EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences
    Sylvain Foissac
    Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326, Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:3742-5. 2003
    ..The current target of EUGENE'HOM is plant sequences. The EUGENE'HOM web site is available at http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl...
  11. doi request reprint Contribution of radiation hybrids to genome mapping in domestic animals
    T Faraut
    INRA, Laboratoire de Génétique Cellulaire and Biométrie et Intelligence Artificielle, Castanet Tolosan, France Thomas faraut toulouse inra fr
    Cytogenet Genome Res 126:21-33. 2009
    ..Finally, current applications of radiation hybrid mapping in the context of whole genome assemblies will be described...
  12. ncbi request reprint Searching RNA motifs and their intermolecular contacts with constraint networks
    P Thebault
    Unité de Biométrie and Intelligence Artificielle, INRA, Chemin de Borde Rouge Auzeville, BP 52627, 31326 Castanet Tolosan, France
    Bioinformatics 22:2074-80. 2006
    ..Even if several programs exist for RNA motif search, none exists that can represent and solve the problem of searching for occurrences of RNA motifs in interaction with other molecules...
  13. ncbi request reprint Rearranged gene order between pig and human in a QTL region on SSC 7
    Olivier Demeure
    Laboratoire de Genetique Cellulaire, INRA, BP 27, 31326 Castanet Tolosan, France
    Mamm Genome 14:71-80. 2003
    ..000 rads panel. The rearranged fragment contains two microsatellites found at the most likely QTL location in the INRA QTL experiment. It also contains the BMP5 gene, which, together with CLPS, could be considered as a possible candidate...
  14. pmc Current methods of gene prediction, their strengths and weaknesses
    Catherine Mathe
    Institut de Pharmacologie et Biologie Structurale, UMR 5089, 205 route de Narbonne, F 31077 Toulouse cedex, France
    Nucleic Acids Res 30:4103-17. 2002
    ..Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered...
  15. pmc Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
    Steven B Cannon
    Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 103:14959-64. 2006
    ..Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar)...
  16. pmc High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly
    Aparna Prasad
    Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G2P5, Alberta, Canada
    BMC Genomics 8:310. 2007
    ..1). We have chosen BTA19 and 29 as candidate chromosomes for mapping, since many Quantitative Trait Loci (QTL) for the traits of carcass merit and residual feed intake have been identified on these chromosomes...