Julie D Thompson

Summary

Country: France

Publications

  1. ncbi request reprint BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
    J D Thompson
    Institut de Genetique et de Biologie Moleculaire et Cellulaire CNRS INSERM ULP, BP 163, 67404 Illkirch Cedex, France
    Bioinformatics 15:87-8. 1999
  2. pmc MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences
    Julie D Thompson
    Institut de Génétique et deBiologie Moléculaire et Cellulaire 1 rue Laurent Fries, B P 10142, 67404 Illkirch Cedex, France
    Nucleic Acids Res 33:4164-71. 2005
  3. pmc MACSIMS: multiple alignment of complete sequences information management system
    Julie D Thompson
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France
    BMC Bioinformatics 7:318. 2006
  4. pmc Controversies in modern evolutionary biology: the imperative for error detection and quality control
    Francisco Prosdocimi
    Department of Integrated Structural Biology, IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS INSERM Université de Strasbourg, 1 rue Laurent Fries, Illkirch, F 67404, France
    BMC Genomics 13:5. 2012
  5. pmc A new protein linear motif benchmark for multiple sequence alignment software
    Emmanuel Perrodou
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Department of Structural Biology and Genomics, F 67400 Illkirch, France
    BMC Bioinformatics 9:213. 2008
  6. doi request reprint Functional insights into the core-TFIIH from a comparative survey
    Florence Bedez
    Laboratoire de bioinformatique et genomique integratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS, INSERM, UDS, BP163, 67404 Illkirch Cedex, France
    Genomics 101:178-86. 2013
  7. pmc OrthoInspector: comprehensive orthology analysis and visual exploration
    Benjamin Linard
    Laboratoire de bioinformatique et genomique integratives, Département de Biologie et Génomique Structurales CNRS INSERM UDS, Institut de Genetique et de Biologie Moleculaire et Cellulaire, 1 rue Laurent Fries, 67404, Illkirch, Cedex, France
    BMC Bioinformatics 12:11. 2011
  8. pmc A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives
    Julie D Thompson
    Département de Biologie Structurale et Génomique, IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS INSERM Université de Strasbourg, Illkirch, France
    PLoS ONE 6:e18093. 2011
  9. pmc Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
    Mohamed Radhouene Aniba
    Department of Structural Biology and Genomics, Institut de Genetique et de Biologie Moleculaire et Cellulaire, The Centre National de la Recherche Scientifique, UMR7104, F 67400 Illkirch and Université de Strasbourg, F 67000 Strasbourg, France
    Nucleic Acids Res 38:7353-63. 2010
  10. pmc PipeAlign: A new toolkit for protein family analysis
    Frederic Plewniak
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM ULP, BP 10142, 67404 Illkirch Cedex, France
    Nucleic Acids Res 31:3829-32. 2003

Collaborators

Detail Information

Publications14

  1. ncbi request reprint BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
    J D Thompson
    Institut de Genetique et de Biologie Moleculaire et Cellulaire CNRS INSERM ULP, BP 163, 67404 Illkirch Cedex, France
    Bioinformatics 15:87-8. 1999
    ..BAliBASE is a database of manually refined multiple sequence alignments categorized by core blocks of conservation sequence length, similarity, and the presence of insertions and N/C-terminal extensions...
  2. pmc MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences
    Julie D Thompson
    Institut de Génétique et deBiologie Moléculaire et Cellulaire 1 rue Laurent Fries, B P 10142, 67404 Illkirch Cedex, France
    Nucleic Acids Res 33:4164-71. 2005
    ....
  3. pmc MACSIMS: multiple alignment of complete sequences information management system
    Julie D Thompson
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France
    BMC Bioinformatics 7:318. 2006
    ..Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family...
  4. pmc Controversies in modern evolutionary biology: the imperative for error detection and quality control
    Francisco Prosdocimi
    Department of Integrated Structural Biology, IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS INSERM Université de Strasbourg, 1 rue Laurent Fries, Illkirch, F 67404, France
    BMC Genomics 13:5. 2012
    ..Most gene sequences are predicted by bioinformatics programs and a number of quality issues have been raised, concerning DNA sequencing errors or badly predicted coding regions, particularly in eukaryotes...
  5. pmc A new protein linear motif benchmark for multiple sequence alignment software
    Emmanuel Perrodou
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Department of Structural Biology and Genomics, F 67400 Illkirch, France
    BMC Bioinformatics 9:213. 2008
    ..As a consequence, poor motif alignment quality is hindering efforts to detect new LMs...
  6. doi request reprint Functional insights into the core-TFIIH from a comparative survey
    Florence Bedez
    Laboratoire de bioinformatique et genomique integratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS, INSERM, UDS, BP163, 67404 Illkirch Cedex, France
    Genomics 101:178-86. 2013
    ..While little information was inferred for P8 and P62, our studies confirm the known role of P52 in repair and suggest for the first time the implication of the core TFIIH in mRNA splicing via P34...
  7. pmc OrthoInspector: comprehensive orthology analysis and visual exploration
    Benjamin Linard
    Laboratoire de bioinformatique et genomique integratives, Département de Biologie et Génomique Structurales CNRS INSERM UDS, Institut de Genetique et de Biologie Moleculaire et Cellulaire, 1 rue Laurent Fries, 67404, Illkirch, Cedex, France
    BMC Bioinformatics 12:11. 2011
    ..Various methods have been developed based on either simple blast all-versus-all pairwise comparisons and/or time-consuming phylogenetic tree analyses...
  8. pmc A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives
    Julie D Thompson
    Département de Biologie Structurale et Génomique, IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS INSERM Université de Strasbourg, Illkirch, France
    PLoS ONE 6:e18093. 2011
    ..We then propose knowledge-enabled, dynamic solutions that will hopefully pave the way to enhanced alignment construction and exploitation in future evolutionary systems biology studies...
  9. pmc Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
    Mohamed Radhouene Aniba
    Department of Structural Biology and Genomics, Institut de Genetique et de Biologie Moleculaire et Cellulaire, The Centre National de la Recherche Scientifique, UMR7104, F 67400 Illkirch and Université de Strasbourg, F 67000 Strasbourg, France
    Nucleic Acids Res 38:7353-63. 2010
    ..Finally, we propose directions for future developments that will ensure that the bioinformatics benchmarks correspond to the challenges posed by the high throughput data...
  10. pmc PipeAlign: A new toolkit for protein family analysis
    Frederic Plewniak
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM ULP, BP 10142, 67404 Illkirch Cedex, France
    Nucleic Acids Res 31:3829-32. 2003
    ..PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/...
  11. pmc LEON: multiple aLignment Evaluation Of Neighbours
    Julie D Thompson
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM ULP, BP 163, 67404 Illkirch Cedex, France
    Nucleic Acids Res 32:1298-307. 2004
    ....
  12. pmc KD4v: Comprehensible Knowledge Discovery System for Missense Variant
    Tien Dao Luu
    Laboratoire de bioinformatique et genomique integratives, Institut de Genetique et de Biologie Moleculaire et Cellulaire, 67404 Illkirch, France
    Nucleic Acids Res 40:W71-5. 2012
    ..These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at http://decrypthon.igbmc.fr/kd4v...
  13. pmc Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
    Valentin Ruano-Rubio
    Laboratoire de Biologie et Génomique Intégrative, Département de Biologie et Génomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM UdS, Illkirch, France
    BMC Bioinformatics 10:383. 2009
    ....
  14. pmc EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data
    Benjamin Linard
    Laboratoire de bioinformatique et genomique integratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS INSERM UDS, Illkirch, France
    Evol Bioinform Online 8:61-77. 2012
    ..A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes...