Julie Dawn Thompson

Institute of Genetics and Molecular and Cellular Biology (IGBMC),
Strasbourg,
France.

Education

1984                B.Sc. University of Sheffield, England
2006                PhD. University of Strasbourg, France
2007                HDR. University of Strasbourg, France

Experience

1984-1986 Vickers Shipbuilding and Engineering Limited, England
1986-1988 Singer Link Miles Limited, England
1988-1990 Rediffusion Simulation Limited, England
1991-1994 European Molecular Biology Laboratory, Germany
1995-2007 Research Engineer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), France
2007-2009 Staff Scientist, Institute of Genetics and Molecular and Cellular Biology (IGBMC), France
2009- Senior Scientist, Institute of Genetics and Molecular and Cellular Biology (IGBMC), France

Publications

Prosdocimi F, Linard B, Pontarotti P, Poch O and Thompson JD. Controversies in modern evolutionary biology: the imperative for error detection and quality control. BMC Genomics 2012 13:5.

Linard B, Nguyen NH, Prosdocimi F, Poch O and Thompson JD. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evolutionary Bioinformatics 2012 8:61-77.

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, et al. Identifying Single Copy Orthologs in Metazoa. PLoS Comput Biol 2011, 7: e1002269.

Sievers F, Wilm A, Dineen D, MacWilliam H, Remmert M, Gibson T, Karplus K, Lopez R, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011, 7:539.

Thompson JD, Linard B, Lecompte O, Poch O. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives. PLoS One 2011, 6:e18093.

Linard B, Thompson JD, Poch O, Lecompte O. OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics. 2011, 12:11.

Anamika K, Krebs AR, Thompson JD, Poch O, Devys D, Tora L. Lessons from genome-wide studies: an integrated definition of the co-activator function of histone acetyl transferases. Epigenetics & Chromatin 2010, 3:18.

Aniba MR, Poch O, Marchler-Bauer A, Thompson JD. Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res. 2010 38:7353-63.

Aniba MR, Poch O, Marchler-Bauer A, Thompson JD. AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res. 2010 38(19):6338-49.

Procter JB, Thompson JD, Letunic I, Creevey C, Jossinet F, Barton GJ. Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods 2010 7:S16-25.

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P. AQUA: Automated quality improvement for multiple sequence alignments. Bioinformatics 2010 26:263-5.

Ruano-Rubio V, Poch O, Thompson JD. Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. BMC Bioinformatics 2009 10:383.

Gouret P, Thompson JD, Pontarotti P. PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. BMC Bioinformatics 2009 10:298.

Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A. Initial Implementation of a Comparative Data Analysis Ontology. Evolutionary Bioinformatics 2009 5:47-66.

Aniba R, Candel S, Friedrich A, Plewniak F, Poch O, Marchler-Bauer A. Thompson JD. Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis. Briefings in Bioinformatics 2009 10:11-23.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics. 2007 23:2947-8.

Garnier N, Friedrich A, Bolze R, Bettler E, Moulinier L, Geourjon C, Thompson JD, Deleage G, Poch O. 2006 MAGOS: multiple alignment and modelling server. Bioinformatics. 22:2164-5.

Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K. (2006) SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr. 62:1184-95.

Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O. (2006) MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics. 7:318.

Thompson JD, Holbrook SR, Katoh K, Koehl P, Moras D, Westhof E, Poch O. (2005) MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res. 33:4164-71.

Thompson JD, Koehl P, Ripp R, Poch O. (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins. 61:127-36.

Bianchetti L, Thompson JD, Lecompte O, Plewniak F, Poch O. vALId: validation of protein sequence quality based on multiple alignment data. J Bioinform Comput Biol. 2005 3:929-47.

Chalmel F, Lardenois A, Thompson JD, Muller J, Sahel JA, Leveillard T, Poch O. (2005) GOAnno: GO annotation based on multiple alignment. Bioinformatics.

Thompson JD, Prigent V, Poch O. (2004) LEON: multiple Evaluation Of Neighbours. Nucleic Acids Res. 4:1298-1307.

Plewniak F, Bianchetti L, Brelivet Y, Carles A, Chalmel F, Lecompte O, Mochel T, Moulinier L, Muller A, Muller J, Prigent V, Ripp R, Thierry JC, Thompson JD, Wicker N, Poch O. (2003) PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res. 13:3829-3832.

Thompson JD, Thierry JC, Poch O. (2003) RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics. 9:1155-1161.

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 13:3497-3500.

Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O. (2001) Towards a reliable objective function for multiple sequence alignments. J Mol Biol. 4:937-951.

Lecompte O, Thompson JD, Plewniak F, Thierry J, Poch O. (2001) Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene. 1:17-30.

Bahr A, Thompson JD, Thierry JC, Poch O. (2001) BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res. 1:323-326.

Plewniak F, Thompson JD, Poch O. (2000) Ballast: blast post-processing based on locally conserved segments. Bioinformatics. 9:750-759.

Thompson JD, Plewniak F, Thierry J, Poch O. (2000) DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.

Nucleic Acids Res. 15:2919-2926.

Thompson JD, Plewniak F, Poch O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. J13:2682-2690.

Thompson JD, Plewniak F, Poch O. (1999) BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics. 1:87-88.

Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci. 10:403-405.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.

Birney E, Thompson JD, Gibson TJ. (1996) PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res. 14:2730-2739.

Higgins DG, Thompson JD, Gibson TJ. (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:383-402.

Thompson JD (1995) Introducing variable gap penalties to sequence alignment in linear space. CABIOS 2:181-186.

Thompson JD, Higgins DG, Gibson TJ. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.

Gibson TJ, Thompson JD. (1994) Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases. Nucleic Acids Res. 13:2552-2556.

Gibson TJ, Thompson JD, Blocker A, Kouzarides T. (1994) Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. Nucleic Acids Res. 6:946-952.

Thompson JD, Higgins DG, Gibson TJ. (1994) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci. 1:19-29.

Gibson TJ, Rice PM, Thompson JD, Heringa J. (1993) KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism. Trends Biochem Sci. 9:331-333.

Gibson TJ, Thompson JD, Heringa J. (1993) The KH domain occurs in a diverse set of RNA-binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid. FEBS Lett. 3:361-366.

Gibson TJ, Thompson JD, Abagyan RA. (1993) Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Eng. 1:41-50.