Emmanuel Quevillon Bioinformatic Applications Developper / Data & Database Manager 15 years experience in bioinformatics applications development
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Contacts	Background	Training	Publications	Skills	Other
Contact Name Emmanuel Surname Quevillon Status Married Born June 18th 1976 Nationality French Phone mobile: +33(0) 6 03 44 32 86 (all day) work: +33(0) 1 44 38 95 98 (work time)   Email Url horkko.free.fr
Background 04/07-today Co-head of Tools & Data group, Institut Pasteur Paris Biological databanks resources manager using BioMAJ. https://biomaj.it.pasteur.fr Official tester for new BioMAJ3 (GitHub) Database manager (PostgreSQL). Team: Centre Informatique pour la Biologie / DSI Contact: Michael Pressigout (email). Bioinformatic applications developper, Institut Pasteur Paris Team: Centre Informatique pour la Biologie Contact: Michael Pressigout (email). Web applications and databases development demultiplex : Automatic demultiplex tool for Illumina FASTQ pipeline analysis dbNucleus : An application for genetical diseases such as Autism, Dyslexia ... BiblioList : Litterature curation tool for annotated organisms Bioinformatics tools CIF : A tool to cut DNA and stay in frame dbmaint : Tool that maintains, formats and index databanks PairedEnd : PairedEnd overlapping sequences searcher Maintenance and support GBrowse: Help, support, installation, development for viewing NGS data using GBrowse dbmaint: Daily checks, installs and updates for databanks needed for biologists at Institut Pasteur. 06/05-04/07 Bioinformatic applications developper, URGI Contact: Marc-Henri Lebrun (marc-henri.lebrun@versailles.inra.fr) & Joelle Amselem (joelle.amselem@versailles.inra.fr) Development of an automatic annoation pipeline for fungal genomes. Perl Oriented objects parser and loader for GMOD tools (GBrowse, chado). Database development for storing, viewing and editing gene and protein annotations Bioinformatic consulting for BayerCropScience. Functional annotation of the fungi Magnaporthe grisea and set up of GMOD tools. 10/02-05/05 Bioinformatic applications developper, European Bioinformatics Institute (EBI) Team: external services group. Contact:Rodrigo Lopez (rls@ebi.ac.uk) & Nicky Mulder (mulder@ebi.ac.uk). Application Development InterProScan : InterPro Protein domains identifier (Perl standalone version) PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees. Web application for FTP log report Maintenance and support Manager of interproscan mailing list (interhelp at ebi dot ac dot uk). Maintainance and support of bioinformatics applications, data updates/integrations,... Course EMBOSS: Bioinformatics Software Development Course (BSDC 2004), 2-4 nov 2004. 09/01-09/02 Bioinformatic developper, Institut Pasteur Team: Genopole, Plateau Technique 4, Intégration et analyse génomique. Contact:Ivan Moszer (moszer@pasteur.fr) Software and database devlopement Desing and settling of a multiorganisms database (Genolist) and its web interface. 12/99-07/01 Master internship, Bio-analyst Institut Pasteur Team: Laboratory of signalisation immunoparasitaire (LSI) (URA 1960). Contact: Gordon Langsley (langsley@pasteur.fr). Comparative bioinformatic Identification of new genes family (see Publications) in Theileria and Plasmodia apicomplex.
Training 1999-2001 Bioinformatic post Master's degree (Professional Bioinformatic Master), University of Rouen, 4th over 17. 1998-1999 Cellular and Molecular Biology post Master's degree (DEA), University of Grenoble. 1997-1998 4th year at university in Biochemistry and Molecular Biology (Maîtrise), University of Rouen, B average. 1996-1997 3rd year at university in Biochemistry(Licence), University of Rouen, B average. 1994-1996 Technicological Diploma of University of Applied Biology (DUT de biologie appliquées), University of Rouen, B average. 1993-1994 Baccalauréat D, College Jeanne d'Arc, Rouen.
Skills    Informatics Algorithms Sorting Pattern search Dynamic programing Modeling UML XML Object oriented programing Databases (Sybase, PostgreSQL, MySQL) Web application (MVC): Perl Catalyst & DBIx::Class Python Bottle: Python web framework Computing Newbie system administration (Linux) Database administration (PostgreSQL) System/Software updates Newbie network administration (Linux) Languages Perl Python C/C++ Java Unix shells Sed/Awk AJAX/Javascript SQL(PostgreSQL, MySQL, Sybase)  Bioinfomatics Softwares Alignment Blast(Wu & NCBI), FastA Multiple alignment ClustalW, Dialign, Multalign, Mafft, SAM Phylogeny PHYLIP Statistics StatGraphics, Splus Statistics Hidden Markov Models AFC Applications Interfaces human/machine Tools (InterProScan,Pandit, ...) Support  Biology Molecular biology RFLP PCR Cloning Microbiology (strain identification, ...) Biochemistry Western blot HPLC Ions exchange chromatography
Publications 2011 Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quevillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collemare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Guldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuveglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Segurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 2011 Aug;7(8):e1002230. Epub 2011 Aug 18. 2007 Lizundia R, Chaussepied M, Naissant B, Masse GX, Quevillon E, Michel F, Monier S, Weitzman JB, Langsley G. The JNK/AP-1 pathway upregulates expression of the recycling endosome rab11a gene in B cells transformed by Theileria. Cell Microbiol. 2007 Aug;9(8):1936-45. Epub 2007 Mar 26 Quevillon E, Dominguez Del V, Fillinger S, Giraud C, Legeai F, Levis C, Luyten I, Pommier C, Pradier J.M, Reboux S, Rouxel T, Simon A, Viaud M, Lebrun M.H, Amselem J. Setup of a fungal genomic annotation platform JOBIM 2007, Marseille France (Poster). 2006 Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D327-31. 2005 E Quevillon, V Silventoinen, S Pillai, N Harte, N Mulder, R Apweiler, R Lopez InterProScan: protein domains identifier. Nucleic Acids Res. 2005 Jul 1;33:W116-20 BOOK : Focus On Genome Research (Clyde R. Williams) (ISBN 1590339606) Chapter V : InterPro-Predictions of Protein Families, Domains and Functionl Site. p169-204, Nova publishers Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH. InterPro, progress and status in 2005. Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D201-5. 2004 Harte N, Silventoinen V, Quevillon E., Robinson S., Kallio K., Fustero X., Patel P., Jokinen P., Lopez R.; European Bioinformatics Institute. Public web-based services from the European Bioinformatics Institute. Nucleic Acids Research. 2004 Jul 1;32(Web Server issue):W3-9. Quevillon E., Silventoinen V., Servant F., Zdobnov E., Lopez R. and Apweiler R. InterProScan : Protein domain wrapper identifier. JOBIM 2004, Montreal Canada (Poster).  Abstract. 2003 Lopez R., Robinson S., Kibria A., Harte N., Patel G., Harper R., Quevillon E., Silventoinen V., Kallio K., Jokinen P. The European Bioinformatics Institute web site: a new view. Bioinformatics. 2003 Mar 1;19(4):546-7. Quevillon E., Spielmann T., Brahimi K., Chattopadhyay D. and Langsley G. (2003) The Plasmodium falciparum family of Rab GTPases. Gene 2003 March 13; 306: 13-25. Quevillon E., Servant F. and Zdobnov E. InterProScan : Standalone Perl based version 3.3. EBI retreat, Wales, England (Talk). 2002 Quevillon E., Leroch A., Jones L., Moszer I. And Danchin A. MultiList : La nouvelle base de données GenoList. JOBIM 2002, Saint-Mâlo, France (Poster).  Abstract.
General Other Driving licence A+B Sports: Diving (CMAS 2), Capoeira, Motorcycle Language: French(mother tongue), English(Fluent)

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