[Research projects]
[Teaching]
[Fellowship]
[Skills]
[Education]
[Academic activities]
[Miscellaneous]

I combines applied research related to bioinformatics for genome analysis and education / formation. My research environment feature extensive collaboration between computational and experimental scientists pursuing biological questions.

Scientific Interests: Sequencing analysis (exome / genome / targeted sequencing), cancer research, regulation of gene expression, transcriptome analysis, human genetic diseases, epigenetics.

Research projects

Please fell free to consult details about my publications, posters and presentations relative to these projects.
Since 2012, Mar. Bioinformatician specialized in NGS analysis heading Institut Curie ICGex Bioinformatics team, in the Institut Curie.
Next Genereation Sequencing bioinformatics team manager. 		Paris
(France)
    Responsibilities
  • Organize and direct the bioinformatics team of ICGex to support Institut Curie's efforts towards personalization of cancer care
  • Provide state-of-the-art NGS data analysis expertise
  • Define innovative analysis strategies, from raw data to biological interpretation, in close collaboration with the core bioinformatics unit, the genetic groups and other stakeholders
  • Liaising between clinical and research staff in multiple sites
  • Provide guidance and support
  • Participate in defining standards for NGS data management in clinical context

    Technologies used at the NGS platform
  • 1 HiSeq 2500
  • 1 HiSeq 2000
  • 1 MiSeq
  • 2 Ion PGM
  • 1 Ion Proton
2010, Mar. to 2012, Mar. Postdoctoral fellowship in the Centre for Molecular Medicine and Therapeutics (CMMT), in Dr. Wyeth W. Wasserman lab.
Exome analysis and identification of regulatory variation.
... More details...
Supervisor: Dr. Wyeth W. Wasserman 		Vancouver, BC
(Canada)
2006, Oct. to 2010, Jan.

3 years & 4 months		 Ph.D. student in bioinformatics at the Plant Genomics Research Unit (URGV), INRA UMR 1165, UEVE, in the Bioinformatics team.
Relationship between Arabidopsis thaliana regulatory element organization, gene function and gene expression: toward the regulatory element annotation.
... More details...
Supervisors: Dr. Alain LECHARNY and Dr. Véronique BRUNAUD
 Evry
(France)
2004, Sept. to 2006 Aug.
2 years		 Trainee in bioinformatics at the Plant Genomics Research Unit (URGV), INRA UMR 1165, CNRS UMR 8114, UEVE, in the Bioinformatics team.
In silico research of motifs involved in the regulation of Arabidopsis thaliana gene expression.
... More details...
Supervisor: Dr. Véronique BRUNAUD
 Evry
(France)
2004, March to Aug.
5 months		 Internship in bioinformatics at the Biotechnology, Biocatalysis and Bioregulation Unit (U3B), CNRS UMR 6204, in the Biocatalysis team.
Investigation of the structure in thumb-shaped loop from Thermobacillus xylanilyticus that controls the access to the catalytic cleft.
... More details...
Supervisor: Pr. Vinh TRAN 		Nantes
(France)
2003, June to Aug.
3 months		 Internship in bioinformatics in the Pitié-Salpêtrière Hospital, at the Laboratory of Molecular Genetics of Neurotransmission (LGN), CNRS UMR 7091. Development of a database on gene regulatory network.
... More details...
Supervisor: Dr. Aurélien MAZURIE 		Paris
(France)
2002 April to Aug.
4 months		 Internship in molecular genetics at the Edouard Herriot Hospital (HEH) at the genetics laboratory.
MeCP2 mutations screening in patients with mental retardation.
... More details...
Supervisor: Dr. Gaëtan LESCA
 Lyon
(France)

Teaching

I was a teaching assistant in France from 2007 to 2010.
Please feel free to view my Teaching page for more details.

Fellowship

2010 Travel Award: ICRH's 2010 Young Investigators (YI) Forum (YI forum), Vancouver, BC, Canada, 2010 May 5th to 7th Funded by the Canadian Institutes of Health Research - Institute of Circulatory and Respiratory Health
(CIHR ICRH)
2009 Travel Award: The 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 7th Annual European Conference on Computational Biology (ISMB / ECCB), Stockholm, Sweden, 2009, June 27 to July 2 Funded by the French Genetics Society (SFG)
2006-2009 MENRT grant: Scholarship for a three-year doctoral program Funded by the French Ministry of National Education, Research and Technology

Skills

Computational Statistics R software: Datamining
Development languages PERL (CGI, DBI), C, JAVA
Web CSS, PHP, HTML, XML
Office automation Microsoft Office, Open Office
Operating Systems Linux, MAC, Windows
Database management system Oracle, Postgres, mySQL
Language French Mother tongue
English Fluent
German Basic

Education

2006 to 2009 Ph.D. degree in bioinformatics Evry University (France)
Doctoral School "From genomes to Organisms" (GAO)
2004 to 2006 M.Sc. BioInformatics, awarded with distinction, 1st/12 Rouen University (France)
EGOISt, a two years apprenticeship course: Bioinformatics and Statistics Tools for Genome Analysis.
2002 to 2004 B.Sc. in Bioinformatics Paris 7 University - Jussieu (France)
Specialization: Multifactorial analysis.
2000 to 2002 DUT (two-year university degree in technology) in Biology Angers University (France)
Specialization: Biological and Biochemical Analysis.

Training

2014, Jun. 30th-Jul. 1st Manage your time and priorities Philippe Belpaeme - Sud Performance
2014, Apr. 9th-10th Handle conflicts Philippe Belpaeme - Sud Performance
2013, Feb. 25th Communication skills appropriate to different interviews Philippe Belpaeme - Sud Performance
2012, Dec. 9th-10th How to manage a unit, a team, a department with regards to research and human aspirations Philippe Belpaeme - Sud Performance
2010, Oct. 28th Orientation Day for Postdoctoral Fellows Postdoctoral Fellows Office, UBC
2010, Oct. 7th pdf Career Day UBC, Medical Genetic Dept.
2009, Apr., 20th to 24th pdf Data analysis (french) Doctoral School MNHN
2009, Mar. 2nd to 6th Doctoriales seminar Doctoral School GAO formation
2008, May 19th to 23rd Réflexives®
For preparing a PhD and for training young scientists: the supervisor-student model		 INRA formation
2007, Nov. "How to construct a career in Europe" INRA formation
2007, Feb. pdf Control of gene expression in Eukaryotes (french) Doctoral School GAO formation
2006, Jun. 9th Exceptional motifs in genomes - R'MES tool use INRA formation - by Dr. Sophie Schbath
2006 - 2007 English Doctoral School GAO formation
2006, Apr. 27th to 28th Identification of non-coding functional regions in genome INSERM formation

Academic activities

Program committees / organizing committees
Associative implication
RSG-France (JeBiF) association
2009-2011: In the board of directors;
2010 (1 year): Secretary.
Association of Bioinformatics M.Sc. students - Paris 7 University (AMBI)
Since 2010: In the board of directors;
2008 to 2009 (2 years): President of the Association.
  • 2011 : Establishment of an mentoring project for Master2 students;
  • Establishment of an annual meeting for B.Sc. and M.Sc. students : graduate student presentation and round table.
    Main objective: counseling improvement;
  • Graduate student follow-up;
  • Newspaper.
Scientific popularization

Miscellaneous

Memberships of professional organisations
  • Since 2009: The French Regional Student Group, a young computer scientist association (RSG-France (JeBiF))
  • Since 2007: Association of Bioinformatics M.Sc. - Paris 7 University (AMBI)
  • Since 2008: International Society for Computational Biology (ISCB)
  • Since 2008: International Society for Computational Biology Student Council (ISCB student council)
  • Since 2008: French Bioinformatics Society (SFBI)
  • 2008-2010: French Genetics Society (SFG)
  • 2008-2009: French Vegetal Biology Society (SFBV)
Hobbies Games playing Board games, strategy games
Sport Hiking, trekking, skiing, volleyball, swimming
Creative leisure
Cooking

My referees

Please feel free to view my referees to have a look to their coordinates.