Work experience

LabEx Milieu Intérieur, Institut Pasteur Paris, France
Engineer, supervised by Darragh Duffy 2016 - June 2017

Sample data management system conception with data formating before implementation. Shiny (R) scripts development.

  • Sample data formating before uploading on software FreezerPro
  • Shiny (R) development to analyse gene expressions
  • Unity's Journal Club presentation (in english)
  • Python scripting and file analysis report with Jupyter
  • Work in progress reports towards research unity (in english)


UMR 946 INSERM-Université Paris Diderot Paris, France
Engineer in bioinformatics, supervised by Dr Florence Demenais May - December 2015

Common process deveropment (annotations, formating, imputations) for the different research fields of laboratory, prepare genetic data for scientific computing, literature monitoring in science and technology.

  • Interspecies compararison for melanoma using EPOs (human-dag): orthologous genes comparison
  • SNPs annotation along genes
  • Literature monitoring in science and technology for the laboratory
  • Writting documentation for scripts and processes
  • User training for scripts and processes realised


AP-HP Cochin Paris, France
Engineer in bioinformatics, supervised by Dr Marie-Françoise Avril and Dr F Demenais 2013 - April 2015

Prepare genetic data for scientific computing and common informatics processes.

  • Prepare genotypic data before imputing
  • SNPs annotation along genes
  • Recovery of orthologous genes human-dog from Ensembl
  • Functional annotation (DNAse, transciption binding site...) with UCSC Genome Browser, help interpreting data shown in function of selected database
  • Development of file formating scripts
  • Literature monitoring in science and technology for the laboratory
  • Writting documentation for scripts and processes


UMR 946 INSERM-Université Paris Diderot Paris, France
Engineer in bioinformatics, supervised by Dr Florence Demenais 2012 - 2013

Identify and use public databases, develop common processes (annotations, formating, imputations) for the different research fields of laboratory, prepare genetic data for scientific computing, literature monitoring in science and technology.

  • Identify public databases
  • Local repository on annotation of genes and SNPs from NCBI
  • SNPs annotation along genes
  • Gene pathway search (KEGG)
  • Support on existing processes
  • Script development in Bash, Perl, VBA (Excel macro)
  • Literature monitoring in science and technology for the laboratory
  • Writting documentation for scripts and processes


Centre de bioinformatique bordelais Bordeaux, France
Engineer in bioinformatics, diected by Macha Nikolski February - May 2011

Web interface development to align short peptids agains protein database for a specific organism. Show peptid sets that match with a same set of proteins and gather proteins information. Allow to determine interactions between genes and protein discovered.

  • Blast of rat's short peptides over UniProt proteins (localy)
  • Search homologous human genes with OrthoMCL and HomoloGene (NCBI)
  • For each recovered gene, show description in a web interface web : Gene (NCBI)
  • Show peptids aligned with matching proteins using MAFFT
  • Web interface developped in Perl, PHP, JavaScript, HTML, CSS

DIMNP (Dynamique des Interactions Membranaires Normales et Pathologiques) Montpellier, France
Trainee, Master 2, supervised by Pr Ovidiu Radulescu March - July 2010

Modelizing the phospholipid metabolism of Plasmodium falciparum
Mathematic approach development to modelise and explain the phospholipid metabolism of Plasmodium falciparum

  • Literature monitoring
  • Modeling with MatLab (SimBiology)

LaBRI (Laboratoire Bordelais de Recherche en Informatique) Bordeaux, France
Trainee, supervised by Pascal Desbarats June - July 2009

Website management software conception
Development of a software to help website management with a graphical interface.

  • Python, wxPython, XML, HTML

 Skills

Programming
  • Python
  • Bash
  • R
  • Perl
  • VBA
  • Java
Web technology
  • HTML
  • XML
  • Django
  • CSS
  • Shiny
  • XSLT
Database
  • CSV text
  • SQL
Bioinformatics tools
  • UCSC Genome Browser
  • MAFFT
  • BLAST
  • Galaxy
  • ClustalW
  • Rasmol
  • ImageJ
Operating system
  • GNU/Linux
  • Windows
  • Mac OS

 Training

Cancéropôle Île-de-France Paris, France
NGS & Cancer : ChIP-Seq Analysis April 2015 (3 days)

Galaxy, peak-calling, Functional and transcriptomic analysis, ChIP-Seq and RNA-Seq crossing data

 Education

Université de Bordeaux Bordeaux, France
Master degree in Biologie Santé, Bioinformatique 2008 - 2010

Functional proteomic and post-genomic, Functional genomic, Division and cell cycle, Computing ressources, Algorithmics, Programming, Database, Data Mining, Imaging


Université Victor Segalen Bordeaux II Bordeaux, France
Bachelor degree in Sciences de la Vie et de la Santé, Biologie Cellulaire et Physiopathologie 2004 - 2008

Immunology, Physiology, Biochemistry, Chemistry (organic, kinetics, enzymatics), Cellular biology (animal, plants), Microbio- logy, Genetics, Statistics

 Publications

 Articles

[1] The COL5A3 and MMP9 genes interact in eczema susceptibility. J Allergy Clin Immunol (2017 (soumis))
Margaritte-Jeannin P, Babron MC, Laprise C, Lavielle N, Sarnowski C, Brossard M, Moffat M, Gagné-Ouellet V, Etcheto A, Lathrop N, Jut J, Cookson WO, Bouzigon E, Demenais F et Dizier MH.
[2] A comprehensive analysis of melanoma Breslow thickness identifies interaction between CDC42 and SCIN genetic variants. Int J of Cancer (2016)
Vaysse A, Fang S, Brossard M, Wei Q, Chen WV, Mohamdi H, Vincent-Fetita L, Margaritte-Jeannin P, Lavielle N, Maubec E, Lathrop M, Avril MF, Amos CI, Lee JE et Demenais F.
[DOI: 10.1002/ijc.30245]
[3] Integrated pathway analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk. Int J of Cancer (2015)
Brossard M, Fang S, Vaysse A, Wei Q, Chen WV, Mohamdi H, Maubec E, Lavielle N, Galan P, Lathrop N, Avril MH, Lee JE, Amos CI et Demenais F.
[DOI: 10.1002/ijc.29570]
[4] Interaction between DNAH9 gene and early smoke exposure on bronchial hyper-responsiveness. ERJ (2015)
Dizier MH, Nadif R, Margaritte-Jeannin P, Barton S, Sarnowski C, Gagné-Ouellet V, Brossard M, Lavielle N, Just J, Lathrop M, Holloway J, Laprise C, Bouzigon E et Demenais F.
[DOI: 10.1183/13993003.00849-2015]
[5] A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults. Clin Exp Allergy (2015)
Bouzigon E, Nadif R, Thompson EE, Concas MP, Kuldanek S, Du G, Brossard M, Lavielle N, Sarnowski C, Vaysse A, Dessen P, van der Valk RJP, Duijts L, Henderson AJ, Jaddoe VWV, de Jongste JC, GABRIEL consortium, EArly Genetics & Lifecourse Epidemiology (EAGLE) Consortium, Casula S, Biino G, Dizier MH, Pin I, Matran R, Lathrop M, Pirastu M, Demenais F et Ober C.
[DOI: 10.1111/cea.12461]
[6] The nuclear factor I/A (NFIA) gene is associated with the ashma plus rhinitis phenotype. J Allergy Clin Immunol (2014)
Dizier MH, Margaritte-Jeanin P, Madore AM, Moffat M, Brossard M, Lavielle N, Sarnowski C, Just J, Cookson W, Lathrop M, Laprise C et Demenais F.
[DOI: 10.1016/j.jaci.2013.12.1074]

 Communications

[7] Network-Assisted Investigation of Signals for Genome-Wide Association Studies in Childhood-onset Asthma.
Liu Y, Brossard M, Margaritte-Jeannin P, Llinares F, Sarnowski C, Al-Shikley L, Lavielle N, Vaysse A, Dizier MH, Bouzigon E et Demenais F.
Capita Selecta in Complex Disease Analysis (CSCDA), 24-26 Nov. 2014, Liège, Belgique.
[8] Integrated pathway and gene-gene interaction analysis reveals novel candidate genes for melanoma.
Brossard M, Fang S, Vaysse A, Wei Q, Mohamdi H, Chen WV, Lavielle N, Maubec E, Avril M-F, Lathrop M, Lee JE, Amos CI, Demenais F et MDACC Melanoma Study Groups.
American Society of Human Genetics (ASHG), 18-22 Oct. 2014, San Diego, États-Unis.
[9] Combined pathway and gene-gene interaction analysis pinpoints biologically relevant genes for a major melanoma prognosis factor.
Vaysse A, Fang S, Brossard M, Mohamdi H, Chen WV, Lavielle N, Maubec E, Wei Q, Lathrop M, Avril M-F, Amos CI, Lee JE, Demenais F, MELARISK et MDACC Melanoma Study Groups.
American Society of Human Genetics (ASHG), 18-22 Oct. 2014, San Diego, États-Unis.
[10] Interactive effect between DNAH9 gene and early-life tobacco smode exposure in bronchial hyper-responsiveness.
Dizier MH, Nadif R, Margaritte-Jeanin P, Barton SJ, Gagné-Ouellet V, Sarnowski C, Brossard M, Lavielle N, Just J, Lathrop M, Holloway JW, Laprise C, Bouzigon E et Demenais F.
International Genetic Epidemiology Society (IGES), 28-30 Aug. 2014, Vienna, Autriche.
[11] Pathways and gene-gene interactions associated with melanoma risk.
Brossard M, Fang S, Vaysse A, Wai Q, Mohamdi H, Chen WV, Lavielle N, Maubec E, Avril M-F, Lathrop M, Lee JE, Amos CI, Demenais F et MDACC Melanoma Study Groups.
Meeting of the Melanoma Genetics Consortium (GenoMEL), 7-9 May 2014, Valencia, Espagne.
[12] Pathay-based analysis of genome-wide SNP data reveals new candidate genes for susceptibility to melanoma.
Brossard M, Vaysse A, Corda E, Jeannin P, Mohamdi H, Chaudru V, Lavielle N, Bressac-de Paillerets B, Avril MF, Lathrop M et Demenais F.
Annual Meeting of the American Society of Human Genetics (ASHG), 6-10 Nov. 2012, San Francisco, États-Unis.

 Miscellaneous

Web development: website management, web server managemont (Nginx), website creation (norore.fr), main developper on web application BioInfuse

Graphics: image modification, photomontage, webdesign (The Gimp, Inkscape), drawing (Krita)

Writting: blogging, short stories

Associative activities:

Active member of Giroll collective (Gironde logiciel libre, giroll.org) October 2008 - February 2012
Autor and reviewer on blog bioinfo-fr.net, since its creation Since March 2012
Editorial manager on blog bioinfo-fr.net April 2015 - Mid-October 2016
Member of RSG France-JeBiF association (Jeunes Bioinformaticiens) Since March 2013
Board member of RSG France-JeBiF association (Jeunes Bioinformaticiens) December 2013 - December 2014
December 2015 - December 2016
Active member of Parinux association Since Novembre 2016
Member of labsquare (labsquare.org) Since February 2017