Members

Hub Members

ALPS

Pierre LECHAT

Group : ALPS - Hub Core

I have been involved in genomic projects for prokaryotic and human genetic studies (GWAS) since 1998. Currently, I am working on novel visualization techniques to explore large and highly complex data sets. I have develop a web based graphical user interface, called SynTView (http://genopole.pasteur.fr/SynTView/) to visualize biological features in comparative genomic studies. The tool allows interactive visualization of microbial genomes to investigate massive amounts of information efficiently. The software is characterized by the presentation of synthetic organisations of microbial genomes and the visualization of polymorphism data. I am extending this work into designing novel dynamic views for comparative analysis of viruses in emerging disease.


Keywords
Data VisualizationDatabaseSofware development and engineeringComparative metagenomicsOrthology and paralogy analysis
Organisms

Projects (20)

Nicolas MAILLET

Group : ALPS - Embedded : Structural Virology

After a PhD in bioinformatics at Inria/IRISA, Université de Rennes 1, Rennes (France), under the supervision of Dominique Lavenier and Pierre Peterlongo, I did a postdoc in bioinformatics at Laboratory of Ecology and Evolution of Plankton in Stazione Zoologica Anton Dohrn of Naples, Italy. Both my thesis and my postdoc were about the Tara Oceans projet and the development of new software to analyze huge quantities of raw reads coming from metagenomics sample. I am currently occupying a research engineer position at the Hub as leader of ALPS group and focus on several different computing problems including metagenomics, protein assembly and several short term developments.


Keywords
AlgorithmicsData managementProteomicsDatabaseProgram developmentScientific computingSofware development and engineeringComparative metagenomics
Organisms

Projects (8)

Bertrand NÉRON

Group : ALPS - Hub Core

Activities Contact for any subject related to IFB. Help scientists to develop new tools (architecture, design, implementation). animate the Python Working Group at pasteur . O|B|F (http://www.open-bio.org/) member. Skills Strong programming experience in Python. Software architecture and design. NoSQL DataBase (MongoDB, CouchDB) XML/YAML continuous integration (github/travis-CI/readthedocs, gitlab/gitlab-CI) containers (Docker, Singularity) linux (Gentoo, Xubuntu) IFB developer Main projects on the campus Mobyle http://Mobyle.pasteur.fr Mobyle: a new full web bioinformatics framework IntegronFinder (ongoing project) MacsyFinder (ongoing project) githubaccess to my projects on github Teaching Unix (Unix-I , Unix-II) Python . Education 2002 Phd in Molecular and cellular biology. “Rôle de deux protéines QN1 et PATF impliquées dans l’arrêt de prolifération des cellules de la neurorétine aviaire au cours du developpement”. 2001 “Informatique En Biologie” course (Pasteur)


Keywords
Data managementDatabaseProgram developmentScientific computingDatabases and ontologies
Organisms
Non applicable
Projects (11)

WINTER

Kenzo-Hugo HILLION

Group : WINTER - Hub Core

After a Master degree in Genetics at Magistère Européen de Génétique, Paris Diderot, I did a second Master in bioinformatics at University of Nantes where I focused my work on the study of mapping strategy for allele specific analysis at the bioinformatics platform of Institut Curie. I then joined Institut Pasteur to work on an ELIXIR project related to the bio.tools registry through the development of a dedicated tool and the participation of several workshops and hackathons. As an engineer of the bioinformatics and Biostatistics Hub, I am involved in several projects from Differential Analysis of RNA-seq data to Metagenomics. I am also in charge of the maintenance of the Galaxy Pasteur instance.


Keywords
ChIP-seqEpigenomicsGenomicsSequence analysisProgram developmentDatabases and ontologiesSofware development and engineeringGeneticsData integrationRead mappingWorkflow and pipeline developmentConfocal Microscopy
Organisms

Projects (4)

Fabien MAREUIL

Group : WINTER - Hub Core

After a Master degree in Genome Analysis and Molecular Modeling at Denis Diderot University, I did a PhD in NMR / bioinformatics at Denis Diderot University, where I worked on the development and use of a software named DaDiModO which uses SAXS data and RDC/NMR data to calculate models of structural proteins. After a postdoc aiming to adapt ARIA software to allow execution on computing grid in the Structural Bioinformatic Team at Institut Pasteur in collaboration with IBCP, I joined CIB/DSI Team where I was responsible for the development of bioinformatics projects and the deployment, maintenance and evolution of the Pasteur Galaxy server. I joined the Hub/C3BI team in 2017 as research engineer where I’m involved in several projects such as structural bioinformatics, softwares and web development. I am also in charge of the maintenance of the Galaxy Pasteur instance.


Keywords
Data managementStructural bioinformaticsDatabaseProgram developmentScientific computingDatabases and ontologiesGrid and cloud computing
Organisms
Non applicable
Projects (9)

Rachel TORCHET

Group : WINTER - Hub Core

In 2012 I completed my master degree at the MicroScope Platform located at Genoscope (the French National Sequencing Center). I was involved in a project aiming at the management of evolution projects which rely on the Next Generation Sequencing (NGS) technologies to try to decipher the dynamics of genomic changes as well as the molecular bases and the mechanisms underlying adaptative evolution of micro-organisms (Remigi et al. 2014). Since November 2014, I joined the Bioinformatics and Biostatistics HUB at Institut Pasteur. I participated to the creation and updates of the C3BI website. I joined the WINTER group where I’m in charge of web and interface development projects. I have completed an UX-Design training to add extra value to my front-end development skills. I design and develop bioinformatics tools and interfaces that are users oriented.


Keywords
Data VisualizationWeb developmentDatabaseGenome analysisScientific computingDatabases and ontologiesSofware development and engineeringWorkflow and pipeline development
Organisms

Projects (5)