Christophe BÉCAVIN

CV Senior Bioinformatician August 2015 – Present : Institut Pasteur, Paris PostDoc fellow 2011 – 2015 : Pascale Cossart’s laboratory, Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris Phd fellow 2007 – 2010 : Institut des Hautes Etudes Scientifiques, ann Ecole Normale Supérieure, Paris Magister of Science, Theoretical Physics 2003 – 2007 : Dynamical systems and statistics of complex matter, Université Paris 7 and Université Paris 6

• Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae(Baharoglu ZEYNEP - Bacterial Genome Plasticity) - Closed
• Finding and Predicting CRISPR-Cas9 Efficiency(Jerome WONG NG - Synthetic Biology) - Closed
• Characterization of a Salmonella mutant carrying a single amino-acid substitution in the stress sigma factor RpoS(Françoise NOREL - Biochemistry of Macromolecular Interactions) - Closed

Bryan BRANCOTTE

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• BIGSdb-Pasteur web pages and design renewal(Federica PALMA - Biological Resource Center of Institut Pasteur (CRBIP)) - In Progress
• Récupération des données associées aux séquences de génomes de Klebsiella pneumoniae téléchargées du NCBI(Nicolas CABANEL - Ecology and Evolution of Antibiotics Resistance) - Pending
• Viral Host Range Databank(Laurent DEBARBIEUX - Molecular Biology of Gene in Extremophiles) - In Progress

Thomas COKELAER

I joined the Bioinformatics and Biostatistics Hub at Institut Pasteur in 2016 where I am currently developing pipelines related to NGS for the Biomics Pôle. I have an interdisciplinary research experience: after a PhD in Astronomy (gravitational wave data analysis), I joined several research institute to work in the fields of plant modelling (INRIA, Montpellier, 2008-2011), System Biology — in particular logical modelling (EMBL-EBI Cambridge, U.K., 2011-2015), and drug discovery (Sanger Institute, Cambridge, U.K.), 2015). On a daily basis, I use data analysis and machine learning techniques within high-quality software to tackle scientific problems.

• VCF filtering script(NJAMKEPO ELISABETH - Enteric Bacterial Pathogens) - Closed
• Looking for the SNPs in evolved Corynebacterium diphtheriae genomes(Sylvain BRISSE - Molecular Prevention and Therapy of Human Diseases) - Pending

Olivia DOPPELT-AZEROUAL

ONGOING PROJECTS Galaxy administration/Maintenance (https://galaxy.web.pasteur.fr) Bioweb: Future directory of bioinformatics resources at the Institut Pasteur ELIXIR Registry SKILLS Galaxy: administration, API/Bioblend expertise Programming: Python, Javascript, Lua, R, Development tools: GIT, Subversion, Emacs Database: NoSQL (couchdb), MySQL, PostgreSQL Bioinformatics: Preprocessing NGS data, MED-SuMo, Protein surface comparison, Protein functional annotation. OTHER ACTIVITIES C3BI seminars and meetings management Involved in Galaxy France Working Group (IFB) FORMER PROJECTS MetaGenSense(https://metagensense.web.pasteur.fr) Disco-Bac (https://disco-bac.web.pasteur.fr)

• Common and phylogenetically widespread coding for peptides by bacterial small RNAs – Follow up of a project regarding its journal review(Benno SCHWIKOWSKI - Systems Biology) - Closed
• A novel MacSyFinder module for detection of bacterial capsule systems on the future Galaxy platform.(Eduardo ROCHA - Microbial Evolutionary Genomics) - Closed
• Development of a web application and new functionalities for the maintenance and curation of iPPI-DB(Olivier SPERANDIO - Center for Innovation and Technological Research) - In Progress

Amine GHOZLANE

After a PhD in informatics on graph analysis (metabolic networks and sRNA-mRNA interaction graphs) at the LaBRI (Université de Bordeaux), I joined the DSIMB team (INTS) for a post-doc on structural modeling. Then, I performed a second post-doc at Metagenopolis – INRA Jouy-en-Josas, where I was initiated to the analysis of metagenomic data. I was recruited at the HUB in 2015, and since I pursue the development of methods dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, the statistics, the protein structural modeling and the graph analysis.

• Regulation of nasopharyngeal microbiome in normal healthy individuals(James DI SANTO - Innate Immunity) - Pending
• Changes in cellular pathways during SARS-CoV-2 infection upon drug treatment(Bjoern MEYER - Viral Populations and Pathogenesis) - Pending
• Identification, structural and functional analyses of peptides from SARS-Cov2 binding with high affinity to MHC-E and impact on NK cell responses in SARS-Cov2 infection(Huot NICOLAS - HIV, Inflammation and Persistence) - Pending

Kenzo-Hugo HILLION

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.

• Impact of gut microbiota on lipid metabolism(Grégoire CHEVALIER - Microenvironment and Immunity) - Closed
• Analysis of IFITM RNA levels in vraious cell types and tissues(Olivier SCHWARTZ - Virus and Immunity) - Closed
• Channels in metagenomics data(Delarue MARC - Structural Dynamics of Macromolecules) - Closed
+ 1 project

Bernd JAGLA

Bernd Jagla received his PhD in bioinformatics (department of Biology, Chemistry, and Parmacy) from the Free University in Berlin, Germany in 1999. Before joining the Institut Pasteur, he worked for almost ten years in New York City, including as an associate research scientist in the Joint Centers for System Biology (Columbia University) and at the Columbia University Screening Center led by Dr J.E. Rothman. He joined the Institut Pasteur in 2009 to take charge of the bioinformatic needs at the Transcriptome et Epigenome platform, focusing on Next Generation Sequencing. As of 2016 he is member of the C3BI – HUB Team detached to the Human immunology center (CIH) and provides support for cytometry, next generation sequencing, and microarray data analysis. His areas of interest include the quality assurance and data analysis and visualization at the facility. He also has strong expertise in developing algorithms for function prediction from sequence data, image analysis, analysis of mass spectrometry data, workflow management systems. While at Pasteur he developed: KNIME extensions for Next Generation Sequencing (Link) Post Alignment Visualization and Characterization of High-Throughput Sequencing Experiments (Link) Post Alignment statistics of Illumina reads (Link)

• A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community(Milena HASAN - Department of Immunology) - In Progress

Pierre LECHAT

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.

• Mosquito vector competence for different RVFV variants(Pei-Shi YEN - Arboviruses and Insect Vectors) - Pending
• Genome organization and synteny analysis of Yersinia pseudotuberculosis strains responsible for the Far-East Scarlatine-Like Fever(Javier PIZARRO-CERDA - Yersinia) - Pending
• Yersinomics SynTView instance deployment for 85 genomes and development of a SynTView javascript local view(Javier PIZARRO-CERDA - Yersinia) - Pending

Frédéric LEMOINE

After a Master degree in bioinformatics and biostatistics, I did a PhD in computer science / bioinformatics at University Paris-Sud (now in University Paris-Saclay), where I worked on integration and analysis of comparative genomics data. After a postdoc in Lausanne, Switzerland where I worked on small-RNA sequencing data, I joined GenoSplice where I was responsible for the development of bioinformatics projects related to next generation sequencing. I joined Institut Pasteur in Nov. 2015, to work in the Evolutionary Bioinformatics Unit and participate in the development of new tools and algorithms that are able to tackle efficiently the ever increasing amount of sequencing data.

Nicolas MAILLET

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.

• Analysis of neuronal population dynamics in rodents during virtual navigation(Christoph SCHMIDT-HIEBER - Neural circuits for spatial navigation and memory) - Pending
• Recombination among enteroviruses(Maël BESSAUD - Biology of Enteric Viruses) - Pending
• Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases(Marc ELOIT - Biology of Infection) - In Progress

Christophe MALABAT

After a PhD in biochemistry of the rapeseed proteins, during which I developed my first automated scripts for handling data processing and analysis, I join Danone research facility center for developing multivariate models for the prediction of milk protein composition using infrared spectrometry.
As I was already developing my own informatics tools, I decided to join the course of informatic for biology of the Institut Pasteur in 2007. At the end of the course I was recruited by the Institute and integrate the unit of “génétique des interactions macromoléculaires” of Alain Jacquier. Within this group, I learn to handle sequencing data and I developed processing and analysis tools using python and R. I also create a genome browser and database system for storing, retrieving and visualizing microarray data. After 8 years within the Alain Jacquier’s lab, I join the Hub of bioinformatics and biostatistics as co-head of the team.

• SHERLOCK4HAT - WP1.1(Brice ROTUREAU - Group: Trypanosome transmission) - In Progress
• Remettre les servers Genolist comme LegioList, TuberclListe, Colibri etc en service(Carmen BUCHRIESER - Biology Of Intracellular Bacteria) - Closed
• Identification of eukaryotic 5'UTRs(Arnaud ECHARD - Membrane Traffic and Cell Division) - Closed

Fabien MAREUIL

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.

• basic alignment/visualisation pipeline(Pablo NAVARRO - Epigenetics of Stem Cells) - In Progress
• Track Analyzer(Arthur MICHAUT - Morphogenesis Regulation In Higher Vertebrates) - In Progress
• Implementation of the ViroScreen workflow in Galaxy(Laurent DACHEUX - Lyssavirus Dynamics and Host Adaptation) - In Progress

Hervé MÉNAGER

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• JASS 2 : Integrating functional annotation to a multi-trait GWAS web application(HANNA JULIENNE - Statistical Genetics) - Pending
• Flemmingsome: A Midbody Remnant Proteome Database(Neetu GUPTA-ROSSI - Membrane Traffic and Cell Division) - Pending
• crispr.pasteur.fr(David BIKARD - Synthetic Biology) - Closed

Damien MORNICO

Graduated in “Structural Genomics and Bioinformatics”, I mainly worked during almost 6 years at the Genoscope (CEA) in the LABGeM team, within the microbial annotation platform MicroScope. I specifically focused on functional annotation and microbial metabolic pathways prediction and reconstruction, through pipeline implementation, database modeling and web interface development. Broadly, interactions in the MicroScope platform allowed me to tackle the whole annotation process: from genome assembly and gene prediction to network reconstruction. I also performed several comparative genomics analyses. As a member of the “Hub team”, I now take part to various projects, linked to HTS data, on different subjects (lncRNAs and stem cells, HIV integration and DNA structure, Ribosomal protein genes and genome evolution, Natural Antisense Transcripts in compact genomes…).

• Setup of bioinformatic pipelines for paleo(meta)genomics(Nicolás RASCOVAN - Department of Genomes and Genetics) - In Progress
• Multiparametric immunophenotyping of whole blood in IFN-treated multiple sclerosis patients(Priyanka DEVI - Cytokine Signaling) - Awaiting Publication
• Genomic DNA sequencing of Burkholderia ambifaria Q53 strain isolated from peanut rizospheric soil(Mathilde BEN ASSAYA - Structural Microbiology) - In Progress

Bertrand NÉRON

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)

• MacSyFinder 2.0(Eduardo ROCHA - Microbial Evolutionary Genomics) - Pending
• Move of the DISCO-BAC server VM to the new DSI infrastructure(Benno SCHWIKOWSKI - Systems Biology) - Closed
• MacSyDBCapsule(Eduardo ROCHA - Microbial Evolutionary Genomics) - Closed

Natalia PIETROSEMOLI

Dr. Natalia Pietrosemoli is an Engineer with a M. Sc. in Modeling and Simulation of Complex Realities from the International Center for Theoretical Physics, ICTP and the International School of Advanced Studies, SISSA (Triest, Italy). During her M. Sc. internships she mostly worked in modeling, optimization, combinatorics and information theory applied to medical imaging. In 2012 she got a Ph. D in Computational Biology from the School of Bioengineering of Rice University (Houston, TX, US), where she specialized in computational structural biology and functional genomics. Her doctoral thesis “Protein functional features extracted with from primary sequences : a focus on disordered regions”, contributed to a better understanding of the functional and evolutionary role of intrinsic disorder in protein plasticity, complexity and adaptation to stress conditions. As part of her Ph. D., Natalia was a visiting scholar in two labs in Madrid: the Structural Computational Biology Group at the Spanish National Cancer Research Centre (CNIO), where she mainly worked in sequence analysis and the functional-structural relationships of proteins, and the Computational Systems Biology Group at the Spanish National Centre for Biotechnology (CNB-CSIC ), where she studied the functional implications of intrinsically disordered proteins at the genomic level for several organisms, collaborating with different experimental and theoretical groups. In 2013, she joined the Swiss Institute of Bioinformatics as a postdoctoral fellow in the Bioinformactics Core Facility. Her main project consisted in the molecular classification of a rare type of lymphoma, which involved the integration of transcriptomic, clinical and mutational data for the identification of molecular markers for classification, diagnosis and prognosis. This work was performed in collaboration with the Pathology Institute at the University Hospital of Lausanne (CHUV). In November of 2015 Natalia joined the Hub Team @ Pasteur C3BI as a Senior Bioinformatician. Natalia is especially interested in the integrative analysis of different omics data, both at large-scale and for small datasets, and loves collaborating in interdisciplinary environments and having feedback from her fellow experimental colleagues. Currently, she’s coordinating several projects performing functional and pathway analysis at the genomic level. By grouping genes, proteins and other biological molecules into the pathways they are involved in, the complexity of the analyses is significantly reduced, while the explanatory power increases with respect to having a list of differentially expressed genes or proteins.

• Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms(Yves JACOB - Molecular Genetics of RNA Viruses) - In Progress
• Mitochondrial polarization identifies functionally mature human NK cells(Laura SURACE - Innate Immunity) - Awaiting Publication
• Proteomic analysis of the intracellular compartments containing Brucella abortus(Javier PIZARRO-CERDA - Yersinia) - In Progress

Najwa TAIB

Najwa has been a postdoctoral fellow funded by the PTR project OM-Nega of the Institut Pasteur. Since January 2018 she has become the permanent bioinformatician of the group as part of the Hub team C3BI of the Institut Pasteur.

Rachel TORCHET

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.

• BIGSdb-Pasteur web pages and design renewal(Federica PALMA - Biological Resource Center of Institut Pasteur (CRBIP)) - In Progress
• Page web modélisation covid-19 pasteur(Simon CAUCHEMEZ - Mathematical Modelling Of Infectious Diseases) - Pending
• French GWAS Covid webpage(Hugues ASCHARD - Statistical Genetics) - In Progress

Anna ZHUKOVA

A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, knowledge inference, ontologies and data visualisation.

• Modeling mitochondrial metabolism dormant Cryptococcus neoformans(Benjamin HOMMEL - Molecular Mycology) - Closed
• Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment(Alice MEIGNIÉ - Viral Genomics and Vaccination) - Closed
• Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation(Olivier GASCUEL - Evolutionary Bioinformatics) - In Progress