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

Giovanni BUSSOTTI

Developing and evaluating bioinformatic tools for: – next generation sequencing data – genome analysis & comparison Specialties:Genome & Transcriptome Bioinformatics

• Tissue-resident stromal cell heterogeneity(Lucie PEDUTO - Stroma, Inflammation and Tissue Repair) - In Progress
• Dissecting Peptidoglycan pathways in human near-haploid cells(Martine FANTON D\'ANDON - Biology and Genetics of Bacterial Cell Wall) - Pending
• Analysis of sequencing data from a Leishmania donovani cosmid library(Pascale PESCHER - Molecular Parasitology and Signaling) - In Progress

Pascal CAMPAGNE

Initially trained in evolutionary and environmental sciences, I studied population genetics and micro-evolutionary processes in a number of postdoctoral research projects. I recently joined the C3BI-Hub at the Institut Pasteur, where I work on various aspects involving Biostatistics and the analysis of genetic data.

• Afribiota-Neuro(Pascale VONAESCH - Molecular Microbial Pathogenesis) - In Progress
• Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur(Xavier MONTAGUTELLI - Mouse Genetics) - In Progress
• Ecological evolution in Klebsiella(Juan Sebastian LOPEZ FERNANDEZ - Molecular Prevention and Therapy of Human Diseases) - In Progress

Freddy CLIQUET

One of my projects consists in developing GRAVITY, a java tool based on Cytoscape to integrate genetic variants within protein-protein interaction networks to allow the visual and statistical interpretation of next-generation sequencing data, ultimately helping geneticists and clinicians to identify causal variants and better diagnose their patients. I’m also involved in several other projects in the lab, taking part in the design of pipelines for the processing and the analysis of genomics data, including SNP arrays, whole-exome and whole-genome sequencing data. This means being confronted to the big data problematic, the unit having to manage hundreds of terabytes of genomics data. Finally, I am now analysing these data in order to identify possible causes for autism, to help clinicians with their diagnosis but also to better understand the biological mechanisms at play in this complex disease. This is done through the project aiming at understanding the genetic architecture of autism in the Faroe Islands, and also with the newly starting IMI2 European project AIMS2-Trials.

Marie-Agnès DILLIES

I obtained an engineering degree in Biomedical engineering from Université de Technologie de Compiègne (UTC) in 1989, a master degree in Control of Complex Systems from UTC in 1990, a PhD in Control of Complex Systems from UTC in 1993, a University Degree in Human Genetics from The University of Rennes 1 in 2001 and a master degree in Functional Genomics from University Paris Diderot (Paris 7) in 2002. I worked as a statistician at the Transcriptome and Epigenome Platform from 2002 to 2017, where I was responsible for the statistical analyses of the data and had an important training activity (on the campus and outside). Since 2015 I have been co-head of the Bioinformatics and Biostatistics Hub within the Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI). I am co-director of the Pasteur course Introduction to Data Analysis and co-organiser of the sincellTE summer school (a school dedicated to single cell transcriptome and epigenome data analysis). I am also co-managing the StatOmique group which gathers more than 60 statisticians from France.

• Biomarqueurs d’identification précoce du sepsis aux urgences (BIPS)(Jean-Marc CAVAILLON - Cytokines and Inflammation) - In Progress
• Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome(Sylvain BAIZE - Biology of Viral Emerging Infections) - In Progress
• Host microbiota modification by the pathogen Listeria monocytogenes(Javier PIZARRO-CERDA - Bacteria-Cell Interactions) - Closed
+ 1 project

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.

• Microbiota dysbiosis in human colon cancer(Iradj SOBHANI - Other) - Pending
• Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar and the impact during the switch from tOPV to bOPV(Patsy POLSTON - Biology of Enteric Viruses) - In Progress
• AIMyc: Analysis of the Impact of antibiotics, antifungals on the Mycobiome of allogeneic stem cell recipients.(Alanio ALEXANDRE - Molecular Mycology) - Closed

Quentin GIAI-GIANETTO

Since September 2016, I am a research engineer in the Bioinformatics and Biostatistics HUB of the Institut Pasteur and detached in the Proteomics facility. I have a PhD in Signal Processing from the Ecole Nationale Supérieure des Télécommunications de Bretagne (Telecom Bretagne) and a Master in Mathematics with a specialty in Statistical Engineering from Rennes 1 University. After my PhD, I was a research and teaching assistant in Mathematics at the Institut National des Sciences Appliquées (INSA) of Rennes, then I worked as a consultant for public local authorities in the company Ressources Consultants Finances. I started working in the field of Proteomics in October 2014 in the EDyP laboratory located in Grenoble (http://www.edyp.fr/). I have been working on the improvement of statistical analysis of bottom-up proteomics data. Today, most of the projects I work on consist of detecting changes in protein abundances using discovery-driven mass spectrometry. I am interested in the development of new methodologies to optimize proteomics data analysis pipelines, from the identification of peptides/proteins to their quantification and the interpretation of results. For this purpose, I worked on several R packages which can be downloaded from the CRAN and Bioconductor: cp4p (https://cran.r-project.org/web/packages/cp4p/index.html), imp4p (https://cran.r-project.org/web/packages/imp4p/index.html), DAPAR (http://bioconductor.org/packages/release/bioc/html/DAPAR.html) and its GUI ProStar.

• Modulation of neutrophil cytosolic proteome in GCSF-treated patients. Impact of sample treatment(Marteyn BENOIT - Molecular Microbial Pathogenesis) - In Progress

Vincent GUILLEMOT

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• Afribiota-Neuro(Pascale VONAESCH - Molecular Microbial Pathogenesis) - In Progress
• Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur(Xavier MONTAGUTELLI - Mouse Genetics) - In Progress
• Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar(Pascale VONAESCH - Molecular Microbial Pathogenesis) - In Progress

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

Gael MILLOT

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• LGP2 binds PACT to regulate RIG-I- and MDA5-mediated antiviral response(Anastassia KOMAROVA - Viral Genomics and Vaccination) - In Progress
• Comparison of matrices of antibody gene usage(Pierre BRUHNS - Antibodies in Therapy and Pathology) - Pending
• Identification of immune response signatures that correlate with therapeutic responses to TNF inhibitors using machine-learning algorithms(Lars ROGGE - Immunoregulation) - In Progress

Thomas OBADIA

Thomas is a biostatistician who holds an engineering degree in Agronomy (Agrocampus Ouest, Rennes, France). He also holds a Ph.D. in biostatistics from Université Pierre et Marie Curie for his work on the spread of nosocomial pathogens on contact networks. During his Ph.D at INSERM, he investigated how high-resolution dynamical contact data could support infection-tracing conducted using more traditional approaches in healthcare settings, e.g. routine swabbing and genetic characterization of strains detected in patients or healthcare workers. He developed a new statistical framework to test the correlation between dynamic close-proximity interaction networks and biological carriage data. While at INSERM, he also developed the R0 package for R that aimed at implementing several computation methods used in estimating reproduction parameters for emerging transmissible diseases. After working as a statistical modeller for a private company in the pharmaceutical industry, he joined the Hub in 2016 as a statistician and is now involved in the projects of the Malaria: parasites and hosts unit headed by Ivo Mueller.

• Impact des contraintes biomécanistiques sur la dynamique des macro-ouverture induits par l'EDIN de Staphylococcus aureus.(Camille MOREL - Bacterial Toxins) - In Progress
• An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe(Pei-Shi YEN - Arboviruses and Insect Vectors) - Pending
• Evaluation de la représentativité génétique d'un pool de souches(Emilie SITTERLÉ - Fungal Biology and Pathogenicity) - In Progress

Emeline PERTHAME

Since February 2017 Research engineer, Hub of Bioinformatics and Biostatistics of the C3BI, Institut Pasteur 2015-2017 Post doctoral position, team MISTIS, INRIA Grenoble Topic: Robust clustering and robust non linear regression in high dimension. Collaboration with Florence Forbes (INRIA). 2012-2015 PhD thesis in Statistics, Applied Mathematics Department of Agrocampus-Ouest, IRMAR UMR 6625 CNRS, Rennes Topic: Stability of variable selection in regression and classification issues for correlated data in high dimension. Supervisor: David Causeur (Agrocampus-Ouest, IRMAR). Education 2015 PhD thesis in Statistics, Applied Mathematics Department of Agrocampus-Ouest, IRMAR UMR 6625 CNRS, Rennes 2012 ISUP degree (Institut de Statistique de l’UPMC), Université Pierre et Marie Curie, Paris 2012 Master 2 of Statistics, Université Pierre et Marie Curie, Paris

• Determination of host response elicited by different Salmonella lifestyles(Chak Hon LUK - Dynamics of Host-Pathogen Interactions) - Pending
• Cellular plasticity during mammary gland development(HAN LI - Cellular Plasticity And Disease Modelling) - Pending
• Rainfalls and water contamination in Antananarivo over 25 years(JAMBOU RONAN - Other) - In Progress

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.

• Analyse transcriptionnelle du cellules cancéreuse intestinal vs normales après co-culture avec la bactérie associée au cancer Streptococcus gallolyticus(Ewa PASQUEREAU - Biology of Gram-Positive Pathogens) - Pending
• Functional interactomics of SKAP2(Jean-François BUREAU - Functional Genetics of Infectious Diseases) - Pending
• Genome annotation of sequenced bacteria of the Culture Collection of the Pasteur Institut(Mery PINA - Biological Resource Center of Institut Pasteur (CRBIP)) - Pending

Hugo VARET

Hugo Varet is a biostatistician engineer from the Ensai (Ecole Nationale de la Statistique et de l’Analyse de l’Information) and has been recruited by the hub of the C3BI (Center of Bioinformatics, Biostatistics and Integrative Biology) to work at the Transcriptome & Epigenome Platform. He is in charge of the statistical analyses of the RNA-Seq data produced by the platform and develops R pipelines that help in this task. One of them is named SARTools and is available on GitHub: https://github.com/PF2-pasteur-fr/SARTools.

• Defining Shigella-targeting of human lamina propria mononuclear cells using CyTOF technology(Katja BRUNNER - Molecular Microbial Pathogenesis) - Closed
• Exploring immunological mechanisms of human graft-verus-host disease after hematopoietic stem cell transplantation(Eleonora LATIS - Immunoregulation) - Closed
• Functional interactions between HP1 proteins and RNA.(Christophe RACHEZ - Epigenetic Regulation) - Closed

Stevenn VOLANT

After a diploma of statistician engineer from the Ensai (Ecole Nationale de la Statistique et de l’Analyse de l’Information) and a Ph.D in applied mathematics in the Statistics & Genome lab (AgroParisTech), I worked as a developer for the XLSTAT software. I have implemented some statistical methods such as mixture models, log-linear regression, mood test, bayesian hierarchical modeling CBC/HB, … Then I worked as a head teacher in statistics for one year. I was recruited in the Bioinformatic and biostatistic hub of the C3BI (Center of Bioinformatics, Biostatistics and Integrative Biology) in 2014, I am in charge of the statistical analysis and the development of R/R shiny pipelines.

• Afribiota-Neuro(Pascale VONAESCH - Molecular Microbial Pathogenesis) - In Progress
• MOODel: Modeling Mood Disorders(Aroldo A. DARGÉL - Perception and Memory) - In Progress
• Analyse statistique d'interactions protéine-protéine(Gouin EDITH - Bacteria-Cell Interactions) - Awaiting Publication