Thomas BIGOT

I joined the C3BI Hub in 2016 after a curriculum widely dedicated to Bioinformatics studies, and more precisely to Phylogeny and Evolution, topics of my PhD thesis. At Institut Pasteur, I am involved in projects dealing with sequences homology : alignments, hmm profiles, making homologous family databases, kmers signatures. I am also a developer (Python / C++) with a solid interest in optimization as well as in developing usable tools for final user such as automated pipeline for metagenomics sequence analysis. I’m currently embedded in Marc Eloit’s team (80% of my work time). My main task in this team is to develop strategies to identify, in their metagenomics samples, new pathogens, or new combination pathogen / symptoms. The rest of my time, I manage small projects and participate to the Hub life. I am currently experimenting with functional programming (for now, using Python) and its applicability to bioinformatics issues.

• DNMT and RNMT in Leishmania(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress
• Targetting the function of a hypothetical protein(Dariusz CZERNECKI - Structural Dynamics of Macromolecules) - Pending
• Defective interfering viral genomes of shrimps' viruses(Anastassia KOMAROVA - Viral Genomics and Vaccination) - Awaiting Publication

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.

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

Yoann DUFRESNE

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• Assessing the integrations of viral sequences into the genomes of Aedes albopictus and Aedes aegypti(Vincent HOUÉ - Arboviruses and Insect Vectors) - Pending
• Implémentation d’un algorithme rapide de génotypage cgMLST(Valérie BOUCHEZ - Molecular Prevention and Therapy of Human Diseases) - In Progress
• characterization of RNA virus populations from untargeted NGS in natural infections samples(Etienne SIMON-LORIERE - Evolutionary Genomics of RNA viruses) - Closed

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

Etienne KORNOBIS

After a PhD in Biology in 2011 on population genetics and phylogeography on amazing little amphipods (Crangonyx, Crymostygius) at the University of Reykjavik (Iceland), I pursued my interest in Bioinformatics and Evolutionary Biology in various post-docs in Spain (MNCN Madrid, UB Barcelona). During this time, I investigated transcriptomic landscapes for various non-model species (groups Conus, Junco and Caecilians) using de novo assemblies and participated in the development of TRUFA, a web platform for de novo RNA-seq analysis. In July 2016, I integrated the Revive Consortium and the Epigenetic Regulation unit at Pasteur Institute, where my main focus were transcriptomic and epigenetic analyses on various thematics using short and long reads technologies, with a special interest in alternative splicing events detection. I joined the Bioinformatics and Biostatistics Hub in January 2018. My latest interests are long reads technologies, alternative splicing and achieving reproducibility in Bioinformatics using workflow managers, container technologies and literate programming.

• Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing(allemand ERIC - Epigenetic Regulation) - In Progress
• Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets(Catherine BOURGOUIN - Functional Genetics of Infectious Diseases) - In Progress
• Mapping of Enhancers from transcriptome data(Christian MUCHARDT - Epigenetic Regulation) - In Progress

François LAURENT

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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

Rachel LEGENDRE

Rachel Legendre is a bioinformatics engineer. She completed her master degree in apprenticeship for two years at INRA in Jouy-en-Josas in the Genetic Animal department. She was involved in a project aiming at the detection and the expression analysis of micro-RNA involved in an equine disease. In 2012, she joined the Genomic, Structure and Translation Team at Paris-Sud (Paris XI) university. She worked principally on Ribosome Profiling data analysis, a new technique that allows to identify the position of the ribosome on the mRNA at the nucleotide level. Since november 2015, she worked at Institut Pasteur. During 4 years, she was detached to the Biomics Platform, where she was in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She was also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics. Since november 2019, she has joined the Hub of Bioinformatics and Biostatistics, et more precisely the Genome Organization Regulation and Expression group.

• basic alignment/visualisation pipeline(Pablo NAVARRO - Epigenetics of Stem Cells) - In Progress
• The master regulator of virulence gene expression in Group B Streptococcus(Arnaud FIRON - Biology of Gram-Positive Pathogens) - Pending
• Transcriptional analysis of injured skeletal muscle(Eleonora ROSSI - Stroma, Inflammation and Tissue Repair) - Closed

Blaise LI

I obtained a PhD in phylogeny in 2008 at the Muséum National d’Histoire Naturelle in Paris, then worked as a post-doc in Torino (Italy, 2009 – 2011) and Faro (Portugal, 2011 – 2013) where I worked on methodological aspects of phylogeny. In 2013, I have been hired as research engineer in bioinformatics at the Institut de Génétique Humaine in Montpellier where I wrote tools to analyse high-throughput sequencing data, especially small RNA-seq. This is also the kind of job I do now at Institut Pasteur, since 2016. I enjoy programming in Python, I’m interested in evolutionary biology, and I find teaching the UNIX command-line and other practical computer skills a rewarding activity. I’m also particularly involved in a course introducing PhD students (and sometimes other staff at Institut Pasteur) to R programming and basic descriptive statistics. The course support is available on-line and can hopefully be studied autonomously: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html One of my main activities is the development of automated data analysis workflows using Snakemake. My published work is available here: http://www.normalesup.org/~bli/useful.html

• The LeiSHield-MATI consortium: Investigating genomic adaptation of Leishmania parasites in endemic areas(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress
• Codon usage dependent translation and antibiotic stress in V. cholerae.(Zeynep BAHAROGLU - Bacterial Genome Plasticity) - In Progress
• Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing(Lisa CHAKRABARTI - Virus and Immunity) - In Progress

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

Hervé MÉNAGER

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• Development of a contributor management webpage for iPPI-DB.(Olivier SPERANDIO - Structural Bioinformatics) - Pending
• 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) - Closed

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) - In Progress
• 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