Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise
Searched keyword : Program development
Related people (19)
Emna has joined the C3BI in 2016 and worked actively in the IGDA platform doing research and education. Now, she is also part of the Viral Populations and Pathogenesis Unit (PVP).
Genome assemblySequence analysisProgram developmentData integrationRead mappingLIMSParallel computingGene predictionShotgun metagenomics
Developing and evaluating bioinformatic tools for: – next generation sequencing data – genome analysis & comparison Specialties:Genome & Transcriptome Bioinformatics
Data managementData VisualizationGenomicsNon coding RNASequence analysisTranscriptomicsGenome analysisBiostatisticsProgram developmentScientific computingData and text miningBiosensors and biomarkersEpidemiology and public health
- Identification of non-coding RNAs under the control of the PerR regulators(Nadia BENAROUDJ - Biology of Spirochetes) - In Progress
- Tissue-resident stromal cell heterogeneity(Lucie PEDUTO - Stroma, Inflammation and Tissue Repair) - In Progress
- Role of small non coding RNAs in the adaptive response to oxidative stress in pathogenic Leptospira(NADIA BENAROUDJ - Biology of Spirochetes) - In Progress
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.
AlgorithmicsData managementData VisualizationGenomicsMachine learningProteomicsGenome analysisBiostatisticsProgram developmentScientific computingApplication of mathematics in sciencesExploratory data analysisSofware development and engineeringData and text miningGenetics
| work as a research engineer in the ßioinƒormatics and ßiostatistics HUß of the |nstitut Pasteur. Holder of a PhD in bioinƒormatics, my main interest is on ƒast but robust phylogenetic inƒerence algorithms and methods ƒrom large genome-scaled datasets. |n consequence, | am oƒten involved in related bioinƒormatics projects, such as perƒorming de novo or ab initio genome assemblies, designing and processing core genome †yping schemes, building and analysing phylogenomics datasets, or implementing and distributing novel tools and methods.
AlgorithmicsClusteringGenome assemblyGenomicsGenotypingPhylogeneticsTaxonomyGenome analysisProgram developmentEvolutionSequence homology analysis
- Long-term preservation of a Campylobacter fetus strain and genomic stability(Dominique CLERMONT - Collection of the Institut Pasteur (CIP)) - In Progress
- DNMT and RNMT in Leishmania(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress
- Séquençage à haut débit (NGS) et traitement de séquences ADN des domaines variables d’anticorps simple chaine d’alpaga (domaines VHH ou Nanobodies®)(Margarida GOMES - Antibody Engineering) - In Progress
Data managementSequence analysisStructural bioinformaticsDatabaseProgram developmentScientific computingLIMS
- 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
AlgorithmicsProgram developmentScientific computingSofware development and engineering
- 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
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.
AlgorithmicsClusteringGenome assemblyGenomicsMetabolomicsModelingNon coding RNASequence analysisStructural bioinformaticsTargeted metagenomicsDatabaseGenome analysisBiostatisticsProgram developmentScientific computingDatabases and ontologiesExploratory data analysisData and text miningIllumina HiSeqComparative metagenomicsRead mappingIllumina MiSeqSequence homology analysisGene predictionMultidimensional data analysisSequencingShotgun metagenomics
- Analysis of microbiota in Anopheles mosquitoes(Patricia BALDACCI - Center for Production and Infection of Anopheles) - Pending
- Assessing the role of gut microbiota in spondyloarthritis patients and impact of anti-TNF treament on its composition(Corinne RICHARD-MICELI - Immunoregulation) - Closed
- Uncovering diversity and improving gene annotation of Leptospira sppo(Mathieu PICARDEAU - Biology of Spirochetes) - Pending
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.
ChIP-seqEpigenomicsGenomicsSequence analysisProgram developmentDatabases and ontologiesSofware development and engineeringGeneticsData integrationRead mappingWorkflow and pipeline developmentConfocal Microscopy
- 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 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)
AlgorithmicsChIP-seqData managementData VisualizationImage analysisMachine learningSequence analysisDatabaseGenome analysisBiostatisticsProgram developmentScientific computingData and text miningIllumina HiSeqGraphics and Image ProcessingIllumina MiSeqHigh Throughput ScreeningFlow cytometry/cell sortingPac Bio
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.
Data managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
- 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
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.
AlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
BacteriaFungiParasiteHumanInsect or arthropodOther animal
- Small RNA signature on RIG-I like receptors(Anastasia KOMAROVA - Molecular Genetics of RNA Viruses) - In Progress
- Determination of RABV RNAs signatures recognized by RLRs(Wahiba AOUADI - Lyssavirus Dynamics and Host Adaptation) - Pending
- Identification of internal methylations of RABV mRNAs using RiboMeth sequencing approach(Wahiba AOUADI - Lyssavirus Dynamics and Host Adaptation) - Pending
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.
AlgorithmicsData managementPhylogeneticsSequence analysisDatabaseGenome analysisProgram developmentScientific computingDatabases and ontologiesSequencingWorkflow and pipeline development
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.
AlgorithmicsData managementProteomicsDatabaseProgram developmentScientific computingSofware development and engineeringComparative metagenomics
- 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
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.
ClusteringData managementSequence analysisTranscriptomicsWeb developmentDatabaseGenome analysisProgram developmentScientific computingExploratory data analysisData and text miningIllumina HiSeqRead mappingLIMSIllumina MiSeqHigh Throughput ScreeningMultidimensional data analysisWorkflow and pipeline developmentRibosome profilingMotifs and patterns detection
- 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
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.
Data managementStructural bioinformaticsDatabaseProgram developmentScientific computingDatabases and ontologiesGrid and cloud computing
- Implementation of the ViroScreen workflow in Galaxy(Laurent DACHEUX - Lyssavirus Dynamics and Host Adaptation) - In Progress
- Implementation of the ViroScreen workflow in Galaxy(Laurent DACHEUX - Lyssavirus Dynamics and Host Adaptation) - Closed
- Intégration d'outils bioinformatique dans Galaxy pour identification bactérienne(ANNE LE FLECHE - Department of Infection & Epidemiology,Environment and Infectious Risks) - Closed
Professional Experience Today - Institut Pasteur,Paris - HUB Team 2017 - Bioinformatician 2001 - 2017 - Institut Pasteur,Paris; CIB/DSI - Engineer 1997 - 2000 Thesis: NMR and molecular modelisation, CEA, Saclay,
Data managementSequence analysisTranscriptomicsGenome analysisProgram developmentScientific computing
FungiCandida albicansCryptococcus gattiiCryptococcus neoformans
- maintenance du site de la Collection des cyanobactéries(Bénédicte BENEDIC - Collection of Cyanobacteria) - Pending
- Trichosporon asahii NGS analysis(Marie DESNOS-OLLIVIER - Molecular Mycology) - In Progress
- Development of a bioinformatics workflow dedicated to the analysis of the viral metagenome: from NGS raw data to the identification of novel viruses(Laurent DACHEUX - Lyssavirus Dynamics and Host Adaptation) - In Progress
Data managementData VisualizationWeb developmentDatabaseProgram developmentDatabases and ontologiesSofware development and engineeringData integrationWorkflow and pipeline development
- Flemmingsome: A Midbody Remnant Proteome Database(Neetu GUPTA-ROSSI - Membrane Traffic and Cell Division) - Pending
- crispr.pasteur.fr(David BIKARD - Synthetic Biology) - Awaiting Publication
- The Flemmingsome: the proteome of intact cytokinetic midbodies(NEETU GUPTA-ROSSI - Membrane Traffic and Cell Division) - Awaiting Publication
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)
Data managementDatabaseProgram developmentScientific computingDatabases and ontologies
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.
AlgorithmicsData VisualizationMetabolomicsModelingPathway AnalysisPhylogeneticsSystems BiologyTool DevelopmentDatabaseProgram developmentScientific computingDatabases and ontologiesApplication of mathematics in sciencesSofware development and engineeringData and text miningEvolutionData integrationGraph theory and analysisWorkflow and pipeline developmentDiscrete and numerical optimization
VirusHuman Immunodeficiency virus (HIV)
- 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
Related projects (5)
Characterization of the role of Argonaute proteins in regulating germline gene expression at the transcriptional and the post-transcriptional levels.
This research project focuses on the characterization of the role of small RNAs and their associated Argonaute proteins in transcriptional and post-transcriptional regulation of germline gene expression. Using the nematode C. elegans, we have recently showed that one of the germline-expressed Argonaute protein, CSR-1, promotes germline transcription. However, CSR-1 also possess an endonucleolytic activity that might participate in post-transcriptional silencing. Therefore, two possible functions of the protein might regulate the germline transcriptome. 1) CSR-1 promotes specific germline transcription programs in the nucleus, and 2) negatively regulates expression of target transcripts in the cytoplasm. To gain mechanistic insights into these two functions, we aim to use RNA-seq, sRNA-seq, ChIP-seq, GRO-seq, Ribo-seq, RIP-seq, iCLIP in wild type worms, knock out and catalytic inactive mutants of CSR-1 protein at different times of germline development.
To study the neuronal mechanisms underlying the generation of distinct memories, it is necessary to perform experiments in which the sensory elements of the environment are under the precise control o
We are interested in Spondyloarthritis. Spondyloarthritis is a chronic inflammatory rheumatism. Currently 2 biologic treatments are available : anti TNF and anti IL-17A. We are analyzing how these
Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing
The rare patients who spontaneously control HIV replication in the absence of therapy show signs of a particularly efficient T cell response. We aim at characterizing the molecular determinants underl
MacSyFinder is a framework to model and detect macromolecular systems in genomes using decision rules (gene content and architecture) and similarity searches (protein profiles). It was initially devel