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 : Web development
Related people (7)
Web developmentDatabases and ontologies
- Récupération des données associées aux séquences de génomes de Klebsiella pneumoniae téléchargées du NCBI(Nicolas CABANEL - Ecology and Evolution of Antibiotics Resistance) - Pending
- Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur(Xavier MONTAGUTELLI - Mouse Genetics) - In Progress
- Viral Host Range Databank(Laurent DEBARBIEUX - Molecular Biology of Gene in Extremophiles) - In Progress
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
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
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
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…).
Data managementGenomicsSequence analysisWeb developmentDatabaseGenome analysisDatabases and ontologiesOrthology and paralogy analysisRead mappingSequence homology analysisGene prediction
- Multiparametric immunophenotyping of whole blood in IFN-treated multiple sclerosis patients(Priyanka DEVI - Cytokine Signaling) - In Progress
- Genomic DNA sequencing of Burkholderia ambifaria Q53 strain isolated from peanut rizospheric soil(Mathilde BEN ASSAYA - Structural Microbiology) - In Progress
- Comparative genomics of Helicobacter pylori bismuth resistant strains(Hilde DE REUSE - Helicobacter Pathogenesis) - Pending
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.
Data VisualizationWeb developmentDatabaseGenome analysisScientific computingDatabases and ontologiesSofware development and engineeringWorkflow and pipeline development
- Development and design of new functionalities for MEMHDX, a web application dedicated to the statistical analysis and vizualization of large HDX-MS datasets.(Sebastien BRIER - Biological NMR Technological Platform) - In Progress
- Development of a Software tool to integrate Bottomp-up, Middle-down and Top-down proteomics data(Mariette MATONDO - Proteomics,Structural Mass Spectrometry and Proteomics) - Pending
- Genomic differences of the same strains preserved in different culture collections(Dominique CLERMONT - Department of Microbiology) - Closed
- CRISPR design tools on crispr.pasteur.fr(David BIKARD - Synthetic Biology) - In Progress
- Gene expression and its regulation during and after inpatient detoxification of cocaine: a link to relapse?(Romain ICICK - Integrative Neurobiology of Cholinergic Systems) - In Progress
- crispr.pasteur.fr(David BIKARD - Synthetic Biology) - Awaiting Publication
Related projects (17)
Development of a web application and new functionalities for the maintenance and curation of iPPI-DB
A new version of the iPPI-DB, a manually curated database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundred modulators of protein-protein interactions.
This new version will include:
- A maintenance application that facilitates and automates the updates of the database. The computation of the various physico-chemical properties of the modulators and chemical similarity screening on the Galaxy server of the Institut Pasteur.
- A new target-centric mode, based on the mapping of all druggable cavities at the core of PPI interfaces throughout the Protein Data Bank.
The ARIA (Ambiguous Restraints for Iterative Assignment) software, developed at the Structural Bioinformatics Unit, automatizes the treatment of NMR data and protein structure calculation by molecular dynamics simulation. To enhance the visibility of the software, it is necessary to develop a new web interface where users will be able to easily manage their data, perform calculations and analyze the results of the ARIA calculations.
In recent years, large genome-wide association studies (GWAS) have been successful in identifying thousands of significant genetic associations for multiple traits and diseases1. In the course of this endeavor, sample size has proven to be the key factor for identifying new variants. For example, GWAS of body mass index (BMI), now including up to 350,000 individuals from more than 100 cohorts, have been able to identify genetic variant that explain as low as 0.02% of BMI variance2. While standard approaches for detecting new genetic variants associated with traits and diseases will go on as sample size increases, multivariate analyses have been proposed as an alternative strategy for both improving detection of new variants and exploring the multidimensional components of complex traits and diseases. Intuitively, multivariate analysis can be used to improve detection of variants displaying a pleiotropic effect3 by accumulating moderate evidence of association across multiple traits and diseases. Several recent examples have been published about not only GWAS hit overlap across related traits4, but also of genome-wide shared genetic effect5. Multivariate analyses of GWAS have also proven useful to understand shared genetics between diseases5, and potential causal relationship between phenotypes using Mendelian randomization (MR)6. Importantly, most of existing multivariate methods are based on GWAS summary statistics, while approaches based on individual-level data have been seldom considered because of major practical and ethical issues. In the continuity of ongoing work on multi-phenotype analysis (Aschard et al 20147, Aschard et al 20158), we developed an effective and robust multivariate approach of GWAS summary statistics that addresses the major barriers of existing approaches, i.e. the presence of correlation between studies that would exists when GWAS analyzed share sample9-16. Our approach consists in a robust omnibus multivariate test of GWAS summary statis
Common and phylogenetically widespread coding for peptides by bacterial small RNAs – Follow up of a project regarding its journal review
Following a collaboration started a few years ago between a postdoc of the System Biology team (Robin Friedman) and Olivia Doppelt-Azeroual, a publication is in review in the journal Genome Biology. One of the reviewers made comments regarding the database and web interface implemented by Olivia at the time and after a brainstorm on the review, the first author (Robin) needs to make a few modifications on the database. This modification requires Olivia's intervention to update the database and adapt the web application accordingly, in order to display the right information: adding a column in the table with the concerned sRNA names.
CRISPR-Cas systems provide immunity to bacteria and archaea. One of the reasons these systems have attracted so much attention in the past few years is due to the discovery of nucleases among the Cas proteins that are guided by small RNAs to bind and degrade homologous DNA. The introduction of breaks in DNA that can be repaired either in a controlled or uncontrolled manner now is a widely used method to introduce mutations in genomes. We are interested in probing the CRISPR-Cas system efficiency for different targets.
The purpose of this short project is to develop a database that can efficiently store millions of unique molecular compounds along with some of their already calculated properties. The database named BD-CheM should be able to deal with extensive sets of data: millions of compounds and several hundreds of molecular properties. The import of new data should deal with the detection of molecule uniqueness to prevent data redundancy and with multiple sources of molecular compounds to keep track of their origin. The motivation for this project is the imperious necessity for our group to properly store this precious chemical information and efficiently extract subsets of data with appropriate database queries. Such subsets are used by our group to carry out dedicated and tailored chemoinformatics analyses for different specific projects on and off campus.
The aim of the project is to develop a powerful software tool to integrate MS data for the visualization of the protein coverage and mapping of Post Translational Modifications (PTMs). Even if some to
The central part of the intercellular bridge connecting the two daughter cells during cytokinesis is a highly dense structure named the Midbody first described by Flemming in 1891. Work in the past te
- The Institut Pasteur genomic taxonomy database of microbial strains (“Pasteur MLST”) is a free, publicly-accessible resource that hosts nucleotide sequence-based definitions of microbial strains, al
Bacteriophages infect bacteria. One bacteriophage can infect several strains. Around the world, many labs have performed spot tests to determine the host range of bacteriophages but this information i
crispr.pasteur.fr is a website providing resources to visualize CRISPR screen data and design CRISPR experiments in bacteria
DISCO-Bac (http://disco-bac.web.pasteur.fr/), a Web server, is a part of a recent publication https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3932-y (Co-authored by former Hub member
The servers like LegioList are used by my group and many groups around the world working on Legionella pathogenesis since its establishment in 2004. This server has provided us with an important reser
Development and design of new functionalities for MEMHDX, a web application dedicated to the statistical analysis and vizualization of large HDX-MS datasets.
Hydrogen Deuterium eXchange followed by Mass Spectrometry (HDX-MS) is a recognized biophysical tool in structural biology capable of probing protein/ligand interactions, conformational changes, and pr
The central part of the intercellular bridge connecting the two daughter cells during cytokinesis is a highly dense structure named the Midbody first described by Flemming in 1891. We set up an experi