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 : Database
Related people (19)
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
BiophysicsMachine learningModelingProteomicsBiostatisticsDatabases and ontologiesHost-pathogen interactions
- 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
Web developmentDatabases and ontologies
- Klebsiella MALDI-Typer(Sebastien BRIDEL - Biodiversity and Epidemiology of Bacterial Pathogens) - Closed
- 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) - Closed
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.
AlgorithmicsData managementData VisualizationGenome assemblyGenomicsMachine learningModelingScientific computingDatabases and ontologiesSofware development and engineeringData and text miningIllumina HiSeqGraph theory and analysisIllumina MiSeq
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) - 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
- Evaluation of a novel mouse model for Primary Antibody Deficiency (PAD)(Lise HUNAULT - Antibodies in Therapy and Pathology) - In Progress
- Measles virus type 1 infection disturbs the mitochondrial network leading to type I interferon production through the RNA polymerase III/RIG-I pathway(Jean-Pierre VARTANIAN - Department of Virology) - Awaiting Publication
- Comparative analysis of choanoflagellate proteomic data(Thibaut BRUNET - Other) - Closed
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
- Identifying new population(s) of NK cells involved in memory to bacterial infection(Melanie HAMON - Chromatin and Infection) - In Progress
- 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
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.
Data VisualizationDatabaseSofware development and engineeringComparative metagenomicsOrthology and paralogy analysis
- Genetic adaptation of pathogenic Leptospira to a superoxide stress(BENAROUDJ NADIA - Biology of Spirochetes) - In Progress
- Detection of newly produced NIRVS in mosquito persistently infected cells(Anna-Bella FAILLOUX - Arboviruses and Insect Vectors) - Pending
- Genetic diversity of arbovirus populations in Aedes aegypti mosquitoes from Colombia(Anna-Bella FAILLOUX - Arboviruses and Insect Vectors) - 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) - Closed
- 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) - Closed
- 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 managementGalaxyStructural bioinformaticsWeb developmentDatabaseProgram developmentScientific computingDatabases and ontologiesWorkflow and pipeline developmentGrid and cloud computing
- SatelliteFinder(Jorge SOUSA - Department of Genomes and Genetics,Microbial Evolutionary Genomics) - In Progress
- Development of a secure API for ARIAweb(Benjamin BARDIAUX - Structural Bioinformatics) - In Progress
- Development of a web server to calculate functional binding sites using Deep Learning(Olivier SPERANDIO - Structural Bioinformatics) - In Progress
Data managementData VisualizationWeb developmentDatabaseProgram developmentDatabases and ontologiesSofware development and engineeringData integrationWorkflow and pipeline development
- An online database of RNA-small molecules complexes for rational drug design(Massimiliano BONOMI - Structural Bioinformatics) - Closed
- Development of a contributor management webpage for iPPI-DB.(Olivier SPERANDIO - Structural Bioinformatics) - In Progress
- JASS 2 : Integrating functional annotation to a multi-trait GWAS web application(HANNA JULIENNE - Statistical Genetics) - In Progress
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
- Virulence and natural anti-sense RNA in Entamoeba histolytica, the agent of human amoebiasis(Nancy GUILLEN - Bioimage Analysis,Biology of Host-parasite Interactions) - In Progress
- Transcriptional analysis of niche cells in the context of tumour progression in the Drosophila brain(Pauline SPÉDER - Brain Plasticity In Response To The Environment) - In Progress
- Setup of bioinformatic pipelines for paleo(meta)genomics(Nicolás RASCOVAN - Department of Genomes and Genetics) - In Progress
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
- SatelliteFinder(Jorge SOUSA - Department of Genomes and Genetics,Microbial Evolutionary Genomics) - In Progress
- Identification of ASD markers using HD-EEG(Lefebvre ALINE - Human Genetics and Cognitive Functions) - In Progress
- MacSyFinder 2.0(Eduardo ROCHA - Microbial Evolutionary Genomics) - In Progress
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.
AlgorithmicsData managementGenomicsImage analysisMachine learningModelingProteomicsSequence analysisStructural bioinformaticsTranscriptomicsDatabaseGenome analysisBiostatisticsScientific computingDatabases and ontologiesApplication of mathematics in sciencesData and text miningGeneticsGraphics and Image ProcessingBiosensors and biomarkersClinical researchCell biology and developmental biologyInteractomicsBioimage analysis
- Exploring pathogenic mechanisms of chronic inflammatory disease: unresolved issues in IL-23/IL-17 biology(YAHIA HANANE - Immunoregulation) - In Progress
- Study of the role of cyclic dimeric guanosine mono-phosphate (c-di-GMP) in the regulation of virulence and biofilm formation in Leptospira interrogans(Gregoire DAVIGNON - Other) - In Progress
- 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
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.
GenomicsSequence analysisDatabaseGenome analysisEvolutionOrthology and paralogy analysis
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
- User experience design for Oncodash(Dreo JOHANN - Systems Biology) - In Progress
- Monitoring tool for scientist who have received MAASCC career guidance(Marion GUESSOUM - Other) - Pending
- An online database of RNA-small molecules complexes for rational drug design(Massimiliano BONOMI - Structural Bioinformatics) - Closed
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) - Closed
Related projects (9)
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.
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.
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 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 ten years revealed that the midbody is a platform that concentrates essential proteins involved in cytokinetic abscission. After abscission, the midbody is cut on both sides, thus generating a midbody remnant (named MBR). The MBR usually interacts with the cell surface of one of the two daughter cells, before being engulfed in a phagocytic-like manner. We also found that the MBR can be easily released from cells before their engulfment by calcium chelation. Of note, MBRs at the cell surface might act as pro-proliferative, signalling entities but the proteins involved and the mechanisms of MBR anchoring are unknown. A previous proteomic study of the midbody conducted by Skop purified intercellular bridges from cell lysates recovered after cell synchronization, microtubule stabilization and detergent treatment. This pioneer proteomic study, although informative, did not allow the recovery of many key known proteins of the midbody. Here, we set up an experimental protocol to purify intact, detergent-free MBRs in order to have the full proteome of this organelle. Quantitative, label-free proteomics enabled us to identify 529 proteins enriched at least 2 times as compared to whole cell lysates, that we named the “Flemmingsome”. Besides known and well-established proteins of the midbody (MKLP1, MgcRacGAP, AuroraB, INCENP, MKLP2, Rab8, Rab11, Rab35, Citron Kinase, ESCRTs…), we identified new and promising candidates potentially involved in cytokinetic abscission. In addition, we identified 27 transmembrane proteins that are excellent candidates for mediating interactions between the MBR and the receiving daughter cells after cytokinetic abscission. We are also currently exploring whether newly identified candidates could participate in the signalling mediated by the MBRs. We would thus like to create a website that recapitulates the findings of our screen. The proteins discovered represent new candidates for the understanding of cytokinesis and tumorigenesis. This should be instrumental in the field as the previous websites are not updated (Microkits, Uniprot) and do not focus on this particular step of cytokinesis.
- 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, along with information on bacterial isolates (provenance data) and their genomic sequences. The Pasteur MLST database provides universal nomenclatures that are largely adopted for important pathogens (Klebsiella, Listeria, …), and represent a unifying language on strains for microbial population biology. - Unified strain taxonomies facilitate the coordinated international surveillance of bacterial pathogens. Several hundred research laboratories and public health agencies worldwide have deposited novel strain types, sequences and provenance data on their bacterial isolates. - Pasteur MLST is powered by the Open source GPL3 BIGSdb web application developed at Oxford University (Keith Jolley & Martin Maiden). (http://bigsdb.pasteur.fr ). Its evolution in terms of functionality is tightly linked to the developments of the software at Oxford U. Its evolution in terms of contents is managed by dedicated international teams of curators for each bacterial pathogenic species, coordinated by the PasteurMLST team. - The genomic taxonomies hosted at Pasteur MLST represent unique, authoritative resources that are highly valued by the community, as testified by the routine use of Pasteur MLST strain tags (e.g., K. pneumoniae ST258) in the scientific literature. Several labs (National Reference Centers or Units) of Institut Pasteur are coordinating the curation of genomic taxonomies (Klebsiella, Listeria, Corynebacteria, Bordetella, Leptospira, Yersinia, ...). The aim of the project is to obtain support from the C3BI HUB for the maintenance of the BIGSdb instance at Pasteur: deployment, upgrades, installation of API functionality developed by our partner, coping with future IT evolutions, ...
Because of the increasing biological data generated due to next-generation sequencing of the genetic material of organisms, storing and analyzing these data have become challenging both for molecular biologists and computer scientists. Here, we propose to design a system that attempts to solve this from building a secure repository up to designing algorithms that process sequences to produce biological insights, particularly mining for sequential patterns present in the sequences. Discovering sequence motifs/patterns has been essential to computational biologists as it is helpful in understanding protein function, structure, and evolution. Given the data generated from the project “A Study of Mosquitoes of Makiling Forest Reserve Areas with Characteristic Land Use and Survey of their Arbovirus Diversity through Vector-enabled Virome Sequencing” (funded by the Department of Science and Technology - Philippine Council of Health Research and Development; DOST-PCHRD) of Dr. Bautista, using the assembled contigs or even substantial portion of viruses’ full genome, we can take a look at the dynamics of genetics of viruses over time when analyzed alongside other publicly available sequences. This is a collaborative project between the University of the Philippines and Institut Pasteur in the context of this funded project that includes btoh partners. Our wish is for the Philippines bioinformatics engineer involved seeks guidance of the development their databse that may eventually be housed at Institut Pasteur.
The majority of approved drugs target proteins, which are encoded in a very small fraction of the human genome. When a pathology is associated with so-called undruggable proteins, an alternative strategy should be sought. In the last twenty years, non-coding RNA molecules have been shown to perform a variety of crucial biological functions, including regulating gene expression, protecting chromosomes from foreign nucleic acids, and guiding telomers synthesis. In this context, targeting either mRNA molecules that are translated into undruggable protein targets or biologically relevant non-coding RNA molecules with small molecules is emerging as a promising therapeutical approach in pathologies such as cancer, viral infections, and neurodegenerative disorders. However, the number of approved drugs that target RNA molecules is still very limited and the existing examples have mostly been found by costly and time-consuming screening experiments. In this project, we aim at building a computational framework to guide the rational design of drugs targeting RNA. To this end, we created a database containing all the experimentally-determined structures of RNA-small molecule complexes deposited in the PDB database. The entries containing drug-like compounds were selected and annotated based on the different biological entities interacting with the ligands. Our database, freely accessible via a web interface, will facilitate i) mapping the chemical space of the small molecules known to bind RNA, ii) understanding the nature of the interactions that drive ligand/RNA recognition, and iii) benchmarking existing tools for in silico protein drug design with RNA targets.
A protein-protein interaction screen has been done beween viral proteins of influenza A viruses and a library of about 100 human factors invovled in RNA processing through RNA exonucleases activity. 20 factors were identified as interactors of viral proteins. To see if this targeting corresponds to specific RNA metabolism focntions of the cell, we analysed using Cytoscape the first neighbors of these factors in the human ORFeome. We then compared using the ClueGo pluging the functional enrichment of the factors targeted by viral factors and the functional enrichment of the non-interacting subset. We need now a statistical analysis of the results the functional enrichment comparison, which is required for further progress of the ongoing research project.
Characterization of a broad spectrum chemical inhibitor targeting the endocytic pathway to prevent bacterial intoxications.
Bacterial toxins can induce a wide range of life threatening diseases and are at risk of bioweapon development due to their extreme toxicity and ease of production. Some AB-like toxins exploit the host cell endocytic machinery to enter into the cell cytosol where they exert their poisoning effects. Host-targeted therapy involving the development of small molecules interfering with key vesicular trafficking components hijacked by bacterial toxins offers to counteract toxin action. We have identified the small compound C910, in a cell-based High-throughput screen (HTS) followed by orthogonal screens described in (Mahtal N et al., 2018), for its cell-protective activity against CNF1 toxin from pathogenic Escherichia coli, as well as diphtheria and Shiga toxins. Therefore, to characterize C910 mechanism of action and find its cellular target we have realized an siRNA wide-genome screening on primary human cells. This screening aims to find genes that can interfere with the trafficking of the CNF1 toxin.