Expertise
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
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Searched keyword : Transcriptomics
Related people (13)

Giovanni BUSSOTTI
Developing and evaluating bioinformatic tools for: – next generation sequencing data – genome analysis & comparison Specialties:Genome & Transcriptome Bioinformatics
KeywordsData managementData VisualizationGenomicsNon coding RNASequence analysisTranscriptomicsGenome analysisBiostatisticsProgram developmentScientific computingData and text miningBiosensors and biomarkersEpidemiology and public health
Organisms
Leishmania
Projects (8)
- Identification of non-coding RNAs under the control of the PerR regulators(Nadia BENAROUDJ - Biology of Spirochetes) - Closed
- Tissue-resident stromal cell heterogeneity(Lucie PEDUTO - Stroma, Inflammation and Tissue Repair) - Closed
- Role of small non coding RNAs in the adaptive response to oxidative stress in pathogenic Leptospira(NADIA BENAROUDJ - Biology of Spirochetes) - Closed

Claudia CHICA
As a computational biologist I have been involved in various projects seeking to answer different biological questions. Those projects have allowed me to define my main research interest, namely the evolutionary study of the emergence, storage and modulation of information in biological systems assisted by computational methods. During my research career I have acquired extensive experience in the analysis of sequence data at the DNA and protein level. I’m trained both in NGS bioinformatic protocols (ChIP-seq, ATAC-seq, RNA-seq, genome assembly) and fine detail sequence analysis. Most importantly, I have gained proficiency in the use of the statistical models that are at the basis of the quantitative analysis of low and high throughput sequence data. Additionally, my experience as a lecturer and instructor has taught me that training researchers about the formal basis of bioinformatic methodologies is the key for a successful collaboration between wet and dry lab. Likewise, I have gained valuable skills by working within two international consortia (TARA Oceans project and TRANSNET): the ability to collaborate with multidisciplinary groups and to coordinate younger researchers.
KeywordsAlgorithmicsGenomicsSequence analysisTranscriptomicsGenome analysisGeneticsEvolutionInteractomics
Organisms
Projects (23)
- fliC locus of Y. pestis(Mara CARLONI - Yersinia) - In Progress
- Mechanisms defining functional heterogeneity of anatomically distinct myogenic populations: insights from single nuclei-ATAC-seq data(Glenda COMAI - Department of Developmental and Stem Cell Biology) - In Progress
- basic alignment/visualisation pipeline(Pablo NAVARRO - Epigenetics of Stem Cells) - In Progress

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.
KeywordsRNA-seqStatistical inferenceTranscriptomicsBiostatisticsApplication of mathematics in sciencesExploratory data analysisIllumina HiSeqStatistical experiment designSequencing
Organisms
Projects (3)
- Biomarqueurs d’identification précoce du sepsis aux urgences (BIPS)(Jean-Marc CAVAILLON - Cytokines and Inflammation) - Closed
- 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
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.
KeywordsData managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
Organisms
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
Projects (3)
- Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing(allemand ERIC - Epigenetic Regulation) - Closed
- Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets(Catherine BOURGOUIN - Functional Genetics of Infectious Diseases) - Closed
- Mapping of Enhancers from transcriptome data(Christian MUCHARDT - Epigenetic Regulation) - Closed

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.
KeywordsAlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
Organisms
BacteriaFungiParasiteHumanInsect or arthropodOther animal
Projects (24)
- Exploring pathogenic mechanisms of chronic inflammatory disease: unresolved issues in IL-23/IL-17 biology(YAHIA HANANE - Immunoregulation) - Pending
- Identification of factors influencing the activity of bacteriophage within the gut of mammals(Devon CONTI - Other) - In Progress
- HKA: systemic analysis of two-component signalling(Arnaud FIRON - Biology of Gram-Positive Pathogens) - In Progress
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
KeywordsGenomicsNon coding RNATranscriptomicsSofware development and engineeringGeneticsWorkflow and pipeline development
Organisms
Insect or arthropodOther animalDrosophila melanogaster (Fruit fly)C. elegans
Projects (10)
- Codon Usage Bias Analysis in Vibrio(Marie-Eve KENNEDY-VAL - Bacterial Genome Plasticity) - In Progress
- Gene conversion and allelic selection drives L. donovani genomic adaptation in experimental Sand fly infection(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress
- The LeiSHield-MATI consortium: Investigating genomic adaptation of Leishmania parasites in endemic areas(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress

Christophe MALABAT
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
Organisms
Projects (10)
- 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

Corinne MAUFRAIS
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,
KeywordsData managementSequence analysisTranscriptomicsGenome analysisProgram developmentScientific computing
Organisms
FungiCandida albicansCryptococcus gattiiCryptococcus neoformans
Projects (11)
- Viral metagenomic in noctule bats from East Europe(Laurent DACHEUX - Lyssavirus Dynamics and Host Adaptation) - In Progress
- Viral metagenomic in Chinese bats and their associated ectoparasites.(Laurent DACHEUX - Lyssavirus Dynamics and Host Adaptation) - In Progress
- Characterization of Salmonella mutants(FRANCOISE NOREL - Biochemistry of Macromolecular Interactions) - In Progress

Adrien PAIN
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KeywordsGenomicsTranscriptomics
Organisms
Mosquito
Projects (9)
- ANR Arbovec- CHIKV/Aedes interactions(Blisnick ADRIEN - Arboviruses and Insect Vectors) - Awaiting Publication
- Biology of noncoding regulatory elements in Anopheles(Kenneth VERNICK - Genetics and Genomics of Insect Vectors) - Pending
- Genetic association of malaria susceptibility by Anopheles population resequencing(Kenneth VERNICK - Genetics and Genomics of Insect Vectors) - Pending

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
KeywordsClusteringModelingStatistical inferenceTranscriptomicsBiostatisticsExploratory data analysisDimensional reductionStatistical experiment designMultidimensional data analysis
Organisms
Projects (22)
- Asymmetric heart morphogenesis(BERNHEIM SÉGOLÈNE - Heart Morphogenesis) - In Progress
- Modulation of Flu transmission in Niger , according to climate variations over the past ten years(Ronan JAMBOU - Other) - Awaiting Publication
- Left-right patterning of heart precursors(Tobias BØNNELYKKE - Heart Morphogenesis) - 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.
KeywordsAlgorithmicsData 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
Organisms
Projects (32)
- Exploring pathogenic mechanisms of chronic inflammatory disease: unresolved issues in IL-23/IL-17 biology(YAHIA HANANE - Immunoregulation) - Pending
- 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) - Pending
- 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

Violaine SAINT-ANDRÉ
After graduating from Paris VI University with a PhD in Genetics on the “Role of histone protein post-translational modifications in splicing regulation” that I performed in the Epigenetic Regulation unit at the Institut Pasteur, I carried out two post-doctoral experiences. I first worked for three years as a postdoctoral associate of the Whitehead Institute for Biomedical Research/MIT in Cambridge (USA). My main project consisted in the integration of genomic and epigenomic data in order to predict the transcription factors that are potentially at the core of the regulation of the cell-type specific gene expression programs. I then joined the Institut Curie where I deepened my experience in multi-omics data analyses and integration to identify non-coding RNAs involved in cancer progression. I have recently joined the HUB-C3BI of the Institut Pasteur where I am performing high-throughput data integration to better understand biological complexity and contribute to precision medicine development.
KeywordsATAC-seqChIP-seqEpigenomicsNon coding RNAPathway AnalysisRNA-seqSingle CellSystems BiologyTool DevelopmentTranscriptomicsData integrationGraph theory and analysisCell biology and developmental biology
Organisms
Human
Projects (1)
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 in 2013 by the Transcriptome & Epigenome Platform of the Biomics Pole. Late 2014 he obtained a permanent position at the Bioinformatics & Biostatistics Hub and has been detached to the platform to continue the statistical analyses of RNA-Seq data and develop R pipelines and Shiny applications that help in this task. One of them is named SARTools and is available on GitHub: https://github.com/PF2-pasteur-fr/SARTools. In December 2019 he left the Biomics Platform and joined the Bioinformatics & Biostatistics Hub as a core-member.
KeywordsMetabolomicsModelingSequence analysisStatistical inferenceTranscriptomicsBiostatisticsScientific computingApplication of mathematics in sciencesExploratory data analysisHigh Throughput ScreeningClinical research
Organisms
Projects (28)
- Evaluation in cellulo of the impact of insecticide usage on arbovirus population(VALLET THOMAS - Viral Populations and Pathogenesis) - In Progress
- Analysis of the molecular pathways induced by the activation of the Nod2 receptor by MDP in hypothalamic neurons(Ilana GABANYI - Perception and Memory) - Pending
- Characterization of a broad spectrum chemical inhibitor targeting the endocytic pathway to prevent bacterial intoxications.(Eléa PAILLARES - Bacterial Toxins) - In Progress
Related projects (53)
Gene regulation in yeast quiescence
Novel regulators of cell wall maintenance in Aspergillus fumigatus
Study of lncRNAs in Cryptococcus neoformans
Systems wide analysis of amastigote and promastigote stages of Leishmania donovani
Molecular analysis of muscle stem cells
Role of SUMO, a new epigenetic mark, in stress response
Identification of Transcription Start Sites and small RNAs in Leptospira interrogans by transcriptome analysis
MicrocystOmics
- Christophe BÉCAVIN
- Rachel LEGENDRE
- Hugo VARET + 1 operator
The Physiological Consequences of Altering Bacterial Cell Wall Synthesis
Transciptomic analysis of dendritic cell response during Lassa virus infection
Listeriomics - Development of a web platform for visualization and analysis of Listeria omics data
Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment
Tac4, a new RNA helicase involved in translation control?
Identification of promoteur-overlaping antisense transcription
Insect Vector Genomics
Modeling mitochondrial metabolism dormant Cryptococcus neoformans
In silico analyses of a novel LincRNA potentially involved in type I IFN response
Discovery of non-annotated transcripts in RNAseq data from Aedes Aegypti
Genotype to phenotype analysis of immune responses in chronic inflammatory diseases
Genomic determinants for initiation and length of natural antisense transcripts in a compact eukaryotic genome and phylogenetic analysis of related Entamoeba species
Analysis of IFITM RNA levels in vraious cell types and tissues
Mapping of Enhancers from transcriptome data
Characterization of the role of Argonaute proteins in regulating germline gene expression at the transcriptional and the post-transcriptional levels.
Transcriptome of epithelial cells challenged with different serotypes of S. pneumoniae
Dynamic and integrative multidimensional OMICs analysis of the cellular senescence fate
Identification of eukaryotic 5'UTRs
Role of the Topoisomerase 1 and Guanine quadruplexes as transcriptional regulators
Antiviral activities of anti-HIV-1 antibodies
Finding SNPs associated with Dengue infection in the mosquito Aedes aegypti
Multiparametric immunophenotyping of whole blood in IFN-treated multiple sclerosis patients
Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing
Identification of non-coding RNAs under the control of the PerR regulators
Deciphering the transcriptome profil during rabies infection in brain in mouse and in human
Identification of internal methylations of RABV mRNAs using RiboMeth sequencing approach
Determination of RABV RNAs signatures recognized by RLRs
Small RNA signature on RIG-I like receptors
Left-right patterning of heart precursors
- Anne BITON
- Rachel LEGENDRE
- Emeline PERTHAME + 1 operator