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 : Genetics
Related people (16)

Anne BITON
I received a Ph.D. in Biostatistics and Bioinformatics applied to Cancer Research in 2011 from the University Paris Sud XI, I was working at the Curie institute under the supervision of Emmanuel Barillot and François Radvanyi. My Ph.D. was about the unsupervised analysis of cancer transcriptome. During my postdoctoral time, I worked on the computational and statistical analysis of NGS data. My areas of interest and expertise include - functional genomics - human genetics - statistical analysis of high-dimensional data - normalization, batch-correction, meta-analysis of high-throughput data - unsupervised learning, independent component analysis - NGS data analysis (RNA-Seq, DNA-Seq, …) - analysis of the non-coding genome, transposable elements
KeywordsMachine learningModelingGenetics
Organisms
Projects (17)
- Left-right patterning of heart precursors(Tobias BØNNELYKKE - Heart Morphogenesis) - In Progress
- Collaboration between CETEA, C2RA and Hub for optimization of experimental designs (3R)(Myriam MATTEI - Center for Animal Resources and Research) - In Progress
- Mechanisms of HIV-1-infected cells susceptibility to Fc effector functions(Timothée BRUEL - Virus and Immunity) - In Progress

Pascal CAMPAGNE
Initially trained in evolutionary and environmental sciences, I studied population genetics and micro-evolutionary processes in a number of postdoctoral research projects. I recently joined the C3BI-Hub at the Institut Pasteur, where I work on various aspects involving Biostatistics and the analysis of genetic data.
KeywordsAssociation studiesGenomicsGenotypingBiostatisticsGeneticsEvolutionPopulation genetics
Organisms
BacteriaParasiteHumanInsect or arthropodOther animal
Projects (23)

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

Freddy CLIQUET
One of my projects consists in developing GRAVITY, a java tool based on Cytoscape to integrate genetic variants within protein-protein interaction networks to allow the visual and statistical interpretation of next-generation sequencing data, ultimately helping geneticists and clinicians to identify causal variants and better diagnose their patients. I’m also involved in several other projects in the lab, taking part in the design of pipelines for the processing and the analysis of genomics data, including SNP arrays, whole-exome and whole-genome sequencing data. This means being confronted to the big data problematic, the unit having to manage hundreds of terabytes of genomics data. Finally, I am now analysing these data in order to identify possible causes for autism, to help clinicians with their diagnosis but also to better understand the biological mechanisms at play in this complex disease. This is done through the project aiming at understanding the genetic architecture of autism in the Faroe Islands, and also with the newly starting IMI2 European project AIMS2-Trials.
KeywordsAlgorithmicsData managementData VisualizationGenomicsMachine learningProteomicsGenome analysisBiostatisticsProgram developmentScientific computingApplication of mathematics in sciencesExploratory data analysisSofware development and engineeringData and text miningGenetics
Organisms
Projects (0)

Alexis CRISCUOLO
| 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.
KeywordsAlgorithmicsClusteringGenome assemblyGenomicsGenotypingPhylogeneticsTaxonomyGenome analysisProgram developmentEvolutionSequence homology analysis
Organisms
Projects (24)
- Comparative genomics analysis of cyclic-di-GMP metabolism across the Leptospira genus(Roman THIBEAUX - Leptospirosis,Other) - In Progress
- Fast and accurate identification of the medoid of a set of genomes(Olivier CHESNEAU - Collection of the Institut Pasteur (CIP)) - Awaiting Publication
- Quick phage data mining(Quentin LAMY-BESNIER - Bacteriophage, Bacterium, Host) - Closed

Julien GUGLIELMINI
After a PhD in Microbiology on bacterial toxin-antitoxin systems at the Free University of Brussels, I joined the Institut Pasteur for a 3 years postdoc in Eduardo Rocha’s lab. During this period, I performed comparative genomics and pylogenetic analysis on bacterial conjugation and type IV secretion systems. Then, I worked 2 years in Olivier Tenaillon’s team on the modelling and evolution of organismal complexity. I joined the HUB in 2015, and I am involved in phylogenetic and comparative genomics projects.
KeywordsGenomicsPhylogeneticsSequence analysisGenome analysisGeneticsEvolutionPopulation genetics
Organisms
ArchaeaBacteriaVirus
Projects (12)
- Centrosome and basal body function in human parasites(Philippe BASTIN - Trypanosome Cell Biology) - New
- Evaluation of the mutation rate per site and dN/dS in the genomes of Yersinia enterocolitica(Cyril SAVIN - Yersinia) - Awaiting Publication
- Phylogenetic analysis of HHD-PDZ containing proteins(Nicolas WOLFF - Channel Receptors) - Closed

Kenzo-Hugo HILLION
After a Master degree in Genetics at Magistère Européen de Génétique, Paris Diderot, I did a second Master in bioinformatics at University of Nantes where I focused my work on the study of mapping strategy for allele specific analysis at the bioinformatics platform of Institut Curie. I then joined Institut Pasteur to work on an ELIXIR project related to the bio.tools registry through the development of a dedicated tool and the participation of several workshops and hackathons. As an engineer of the bioinformatics and Biostatistics Hub, I am involved in several projects from Differential Analysis of RNA-seq data to Metagenomics. I am also in charge of the maintenance of the Galaxy Pasteur instance.
KeywordsChIP-seqEpigenomicsGenomicsSequence analysisProgram developmentDatabases and ontologiesSofware development and engineeringGeneticsData integrationRead mappingWorkflow and pipeline developmentConfocal Microscopy
Organisms
Projects (4)
- 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

Hanna JULIENNE
I am seeking to apply my knowledge in computer science and statistics to understand real world data. I have interdisciplinary background spanning complex systems, Big Data, machine learning, biostatistics and genomics. I have completed a PhD in which I applied clustering and PCA to epigenomics data and discovered new insights on the coupling between replication and epigenetics. I worked at Dataiku, a dynamic start up in which I was actively engaged to help their clients to build their Big Data strategy and draw value from their data. I studied the human microbiota during two years at MetaGenoPolis (MGP), an innovative research center. We aim at improving human health by developing strategies (eg. nutritional, therapeutical, preventive…) to restore dysbiosed microbiota with our industrial and academical partners. I currently work in the statistical genetics group at the Pasteur Institut where I apply my software development and data science skills to quantify the impact of the human genome variation on diverse health parameters.
KeywordsClusteringData managementGenomicsGenome analysisExploratory data analysisGeneticsComparative metagenomicsDimensional reductionMultidimensional data analysis
Organisms
Projects (2)
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

Frédéric LEMOINE
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.
KeywordsAlgorithmicsData managementPhylogeneticsSequence analysisDatabaseGenome analysisProgram developmentScientific computingDatabases and ontologiesSequencingWorkflow and pipeline development
Organisms
Projects (1)
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

Gael MILLOT
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KeywordsImage analysisStatistical inferenceBiostatisticsGeneticsSequencingDiagnostic tools
Organisms
Projects (22)
- Research of homopolymers in the integron integrase genes(Céline LOOT - Bacterial Genome Plasticity) - In Progress
- Effect of Chlamydia trachomatis infection on histone methylation and consequences(Agathe SUBTIL - Cellular Biology of Microbial Infection) - Pending
- Modification and reliance of Chlamydia trachomatis on host cell metabolism(Agathe SUBTIL - Cellular Biology of Microbial Infection) - Awaiting Publication

Amandine PERRIN
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KeywordsGenetics
Organisms
Projects (3)
- Add unit tests to IntegronFinder(Eduardo ROCHA - Microbial Evolutionary Genomics) - Closed
- Modeling mitochondrial metabolism dormant Cryptococcus neoformans(Benjamin HOMMEL - Molecular Mycology) - Closed
- a web interface for MacSyFinder (a tool to detect macromolecular systems in genomes).(Eduardo ROCHA - Microbial Evolutionary Genomics) - Closed

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

Anna ZHUKOVA
A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, knowledge inference, ontologies and data visualisation.
KeywordsAlgorithmicsData 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
Organisms
VirusHuman Immunodeficiency virus (HIV)
Projects (6)
- 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
Amaury VAYSSE
Amaury
KeywordsOrganisms
Human
Projects (6)
- Understanding the mode of action of epigenetic inhibitors active against Plasmodium falciparum(Irina DOBRESCU - Biology of Host-parasite Interactions) - Pending
- A cost-effective molecular Tool for Strengthening Antimalarial drug Resistance surveillance in Africa (TSARA)(Didier MENARD - Group : Malaria Genetic and Resistance) - In Progress
- Search for genetic determinants of aminoglycoside tolerance(Zeynep BAHAROGLU - Bacterial Genome Plasticity) - In Progress
Related projects (48)
Genotype to phenotype analysis of immune responses in chronic inflammatory diseases
Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing
Evolutionary relationships between giant viruses and eukaryotes
Candida albicans population genomics
Phylogenetic analysis of the Leishmania HSP70 protein family
Whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology
Methods to identify and characterize orthologs of genes encoding small proteins
Characterization of an unusual Leishmania major HSP70-related protein
Updating the Topo IB gene tree
Regulation by phase variation and attenuation: looking for leader peptides containing repeats in the intergenic regions of streptococcal genomes
Pasteur International Bioresources Network (PIBnet) bioinformatics: whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology
N/A
L'analyses phylogénétique par séquence protéique, temporal et géographical
Comparative genomic and phylogenetic analysis of 14 Clostridium tetani strains
Bioinformatic analysis of phospholipase A2 (PLA2) from P. falciparum
Comparative genomic and phylogenetic analysis of Clostridium baratii strains
Comparative genomic and phylogenetic analysis of Clostridium botulinum strains
Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation
Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases
Novel protein interaction in the assembly of photosynthetic prokaryotic complexes
Histone Methyltransferase and Demethylase in Leishmania
viral evolution around Ebola Treatment Center in Macenta
Genomic determinants for initiation and length of natural antisense transcripts in a compact eukaryotic genome and phylogenetic analysis of related Entamoeba species
Next Generation Surveillance of Salmonella and Shigella infections
Fusion proteins in mammals and yeasts
Antimalarial drug resistance in Africa: A comprehensive molecular analysis of the emergence of artemisinin resistant parasites in Africa
Ecological evolution in Klebsiella
DNMT and RNMT in Leishmania
Evaluation of the mutation rate per site and dN/dS in the genomes of Yersinia enterocolitica
Setup of bioinformatic pipelines for paleo(meta)genomics
Centrosome and basal body function in human parasites
Comparative genomics analysis of cyclic-di-GMP metabolism across the Leptospira genus
Insect Vector Genomics
JASS: an online tool for the joint analysis of GWAS summary statistics
- Vincent GUILLEMOT
- Hanna JULIENNE
- Pierre LECHAT + 1 operator
Genetic profile of patients with dyslexia
Heritability of the melatonin synthesis pathway in Autism Spectrum Disorders
Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur
- Pascal CAMPAGNE
- Vincent GUILLEMOT
- Rachel TORCHET + 1 operator