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.

• Analyse statistique de données de phénotypage à haut débit(Melanie LEGRAND - Fungal Biology and Pathogenicity) - Pending
• Identification of the genetic basis of bacteriophage-resistant isolates(Laurent DEBARBIEUX - Molecular Biology of Gene in Extremophiles) - Pending
• Effect of metabolic disturbance on the host transcriptional profile during Chlamydia infection(Agathe SUBTIL - Cellular Biology of Microbial Infection) - Pending

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.

• Mitochondrial polarization identifies functionally mature human NK cells(Laura SURACE - Innate Immunity) - In Progress
• Identification of mouse skin macrophage subpopulations(Dorian OBINO - Pathogenesis of vascular infections) - In Progress
• Identifying subpopulation-specific signatures of tuberculosis persistence for enhanced diagnostics.(Giulia MANINA - Microbial Individuality and Infection) - In Progress

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.

• Long-term preservation of a Campylobacter fetus strain and genomic stability(Dominique CLERMONT - Collection of the Institut Pasteur (CIP)) - In Progress
• DNMT and RNMT in Leishmania(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress
• Séquençage à haut débit (NGS) et traitement de séquences ADN des domaines variables d’anticorps simple chaine d’alpaga (domaines VHH ou Nanobodies®)(Margarida GOMES - Antibody Engineering) - In Progress

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.

• 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) - Awaiting Publication
• Phylogenetic analysis of insect-specific flaviviruses(Artem BAIDALIUK - Insect-Virus 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.

• 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

Najwa TAIB

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.

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.

• Modeling mitochondrial metabolism dormant Cryptococcus neoformans(Benjamin HOMMEL - Molecular Mycology) - Closed
• Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment(Alice MEIGNIÉ - Viral Genomics and Vaccination) - Closed
• Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation(Olivier GASCUEL - Evolutionary Bioinformatics) - In Progress