PUTHIER Denis

Telephone
+33 (0)4 91 82 87 13
Présentation

Scientific and administrative responsabilities

 

Research Interests

Prof. Puthier has been Professor in bioinformatics and genomics at AMU since 2005. He has a long-standing experience in epigenomic data analysis. After completing a PhD in oncoimmunology at the University of Nantes (1999, Inserm U463), he joined the CIML (Dr. C. Nguyen’s team) and started experimenting with microarrays and developed the project “Molecular microdissection of the thymus” in the early 2000s. He is leading the group "Bioinformatics of epigenomics" at TAGC. His main research topics are related to the understanding of the transcriptional mechanisms driving cell development with a particular interest in epigenomics, non-coding RNA world. With his long-time collaborator, Salvatore Spicuglia, he has been studying numerous features of the regulatory elements controlling T-cell development that led to the discovery of Epromoters, a particular class of promoters with enhancer activity that are involved in topologically coordinated gene responses. Additionally, Prof. Puthier has a long lasting experience in software development and is leading the “Python GTF toolkit” project, a set of utilities for handling of genomic coordinates and the Scigenex project for single-cell and spatial transcriptomic data analysis. He is co-head of the Transcriptomics and Genomics Marseille Luminy (TGML) sequencing facility and deputy director of education at the Marseille Institute for Rare Diseases (MarMaRa). Prof. Puthier is highly involved in training abroad (e.g. University of Saint JĂ©r

Teaching 

2004-current, Teacher in Genomics, Bioinformatics, Informatics and Statistics, Aix-Marseille University, France (192 hours/year in Bachelor & Master levels)
2013-2022 Trainer in Genomics and Bioinformatics, AVIESAN-IFB-Inserm Bioinformatics school level I, Station Biologique de Roscoff, France (40 hours/year)
2021-2022 Trainer in Genomics and Bioinformatics, AVIESAN-IFB-Inserm Bioinformatics school level II, Station Biologique de Roscoff, France (40 hours/year)
2022-current Co-organizer of MarMaRa’s summer School (1 week).
2022-current MarMaRa PhD Program, Aix-Marseille University, France (16/year hours).

Collaborations 

Dr. Salvatore Spicuglia, Epigenomic characterization of T-cell development, TAGC, AMU, France (14 publications); Dr. Saadi Khochbin, Epigenomic characterization of spermiogenesis, IAB, Grenoble, France (6 publications); Dr. Vahid Asnafi, Epigenomic characterization of T-cell leukemia, Necker Hospital, Paris, France (4 publications); Prof. Cécile Capponi, Machine-Learning applied to functional annotation of the genome, LIS, AMU, France (3 publications); Prof. Kaj Chokeshaiusaha, Epigenomic characterization of animal genomes using bioinformatics, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-Ok, Thailand (6 publications); Prof EA Donadi, Transcriptomic analyzes to decipher the physiopathology of diabetes mellitus, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Brazil (3 publications); Dr. Magali Irla, Genomic characterization of the thymus, CIML, AMU, France (4 publications, one publication under preparation); Prof. Arnauld Sergé, Thymic medulla characterization, Laboratory of Adhesion and Inflammation, LAI, AMU, France (one publication under preparation).

Funding

 

External references

 SOFTWARE DEVELOPMENT (see https://github.com/dputhier )
2023 - Scigenex ; 2024 - STarlight; 2021 - OLOGRAM-MODL ; 2020 - OLOGRAM ; 2019 - Python GTF toolkit; 2019 - libgtftk ; 2009 - RTools4TB ; 2008 - TranscriptomeBrowser ;

Author publications