Frédéric Chalmel Integrative genomics, physiology and physiopathology of the male urogenital tract

Course and current status

Personal information

Date and place of birth: August 13th 1977, Paris 10ième

Nationality : French

Marital status : Couple, two daughters

Current position : Research Associate (Chargé de Recherche 1ère classe), Inserm U1085-Irset

Professional address : Inserm U1085-Irset, Université de Rennes 1, 263 av. du Général Leclerc, 35042 Rennes, France


Work experience

2013: Research Associate (CR1), team “Viral and Chemical Environment and Reproduction”, lead by Pr. B. Jégou and Dr. N. Dejucq-Rainsford, Inserm U1085-Irset, Rennes, France.

2007-2013: Research Associate (CR2 then CR1 in 2011), team “Reproductive and Cancer Genomics”, lead by Dr M. Primig, Inserm U1085-Irset, Rennes, France.

2005 - 2007: Postdoctoral fellowship in the team of Dr. M. Primig, Biozentrum, University of Basel, Switzerland.

2001 – 2005: PhD in bioinformatics, supervised by O. Poch, team “Integrative Bioinformatics and Genomics” (LBGI.), IGBMC, Strasbourg, France.


Degrees and diplomas

2015 : Habilitation to supervise research (HDR), University of Rennes 1, Rennes

2005 : PhD in bioinformatics, IGBMC, Strasbourg, France

2000-2001 : DEA in Biomathematics, University of Paris VI, Paris

1998-2001 : Master in Biochemistry, University of Paris VI, Paris

Scientific summary

Biographical sketch: I have a 15 years’ experience in functional genomics. For the last 10 years my researches have been focusing on the “omic-biology” of mammalian spermatogenesis with emphasis on transcriptomic and integrative genomics. I recently joined Nathalie Dejucq-Rainsford & Bernard Jégou’s lab (January 2013) to deploy integrative genomics methodologies applied to reproductive biology and reproductive toxicology. These researches focus on the effects of xenobiotics on transcriptional and epigenetic dynamics during male germ cell differentiation as well as gonad development in human.


Reproductive toxicogenomics and predictive toxicology: The “omics” technologies represent extremely powerful tools to highlight toxicogenomic signatures with a high predictive potential as it is well established that two substances with similar transcriptional signatures/responses are usually associated with close toxicological effects. Our aims are to: 1) gain insight into the mechanisms of actions several environmental contaminants that exhibit endocrine disrupting and/or repro-toxic properties by making use of integrative toxicogenomic approaches; 2) Identify, classify and prioritize novel endocrine disruptors and repro-toxicants by combining bioinformatics approaches and massive toxicogenomics available in public repositories.


Reprogenomics & the genome biology of mammalian testis: The current axis intends to improve the knowledge on testis development and function in humans, and on how endocrine disruptors and/or repro-toxicants may interfere with these biological processes. To gain insight into molecular mechanisms controlling these processes we study the transcriptional regulatory network that governs spermatogenesis and gonad development in human and rodents. In 2007, we were among the first to publish highly reproducible genome-wide testicular expression data for rodents and human which have been a rich source of discovery for the basic and clinical research communities (Chalmel and Rolland et al., PNAS, 2007). In 2012, we published the post-natal human testicular transcriptome at the level of cell populations (Chalmel et al. , Hum. Reprod., 2012). Since 2011, I’m working on the comprehensive transcriptome analysis of different adult testicular cell populations in the rat (Chalmel et al., 2014) and in humans (in prep.) using deep sequencing (RNA-seq). In addition, we have recently initiated a project aiming at characterizating the transcriptional lanscape of human fetal gonads.


Genomic tools and data dissemination: To support our genome biological research, I am also involved in the development and maintenance of bioinformatics tools for high-throughput data analysis (AMEN,, GPSy, and dissemination (the Reproductive Genomics Viewer, that facilitate the arduous and challenging task of data analysis and interpretation (Chalmel et al., 2008; Britto et al., 2012; Darde et al., 2015).

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