CV Science

Frédéric Chalmel Physiology & physiopathology of the urogenital tract (UrGenT)

Course and current status

Personal information

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

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

•    2024-present: Chief Scientific Officer at the biotech company SciLicium (20% part-time position) 

•    2022-present: Inserm U1085-Irset, co-head of the UrGenT team with with N. Dejucq-Rainsford.

•    2019-present: Inserm U1085-Irset, Senior scientist at Inserm (DR2).

•    2013-present: Inserm U1085-Irset, head of the “Physiogenomics and toxicogenomics of the urogenital tract” group in the UrGenT team headed by N. Dejucq-Rainsford.

•    2007-2013: Inserm U1085-Irset, Post-doctorate, and then researcher in the team “Reproductive and Cancer Genomics” headed by M. Primig.

•    2005-2007: Biozentrum (Basel), Post-doctorate in the transcriptomic platform headed by M. Primig.

•    2001 - 2005: IGBMC, PhD in bioinformatics under the supervision of D. O. Poch.

 

Degrees and diplomas

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

2001 – 2005 : PhD in Bioinformatics, under the supervision of Dr O. Poch,

Laboratoire de Bioinformatique et Génomique Intégratives (LBGI.),

IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), Strasbourg.

2000 – 2001 : Master (M2) in Biomathematics. University of Paris VI.

1998 – 2000 : Master (M1) in Biochemistry, University of Paris VI.

1996 – 1998 : Associate's degree in Life Sciences, University of Paris XI.

1995 – 1996 : PCS0 et Baccalauréat S, option SVT, Faculté Paris XI.

 

Professional memberships

•    2025: Coordinator of the “Biomathematics, Bioinformatics and Biophysics for Reproduction” working group within the French Reproduction Research Network (GdR Repro).

•    2023: POC-member of the European Testis Workshop (ETW), Caux Palace, Montreux, France.

•    2023-present: Management Committee (MC) member of ANDRONET - "European Andrology Network– research coordination, education and public awareness”. 

•    2022-present: Member of the Inserm specialized scientific commissions (CSS3) ‘Physiology and physiopathology of large systems”.

•    2021: POC-member of the European Testis Workshop (ETW), Virtual Edition.

•    2020-present: Member of the University Hospital Federation (FHU) Camin (Cancer, micro-environnement and innovation) and workpackage leader.

•    2018-present: Member of the Permanent Scientific Committee of the European Testis Workshop, Obidos, Portugal.

•    2018: POC-member of the European Doctoral College on Environment and Health, Rennes, France.

•    2018-present: Academician of the European Academy of Andrology.

•    2015-2018: Member of the European Academy of Andrology, Rotterdam, France.

•    2016: POC-member of the European Testis Workshop (ETW), St Malo, France.

•    2016: POC-member of the European Congress of Andrology, Rotterdam, Netherlands.

•    2005-2007: Member of the Swiss Institute of Bioinformatics (SIB).

 

 

Awards

• 2024: Recipient of the RIPEC incentive award (Inserm).
• 2023: Personal letter of congratulations from the President and CEO of Inserm, Prof. Didier Samuel, for my participation in several European projects (HuGoDeCA, FREIA, PARC, MERLON).

• 2016 : « Remarkable evaluation » attributed by the Director General of the French National Institute of Health and Medical Research (Inserm) for his research activities during the 2014-2015 period.

• 2015: International Network of Young Researchers in Male Fertility (INYRMF) “Young Researcher Award 2015”, Florence, Italia.
• 2014: 8^th European Congress of Andrology (ECA) Travel grants, Barcelona, Spain.

 

10 publications out of a list of 101 scientific publications and 6 reviews (h index = 33, 3,764 citations)

• Lardenois A*, Suglia A*, …, Chalmel F* (co-corresponding author), Rolland AD*. Single-cell exploration of gonadal somatic cell lineage specification during human sex determination. Dev Cell. 2025. PMID:41072414
• Bellutti L*, Chan Sock Peng E*, …, Chalmel F (co-corresponding author), Livera G. Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice. Nucleic Acids Res. 2025. PMID:40103226
• Lecuyer GCV, Lardenois A, Chalmel F; Uro-oncogenomics Viewer Group. UncoVer: A Web-based Resource for Single-cell and Spatially Resolved Omics Data in Uro-oncology. . Eur Urol Oncol. 2024 Apr 29:S2588-9311(24)00100-7. doi: 10.1016/j.euo.2024.04.008. PMID: 38688769
• Souali-Crespo, …, Chalmel F*, Ghyselinck N*. Loss of NR5A1 in mouse Sertoli cells after sex determination changes cellular identity and induces cell-death by anoikis. Development. 2023.
• Gregoire EP, …, Chalmel F, Schedl A, Chaboissier MC. The -KTS splice variant of WT1 is essential for ovarian determination in mice. Science. 2023 Nov 3;382(6670):600-606. doi: 10.1126/science.add8831. Epub 2023 Nov 2. PMID: 37917714
• Saout JR, …, Chalmel F. Single-cell Deconvolution of a Specific Malignant Cell Population as a Poor Prognostic Biomarker in Low-risk Clear Cell Renal Cell Carcinoma Patients. Eur Urol. 2023 Feb 15:S0302-2838(23)02580-0. doi: 10.1016/j.eururo.2023.02.008. Online ahead of print. PMID: 36801089
• Lecluze E, …, Chalmel F. Dynamics of the transcriptional landscape during human fetal testis and ovary development. Hum Reprod. 2020 May 1;35(5):1099-1119. doi: 10.1093/humrep/deaa041. PMID: 32412604.
• Rolland AD, …, Chalmel F*, Jégou B*. RNA profiling of human testicular cells identifies syntenic lncRNAs associated with spermatogenesis. Hum Reprod. 2019 Jul 8;34(7):1278-1290. doi: 10.1093/humrep/dez063. PubMed PMID: 31247106.
• Jégou B., …, Chalmel F. (2017). Meiotic Genes Are Enriched in Regions of Reduced Archaic Ancestry. Mol Biol Evol. 2017 Aug 1;34(8):1974-1980.
• Chalmel F., et al. (2007). The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci USA 104:8346-51.

29 presentations as invited speakers

 

-          Grants

2025 : University of Rennes « Projets scientifiques émergents 2025 » (PI), (10 k€)

2024 : Ligue contre le cancer 35 (PI), (30 k€)

2023 : UE, project “Merging scientific Evidence with Regulatory practices and Leveraging identification Of endocrine disruptors using New approach methodologies” (MERLON) (Partner), (~717k€)

2023 : Inserm, Programme transversal "HuDeCA2 : Human Development Cell Atlas" (Partner), (216.0k€)

2022: UE, project PARC “Partnership for the Assessment of Risks from Chemicals” (Partner), (80k€)

2021 : ANR, projet « INNATESTIS » (Partner), (118k€)

2021 : ANR, projet « InvitroSperm » (Partner), (125k€)

2020: Cancéropole Grand-Ouest, “Oncologie 4.0” (PI), (17.871k€)

2019 : Inserm, Programme transversal "HuDeCA : Human Development Cell Atlas" (Partner), (394.7k€)

2019 : ANR, project « SexDiff » (Partner), (151.632 k€)

2019: Région Bretagne, ½ allocation doctorale, (~50k€)

2019 : University of Rennes 1 « Collaborations internationales 2019 », (1k€)

2018 : ANSES, project Massive Attack (PI), (200 k€).

2018 : French Research National Agency (ANR), project « MEIOSIL » (partner), (141.7 k€)

2018 : UE, project “Female Reproductive toxicity of Endocrine disrupting chemicals (EDCs): a human evidence-based screening and Identification Approach” (FREIA), (~102k€)

2018 : University of Rennes 1 « Collaborations internationales 2018 », (1k€)

2018 : Doctoral scholarship from « La Ligue/ARED », (~102k€)

2017: Ligue contre le cancer 35, (30 k€)

2016 : Swiss National Foundation (SNF), project Sinergia (partner), (~590 kchf)

2016 : French Research National Agency (ANR), project « ARESSEC » (partner), (123 k€)

2016 : University of Rennes 1 « Projets scientifiques émergents 2011 », project PROMPTO (7.5 k€)

2014 : FEDER, «Compétitivité Régionale et Emploi», project Asquisition d’un SIHP en biosanté (20 k€).

2013 : Medical Research Foundation (FRM), project ChemPSy (294 k€).

2013 : ANSES, project ChemPSy (49,4 k€).

2011 : University of Rennes 1 « Projets scientifiques émergents 2011 », project FAIRE-seq (10 k€)

 

Patents

2023: METHODS FOR THE PROGNOSIS OF CLEAR CELL RENAL CELL CARCINOMA (PCT/IB2023/000051); Frédéric Chalmel (50%)

2014: METHODS AND PHARMACEUTICAL COMPOSITIONS FOR TREATMENT OF PROSTATE CANCER (PCT/EP2014/053144). Frédéric Chalmel (40%), Romain Mathieu (40%), Michael Primig (10%)

 

License

2023-present: TOXsIgN: a cross-species repository for toxicogenomic signatures (DA22342/CHALMEL/AF-GP_APP), company SciLicium

 

Startup

2019-present: Founder (2019) and Chief Scientific Officer (2024) of the biotech company SciLicium (Rennes)

2023 : Concours scientifique (2023)

 

Scientific summary

Since 2022, I co-lead the UrGenT team (Physiology and Physiopathology of the Urogenital Tract) alongside Dr. Nathalie DeJucq-Rainsford at the Research Institute for Environmental and Occupational Health (IRSET, UMR 1085) in Rennes. I have been working in the field of functional genomics since 2001, with a specialization in transcriptomics and integrative genomics applied to mammalian urogenital tract development and physiology.

I earned my PhD in Bioinformatics from the University of Strasbourg in 2005 under the supervision of Dr. Olivier Poch, focusing on retinal degeneration. Following my PhD, I completed a postdoctoral fellowship at the Biozentrum in Basel (Switzerland) within a transcriptomics platform led by Dr. Michael Primig, where I investigated the evolutionary conservation of gene expression programs controlling spermatogenesis in mammals (2005–2007). I then joined Prof. Bernard Jégou’s laboratory (GERHM, U625) in Rennes for a second postdoctoral position, pursuing the research initiated during my previous fellowship. In 2008, I was appointed as a Research Scientist (CR2) at Inserm, and in 2015, I obtained my Habilitation to Direct Research (HDR).

In 2013, I joined Dr. Nathalie DeJucq-Rainsford’s team at IRSET to co-supervise, together with Dr. A.-D. Rolland (Associate Professor, University of Rennes), the activities of the “Physiogenomics and Toxicogenomics of the Urogenital Tract” group. Since then, I have been advancing research on the effects of xenobiotics on human urogenital tract development and physiology, employing cutting-edge technologies such as single-cell and spatial genomics.

My team is actively involved in several European projects, including HuDeCA, FREIA, PARC, and MERLON, which focus on reproductive health and the impact of endocrine disruptors. Since 2017, I have also expanded my research to urological cancers, particularly clear cell renal carcinoma, applying integrative genomics to uncover novel insights into their pathophysiology.

As part of the Human Cell Atlas (HCA) initiative, my group contributes to building a comprehensive atlas of human embryonic and fetal cell types. I also lead the development of innovative bioinformatics tools and genomic resources—such as ReproGenomics Viewer, UncoVer, TOXsIgN, and AMEN—in collaboration with the GenOuest Bioinformatics Platform.

In addition, my research activities led me to co-found in 2019 a young innovative company, SciLicium, with my former PhD student, Dr. Thomas Darde. In 2023, I successfully passed the Inserm scientific mobility competition, allowing me to join SciLicium in January 2024 as Chief Scientific Officer (20%), where I contribute to the company’s strategic research and development programs at the interface between academic genomics and translational applications.