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Génétique Quantitative et Évolution - Le Moulon



Junior Investigator, INRAE

Molecular bases of maize adaptation to single and combined environmental constraints

  • Computational biology,
  • System Biology,
  • Gene networks,
  • Population genomics,
  • Epigenetics/Epigenomics,
  • Transcriptomics,
  • Human Genomics,
  • Maize Genomics,
  • Transposable elements


+33 (0)1 69 33 23 51


  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • 12 route 128
  • 91190 Gif-sur-Yvette

Positions and education

  • 2021-07-01 to present : Junior Researcher, GQE-Le Moulon, INRAE, Gif-sur-Yvette, France
  • 2020-04-01 to 2021-06-30 : Postdoctoral fellow, MNHN, Eco-anthropology, CNRS, Paris, France - Marie Sklodowska-Curie (IF) “PATTERNS” grant
  • 2019-01-01 to 2020-03-31: Postdoctoral fellow, GQE-Le Moulon, INRAE, Gif-sur-Yvette, France
  • 2018-01-09 to 2018-10-31 : Postdoctoral fellow, LEE, CNRGH, Evry, France
  • 2015-11-09 to 2017-12-31: Postdoctoral fellow, Quackenbush lab, Harvard T.H. Chan School of Public Health, Boston, MA, USA
  • 2012-09-01 to 2015-08-31: PhD student, Human Evolutionnary Genetics, Institut Pasteur, Paris, France
  • 2009-09-01 to 2012-06-30: Student at the Ecole Normale Supérieure de Lyon, Lyon, France

Research Interests

My research is focused on understanding the regulation of the expression of genes determining complex phenotypes at the molecular level, and their evolution. For more details on my research and links to my publications in open access, please see my personal webpage.

Current Collaborations

  • International: John Quackenbush (Harvard T.H. Chan School of Public Health, Boston, MA, USA); Kimberly Glass (Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA); Megha Padi (University of Arizona, Tucson, AZ, USA); Marieke Kuijjer, NCMM, Oslo, Norway; Maike Stam (University of Amsterdam, Amsterdam, The Netherlands); Shujun Ou (Iowa State University, Ames, IA, USA).

  • National: Frédéric Austerlitz and Raphaëlle Chaix from the Éco-anthropologie lab, Musée de l’Homme, Paris, France; Guillaume Laval, Etienne Patin and Lluis Quintana-Murci from the Human Evolutionary Genetics lab, Institut Pasteur, Paris, France; Hadi Quesneville from the URGI, INRA, Versailles, France.

  • Local: Clémentine Vitte, Maud Tenaillon, Amandine Cornille, Maéva Mollion and Johann Joets from GEvAD; Mélisande Blein-Nicolas and Élodie Marchadier from BASE; Stéphane Nicolas, Laurence Moreau and Alain Charcosset from GQMS .


My PhD was funded by a doctorate fellowship from the École Normale Supérieure de Lyon. In 2019, I received a Marie Słodowska Curie Individual Fellowship. My project, PATTERNS, aims at studying the polygenic selection targeting the regulatory regions of the genome and will be done in collaboration with Frédéric Austerlitz (Musée de l’Homme, Paris).

Useful links

My ORCID profile.

My Google Scholar profile with interesting statistics about my publications can be found here.


  • Stone K., Platig J., Quackenbush J., Fagny M. . (2024) Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. Systems Biology,
  • Ben Guebila M., Weighill D., Lopes-Ramos CM., Burkholz R., Pop RT., Palepu K., Shapoval M., Fagny M. , Schlauch D., Glass K., Altenbuchinger M., Kuijjer ML., Platig J., Quackenbush J.. (2022) An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Methods, 5 (19) 511-513
  • Fagny M. , Glass K., Kuijjer ML.. (2022) Editorial: Applications and Methods in Genomic Networks. Front. Genet., (13) 936015
  • Gaynor SM., Fagny M. , Lin X., Platig J., Quackenbush J.. (2022) Connectivity in eQTL networks dictates reproducibility and genomic properties. Cell Reports Methods, 5 (2) 100218
  • Fagny M. , Kuijjer ML., Stam M., Joets J., Turc O., Rozière J., Pateyron S., Venon A., Vitte C.. (2021) Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Frontiers in Genetics, (11) 1703
  • Fagny M. , Austerlitz F.. (2021) Polygenic Adaptation: Integrating Population Genetics and Gene Regulatory Networks. Trends in Genetics, 7 (37) 631-638
  • Chaix R., Fagny M. , Cosin-Tomás M., Alvarez-López M., Lemee L., Regnault B., Davidson RJ., Lutz A., Kaliman P.. (2020) Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways. Brain, Behavior, and Immunity, (84) 36-44
  • Fagny M. , Platig J., Kuijjer ML., Lin X., Quackenbush J.. (2020) Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. Br J Cancer, 4 (122) 569-577
  • Lopes-Ramos CM., Chen CY., Kuijjer ML., Paulson JN., Sonawane AR., Fagny M. , Platig J., Glass K., Quackenbush J., DeMeo DL.. (2020) Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports, 12 (31) 107795
  • Barry JD., Fagny M. , Paulson JN., Aerts HJWL., Platig J., Quackenbush J.. (2018) Histopathological Image QTL Discovery of Immune Infiltration Variants. iScience, (5) 80-89
  • Weber A., Schwarz SC., Tost J., Trümbach D., Winter P., Busato F., Tacik P., Windhorst AC., Fagny M. , Arzberger T., McLean C., van Swieten JC., Schwarz J., Vogt Weisenhorn D., Wurst W., Adhikary T., Dickson DW., Höglinger GU., Müller U.. (2018) Epigenome-wide DNA methylation profiling in Progressive Supranuclear Palsy reveals major changes at DLX1. Nature Communications, 1 (9)
  • Chaix R., Alvarez-López MJ., Fagny M. , Lemee L., Regnault B., Davidson RJ., Lutz A., Kaliman P.. (2017) Epigenetic clock analysis in long-term meditators. Psychoneuroendocrinology, (85) 210-214
  • Fagny M. , Paulson JN., Kuijjer ML., Sonawane AR., Chen CY., Lopes-Ramos CM., Glass K., Quackenbush J., Platig J.. (2017) Exploring regulation in tissues with eQTL networks. PNAS, 37 (114) E7841-E7850
  • Gopalan S., Carja O., Fagny M. , Patin E., Myrick JW., McEwen LM., Mah SM., Kobor MS., Froment A., Feldman MW., Quintana-Murci L., Henn BM.. (2017) Trends in DNA Methylation with Age Replicate Across Diverse Human Populations. Genetics,
  • Lopes-Ramos CM., Paulson JN., Chen CY., Kuijjer ML., Fagny M. , Platig J., Sonawane AR., DeMeo DL., Quackenbush J., Glass K.. (2017) Regulatory network changes between cell lines and their tissues of origin. BMC Genomics, 1 (18) 723
  • Paulson JN., Chen CY., Lopes-Ramos CM., Kuijjer ML., Platig J., Sonawane AR., Fagny M. , Glass K., Quackenbush J.. (2017) Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics, 1 (18)
  • Sonawane AR., Platig J., Fagny M. , Chen CY., Paulson JN., Lopes-Ramos CM., DeMeo DL., Quackenbush J., Glass K., Kuijjer ML.. (2017) Understanding Tissue-Specific Gene Regulation. Cell Reports, 4 (21) 1077-1088
  • Deschamps M., Laval G., Fagny M. , Itan Y., Abel L., Casanova JL., Patin E., Quintana-Murci L.. (2016) Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. Am. J. Hum. Genet., 1 (98) 5-21
  • Horvath S., Gurven M., Levine ME., Trumble BC., Kaplan H., Allayee H., Ritz BR., Chen B., Lu AT., Rickabaugh TM., Jamieson BD., Sun D., Li S., Chen W., Quintana-Murci L., Fagny M. , Kobor MS., Tsao PS., Reiner AP., Edlefsen KL., Absher D., Assimes TL.. (2016) An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biology, 1 (17)
  • Fagny M. , Patin E., MacIsaac JL., Rotival M., Flutre T., Jones MJ., Siddle KJ., Quach H., Harmant C., McEwen LM., Froment A., Heyer E., Gessain A., Betsem E., Mouguiama-Daouda P., Hombert JM., Perry GH., Barreiro LB., Kobor MS., Quintana-Murci L.. (2015) The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nature Communications, (6)
  • Fagny M. , Patin E., Enard D., Barreiro LB., Quintana-Murci L., Laval G.. (2014) Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing data sets. Mol. Biol. Evol., 7 (31) 1850-1868