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Génétique Quantitative et Évolution - Le Moulon



Postdoctoral Fellow, INRAE

Role of transposable elements in the tissue-specific enhancer-mediated regulation of gene expression in Maize

  • 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
  • Ferme du Moulon
  • F-91190 Gif-sur-Yvette

Positions and education

  • 2019-01-01 to present: Postdoctoral fellow, GQE-Le Moulon, INRA, 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 complex phenotypes at the molecular level, and their evolution.

I'm currently developping a project aiming at studying the role of transposable elements in the enhancer-mediated tissue-specific regulation of gene expression in maize tissues. The aim is to understand how transposable elements inserted in the neighborhood of genes have been shaping the tissue-specific gene regulatory networks. To this end, I use maize as a model, and I combine approaches from comparative genomics, systems biology and computational biology.

I am also investigating whether the high variability in intergenic transposable elements insertions between maize lines may be at the origin of genotype-specific, tissue-specific gene expression patterns. To this end, I uses the GeneAtlas dataset, that includes genomic and transcriptomic data from 13 tissues from 8 European and North American maize lines. My research takes place within the French investment for the future Amaizing program.

I did my PhD in population genomics and epigenomics. I studied the impact of the global environment on the genetic and epigenetic diversity. I investigated the role of a particular type of positive selection, selective sweeps, in shaping the human genome diversity. I also investigated the relative impact of genetic and environmental factors on the DNA methylation profiles between population.

During my postdocs, I started investigating the genetic bases of the regulation of the expression of complex phenotypes, using system biology approaches based on bipartite network representation. I notably characterized the regulatory role of germinal mutations increasing the risk to develop cancers.

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

For more details on my research and links to my publications in open access, please see my personal webpage.

My ORCID profile.

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


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
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