Publications

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Polygenic Adaptation: Integrating Population Genetics and Gene Regulatory Networks
Maud Fagny, Frédéric Austerlitz
PDF DOI Project
Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks
Maud Fagny, Marieke Lydia Kuijjer, Maike Stam, Johann Joets, Olivier Turc, Julien Roziere, Stéphanie Pateyron, Anthony Venon, Clémentine Vitte
PDF DOI Project
Sex differences in gene expression and regulatory networks across twenty-nine human tissues
Camila Lopes-Ramos, Cho-Yi Chen, Marieke L. Kuijjer, Joseph N. Paulson, Abhijeet R. Sonawane, Maud Fagny, John Platig, Kimberly Glass, John Quackenbush, Dawn L. DeMeo
PDF DOI Project
Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways
R. Chaix, M. Fagny, M. Cosin-Tomás, M. Alvarez-López, L. Lemee, B. Regnault, R.J. Davidson, A. Lutz, P. Kaliman
PDF DOI Project
PUMA: PANDA Using MicroRNA Associations
Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass
PDF DOI Project
Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function
Maud Fagny, John Platig, Marieke Lydia Kuijjer, Xihong Lin, John Quackenbush
PDF DOI Project
Deregulation of microRNA expression in monocytes and CD4+ T lymphocytes from patients with axial spondyloarthritis
Olivier Fogel, Andreas Bugge Tinggaard, Maud Fagny, Nelly Sigrist, Elodie Roche, Laurence Leclere, Jean-François Deleuze, Frederic Batteux, Maxime Dougados, Corinne Miceli-Richard, Jörg Tost
PDF DOI
Connectivity of variants in eQTL networks dictates reproducibility and functionality
Sheila Gaynor, Maud Fagny, Xihong Lin, John Platig, John Quackenbush
PDF DOI Project
Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation
Lucas T. Husquin, Maxime Rotival, Maud Fagny, Hélène Quach, Nora Zidane, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Hugues Aschard, Etienne Patin, Lluis Quintana-Murci
PDF DOI Project
Epigenome-wide DNA methylation profiling in Progressive Supranuclear Palsy reveals major changes at DLX1
Axel Weber, Sigrid C. Schwarz, Jörg Tost, Dietrich Trümbach, Pia Winter, Florence Busato, Pawel Tacik, Anita C. Windhorst, Maud Fagny, Thomas Arzberger, Catriona McLean, John C. van Swieten, Johannes Schwarz, Daniela Vogt Weisenhorn, Wolfgang Wurst, Till Adhikary, Dennis W. Dickson, Günter U. Höglinger, Ulrich Müller
PDF DOI
Histopathological Image QTL Discovery of Immune Infiltration Variants
Joseph D. Barry, Maud Fagny, Joseph N. Paulson, Hugo J.W.L. Aerts, John Platig, John Quackenbush
PDF DOI Project
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
PDF DOI Project
Epigenetic clock analysis in long-term meditators
Raphaëlle Chaix, Maria Jesús Alvarez-López, Maud Fagny, Laure Lemee, Béatrice Regnault, Richard J. Davidson, Antoine Lutz, Perla Kaliman
PDF DOI Project
Understanding Tissue-Specific Gene Regulation
Abhijeet Rajendra Sonawane, John Platig, Maud Fagny, Cho-Yi Chen, Joseph Nathaniel Paulson, Camila Miranda Lopes-Ramos, Dawn Lisa DeMeo, John Quackenbush, Kimberly Glass, Marieke Lydia Kuijjer
PDF DOI Project
Regulatory network changes between cell lines and their tissues of origin
Camila M. Lopes-Ramos, Joseph N. Paulson, Cho-Yi Chen, Marieke L. Kuijjer, Maud Fagny, John Platig, Abhijeet R. Sonawane, Dawn L. DeMeo, John Quackenbush, Kimberly Glass
PDF DOI Project
Exploring regulation in tissues with eQTL networks
Maud Fagny, Joseph N. Paulson, Marieke L. Kuijjer, Abhijeet R. Sonawane, Cho-Yi Chen, Camila M. Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig
PDF DOI Project
Trends in DNA Methylation with Age Replicate Across Diverse Human Populations
Shyamalika Gopalan, Oana Carja, Maud Fagny, Etienne Patin, Justin W. Myrick, Lisa M. McEwen, Sarah M. Mah, Michael S. Kobor, Alain Froment, Marcus W. Feldman, Lluis Quintana-Murci, Brenna M. Henn
PDF DOI Project
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease
Steve Horvath, Michael Gurven, Morgan E. Levine, Benjamin C. Trumble, Hillard Kaplan, Hooman Allayee, Beate R. Ritz, Brian Chen, Ake T. Lu, Tammy M. Rickabaugh, Beth D. Jamieson, Dianjianyi Sun, Shengxu Li, Wei Chen, Lluis Quintana-Murci, Maud Fagny, Michael S. Kobor, Philip S. Tsao, Alexander P. Reiner, Kerstin L. Edlefsen, Devin Absher, Themistocles L. Assimes
PDF DOI Project
Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes
Matthieu Deschamps, Guillaume Laval, Maud Fagny, Yuval Itan, Laurent Abel, Jean-Laurent Casanova, Etienne Patin, Lluis Quintana-Murci
PDF DOI Project
The epigenomic landscape of African rainforest hunter-gatherers and farmers
Maud Fagny, Etienne Patin, Julia L. MacIsaac, Maxime Rotival, Timothee Flutre, Meaghan J. Jones, Katherine J. Siddle, Helene Quach, Christine Harmant, Lisa M. McEwen, Alain Froment, Evelyne Heyer, Antoine Gessain, Edouard Betsem, Patrick Mouguiama-Daouda, Jean-Marie Hombert, George H. Perry, Luis B. Barreiro, Michael S. Kobor, Lluis Quintana-Murci
PDF DOI Project
Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing data sets
Maud Fagny, Etienne Patin, David Enard, Luis B. Barreiro, Lluis Quintana-Murci, Guillaume Laval
PDF DOI Project