Maud Fagny

Chargée de Recherche INRAE - GQE Le Moulon - IDEEV - Gif-sur-Yvette, France
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Documents
Affiliation actuelle
  • Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon)
Contact

Présentation

Domaines de recherche

Sciences du Vivant [q-bio] Bio-Informatique, Biologie Systémique [q-bio.QM] Génétique des plantes Génétique des populations [q-bio.PE]

Compétences

Génomique Biologie des systèmes Réseaux de régulation Bioinformatique Analyses de données OMICS Programmation (bash, python, R, perl) Statistiques Épigénomique Transcriptomique Encadrement

Publications

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Publications

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An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks

Marouen Ben Guebila , Deborah Weighill , Camila Lopes-Ramos , Rebekka Burkholz , Romana Pop et al.
Nature Methods, 2022, 19 (5), pp.511-513. ⟨10.1038/s41592-022-01479-2⟩
Article dans une revue hal-03694550 v1
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Connectivity in eQTL networks dictates reproducibility and genomic properties

Sheila Gaynor , Maud Fagny , Xihong Lin , John Platig , John Quackenbush
Cell Reports Methods, 2022, 2 (5), pp.100218. ⟨10.1016/j.crmeth.2022.100218⟩
Article dans une revue hal-03694556 v1
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Editorial: Applications and Methods in Genomic Networks

Maud Fagny , Kimberly Glass , Marieke Kuijjer
Frontiers in Genetics, 2022, 13, pp.936015. ⟨10.3389/fgene.2022.936015⟩
Article dans une revue hal-03694544 v1
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Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks

Maud Fagny , Marieke Lydia Kuijjer , Maike Stam , Johann J. Joets , Olivier Turc et al.
Frontiers in Genetics, 2021, 11, ⟨10.3389/fgene.2020.606285⟩
Article dans une revue hal-03152056 v1
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Polygenic Adaptation: Integrating Population Genetics and Gene Regulatory Networks

Maud Fagny , Frederic Austerlitz
Trends in Genetics, 2021, 37 (7), pp.631-638. ⟨10.1016/j.tig.2021.03.005⟩
Article dans une revue hal-03100982 v1
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PUMA: PANDA Using MicroRNA Associations

Marieke Kuijjer , Maud Fagny , Alessandro Marin , John Quackenbush , Kimberly Glass
Bioinformatics, 2020, 36 (18), pp.4765-4773. ⟨10.1093/bioinformatics/btaa571⟩
Article dans une revue hal-03642316 v1
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Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues

Camila Lopes-Ramos , Cho-Yi Chen , Marieke Kuijjer , Joseph Paulson , Abhijeet Sonawane et al.
Cell Reports, 2020, 31 (12), pp.107795. ⟨10.1016/j.celrep.2020.107795⟩
Article dans une revue hal-03642288 v1
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Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function

Maud Fagny , John Platig , Marieke Lydia Kuijjer , Xihong Lin , John Quackenbush
British Journal of Cancer, 2020, 122 (4), pp.569-577. ⟨10.1038/s41416-019-0614-3⟩
Article dans une revue hal-02964020 v1
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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 , Laure Lemee et al.
Brain, Behavior, and Immunity, 2019, pp.30879-7. ⟨10.1016/j.bbi.2019.11.003⟩
Article dans une revue hal-02404337 v1
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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 et al.
Arthritis Research & Therapy, 2019, 21 (1), pp.1-14. ⟨10.1186/s13075-019-1829-7⟩
Article dans une revue hal-03642295 v1

Histopathological Image QTL Discovery of Immune Infiltration Variants

Joseph Barry , Maud Fagny , Joseph Paulson , Hugo J.W.L. Aerts , John Platig et al.
iScience, 2018, 5, pp.80-89. ⟨10.1016/j.isci.2018.07.001⟩
Article dans une revue hal-03642302 v1
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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 et al.
Genome Biology, 2018, 19, pp.222. ⟨10.1186/s13059-018-1601-3⟩
Article dans une revue hal-02352909 v1

Histopathological Image QTL Discovery of Immune Infiltration Variants

Joseph Barry , Maud Fagny , Joseph Paulson , Hugo J.W.L. Aerts , John Platig et al.
iScience, 2018, 5, pp.80-89. ⟨10.1016/j.isci.2018.07.001⟩
Article dans une revue hal-04310333 v1
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Epigenome-wide DNA methylation profiling in Progressive Supranuclear Palsy reveals major changes at DLX1

Axel Weber , Sigrid C. Schwarz , Jorg Tost , Dietrich Trümbach , Pia Winter et al.
Nature Communications, 2018, 9, pp.2929. ⟨10.1038/s41467-018-05325-y⟩
Article dans une revue cea-01877684 v1

Exploring regulation in tissues with eQTL networks

Maud Fagny , Joseph Paulson , Marieke Kuijjer , Abhijeet Sonawane , Cho-Yi Chen et al.
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (37), ⟨10.1073/pnas.1707375114⟩
Article dans une revue hal-03642025 v1
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Epigenetic clock analysis in long-term meditators

Raphaëlle Chaix , Maria Jesús Alvarez-López , Maud Fagny , Laure Lemee , Béatrice Regnault et al.
Psychoneuroendocrinology, 2017, 85, pp.210-214. ⟨10.1016/j.psyneuen.2017.08.016⟩
Article dans une revue pasteur-02555207 v1

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

Joseph Paulson , Cho-Yi Chen , Camila Lopes-Ramos , Marieke Kuijjer , John Platig et al.
BMC Bioinformatics, 2017, 18 (1), pp.437. ⟨10.1186/s12859-017-1847-x⟩
Article dans une revue hal-03642307 v1

Trends in DNA Methylation with Age Replicate Across Diverse Human Populations

Shyamalika Gopalan , Oana Carja , Maud Fagny , Etienne Patin , Justin Myrick et al.
Molecular Biology and Evolution, 2017, 206 (3), pp.1659-1674. ⟨10.1534/genetics.116.195594⟩
Article dans une revue hal-03642039 v1

Regulatory network changes between cell lines and their tissues of origin

Camila Lopes-Ramos , Joseph Paulson , Cho-Yi Chen , Marieke Kuijjer , Maud Fagny et al.
BMC Genomics, 2017, 18 (1), pp.723. ⟨10.1186/s12864-017-4111-x⟩
Article dans une revue hal-03642306 v1

Understanding Tissue-Specific Gene Regulation

Abhijeet Rajendra Sonawane , John Platig , Maud Fagny , Cho-Yi Chen , Joseph Nathaniel Paulson et al.
Cell Reports, 2017, 21 (4), pp.1077-1088. ⟨10.1016/j.celrep.2017.10.001⟩
Article dans une revue hal-04272697 v1
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An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease

Steve Horvath , Michael Gurven , Morgan Levine , Benjamin Trumble , Hillard Kaplan et al.
Genome Biology, 2016, 17 (1), pp.171. ⟨10.1186/s13059-016-1030-0⟩
Article dans une revue hal-03642312 v1

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 et al.
American Journal of Human Genetics, 2016, 98 (1), pp.5-21. ⟨10.1016/j.ajhg.2015.11.014⟩
Article dans une revue hal-03642313 v1
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The epigenomic landscape of African rainforest hunter-gatherers and farmers

Maud Fagny , Etienne Patin , Maxime Rotival , Julia L. Macisaac , Timothée Flutre et al.
Nature Communications, 2015, 6, 11 p. ⟨10.1038/ncomms10047⟩
Article dans une revue pasteur-01238387 v1

Exploring the Occurrence of Classic Selective Sweeps in Humans Using Whole-Genome Sequencing Data Sets

Maud Fagny , Etienne Patin , David Enard , Luis Barreiro , Lluis Quintana-Murci et al.
Molecular Biology and Evolution, 2014, 31 (7), pp.1850-1868. ⟨10.1093/molbev/msu118⟩
Article dans une revue hal-03642315 v1
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The adaptation of polygenic traits: from genes to phenotypes, are regulatory networks the missing link?

Katherine Stone , John Platig , John Quackenbush , Maud Fagny
Euro Evo Devo 2024, Claudius Kratochwil, Jun 2024, Helsinki, Finland
Communication dans un congrès hal-04646272 v1
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Gene regulatory network structure help us understand how polygenic phenotypes adapt

Katherine Stone , John Platig , Frederic Austerlitz , John Quackenbush , Maud Fagny
Evolution 2024 - Virtual, Mark McPeek, Dartmouth; Tracy Heath, Iowa State University; Mike Whitlock, University of British Columbia; Howard Rundle, University of Ottawa; Brian Hollis, University of South Carolina; Alex Wong, Carleton University; April Wright, Southeastern Louisiana University; Mike Wiser, Michigan State University, Jun 2024, Montréal (Québec), Canada
Communication dans un congrès hal-04646291 v1

MITE-driven dissemenitation of cis-regulatory elements in the maize genome

Klaus Von Grafenstein , Abirami Soundiramourtty , Maud Fagny , Karine Alix , Johann Joets et al.
CNET2022, Jul 2022, Gif-sur-Yvette, France
Communication dans un congrès hal-04478810 v1
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Distal cis-regulatory elements regulate tissue-specific water-deficit response

Maud Fagny
14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges RSGDREAM 2022, Nov 2022, online/Las Vegas, Nevada, United States
Communication dans un congrès hal-04343921 v1

Deciphering tissue-specific regulation and contribution of transposable elements to cis-regulatory sequences

Maud Fagny , Marieke L. Kuijjer , Maike Stam , Johann Joets , Olivier Turc et al.
UCLLN invited seminars, May 2022, Louvain- la-Neuve, Belgium
Communication dans un congrès hal-04351623 v1

Identifying key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

Maud Fagny
2021 63rd Annual Maize Genetics Meeting, Marna Yandeau-Nelson (Chair) - Iowa State University; Erin Sparks (co-Chair) - University of Delaware, Mar 2021, Virtual conference, United States
Communication dans un congrès hal-04330808 v1

Identification of key tissue-specific, biological processes through integration of enhancer information in maize gene regulatory networks

Maud Fagny , Marieke Kuijjer , Maike Stam , Johann Joets , Olivier Turc et al.
LEPSE invited seminars, Oct 2020, Visiconférence, France
Communication dans un congrès hal-04351597 v1

Investigating cancer risk germline mutations using eQTL networks

Maud Fagny
2018 RECOMB meeting - satellite RECOMB-Genetics, Itsik Pe’er, Columbia University; Eleazar Eskin, University of California, Los Angeles, Apr 2018, Paris, France
Communication dans un congrès hal-04330963 v1

Human epigenomic variation is driven by historical and recent changes in habitat and lifestyle

Maud Fagny
SMBE 2015 Vienna, 2015, Vienne (Austria), Austria
Communication dans un congrès hal-04330834 v1

Genetic and epigenetic determinants of human adaptation to different lifestyles and modes of subsistence

Maud Fagny
2014 HUMAN GENOME MEETING: GENOME VARIATION AND HUMAN HEALTH, Apr 2014, Genève (Suisse), Switzerland
Communication dans un congrès hal-04330923 v1
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Gene regulatory network structure help us understand how complex phenotypes adapt

Katherine Stone , John Platig , Frederic Austerlitz , John Quackenbush , Maud Fagny
Evolution 2024, Jul 2024, Montréal (Québec), Canada
Poster de conférence hal-04646904 v1
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Identifying key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

Maud Fagny , Marieke L. Kuijjer , Maike Stam , Johann Joets , Olivier Turc et al.
Symposium "Signaling through Chromatin" from molecules to ecosystems, Oct 2023, Grenoble, France.
Poster de conférence hal-04353449 v1

Identifying key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

Maud Fagny , Marieke L. Kuijjer , Maike Stam , Johann Joets , Olivier Turc et al.
PAG 30, Jan 2023, San Diego (California), United States
Poster de conférence hal-04353912 v1
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Distal cis-regulatory elements regulate tissue-specific water-deficit response

Maud Fagny , Johann Joets , Olivier Turc , Claude Welcker , Anthony Venon et al.
14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges RSGDREAM 2022, Nov 2022, Online/Las Vegas, Nevada., United States.
Poster de conférence hal-04343914 v1
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Distal cis-regulatory elements regulate tissue-specific water-deficit response

Maud Fagny , Olivier Turc , Claude Welcker , Anthony Venon , Harry Belcram et al.
CSHL Network Biology Meeting 2021, Mar 2021, Cold Spring Harbor (NY), United States.
Poster de conférence hal-04347190 v1
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The role of transposable elements on gene expression regulation in maize and its response to drought

Maud Fagny , Véronique Jamilloux , Johann Joets , Clémentine Vitte
22nd national congress on transposable elements, Jul 2019, Lyon, France
Poster de conférence hal-04330779 v1
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Bio0 - Bases de la génétique

Maud Fagny
Master. Bio 0 - Bases de la génétique, Gif-sur Yvette, France. 2024
Cours hal-04709508 v1
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Using eQTL networks to decipher the architecture of complex traits

Maud Fagny
Doctoral. NCMM PhD Course in Multi-Omics, NCMM, Oslo, Norway. 2023
Cours hal-04330996 v1
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Using eQTL networks to functionally characterize regulatory mutations

Maud Fagny
Doctoral. NCMM PhD Courses in Multi-Omics, NCMM, Oslo, Norway. 2022
Cours hal-04331011 v1