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

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Publications

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The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution

Katherine L Stone , John Platig , John Quackenbush , Maud Fagny

Molecular Biology and Evolution, 2025, 42 (8), pp.msaf174. ⟨10.1093/molbev/msaf174⟩

Article dans une revue hal-05314722v1
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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-03694544v1
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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-03694550v1
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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-03694556v1
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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-03100982v1
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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-03152056v1
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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-03642288v1
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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-03642316v1
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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-02964020v1
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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-03642295v1
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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-02404337v1

Effects of anti-TNF on MiR expression in monocytes and CD4(+) T-Lymphocytes in spondyloarthritis

Olivier Fogel , Maud Fagny , Elodie Roche , Nelly Sigrist , Jean-François Deleuze et al.

Arthritis & rheumatology, 2019, 71

Article dans une revue cea-04457182v1
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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-03642302v1
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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-02352909v1
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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-01877684v1

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-04272697v1
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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-02555207v1

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-03642025v1

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-03642307v1

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-03642039v1

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-03642306v1
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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-03642312v1

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-03642313v1
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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-01238387v1

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-03642315v1
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The Importance of Regulatory Network Structure for Polygenic Trait Heritability and Evolution

Maud Fagny

PopGroup 59, Diala Abu Awad; Vincent Castric; Thomas Lesaffre; Camille Roux; Roman Stetsenko, Jan 2026, Lille, France

Communication dans un congrès hal-05453388v1

Revisiting the functional features of maize dispensable genes

Johann Joets. , Maud Fagny , Kevin Baudry , Maëla Mollion , Olivier Turc et al.

PAG32, Jan 2025, San Diego (CA), United States

Communication dans un congrès hal-05366305v1

Identifying the contribution of transposable elements to cis-regulatory elements in plants

Maud Fagny , Johann Joets , Basile Leduque , Leandro Quadrana , Hadi Quesneville et al.

IBRC2025, Jul 2025, Monte Verità, Switzerland

Communication dans un congrès hal-05227710v1
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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-04646291v1
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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-04646272v1

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-04351623v1

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-04478810v1
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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-04343921v1

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

Fagny Maud , Kuijer Marieke L. , Stam Maike , Joets Johann , Turc Olivier et al.

Epiplant III, Feb 2021, Online, France

Communication dans un congrès hal-04351579v1

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

Fagny Maud , Kuijjer Marieke L. , Stam Maike , Joets Johann , Turc Olivier et al.

63. Annual Maize Genetics Conference, Mar 2021, Online, United States

Communication dans un congrès hal-04478817v1

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, Online, France

Communication dans un congrès hal-04351597v1

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-04330963v1

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-04330834v1

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-04330923v1
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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-04646904v1
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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-04353449v1

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.

30. Plant and Animal Genome Conference (PAG 30), Jan 2023, San Diego, United States

Poster de conférence hal-04353912v1
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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.

14. annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges RSGDREAM 2022, Nov 2022, Online, United States.

Poster de conférence hal-04343914v1
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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, New-York, United States.

Poster de conférence hal-04347190v1
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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-04330779v1
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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-04709508v1
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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-04330996v1
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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-04331011v1