Bioinformatics Research In Disease Genomics (BRIDGe)

Team 4

Keywords: genomics, gene-enhancer relationship, structural variant, pangenome

Research Program

The Bioinformatics Research In Disease Genomics (BRIDGe) team studies the functional impact of genomic variations on diseases. While the core of our research is hypothesis-free, our goal is to apply our methods and analyses primarily to digestive health conditions studied in the lab in order to leverage the lab’s expertise and validate our findings.

If many genome-wide association studies have identified thousands of variants associated with common diseases, two important problems hinder a thorough understanding of the biological mechanisms underlying these diseases and the development of new treatments: 1) the actual causal variants very often remain unknown, 2) the set of identified variants do not entirely explain the heritability of the disease. In reality, these two problems stem from the fact that 1) only small variants (SNPs) are tested for the association with the disease and that 2) the vast majority of associated variants are located in non-coding regulatory regions of the genome. For these reasons, we are focusing our efforts on:

  • Extending association studies to longer and more complex variants, Structural Variants (SVs such as duplications, deletions, insertions, translocations) using pangenomic approaches
  • Deriving cell-type-specific functional genomic annotations and incorporate them into disease studies
  • Integrating structural variants and functional annotation to improve the molecular diagnosis in rare genetic disease studies.

Keywords: Genomics, Gene-Enhancer relationship, Structural Variants, Pangenome.

Members

Former members

Tools and Methods

  • Transcriptome sequencing nalysis (RNA-seq, miRNA-seq)
  • 3D DNA conformation analysis (Hi-C, promoter capture Hi-C)
  • Integrative multi-omics methods (e.g. mixOmics)
  • Genome sequencing analysis from short-read (Illumina) or long-read (Oxford Nanopore) data
  • Sequencing data analysis using human pangenomes (pangenome construction, read alignment, variant calling)
  • Genome-wide association tests (GWAS)
  • Rare disease variant calling from long-read data (phased de novo assembly, structural variants, annotation), including for complex regions (e.g. RCCX module)

Members of the team contributed to several public softwares, some of them highlighted below:

  • ChimPipe: a tool to detect novel chimeric transcripts and fusion genes from RNA-seq data. GitHub, Rodríguez-Martín et al. BMC Genomics 2017
  • TAGADA: a comprehensice RNA-Seq pipeline, including modules to create novel transcript annotation, and quantify genes and transcripts expression. GitHub, Kurylo, Guyomar, Foissac and Djebali NAR Genomics and Bioinformatics 2023
  • PaintorPipe: a pipeline to perform fine-mapping analysis of GWAS results using diverse functionnal annotations. GitHub, Gerber et al. Bioinformatics Advances 2024
  • sveval: R package to manipulate and benchmark structural variants. GitHub, Heller, Hickey, Monlong et al. Genome Biology 2020
  • vg: variation graph toolkit to manipulate pangenomes and analyze sequencing data. Includes the fast read mapper Giraffe. GitHub, Sirén, Monlong, Chang, Novak, Eizenga et al. Science 2021
  • Minigaph-Cactus: pangenome construction pipeline from high-quality genome assemblies. GitHub, Hickey, Monlong, et al. Nature Biotechnology 2024
  • Parakit: a pangenome-based tool to characterize the complex RCCX module from long-read data. GitHub, Monlong et al. medRxiv 2025

Recruitment

We are actively looking to expand and welcome new researchers in genomics and bioinformatics to join our team. Some projects could benefit from new expertise: advanced statistical skills to help with variant imputation, single-cell transcriptomics to enrich our cell-specific characterization of gene regulation, or machine learning to assist in the prediction of functional elements in the genome or functional non-coding variants. Complementary research could also include approaches that would benefit from integrating more variants (e.g. structural variants) or variants with better functional annotation (e.g. in cell-specific regulatory regions), for example developing finer evolutionary metrics or polygenic risk scores. Don’t hesitate to reach out to Sarah and Jean if you are interested in joining the team!

Publications

Article type:

Data for "Evolution of regulatory chromatin contacts: insights from duplicated genes". Victor Lefebvre, Sylvain Foissac, Sarah Djebali, et al., 2026. DOI: 10.5281/zenodo.21392106

Data for "Evolution of regulatory chromatin contacts: insights from duplicated genes". Victor Lefebvre, Sylvain Foissac, Sarah Djebali, et al., 2026. DOI: 10.5281/zenodo.21392107

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation. Julian Lucas, Prajna Hebbar, ..., Jean Monlong, et al., bioRxiv 2026. DOI: 10.64898/2026.07.21.739710

vgteam/vg: vg 1.71.0 - Cera. Adam Novak, Erik Garrison, ..., Jean Monlong, et al., 2026. DOI: 10.5281/zenodo.18164686

vgteam/vg: vg 1.71.0 - Cera. Adam Novak, Erik Garrison, ..., Jean Monlong, et al., 2026. DOI: 10.5281/zenodo.18163949

Surmonter la complexité de CYP21A2 : une stratégie NGS optimisée pour le diagnostic moléculaire du déficit en 21-hydroxylase – à propos d’un cas clinique. Julie Milandri, Jean Monlong, et al., Annales d'Endocrinologie 2026. DOI: 10.1016/j.ando.2026.102540

nf-core/smrnaseq: v2.4.1 - 2026-01-07 - Navy Iron Boxer Patch. Alexander Peltzer, Anabella Trigila, ..., Sarah Djebali, et al., 2026. DOI: 10.5281/zenodo.18173574

Catestatin decreases duodenal hypermotility to improve glucose homeostasis in diabetic male mice. Anne Abot, Céline El Samrout, ..., Sarah Djebali, et al., Gut Science 2026. DOI: 10.1136/gutsci-2026-000021

Evolution of regulatory chromatin contacts: insights from duplicated genes. Victor Lefebvre, Sylvain Foissac, Sarah Djebali, et al., bioRxiv 2026. DOI: 10.64898/2026.07.22.739131

Taxonomic-free metagenome GWAS to identify gut microbiome functions influencing host phenotypes. Raphael Malak, Arthur Frouin, et al., bioRxiv 2026. DOI: 10.64898/2026.01.15.699651

A versatile multi-components mixed model for bacterial-Genome Wide association studies. Arthur Frouin, Fabien Laporte, et al., Nature Communications 2026. DOI: 10.1038/s41467-026-72305-y

Strigolactones and sesquiterpene lactones induce *Orobanche cumana* germination via KAI2d receptors through distinct processes. Julien Affholder, Louis Lambret, ..., Stéphane Muños, et al., The Plant Journal 2026. DOI: 10.1111/tpj.70852

Co‐Occurring Non‐Cardiac Congenital Anomalies Among Cases With Congenital Heart Defects. Claude Stoll, Yves Alembik, Marie‐Paule Roth, American Journal of Medical Genetics Part A 2026. DOI: 10.1002/ajmga.70002

A cell-nonautonomous heme acquisition pathway enables erythroid hemoglobinization under stress. Audrey Belot, Andrew Rock, et al., Science 2026. DOI: 10.1126/science.aea0552

Effect of 12 weeks with a 30-min nap opportunity during the night shift of healthcare workers on early cardiovascular risk biomarkers: the NAPWORK study protocol of a randomised controlled trial. Yanis Bouchou, Mathilde Monnier, ..., Mathieu Berger, BMJ Open 2026. DOI: 10.1136/bmjopen-2025-110108

Travail posté et santé vasculaire : revue des altérations de la fonction endothéliale et des biomarqueurs cardiovasculaires associés. Yanis Bouchou, Frederic Roche, ..., Mathieu Berger, Médecine du Sommeil 2026. DOI: 10.1016/j.msom.2025.12.073

Goffman et le politique. Mathieu Berger, Daniel Céfaï, et al., Goffman et les politiques de l'interaction 2026. DOI: 10.4000/164hv

Pas vraiment une discussion. Mathieu Berger, Goffman et les politiques de l'interaction 2026. DOI: 10.4000/164h9

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. Shloka Negi, Sarah L. Stenton, ..., Jean Monlong, et al., The American Journal of Human Genetics 2025. DOI: 10.1016/j.ajhg.2025.01.002

Empowering bioinformatics communities with Nextflow and nf-core. Björn E. Langer, Andreia Neves do Amaral, ..., Sarah Djebali, et al., Genome Biology 2025. DOI: 10.1186/s13059-025-03673-9

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets. Smahane Chalabi, Linda M. P. Loonen, ..., Sarah Djebali, et al., Genomics 2025. DOI: 10.1016/j.ygeno.2025.110995

Polygenic risk score prediction accuracy convergence. Léo Henches, Jihye Kim, ..., Arthur Frouin, ..., Sarah Djebali, et al., Human Genetics and Genomics Advances 2025. DOI: 10.1016/j.xhgg.2025.100457

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. Xian Chang, Adam M. Novak, ..., Jean Monlong, et al., bioRxiv 2025. DOI: 10.1101/2025.09.29.678807

Long-read sequencing resolves the clinically relevant *CYP21A2* locus, supporting a new clinical test for Congenital Adrenal Hyperplasia. Jean Monlong, Xiao Chen, et al., medRxiv 2025. DOI: 10.1101/2025.02.07.25321404

Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development. Fanny Mollandin, Hervé Acloque, ..., Sarah Djebali, et al., bioRxiv 2025. DOI: 10.1101/2025.03.05.641618

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. Benedict Paten, Xian Chang, ..., Jean Monlong, et al., Research Square 2025. DOI: 10.21203/rs.3.rs-7747403/v1

Porcine Intestinal Organoids as Models of Regional Gut and Animal Identities: a Transcriptomic Approach. Fany Blanc, Smahane Chalabi, ..., Sarah Djebali, et al., bioRxiv 2025. DOI: 10.1101/2025.10.29.679705

Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development. Fanny Mollandin, Hervé Acloque, ..., Sarah Djebali, et al., Genomics 2025. DOI: 10.1016/j.ygeno.2025.111158

Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle. Ervin Shishmani, Andréa Rau, Sarah Djebali, et al., bioRxiv 2025. DOI: 10.1101/2025.11.27.690935

Single-cell omics uncover gene dynamics shaping embryonic and extra embryonic lineages in pig blastocysts. Adrien Dufour, Marie-Noëlle M.-N. Rossignol, ..., Sarah Djebali, et al., iScience 2025. DOI: 10.1016/j.isci.2025.114519

Single-cell omics reveal distinct gene regulatory dynamics underpinning embryonic and extraembryonic lineage functions during pig blastocyst development. Adrien Dufour, Marie‐Noëlle Rossignol, ..., Sarah Djebali, et al., bioRxiv 2025. DOI: 10.1101/2025.06.15.657618

Single-Cell Omics Reveal Distinct Gene Regulatory Dynamics Underpinning Embryonic and Extraembryonic Lineage Functions During Pig Blastocyst Development. Adrien Dufour, Marie‐Noëlle Rossignol, ..., Sarah Djebali, et al., 2025. DOI: 10.2139/ssrn.5362267

Empowering multitrait brain phenotypes GWAS. Antoine Auvergne, Nicolas Traut, ..., Arthur Frouin, et al., bioRxiv 2025. DOI: 10.1101/2025.05.04.652120

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals. Christophe Boetto, Violeta Basten Romero, ..., Arthur Frouin, et al., Communications Biology 2025. DOI: 10.1038/s42003-025-08895-y

Co-occurring non-urinary congenital anomalies among cases with congenital anomalies of the kidney and urinary tract. Claude Stoll, Béatrice Dott, ..., Marie‐Paule Roth, European Journal of Medical Genetics 2025. DOI: 10.1016/j.ejmg.2025.105000

Functional characterization of Sec14L4 in hudep-2 and mouse knockout models reveals its essential role in erythropoiesis.. Mouna Ouchari, Audrey Belot, et al., Blood 2025. DOI: 10.1182/blood-2025-607

Assessing heart rate fragmentation to predict atrial fibrillation in the general population aged 65: the PROOF-AF study. Jean-Baptiste Guichard, David Hupin, ..., Mathieu Berger, et al., European Heart Journal Open 2025. DOI: 10.1093/ehjopen/oeaf030

Barriers and Levers to the Implementation of Napping During Night Shift Work in Healthcare Workers: A Qualitative Study in a French University Hospital. Maryame Mazouz, Pauline Gouttefarde, ..., Mathieu Berger, Journal of Nursing Management 2025. DOI: 10.1155/jonm/5279651

Fundamentos de fisiología del esfuerzo: adaptaciones cardíacas, vasculares y respiratorias. Pierre Labeix, M. Fanget, Mathieu Berger, EMC - Kinesiterapia - Medicina Física 2025. DOI: 10.1016/s1293-2965(24)49904-0

Basi di fisiologia dello sforzo: adattamenti cardiaci, vascolari e respiratori. Pierre Labeix, M. Fanget, Mathieu Berger, EMC - Medicina Riabilitativa 2025. DOI: 10.1016/s1283-078x(24)50008-6

Intérêt des paramètres hypoxémiques du Holter cardiorespiratoire dans le post-AVC ischémique pour le dépistage des pathologies respiratoires du sommeil. Marie Roux, Pierre Garnier, ..., Mathieu Berger, et al., Médecine du Sommeil 2025. DOI: 10.1016/j.msom.2025.01.005

Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Dylan J. Taylor, Jordan M. Eizenga, ..., Jean Monlong, et al., Annual Review of Genomics and Human Genetics 2024. DOI: 10.1146/annurev-genom-021623-081639

Personalized pangenome references. Jouni Sirén, Parsa Eskandar, ..., Jean Monlong, et al., Nature Methods 2024. DOI: 10.1038/s41592-024-02407-2

The microbiota and the host organism switch between cooperation and competition based on dietary iron levels. Marie-Louise Noordine, Yohannes Seyoum, ..., François Canonne‐Hergaux, et al., Gut Microbes 2024. DOI: 10.1080/19490976.2024.2361660

Mapping the scientific output of organoids for animal and human modeling infectious diseases: a bibliometric assessment. Yan Jin, Jean Monlong, ..., Agnès Wiedemann, Veterinary Research 2024. DOI: 10.1186/s13567-024-01333-7

A human anti-matriptase-2 antibody limits iron overload, α-globin aggregates, and splenomegaly in β-thalassemic mice. Matthew Wake, Anaïs Palin, Audrey Belot, Mathieu Berger, ..., Céline Besson‐Fournier, Chloé Latour, ..., Hélène Coppin, Marie‐Paule Roth, ..., Delphine Meynard, Blood Advances 2024. DOI: 10.1182/bloodadvances.2023012010

Empowering bioinformatics communities with Nextflow and nf-core. Björn E. Langer, Andreia J. Amaral, ..., Sarah Djebali, et al., bioRxiv 2024. DOI: 10.1101/2024.05.10.592912

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. Shloka Negi, Sarah L. Stenton, ..., Jean Monlong, et al., medRxiv 2024. DOI: 10.1101/2024.08.22.24312327

Efficient indexing and querying of annotations in a pangenome graph. Adam M. Novak, Dickson Chung, ..., Sarah Djebali, ..., Jean Monlong, bioRxiv 2024. DOI: 10.1101/2024.10.12.618009

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets. Smahane Chalabi, Linda M. P. Loonen, ..., Sarah Djebali, et al., bioRxiv 2024. DOI: 10.1101/2024.08.13.607725

Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Elena Kuzmin, Toby M. Baker, ..., Jean Monlong, et al., Cell Reports 2024. DOI: 10.1016/j.celrep.2024.113988

Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, et al., Genome Research 2024. DOI: 10.1101/gr.278268.123

Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation. Kimberley J. Billingsley, Melissa Meredith, ..., Jean Monlong, et al., bioRxiv 2024. DOI: 10.1101/2024.12.16.628723

P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia*. Emmanuèle C. Délot, Jean Monlong, et al., Genetics in Medicine Open 2024. DOI: 10.1016/j.gimo.2024.101732

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes. Lukas Hafner, Enzo Gadin, ..., Arthur Frouin, et al., Nature Microbiology 2024. DOI: 10.1038/s41564-024-01859-8

MANOCCA: a robust and computationally efficient test of covariance in high-dimension multivariate omics data. Christophe Boetto, Arthur Frouin, et al., Briefings in Bioinformatics 2024. DOI: 10.1093/bib/bbae272

Multitrait Analysis to Decipher the Intertwined Genetic Architecture of Neuroanatomical Phenotypes and Psychiatric Disorders. Antoine Auvergne, Nicolas Traut, ..., Arthur Frouin, et al., Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 2024. DOI: 10.1016/j.bpsc.2024.08.018

Gut microbiome co-abundance networks varies with age, sex, smoking status and body mass index. Christophe Boetto, Violeta Basten Romero, ..., Arthur Frouin, et al., medRxiv 2024. DOI: 10.1101/2024.04.30.24306630

Development and characterization of a new sunflower source of resistance to race G of Orobanche cumana Wallr. derived from Helianthus anomalus. Belén Fernández-Melero, Lidia del Moral, ..., Stéphane Muños, et al., Theoretical and Applied Genetics 2024. DOI: 10.1007/s00122-024-04558-4

Mapping an avirulence gene in the sunflower parasitic weed Orobanche cumana and characterization of host selection based on virulence alleles. Álvaro Calderón-González, Belén Fernández-Melero, ..., Stéphane Muños, et al., BMC Plant Biology 2024. DOI: 10.1186/s12870-024-05855-2

microRNA‐encoded peptides inhibit seed germination of the root parasitic plant *Orobanche cumana*. Sabine Tourneur, Jean‐Philippe Combier, ..., Stéphane Muños, et al., PLANTS, PEOPLE, PLANET 2024. DOI: 10.1002/ppp3.10501

A cluster of putative resistance genes is associated with a dominant resistance to sunflower broomrape. Camille Pubert, Marie‐Claude Boniface, ..., Stéphane Muños, Theoretical and Applied Genetics 2024. DOI: 10.1007/s00122-024-04594-0

Associated Anomalies in Radial Ray Deficiency. Claude Stoll, Yves Alembik, Marie‐Paule Roth, American Journal of Medical Genetics Part A 2024. DOI: 10.1002/ajmg.a.63874

Anatomy and physiology of the autonomic nervous system: Implication on the choice of diagnostic/monitoring tools in 2023. Frédéric Roche, Vincent Pichot, ..., Mathieu Berger, et al., Revue Neurologique 2024. DOI: 10.1016/j.neurol.2023.12.003

Sleep disturbances and incident risk of major depressive disorder in a population-based cohort. Geoffroy Solelhac, Théo Imler, ..., Mathieu Berger, et al., Psychiatry Research 2024. DOI: 10.1016/j.psychres.2024.115934

Sleep Habits and Disturbances in Healthcare Workers: A Cross-Sectional Survey in French Public Hospitals. Yanis Bouchou, Lorine Giffard-Quillon, ..., Mathieu Berger, Nature and Science of Sleep 2024. DOI: 10.2147/nss.s461993

The Frame Analysis of Participation: A Goffmanian Take on Democratic Interaction and its Ambiguities. Mathieu Berger, Symbolic Interaction 2024. DOI: 10.1002/symb.1211

An AI-based approach for detecting COVID-19 long-haul patients through sleep polysomnography analysis: the pandore-IA project. Hugo Lerogeron, Anis Aloulou, ..., Mathieu Berger, et al., Sleep Medicine 2024. DOI: 10.1016/j.sleep.2023.11.456

Prediction of driving performance on simulator using clinical and sleep parameters: The PANDORE-IA project. Miriam Benballa, Mathieu Berger, et al., Sleep Medicine 2024. DOI: 10.1016/j.sleep.2023.11.245

Association entre sommeil et risque prospectif de trouble dépressif majeur (TDM) dans la cohorte de population générale CoLaus|HypnoLaus. Geoffroy Solelhac, Théo Imler, ..., Mathieu Berger, et al., Médecine du Sommeil 2024. DOI: 10.1016/j.msom.2023.12.019

La sieste au travail : freins et leviers à l’implémentation d’une salle de sieste en milieu hospitalier pour les soignants en poste de 12 h alternant. Maryame Mazouz, Pauline Gouttefarde, ..., Mathieu Berger, Médecine du Sommeil 2024. DOI: 10.1016/j.msom.2023.12.184

Insomnie et COVID long : une analyse assistée par l’IA pour explorer la microarchitecture du sommeil des patients. Hugo Lerogeron, Anis Aloulou, ..., Mathieu Berger, et al., Médecine du Sommeil 2024. DOI: 10.1016/j.msom.2023.12.013

Évolution du syndrome d’apnée du sommeil entre 68 et 85 ans et relation avec l’activité autonomique (cohorte PROOF-SYNAPSE). Vincent Pichot, Mathieu Berger, et al., Médecine du Sommeil 2024. DOI: 10.1016/j.msom.2023.12.007

COVISLEEP: A sleep dataset to investigate the impact of long-COVID on chronic insomnia.. Hugo Lerogeron, Anis Aloulou, ..., Mathieu Berger, et al., 2024. DOI: 10.5281/zenodo.10527276

COVISLEEP: A sleep dataset to investigate the impact of long-COVID on chronic insomnia.. Hugo Lerogeron, Anis Aloulou, ..., Mathieu Berger, et al., 2024. DOI: 10.5281/zenodo.10527275

PO-03-088 ASSESSING HEART RATE FRAGMENTATION TO PREDICT ATRIAL FIBRILLATION IN THE GENERAL POPULATION AGED 65. Jean-Baptiste Guichard, David Hupin, ..., Mathieu Berger, et al., Heart Rhythm 2024. DOI: 10.1016/j.hrthm.2024.03.1089

Qualité et habitudes de sommeil des soignants du GHT Loire. Yanis Bouchou, Lorine Riffart, ..., Mathieu Berger, Archives des Maladies Professionnelles et de l'Environnement 2024. DOI: 10.1016/j.admp.2024.102582

Évaluation des habitudes de sommeil des soignants en fonction du rythme de travail : une étude transversale monocentrique. Lorine Giffard-Quillon, Yanis Bouchou, ..., Mathieu Berger, et al., Archives des Maladies Professionnelles et de l'Environnement 2024. DOI: 10.1016/j.admp.2024.102055

A draft human pangenome reference. Wen‐Wei Liao, Mobin Asri, ..., Jean Monlong, et al., Nature 2023. DOI: 10.1038/s41586-023-05896-x

Pangenome graph construction from genome alignments with Minigraph-Cactus. Glenn Hickey, Jean Monlong, et al., Nature Biotechnology 2023. DOI: 10.1038/s41587-023-01793-w

Recombination between heterologous human acrocentric chromosomes. Andrea Guarracino, Silvia Buonaiuto, ..., Jean Monlong, et al., Nature 2023. DOI: 10.1038/s41586-023-05976-y

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Mikhail Kolmogorov, Kimberley J. Billingsley, ..., Jean Monlong, et al., Nature Methods 2023. DOI: 10.1038/s41592-023-01993-x

Increased mutation and gene conversion within human segmental duplications. Mitchell R. Vollger, Philip C. Dishuck, ..., Jean Monlong, et al., Nature 2023. DOI: 10.1038/s41586-023-05895-y

A draft human pangenome reference. Wen‐Wei Liao, Mobin Asri, ..., Jean Monlong, et al., Yearbook of Paediatric Endocrinology 2023. DOI: 10.1530/ey.20.12.1

The genomics of linkage drag in inbred lines of sunflower. Kaichi Huang, Mojtaba Jahani, ..., Stéphane Muños, et al., Proceedings of the National Academy of Sciences 2023. DOI: 10.1073/pnas.2205783119

Associated anomalies inPierre Robin sequence. Claude Stoll, Yves Alembick, Marie‐Paule Roth, American Journal of Medical Genetics Part A 2023. DOI: 10.1002/ajmg.a.63344

Obstructive sleep apnoea and 5-year cognitive decline in the elderly. Nicola Andrea Marchi, Geoffroy Solelhac, Mathieu Berger, et al., European Respiratory Journal 2023. DOI: 10.1183/13993003.01621-2022

Pulse Wave Amplitude Drops Index: A Biomarker of Cardiovascular Risk in Obstructive Sleep Apnea. Geoffroy Solelhac, Manuel Sánchez‐de‐la‐Torre, ..., Mathieu Berger, et al., American Journal of Respiratory and Critical Care Medicine 2023. DOI: 10.1164/rccm.202206-1223oc

Objective polysomnography-based sleep features and major depressive disorder subtypes in the general population. Geoffroy Solelhac, Mathieu Berger, et al., Psychiatry Research 2023. DOI: 10.1016/j.psychres.2023.115213

ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity. Anne Fougerat, Gabriele Schoiswohl, ..., Delphine Meynard, et al., Cell Reports 2022. DOI: 10.1016/j.celrep.2022.110910

Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. John E. Gorzynski, Sneha D. Goenka, ..., Jean Monlong, et al., New England Journal of Medicine 2022. DOI: 10.1056/nejmc2112090

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Sneha D. Goenka, John E. Gorzynski, ..., Jean Monlong, et al., Nature Biotechnology 2022. DOI: 10.1038/s41587-022-01221-5

Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cells. Charles Couturier, Javad Nadaf, ..., Jean Monlong, et al., Neuro-Oncology 2022. DOI: 10.1093/neuonc/noac085

Identification of risk loci for primary aldosteronism in genome-wide association studies. Édith Le Floch, Teresa Cosentino, ..., Arthur Frouin, et al., Nature Communications 2022. DOI: 10.1038/s41467-022-32896-8

The ecologically relevant genetics of plant–plant interactions. Claude Becker, Richard Berthomé, ..., Stéphane Muños, et al., Trends in Plant Science 2022. DOI: 10.1016/j.tplants.2022.08.014

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Jouni Sirén, Jean Monlong, et al., Science 2021. DOI: 10.1126/science.abg8871

RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. Frédéric Jehl, Fabien Degalez, ..., Sarah Djebali, et al., Frontiers in Genetics 2021. DOI: 10.3389/fgene.2021.655707

Expanded encyclopaedias of DNA elements in the human and mouse genomes. Federico Abascal, Reyes Acosta, ..., Sarah Djebali, et al., Nature 2020. DOI: 10.1038/s41586-020-2493-4

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Kishwar Shafin, Trevor Pesout, ..., Jean Monlong, et al., Nature Biotechnology 2020. DOI: 10.1038/s41587-020-0503-6

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Charles Couturier, Shamini Ayyadhury, ..., Jean Monlong, et al., Nature Communications 2020. DOI: 10.1038/s41467-020-17186-5

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Bernardo Rodríguez–Martín, Eva G. Alvarez, ..., Jean Monlong, et al., Nature Genetics 2020. DOI: 10.1038/s41588-019-0562-0

Genotyping structural variants in pangenome graphs using the vg toolkit. Glenn Hickey, David N. Heller, Jean Monlong, et al., Genome Biology 2020. DOI: 10.1186/s13059-020-1941-7

Genetic effects on gene expression across human tissues. Eric Haugen, Yuan He, ..., Jean Monlong, et al., 2020. DOI: 10.17615/p82n-gb73

Perspectives on ENCODE. Federico Abascal, Reyes Acosta, ..., Sarah Djebali, et al., Nature 2020. DOI: 10.1038/s41586-020-2449-8

Massive haplotypes underlie ecotypic differentiation in sunflowers. Marco Todesco, Gregory L. Owens, ..., Stéphane Muños, et al., Nature 2020. DOI: 10.1038/s41586-020-2467-6

Gene banks for wild and cultivated sunflower genetic resources. S. Terzić, Marie‐Claude Boniface, ..., Stéphane Muños, et al., OCL 2020. DOI: 10.1051/ocl/2020004

Stalled developmental programs at the root of pediatric brain tumors. Selin Jessa, Alexis Blanchet-Cohen, ..., Jean Monlong, et al., Nature Genetics 2019. DOI: 10.1038/s41588-019-0531-7

Multi-species annotation of transcriptome and chromatin structure in domesticated animals. Sylvain Foissac, Sarah Djebali, et al., BMC Biology 2019. DOI: 10.1186/s12915-019-0726-5

Thrombolysis During Resuscitation for Out-of-Hospital Cardiac Arrest Caused by Pulmonary Embolism Increases 30-Day Survival. François Javaudin, Jean-Baptiste Lascarrou, ..., Chloé Latour, et al., Chest 2019. DOI: 10.1016/j.chest.2019.07.015

A receptor-like kinase enhances sunflower resistance to Orobanche cumana. Pauline Duriez, Sonia Vautrin, ..., Stéphane Muños, Nature Plants 2019. DOI: 10.1038/s41477-019-0556-z

Regulators of hepcidin expression. Marie‐Paule Roth, Delphine Meynard, Hélène Coppin, Vitamins and Hormones 2019. DOI: 10.1016/bs.vh.2019.01.005

Associated anomalies in cases with agenesis of the corpus callosum. Claude Stoll, Béatrice Dott, Marie‐Paule Roth, American Journal of Medical Genetics Part A 2019. DOI: 10.1002/ajmg.a.61330

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Alvaro Barbeira, Scott Dickinson, ..., Jean Monlong, et al., Nature Communications 2018. DOI: 10.1038/s41467-018-03621-1

Global characterization of copy number variants in epilepsy patients from whole genome sequencing. Jean Monlong, Simon Girard, et al., PLOS Genetics 2018. DOI: 10.1371/journal.pgen.1007285

Human copy number variants are enriched in regions of low mappability. Jean Monlong, Patrick Cossette, et al., Nucleic Acids Research 2018. DOI: 10.1093/nar/gky538

Whole-genome landscape of Medicago truncatula symbiotic genes. Yann Pécrix, S. Evan Staton, ..., Stéphane Muños, et al., Nature Plants 2018. DOI: 10.1038/s41477-018-0286-7

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Sariel Hübner, Natalia Bercovich, ..., Stéphane Muños, et al., Nature Plants 2018. DOI: 10.1038/s41477-018-0329-0

Ten Broad Spectrum Resistances to Downy Mildew Physically Mapped on the Sunflower Genome. Yann Pécrix, Charlotte Penouilh-Suzette, Stéphane Muños, et al., Frontiers in Plant Science 2018. DOI: 10.3389/fpls.2018.01780

Shift in skin microbiota of Western European women across aging. Romain Jugé, Pauline Rouaud, ..., Marie‐Paule Roth, Hélène Coppin, et al., Journal of Applied Microbiology 2018. DOI: 10.1111/jam.13929

The histone demethylase Phf2 acts as a molecular checkpoint to prevent NAFLD progression during obesity. Julien Bricambert, Marie‐Clotilde Alves‐Guerra, ..., François Canonne‐Hergaux, et al., Nature Communications 2018. DOI: 10.1038/s41467-018-04361-y

An atlas of human long non-coding RNAs with accurate 5′ ends. Chung-Chau Hon, Jordan A. Ramilowski, ..., Sarah Djebali, et al., Nature 2017. DOI: 10.1038/nature21374

Deletion of BMP6 worsens the phenotype of HJV-deficient mice and attenuates hepcidin levels reached after LPS challenge. Chloé Latour, Céline Besson‐Fournier, ..., Delphine Meynard, Marie‐Paule Roth, Hélène Coppin, Blood 2017. DOI: 10.1182/blood-2017-07-795658

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Hélène Badouin, Jérôme Gouzy, ..., Stéphane Muños, et al., Nature 2017. DOI: 10.1038/nature22380

Potential impact of the herbicide 2,4-dichlorophenoxyacetic acid on human and ecosystems. Faisal Islam, Jian Wang, ..., Stéphane Muños, et al., Environment International 2017. DOI: 10.1016/j.envint.2017.10.020

Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modelling and genome‐wide association. Brigitte Mangin, Pierre Casadebaig, ..., Stéphane Muños, et al., Plant, Cell & Environment 2017. DOI: 10.1111/pce.12961

The genetics underlying natural variation of plant–plant interactions, a beloved but forgotten member of the family of biotic interactions. Harihar Jaishree Subrahmaniam, Cyril Libourel, ..., Stéphane Muños, et al., The Plant Journal 2017. DOI: 10.1111/tpj.13799

Associated anomalies in cases with esophageal atresia. Claude Stoll, Yves Alembik, ..., Marie‐Paule Roth, American Journal of Medical Genetics Part A 2017. DOI: 10.1002/ajmg.a.38303

A benchmark for RNA-seq quantification pipelines. Mingxiang Teng, Michael I. Love, ..., Sarah Djebali, et al., Genome Biology 2016. DOI: 10.1186/s13059-016-0940-1

Gene-specific patterns of expression variation across organs and species. Alessandra Breschi, Sarah Djebali, et al., Genome Biology 2016. DOI: 10.1186/s13059-016-1008-y

Bioinformatics Pipeline for Transcriptome Sequencing Analysis. Sarah Djebali, Valentin Wucher, et al., Methods in Molecular Biology 2016. DOI: 10.1007/978-1-4939-4035-6_14

Limiting hepatic Bmp-Smad signaling by matriptase-2 is required for erythropoietin-mediated hepcidin suppression in mice. Antonella Nai, Aude Rubio, ..., Chloé Latour, Céline Besson‐Fournier, ..., Hélène Coppin, ..., Delphine Meynard, Blood 2016. DOI: 10.1182/blood-2015-11-681494

Hepcidin upregulation by inflammation is independent of Smad1/5/8 signaling by activin B. Céline Besson‐Fournier, Aurélie Gineste, Chloé Latour, ..., Delphine Meynard, ..., Éric Oswald, Hélène Coppin, Marie‐Paule Roth, Blood 2016. DOI: 10.1182/blood-2016-10-748541

Extraction of High-Molecular-Weight Genomic DNA for Long-Read Sequencing of Single Molecules. Baptiste Mayjonade, Jérôme Gouzy, ..., Stéphane Muños, BioTechniques 2016. DOI: 10.2144/000114460

Sunflower Resistance to Broomrape (Orobanche cumana) Is Controlled by Specific QTLs for Different Parasitism Stages. Johann Louarn, Marie‐Claude Boniface, ..., Stéphane Muños, Frontiers in Plant Science 2016. DOI: 10.3389/fpls.2016.00590

RXLR and CRN Effectors from the Sunflower Downy Mildew Pathogen Plasmopara halstedii Induce Hypersensitive-Like Responses in Resistant Sunflower Lines. Quentin Gascuel, Luis Buendia, ..., Stéphane Muños, et al., Frontiers in Plant Science 2016. DOI: 10.3389/fpls.2016.01887

Decreased Bone Formation Explains Osteoporosis in a Genetic Mouse Model of Hemochromatosiss. Mathilde Doyard, Daniel Chappard, ..., Marie‐Paule Roth, et al., PLOS ONE 2016. DOI: 10.1371/journal.pone.0148292