Lemoine Frédéric

Publications

Communication dans un congrès (3)

A Standards-Based Knowledge Graph that Bridges Scientific Workflows, Run-Time Provenance, and Tool Registries Marie Schmit,Ulysse Le Clanche,George Marchment,Sarah Cohen-Boulakia,Olivier Dameronet al. SWAT4HCLS 2026, Mar 2026, Amsterdam, Netherlands Communication dans un congrès hal-05517640v1
Computational Reproducibility With Scientific Workflows: Analysing viral genomes with Nextflow George Marchment,Sarah Cohen-Boulakia,Frédéric Lemoine ACM REP'25 ACM Conference on Reproducibility and Replicability, Jul 2025, Vancouver, Canada Communication dans un congrès hal-05525260v1
Deep learning from phylogenies to understand the dynamics of epidemics Jakub Voznica,Anna Zhukova,Tristan Dot,Kary Ocaña,Frédéric Lemoineet al. Epidemics - 7th International Conference on Infectious Disease Dynamics, Dec 2019, Charleston, United States Communication dans un congrès pasteur-02405720v1

Article dans une revue (38)

Pre-European contact leprosy in the Americas and its current persistence Maria Lopopolo,Charlotte Avanzi,Sebastian Duchene,Pierre Luisi,Alida de Flaminghet al. Science, In press, pp.eadu7144. ⟨10.1126/science.adu7144⟩ Article dans une revue pasteur-05106303v2
Antibody-secreting cell repertoires hold high-affinity anti-rocuronium specificities that can induce anaphylaxis in vivo Alice Dejoux,Qianqian Zhu,Adam Woolfe,Ophélie Godon,Sami Ellouzeet al. Journal of Allergy and Clinical Immunology, 2025, 155 (5), pp.1557-1574. ⟨10.1016/j.jaci.2025.01.025⟩ Article dans une revue pasteur-04961215v1
Escape of SARS-CoV-2 Variants KP.1.1, LB.1, and KP.3.3 From Approved Monoclonal Antibodies Delphine Planas,Isabelle Staropoli,Cyril Planchais,Emilie Yab,Banujaa Jeyarajahet al. Pathogens and Immunity, 2024, 10 (1), pp.1-11. ⟨10.20411/pai.v10i1.752⟩ Article dans une revue pasteur-04748459v1
The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches Frédéric Lemoine,Olivier Gascuel Molecular Biology and Evolution, 2024, 41 (11), pp.msae238. ⟨10.1093/molbev/msae238⟩ Article dans une revue pasteur-04967436v1
BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization George Marchment,Bryan Brancotte,Marie Schmit,Frédéric Lemoine,Sarah Cohen-Boulakia NAR Genomics and Bioinformatics, 2024, 6 (3), pp.lqae092. ⟨10.1093/nargab/lqae092⟩ Article dans une revue pasteur-04670359v1
Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor Marie Morel,Anna Zhukova,Frédéric Lemoine,Olivier Gascuel Genome Biology and Evolution, 2024, 16 (4), pp.evae040. ⟨10.1093/gbe/evae040⟩ Article dans une revue pasteur-04601784v2
Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion Delphine Planas,Isabelle Staropoli,Vincent Michel,Frederic Lemoine,Flora Donatiet al. Nature Communications, 2024, 15 (1), pp.2254. ⟨10.1038/s41467-024-46490-7⟩ Article dans une revue pasteur-04530809v1
Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites Céline Loot,Gael A Millot,Egill Richard,Eloi Littner,Claire Vitet al. Nature Microbiology, 2024, 9 (1), pp.228-240. ⟨10.1038/s41564-023-01548-y⟩ Article dans une revue pasteur-04384854v1
APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak Rodolphe Suspène,Kyle A Raymond,Laetitia Boutin,Sophie Guillier,Frédéric Lemoineet al. Journal of Infectious Diseases, 2023, 228 (10), pp.1421-1429. ⟨10.1093/infdis/jiad165⟩ Article dans une revue pasteur-04328451v1
Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages Franck Touret,Emilie Giraud,Jérôme Bourret,Flora Donati,Jaouen Tran-Rajauet al. iScience, 2023, 26 (4), pp.106413. ⟨10.1016/j.isci.2023.106413⟩ Article dans une revue pasteur-04072734v1
In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control Pauline Trémeaux,Frédéric Lemoine,Adeline Mélard,Marine Gousset,Faroudy Boufassaet al. Microbiology Spectrum, 2023, 11 (1), ⟨10.1128/spectrum.03267-22⟩ Article dans une revue pasteur-04296534v1
Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling Paul Zaharias,Frédéric Lemoine,Olivier Gascuel Systematic Biology, 2023, pp.syad052. ⟨10.1093/sysbio/syad052⟩ Article dans une revue hal-04296245v1
BioConvert: a comprehensive format converter for life sciences Hugo Caro,Sulyvan Dollin,Anne Biton,Bryan Brancotte,Dimitri Desvillechabrolet al. NAR Genomics and Bioinformatics, 2023, 5 (3), ⟨10.1093/nargab/lqad074⟩ Article dans une revue pasteur-04279554v2
Reprohackathons: promoting reproducibility in bioinformatics through training Thomas Cokelaer,Sarah Cohen-Boulakia,Frédéric Lemoine Bioinformatics, 2023, 39 (Sup 1), pp.i11 - i20. ⟨10.1093/bioinformatics/btad227⟩ Article dans une revue hal-04402365v1
Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems Marine Djaffardjy,George Marchment,Clémence Sebe,Raphaël Blanchet,Khalid Belhajjameet al. Computational and Structural Biotechnology Journal, 2023, 21, pp.2075-2085. ⟨10.1016/j.csbj.2023.03.003⟩ Article dans une revue hal-04037221v2
Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection Samir Amrane,Chloé Jaubert,Amina Bedrat,Tiffany Rundstadler,Patricia Recordon-Pinsonet al. Nucleic Acids Research, 2022, 50 (21), pp.12328-12343. ⟨10.1093/nar/gkac1030⟩ Article dans une revue hal-03874577v1
Deep Learning From Phylogenies To Uncover The Epidemiological Dynamics Of Outbreaks J. Voznica,A. Zhukova,V. Boskova,E. Saulnier,F. Lemoineet al. Nature Communications, 2022, 13 (1), pp.3896. ⟨10.1038/s41467-022-31511-0⟩ Article dans une revue hal-03861407v1
Considerable escape of SARS-CoV-2 Omicron to antibody neutralization Delphine Planas,Nell Saunders,Piet Maes,Florence Guivel-Benhassine,Cyril Planchaiset al. Nature, 2022, 602 (7898), pp.671-675. ⟨10.1038/s41586-021-04389-z⟩ Article dans une revue pasteur-03654259v1
Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows Frédéric Lemoine,Olivier Gascuel NAR Genomics and Bioinformatics, 2021, 3 (3), pp.lqab075. ⟨10.1093/nargab/lqab075⟩ Article dans une revue pasteur-03427582v1
COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM Frédéric Lemoine,Luc Blassel,Jakub Voznica,Olivier Gascuel Bioinformatics, 2021, pp.btaa871. ⟨10.1093/bioinformatics/btaa871⟩ Article dans une revue pasteur-02995703v1
Origin, evolution and global spread of SARS-CoV-2 Anna Zhukova,Luc Blassel,Frédéric Lemoine,Marie Morel,Jakub Voznicaet al. Comptes Rendus. Biologies, 2021, pp.1-19. ⟨10.5802/crbiol.29⟩ Article dans une revue pasteur-03038752v1
Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde Oumar Faye,Maria de Lourdes Monteiro,Bram Vrancken,Matthieu Prot,Sebastian Lequimeet al. Emerging Infectious Diseases, 2020, 26 (6), pp.1084-1090. ⟨10.3201/eid2606.190928⟩ Article dans une revue pasteur-02862296v1
SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data Raphaël Leman,Valentin Harter,Alexandre Atkinson,Grégoire Davy,Antoine Rousselinet al. Bioinformatics, 2019, 36 (5), pp.1634-1636. ⟨10.1093/bioinformatics/btz784⟩ Article dans une revue pasteur-02862337v1
NGPhylogeny.fr: new generation phylogenetic services for non-specialists Frédéric Lemoine,Damien Correia,Vincent Lefort,Olivia Doppelt-Azeroual,Fabien Mareuilet al. Nucleic Acids Research, 2019, 47 (W1), pp.W260-W265. ⟨10.1093/nar/gkz303⟩ Article dans une revue hal-02341225v1
Distribution and asymptotic behavior of the phylogenetic transfer distance Miraine Dávila Felipe,Jean-Baka Domelevo Entfellner,Frédéric Lemoine,Jakub Truszkowski,Olivier Gascuel Journal of Mathematical Biology, 2019, 79 (2), pp.485-508. ⟨10.1007/s00285-019-01365-0⟩ Article dans une revue pasteur-02404376v1
Identification of novel recurrent ETV6-IgH fusions in primary central nervous system lymphoma Aurélie Bruno,Karim Labreche,Mailys Daniau,Blandine Boisselier,Guillaume Gauchotteet al. Neuro-Oncology, 2018, 20 (8), pp.1092-1100. ⟨10.1093/neuonc/noy019⟩ Article dans une revue hal-02862388v1
Renewing Felsenstein’s phylogenetic bootstrap in the era of big data Fréderic Lemoine,Jean-Baka Domelevo Entfellner,Eduan K. Wilkinson,Damien Correia,Miraine Dávila Felipeet al. Nature, 2018, 556 (7702), pp.452-456. ⟨10.1038/s41586-018-0043-0⟩ Article dans une revue lirmm-02078445v1
Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer Grégoire Davy,Antoine Rousselin,Nicolas Goardon,Laurent Castéra,Valentin Harteret al. European Journal of Human Genetics, 2017, 25 (10), pp.1147-1154. ⟨10.1038/ejhg.2017.116⟩ Article dans une revue hal-02336114v1
Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities Sarah Cohen-Boulakia,Khalid Belhajjame,Olivier Collin,Jérôme Chopard,Christine Froidevauxet al. Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩ Article dans une revue hal-01516082v1
Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads. Aurélie Auguste,Laurianne Bessière,Anne-Laure Todeschini,Sandrine Caburet,Sabine Sarnackiet al. Human Molecular Genetics, 2015, 24 (23), pp.6687-98. ⟨10.1093/hmg/ddv373⟩ Article dans une revue hal-01266741v1
Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma Nicolas Vogt,Anne Gibaud,Fréderic Lemoine,Pierre de La Grange,Michelle Debatisseet al. Nucleic Acids Research, 2014, 42 (21), pp.13194-13205. ⟨10.1093/nar/gku1101⟩ Article dans une revue hal-01332776v1
Lipocalin 2, the TNF-like receptor TWEAKR and its ligand TWEAK act downstream of NFAT1 to regulate breast cancer cell invasion. Benoît Gaudineau,Marjorie Fougère,Frédéric Guaddachi,Frédéric Lemoine,Pierre de La Grangeet al. Journal of Cell Science, 2012, 125 (Pt 19), pp.4475-86. ⟨10.1242/jcs.099879⟩ Article dans une revue inserm-00715876v1
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes Frédéric Lemoine,Bernard Labedan,Olivier Lespinet BMC Bioinformatics, 2008, 9 (1), pp.536. ⟨10.1186/1471-2105-9-536⟩ Article dans une revue hal-04011218v1
GenoQuery: a new querying module for functional annotation in a genomic warehouse. Frédéric Lemoine,Bernard Labedan,Christine Froidevaux Bioinformatics, 2008, 24 (13), pp.i322-9. ⟨10.1093/bioinformatics/btn159⟩ Article dans une revue hal-00297225v1
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. Frederic Lemoine,Bernard Labedan,Olivier Lespinet BMC Bioinformatics, 2008, 9 (1), pp.536. ⟨10.1186/1471-2105-9-536⟩ Article dans une revue hal-00354657v1
The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species Stéphane Descorps-Declère,Frédéric Lemoine,Quentin Sculo,Olivier Lespinet,Bernard Labedan Biochimie, 2008, 90 (4), pp.595-608. ⟨10.1016/j.biochi.2007.09.010⟩ Article dans une revue istex hal-04011244v1
Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. Frederic Lemoine,Olivier Lespinet,Bernard Labedan BMC Evolutionary Biology, 2007, 7 (1), pp.237. ⟨10.1186/1471-2148-7-237⟩ Article dans une revue hal-00194466v1
The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. Stéphane Descorps-Declère,Frédéric Lemoine,Quentin Sculo,Olivier Lespinet,Bernard Labedan Biochimie, 2007, epub ahead of print. ⟨10.1016/j.biochi.2007.09.010⟩ Article dans une revue istex hal-00195158v1

Logiciel (1)

ShareFAIR-KG Marie Schmit,Ulysse Le Clanche,George Marchment,Sarah Cohen-Boulakia,Olivier Dameronet al. 2025, ⟨swh:1:rev:a96c28345857df13aafbc85461df2ab0cf259ef8;origin=https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG.git;visit=swh:1:snp:e53f57ef45e971e1b9b76477d1f39f4fbe3de77f⟩ Logiciel hal-05517690v1

Pré-publication, Document de travail (5)

Global evolutionary patterns of Yersinia pestis and its spread into Africa Guillem Mas Fiol,Frédéric Lemoine,Damien Mornico,Guillaume Bouvier,Aida Andrades Valtueñaet al. 2024 Pré-publication, Document de travail hal-05132518v1
Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe Etienne Simon-Loriere,Xavier Montagutelli,Frederic Lemoine,Flora Donati,Franck Touretet al. 2022 Pré-publication, Document de travail pasteur-04067089v1
A new route for integron cassette dissemination among bacterial genomes Céline Loot,Gael A Millot,Egill Richard,Claire Vit,Baptiste Darracqet al. 2022 Pré-publication, Document de travail pasteur-03826688v1
Deep learning from phylogenies to uncover the transmission dynamics of epidemics J Voznica,Anna Zhukova,V Boskova,E Saulnier,Fréderic Lemoineet al. 2021 Pré-publication, Document de travail hal-03428718v1
Sensitive Detection of Site-wise Convergent Evolution in Large Protein Alignments with ConDor Marie Morel,Frédéric Lemoine,Olivier Gascuel 2021 Pré-publication, Document de travail hal-03428682v1

Poster de conférence (1)

Representing bioinformatics Nextflow workflows in RO-Crate : challenges and opportunities George Marchment,Marie Schmit,Clémence Sebe,Frédéric Lemoine,Hervé Ménageret al. Semantic Web Applications and Tools for Health Care and Life Sciences, Feb 2024, Leiden, Netherlands. Zenodo, 2024, ⟨10.5281/zenodo.10822156⟩ Poster de conférence hal-04540040v1