Lemoine Frédéric

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Publications

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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 Dameron et al.

SWAT4HCLS 2026, Mar 2026, Amsterdam, Netherlands

Communication dans un congrès hal-05517640v1
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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 Lemoine et al.

Epidemics - 7th International Conference on Infectious Disease Dynamics, Dec 2019, Charleston, United States

Communication dans un congrès pasteur-02405720v1
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Pre-European contact leprosy in the Americas and its current persistence

Maria Lopopolo , Charlotte Avanzi , Sebastian Duchene , Pierre Luisi , Alida de Flamingh et al.

Science, In press, pp.eadu7144. ⟨10.1126/science.adu7144⟩

Article dans une revue pasteur-05106303v2
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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 Ellouze et 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
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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
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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
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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
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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 Donati et al.

Nature Communications, 2024, 15 (1), pp.2254. ⟨10.1038/s41467-024-46490-7⟩

Article dans une revue pasteur-04530809v1
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Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites

Céline Loot , Gael A Millot , Egill Richard , Eloi Littner , Claire Vit et al.

Nature Microbiology, 2024, 9 (1), pp.228-240. ⟨10.1038/s41564-023-01548-y⟩

Article dans une revue pasteur-04384854v1
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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 Lemoine et al.

Journal of Infectious Diseases, 2023, 228 (10), pp.1421-1429. ⟨10.1093/infdis/jiad165⟩

Article dans une revue pasteur-04328451v1
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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
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BioConvert: a comprehensive format converter for life sciences

Hugo Caro , Sulyvan Dollin , Anne Biton , Bryan Brancotte , Dimitri Desvillechabrol et al.

NAR Genomics and Bioinformatics, 2023, 5 (3), ⟨10.1093/nargab/lqad074⟩

Article dans une revue pasteur-04279554v2
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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 Boufassa et al.

Microbiology Spectrum, 2023, 11 (1), ⟨10.1128/spectrum.03267-22⟩

Article dans une revue pasteur-04296534v1
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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
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Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems

Marine Djaffardjy , George Marchment , Clémence Sebe , Raphaël Blanchet , Khalid Belhajjame et al.

Computational and Structural Biotechnology Journal, 2023, 21, pp.2075-2085. ⟨10.1016/j.csbj.2023.03.003⟩

Article dans une revue hal-04037221v2
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Deep Learning From Phylogenies To Uncover The Epidemiological Dynamics Of Outbreaks

J. Voznica , A. Zhukova , V. Boskova , E. Saulnier , F. Lemoine et 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 Planchais et al.

Nature, 2022, 602 (7898), pp.671-675. ⟨10.1038/s41586-021-04389-z⟩

Article dans une revue pasteur-03654259v1
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Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection

Samir Amrane , Chloé Jaubert , Amina Bedrat , Tiffany Rundstadler , Patricia Recordon-Pinson et al.

Nucleic Acids Research, 2022, 50 (21), pp.12328-12343. ⟨10.1093/nar/gkac1030⟩

Article dans une revue hal-03874577v1
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Origin, evolution and global spread of SARS-CoV-2

Anna Zhukova , Luc Blassel , Frédéric Lemoine , Marie Morel , Jakub Voznica et al.

Comptes Rendus. Biologies, 2021, pp.1-19. ⟨10.5802/crbiol.29⟩

Article dans une revue pasteur-03038752v1
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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
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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
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Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde

Oumar Faye , Maria de Lourdes Monteiro , Bram Vrancken , Matthieu Prot , Sebastian Lequime et 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 Rousselin et al.

Bioinformatics, 2019, 36 (5), pp.1634-1636. ⟨10.1093/bioinformatics/btz784⟩

Article dans une revue pasteur-02862337v1
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NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Frédéric Lemoine , Damien Correia , Vincent Lefort , Olivia Doppelt-Azeroual , Fabien Mareuil et al.

Nucleic Acids Research, 2019, 47 (W1), pp.W260-W265. ⟨10.1093/nar/gkz303⟩

Article dans une revue hal-02341225v1
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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 Gauchotte et al.

Neuro-Oncology, 2018, 20 (8), pp.1092-1100. ⟨10.1093/neuonc/noy019⟩

Article dans une revue hal-02862388v1
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Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Fréderic Lemoine , Jean-Baka Domelevo Entfellner , Eduan K. Wilkinson , Damien Correia , Miraine Dávila Felipe et 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 Harter et al.

European Journal of Human Genetics, 2017, 25 (10), pp.1147-1154. ⟨10.1038/ejhg.2017.116⟩

Article dans une revue hal-02336114v1
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia , Khalid Belhajjame , Olivier Collin , Jérôme Chopard , Christine Froidevaux et 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 Sarnacki et al.

Human Molecular Genetics, 2015, 24 (23), pp.6687-98. ⟨10.1093/hmg/ddv373⟩

Article dans une revue hal-01266741v1
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Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma

Nicolas Vogt , Anne Gibaud , Fréderic Lemoine , Pierre de La Grange , Michelle Debatisse et al.

Nucleic Acids Research, 2014, 42 (21), pp.13194-13205. ⟨10.1093/nar/gku1101⟩

Article dans une revue hal-01332776v1
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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 Grange et al.

Journal of Cell Science, 2012, 125 (Pt 19), pp.4475-86. ⟨10.1242/jcs.099879⟩

Article dans une revue inserm-00715876v1

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

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
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Representing bioinformatics Nextflow workflows in RO-Crate : challenges and opportunities

George Marchment , Marie Schmit , Clémence Sebe , Frédéric Lemoine , Hervé Ménager et 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