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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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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
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Integron cassettes 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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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
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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
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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
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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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Deep learning from phylogenies to uncover the transmission dynamics of epidemics

 J Voznica , Anna Zhukova , V Boskova , E Saulnier , Fréderic Lemoine , et al.
2021
Pré-publication, Document de travail hal-03428718v1
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Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems

 Marine Djaffardjy , George Marchment , Clémence Sebe , Raphael 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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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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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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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
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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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Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor

 Marie Morel , Frédéric Lemoine , Anna Zhukova , Olivier Gascuel
2022
Pré-publication, Document de travail hal-04296479v1

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

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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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

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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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

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

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

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 pasteur-02862388v1

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
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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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A new route for integron cassette dissemination among bacterial genomes

 Céline Loot , Gael A Millot , Egill Richard , Claire Vit , Baptiste Darracq , et al.
2022
Pré-publication, Document de travail pasteur-03826688v1

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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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

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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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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