• 2024
  Lemoine F, Gascuel O, The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches., Mol Biol Evol 2024 Nov; 41(11): .
• 2024
  Fourati S, Reslan A, Bourret J, Casalegno JS, Rahou Y, Chollet L, Pillet S, Tremeaux P, Dossou NC, Gault E, Salmona M, Imbert-Marcille BM, Mirand A, Larrat S, Moisan A, Marot S, Schnuriger A, Veyrenche N, Engelmann I, Handala L, Henry A, Stephan V, Brichler S, Avettand-Fenoel V, Zemali N, Lefeuvre C, Pronier C, Deroche L, Jaffar-Bandjee MC, Mouna L, Francois C, Regueme A, Hartard C, Rogez S, Gallais F, Ly A, Rodriguez C, Dos Santos G, Simon-Loriere E, Schwartz O, Buchrieser J, Pawlotsky JM, Lemoine F, Audureau E, Rameix-Welti MA, Genotypic and phenotypic characterisation of respiratory syncytial virus after nirsevimab breakthrough infections: a large, multicentre, observational, real-world study., Lancet Infect Dis 2024 Oct; (): .
• 2024
  Delphine Planas, Isabelle Staropoli, Cyril Planchais, Emilie Yab, Banujaa Jeyarajah, Yannis Rahou, Matthieu Prot, Florence Guivel-Benhassine, Frederic Lemoine, Vincent Enouf, Etienne Simon-Loriere, Hugo Mouquet, Marie-Anne Rameix-Welti, Olivier Schwartz, Escape of SARS-CoV-2 Variants KP.1.1, LB.1, and KP.3.3 From Approved Monoclonal Antibodies, Pathogens and Immunity, 2024, 10 (1), pp.1-11. ⟨10.20411/pai.v10i1.752⟩.
• 2024
  Marchment G, Brancotte B, Schmit M, Lemoine F, Cohen-Boulakia S, BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization., NAR Genom Bioinform 2024 Sep; 6(3): lqae092.
• 2024
  Planas D, Staropoli I, Michel V, Lemoine F, Donati F, Prot M, Porrot F, Guivel-Benhassine F, Jeyarajah B, Brisebarre A, Dehan O, Avon L, Bolland WH, Hubert M, Buchrieser J, Vanhoucke T, Rosenbaum P, Veyer D, Péré H, Lina B, Trouillet-Assant S, Hocqueloux L, Prazuck T, Simon-Loriere E, Schwartz O, Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion., Nat Commun 2024 Mar; 15(1): 2254.
• 2024
  Morel M, Zhukova A, Lemoine F, Gascuel O, Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor., Genome Biol Evol 2024 Mar; (): .
• 2024
  Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D, Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites., Nat Microbiol 2024 Jan; 9(1): 228-240.
• 2023
  Caro H, Dollin S, Biton A, Brancotte B, Desvillechabrol D, Dufresne Y, Li B, Kornobis E, Lemoine F, Maillet N, Perrin A, Traut N, Néron B, Cokelaer T, BioConvert: a comprehensive format converter for life sciences., NAR Genom Bioinform 2023 Sep; 5(3): lqad074.
• 2023
  Zaharias P, Lemoine F, Gascuel O, Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling., Syst Biol 2023 Aug; (): .
• 2023
  Cokelaer T, Cohen-Boulakia S, Lemoine F, Reprohackathons: promoting reproducibility in bioinformatics through training., Bioinformatics 2023 Jun; 39(39 Suppl 1): i11-i20.
• 2023
  Suspène R, Raymond KA, Boutin L, Guillier S, Lemoine F, Ferraris O, Tournier JN, Iseni F, Simon-Lorière E, Vartanian JP, APOBEC3F is a mutational driver of the human Monkeypox virus identified in the 2022 outbreak., J Infect Dis 2023 May; (): .
• 2023
  Touret F, Giraud E, Bourret J, Donati F, Tran-Rajau J, Chiaravalli J, Lemoine F, Agou F, Simon-Lorière E, van der Werf S, de Lamballerie X, Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages., iScience 2023 Apr; 26(4): 106413.
• 2023
  Trémeaux P, Lemoine F, Mélard A, Gousset M, Boufassa F, Orr S, Monceaux V, Gascuel O, Lambotte O, Hocqueloux L, Saez-Cirion A, Rouzioux C, Avettand-Fenoel V, , In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control., Microbiol Spectr 2023 Feb; 11(1): e0326722.
• 2023
  Djaffardjy M, Marchment G, Sebe C, Blanchet R, Bellajhame K, Gaignard A, Lemoine F, Cohen-Boulakia S, , Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems., Comput Struct Biotechnol J 2023 ; 21(): 2075-2085.
• 2022
  Amrane S, Jaubert C, Bedrat A, Rundstadler T, Recordon-Pinson P, Aknin C, Guédin A, De Rache A, Bartolucci L, Diene I, Lemoine F, Gascuel O, Pratviel G, Mergny JL, Andreola ML, , Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection., Nucleic Acids Res 2022 Nov; 50(21): 12328-12343.
• 2022
  Voznica J, Zhukova A, Boskova V, Saulnier E, Lemoine F, Moslonka-Lefebvre M, Gascuel O, , Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks., Nat Commun 2022 Jul; 13(1): 3896.
• 2022
  Planas D, Saunders N, Maes P, Guivel-Benhassine F, Planchais C, Buchrieser J, Bolland WH, Porrot F, Staropoli I, Lemoine F, Péré H, Veyer D, Puech J, Rodary J, Baele G, Dellicour S, Raymenants J, Gorissen S, Geenen C, Vanmechelen B, Wawina-Bokalanga T, Martí-Carreras J, Cuypers L, Sève A, Hocqueloux L, Prazuck T, Rey FA, Simon-Loriere E, Bruel T, Mouquet H, André E, Schwartz O, , Considerable escape of SARS-CoV-2 Omicron to antibody neutralization., Nature 2022 Feb; 602(7898): 671-675.
• 2021
  Lemoine F, Gascuel O, , Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows., NAR Genom Bioinform 2021 Sep; 3(3): lqab075.
• 2021
  Grant R, Nguyen TTT, Dao MH, Pham HTT, Piorkowski G, Pham TDT, Cao TM, Huynh LTK, Nguyen QH, Vien LDK, Lemoine F, Zhukova A, Hoang DTN, Nguyen HT, Nguyen NT, Le LB, Ngo MNQ, Tran TC, Le NNT, Nguyen MN, Pham HT, Hoang TTD, Dang TV, Vu AT, Nguyen QNT, de Lamballerie X, Pham QD, Luong QC, Fontanet A, , Maternal and neonatal outcomes related to Zika virus in pregnant women in Southern Vietnam: An epidemiological and virological prospective analysis., Lancet Reg Health West Pac 2021 Jun; 11(): 100163.
• 2020
  Zhukova A, Blassel L, Lemoine F, Morel M, Voznica J, Gascuel O, Origin, evolution and global spread of SARS-CoV-2, Comptes Rendus Biologies 2020; 20 p.
• 2020
  Lemoine F, Blassel L, Voznica J, Gascuel O, , COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM., Bioinformatics 2020 Oct; (): .
• 2020
  Faye O, de Lourdes Monteiro M, Vrancken B, Prot M, Lequime S, Diarra M, Ndiaye O, Valdez T, Tavarez S, Ramos J, da Veiga Leal S, Pires C, Moreira A, Tavares MF, Fernandes L, Barreto JN, do Céu Teixeira M, de Lima Mendonça MDL, Gomes CCDSL, Castellon MS, Ma L, Lemoine F, Gámbaro-Roglia F, Delaune D, Fall G, Fall IS, Diop M, Sakuntabhai A, Loucoubar C, Lemey P, Holmes EC, Faye O, Sall AA, Simon-Loriere E, , Genomic Epidemiology of 2015-2016 Zika Virus Outbreak in Cape Verde., Emerg Infect Dis 2020 06; 26(6): 1084-1090.
• 2019
  Leman R, Harter V, Atkinson A, Davy G, Rousselin A, Muller E, Castéra L, Lemoine F, de la Grange P, Guillaud-Bataille M, Vaur D, Krieger S, SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data, Bioinformatics 2019 Oct;.
• 2019
  Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F, Cohen-Boulakia S, Gascuel O, NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Res. 2019 Jul;47(W1):W260-W265.
• 2019
  Dávila Felipe M, Domelevo Entfellner JB, Lemoine F, Truszkowski J, Gascuel O, , Distribution and asymptotic behavior of the phylogenetic transfer distance., J Math Biol 2019 07; 79(2): 485-508.
• 2018
  Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O, Renewing Felsenstein’s phylogenetic bootstrap in the era of big data, Nature 2018 Apr;.
• 2018
  Bruno A, Labreche K, Daniau M, Boisselier B, Gauchotte G, Royer-Perron L, Rahimian A, Lemoine F, de la Grange P, Guégan J, Bielle F, Polivka M, Adam C, Meyronet D, Figarella-Branger D, Villa C, Chrétien F, Eimer S, Davi F, Rousseau A, Houillier C, Soussain C, Mokhtari K, Hoang-Xuan K, Alentorn A, Identification of novel recurrent ETV6-IGH fusions in primary central nervous system lymphoma, Neuro-oncology 2018 Feb;.
• 2017
  Davy G, Rousselin A, Goardon N, Castéra L, Harter V, Legros A, Muller E, Fouillet R, Brault B, Smirnova AS, Lemoine F, de la Grange P, Guillaud-Bataille M, Caux-Moncoutier V, Houdayer C, Bonnet F, Blanc-Fournier C, Gaildrat P, Frebourg T, Martins A, Vaur D, Krieger S, Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer, Eur. J. Hum. Genet. 2017 Oct;25(10):1147-1154.
• 2017
  Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, Christophe Blanchet, Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems.
• 2016
  Mauger O, Lemoine F, Scheiffele P, Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity, Neuron 2016 Dec;92(6):1266-1278.
• 2015
  Auguste A, Bessière L, Todeschini AL, Caburet S, Sarnacki S, Prat J, D'angelo E, De La Grange P, Ariste O, Lemoine F, Legois B, Sultan C, Zider A, Galmiche L, Kalfa N, Veitia RA, Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads, Hum. Mol. Genet. 2015 Dec;24(23):6687-98.
• 2014
  Vogt N, Gibaud A, Lemoine F, de la Grange P, Debatisse M, Malfoy B, Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma, Nucleic Acids Res. 2014 Dec;42(21):13194-205.
• 2013
  Zhang Z, Convertini P, Shen M, Xu X, Lemoine F, de la Grange P, Andres DA, Stamm S, Valproic acid causes proteasomal degradation of DICER and influences miRNA expression, PLoS ONE 2013;8(12):e82895.
• 2013
  Gandoura S, Weiss E, Rautou PE, Fasseu M, Gustot T, Lemoine F, Hurtado-Nedelec M, Hego C, Vadrot N, Elkrief L, Lettéron P, Tellier Z, Pocidalo MA, Valla D, Lebrec D, Groyer A, Monteiro RC, de la Grange P, Moreau R, Gene- and exon-expression profiling reveals an extensive LPS-induced response in immune cells in patients with cirrhosis, J. Hepatol. 2013 May;58(5):936-48.
• 2012
  Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H, Birth and expression evolution of mammalian microRNA genes, Genome Res. 2013 Jan;23(1):34-45.
• 2012
  Gaudineau B, Fougère M, Guaddachi F, Lemoine F, de la Grange P, Jauliac S, Lipocalin 2, the TNF-like receptor TWEAKR and its ligand TWEAK act downstream of NFAT1 to regulate breast cancer cell invasion, J. Cell. Sci. 2012 Oct;125(Pt 19):4475-86.
• 2010
  Pradervand S, Weber J, Lemoine F, Consales F, Paillusson A, Dupasquier M, Thomas J, Richter H, Kaessmann H, Beaudoing E, Hagenbüchle O, Harshman K, Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs, BioTechniques 2010 Mar;48(3):219-22.
• 2008
  Lemoine F, Labedan B, Lespinet O, SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes, BMC Bioinformatics 2008;9:536.
• 2008
  Lemoine F, Labedan B, Froidevaux C, GenoQuery: a new querying module for functional annotation in a genomic warehouse, Bioinformatics 2008 Jul;24(13):i322-9.
• 2007
  Lemoine F, Lespinet O, Labedan B, Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data, BMC Evol. Biol. 2007;7:237.
• 2007
  Descorps-Declère S, Lemoine F, Sculo Q, Lespinet O, Labedan B, The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species, Biochimie 2008 Apr;90(4):595-608.