• 2023
  Fourgeaud J, Regnault B, Ok V, Da Rocha N, Sitterlé É, Mekouar M, Faury H, Milliancourt-Seels C, Jagorel F, Chrétien D, Bigot T, Troadec É, Marques I, Serris A, Seilhean D, Neven B, Frange P, Ferroni A, Lecuit M, Nassif X, Lortholary O, Leruez-Ville M, Pérot P, Eloit M, Jamet A, Performance of clinical metagenomics in France: a prospective observational study., Lancet Microbe 2023 Dec; (): .
• 2023
  Bianca Elena Bratuleanu, Cristian Răileanu, Amal Bennouna, Delphine Chretien, Thomas Bigot, Pablo Guardado-Calvo, Gheorghe Savuta, Sara Moutailler, Marc Eloit, Sarah Temmam, Diversity of Viruses in Ixodes ricinus in Europe including Novel and Potential Arboviruses, Transboundary and emerging diseases, 2023, 2023, pp.1-14. ⟨10.1155/2023/6661723⟩.
• 2023
  Zhukova A, Hecht F, Maday Y, Gascuel O, Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees., Syst Biol 2023 Sep; (): .
• 2023
  Temmam S, Tu TC, Regnault B, Bonomi M, Chrétien D, Vendramini L, Duong TN, Phong TV, Yen NT, Anh HN, Son TH, Anh PT, Amara F, Bigot T, Munier S, Thong VD, van der Werf S, Nam VS, Eloit M, Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence., Viruses 2023 Sep; 15(9): .
• 2023
  Bennouna A, Tantely ML, Raharinosy V, Andriamandimby SF, Bigot T, Chrétien D, Jacquemet E, Volant S, Temmam S, Dussart P, Lacoste V, Girod R, Eloit M, Comprehensive Characterization of Viral Diversity of Female Mosquitoes in Madagascar., Viruses 2023 Aug; 15(9): .
• 2023
  Holtz A, Baele G, Bourhy H, Zhukova A, Integrating full and partial genome sequences to decipher the global spread of canine rabies virus., Nat Commun 2023 Jul; 14(1): 4247.
• 2023
  Zhukova A, Dunn D, Gascuel O, Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK., Viruses 2023 May; 15(6): .
• 2023
  Kende J, Bonomi M, Temmam S, Regnault B, Pérot P, Eloit M, Bigot T, Virus Pop-Expanding Viral Databases by Protein Sequence Simulation., Viruses 2023 May; 15(6): .
• 2023
  Temmam S, Montagutelli X, Herate C, Donati F, Regnault B, Attia M, Baquero Salazar E, Chretien D, Conquet L, Jouvion G, Pipoli Da Fonseca J, Cokelaer T, Amara F, Relouzat F, Naninck T, Lemaitre J, Derreudre-Bosquet N, Pascal Q, Bonomi M, Bigot T, Munier S, Rey FA, Le Grand R, van der Werf S, Eloit M, SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19., EMBO Rep 2023 Apr; 24(4): e56055.
• 2022
  Julien Guglielmini, Morgan Gaia, Violette Da Cunha, Alexis Criscuolo, Mart Krupovic, Patrick Forterre, Viral origin of eukaryotic type IIA DNA topoisomerases, Virus Evolution 2022;8(2):veac097.
• 2022
  Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, , Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O, , Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems., Elife 2022 Aug; 11(): .
• 2022
  Savin C, Le Guern AS, Chereau F, Guglielmini J, Heuzé G, Demeure C, Pizarro-Cerdá J, , First Description of a Yersinia pseudotuberculosis Clonal Outbreak in France, Confirmed Using a New Core Genome Multilocus Sequence Typing Method., Microbiol Spectr 2022 Jul; (): e0114522.
• 2022
  Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero, Sandie Munier, Massimiliano Bonomi, Béatrice Regnault, Bounsavane Douangboubpha, Yasaman Karami, Delphine Chrétien, Daosavanh Sanamxay, Vilakhan Xayaphet, Phetphoumin Paphaphanh, Vincent Lacoste, Somphavanh Somlor, Khaithong Lakeomany, Nothasin Phommavanh, Philippe Pérot, Océane Dehan, Faustine Amara, Flora Donati, Thomas Bigot, Michael Nilges, Félix Rey, Sylvie van Der Werf, Paul Brey, Marc Eloit, Bat coronaviruses related to SARS-CoV-2 and infectious for human cells, Nature, 2022, 604 (7905), pp.330-336. ⟨10.1038/s41586-022-04532-4⟩.
• 2022
  Bianca Elena Bratuleanu, Sarah Temmam, Sandie Munier, Delphine Chrétien, Thomas Bigot, Sylvie van Der Werf, Gheorghe Savuta, Marc Eloit, Detection of Phenuiviridae, Chuviridae Members, and a Novel Quaranjavirus in Hard Ticks From Danube Delta, Frontiers in Veterinary Science, 2022, 9, pp.863814. ⟨10.3389/fvets.2022.863814⟩.
• 2021
  Colcombet-Cazenave B, Druart K, Bonnet C, Petit C, Spérandio O, Guglielmini J, Wolff N, , Phylogenetic analysis of Harmonin homology domains., BMC Bioinformatics 2021 Apr; 22(1): 190.
• 2021
  Jamet A, Guglielmini J, Brancotte B, Coureuil M, Euphrasie D, Meyer J, Roux J, Barnier JP, Bille E, Ferroni A, Magny JF, Bôle-Feysot C, Charbit A, Nassif X, Brisse S, , High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones., J Clin Microbiol 2021 Feb; 59(3): .
• 2021
  Woo AC, Gaia M, Guglielmini J, Da Cunha V, Forterre P, , Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy., Front Microbiol 2021 ; 12(): 704052.
• 2020
  Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č, Diversity and evolution of B-family DNA polymerases, Nucleic Acids Res 2020 Oct; 48(18): 10142-10156.
• 2020
  Baidaliuk A, Lequime S, Moltini-Conclois I, Dabo S, Dickson LB, Prot M, Duong V, Dussart P, Boyer S, Shi C, Matthijnssens J, Guglielmini J, Gloria-Soria A, Simon-Lorière E, Lambrechts L, , Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations., Virus Evol 2020 Jan; 6(1): veaa018.
• 2019
  Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M, Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes, Proc. Natl. Acad. Sci. U.S.A. 2019 Sep;116(39):19585-19592.
• 2019
  Nicolas Maillet, Rapid Peptides Generator: fast and efficient in silico protein digestion, NAR Genomics and Bioinformatics 2020 Mar;2(1):lqz004.
• 2019
  Singh P, Alaganan A, More KR, Lorthiois A, Thiberge S, Gorgette O, Guillotte Blisnick M, Guglielmini J, Aguilera SS, Touqui L, Singh S, Chitnis CE, , Role of a patatin-like phospholipase in Plasmodium falciparum gametogenesis and malaria transmission., 2019 08; 116(35): 17498-17508.
• 2019
  Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M, , Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance., PLoS Negl Trop Dis 2019 04; 13(4): e0007374.
• 2019
  Luigi Caputi, Quentin Carradec, Damien Eveillard, Amos Kirilovsky, Eric Pelletier, Juan J. Pierella Karlusich, Fabio Rocha Jimenez Vieira, Emilie Villar, Samuel Chaffron, Shruti Malviya, Eleonora Scalco, Silvia G. Acinas, Adriana Alberti, Jean‐Marc Aury, Anne‐Sophie Benoiston, Alexis Bertrand, Tristan Biard, Lucie Bittner, Martine Boccara, Jennifer R. Brum, Christophe Brunet, Greta Busseni, Anna Carratalà, Hervé Claustre, Luis Pedro Coelho, Sébastien Colin, Salvatore D'Aniello, Corinne Da Silva, Marianna Del Core, Hugo Doré, Stéphane Gasparini, Florian Kokoszka, Jean‐Louis Jamet, Christophe Lejeusne, Cyrille Lepoivre, Magali Lescot, Gipsi Lima‐Mendez, Fabien Lombard, Julius Lukeš, Nicolas Maillet, Mohammed‐Amin Madoui, Elodie Martinez, Maria Grazia Mazzocchi, Mario B. Néou, Javier Paz‐Yepes, Julie Poulain, Simon Ramondenc, Jean‐Baptiste Romagnan, Simon Roux, Daniela Salvagio Manta, Remo Sanges, Sabrina Speich, Mario Sprovieri, Shinichi Sunagawa, Vincent Taillandier, Atsuko Tanaka, Leila Tirichine, Camille Trottier, Julia Uitz, Alaguraj Veluchamy, Jana Veselá, Flora Vincent, Sheree Yau, Stefanie Kandels‐Lewis, Sarah Searson, Céline Dimier, Marc Picheral, Tara Oceans Coordinators, Peer Bork, Emmanuel Boss, Colomban de Vargas, Michael J. Follows, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Eric Karsenti, Paolo Sordino, Lars Stemmann, Matthew B. Sullivan, Alessandro Tagliabue, Adriana Zingone, Laurence Garczarek, Fabrizio d'Ortenzio, Pierre Testor, Fabrice Not, Maurizio Ribera d'Alcalà, Patrick Wincker, Chris Bowler, Daniele Iudicone, Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems, Global Biogeochemical Cycles 2019 Jan;33(3):391-419.
• 2014
  Maillet N, Collet G, Vannier T, Lavenier D, Peterlongo P, COMMET: comparing and combining multiple metagenomic datasets, BIBM, IEEE 2014 Nov.
• 2012
  Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics 2012;13 Suppl 19:S10.