• 2025
  Cyril Savin, Pierre Lê-Bury, Julien Guglielmini, Thibaut Douché, Guillem Mas Fiol, Rodolphe Buzelé, Cécile Le Brun, Frédéric Bastides, Maud François, Béatrice Birmelé, Laura Guichard, Julien Madej, Rémi Beau, Nicolas Cabanel, Laurent Dortet, Mariette Matondo, Olivier Dussurget, Elisabeth Carniel, Philippe Lanotte, Javier Pizarro-Cerdá, In-host evolution of Yersinia enterocolitica during a chronic human infection, Nature Communications, 2025, 16 (1), pp.5637. ⟨10.1038/s41467-025-60782-6⟩.
• 2025
  Zhukova A, Gascuel O, Accounting for contact tracing in epidemiological birth-death models., PLoS Comput Biol 2025 May; 21(5): e1012461.
• 2025
  Salim Chibani, Elhem Yacoub, Safa Boujemaa, Helmi Mardassi, J. Guglielmini, Amaury Vaysse, Nadine Khadraoui, Béhija Mlik, Boutheina Ben Abdelmoumen Mardassi, A genome-wide investigation of Mycoplasma hominis genes associated with gynecological infections or infertility, Frontiers in Microbiology, In press, 16, pp.1561378. ⟨10.3389/fmicb.2025.1561378⟩.
• 2024
  Gauthier Delvallez, Laure Diancourt, Julien Guglielmini, Anne-Laure Michon, Sylvain Brisse, B. Dupuy, Alexis Criscuolo, Comment on: Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis Division II strain: an unexpected finding, Journal of Antimicrobial Chemotherapy, 6:dkae427. ⟨10.1093/jac/dkae427⟩.
• 2024
  Xie R, Adam DC, Hu S, Cowling BJ, Gascuel O, Zhukova A, Dhanasekaran V, Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach., Mol Biol Evol 2024 Nov; (): .
• 2024
  Maestri R, Perez-Lamarque B, Zhukova A, Morlon H, Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses., Elife 2024 Aug; 13(): .
• 2024
  Marie C Schoelmerich, Lynn Ly, Jacob West-Roberts, Ling-Dong Shi, Cong Shen, Nikhil S Malvankar, Najwa Taib, Simonetta Gribaldo, Ben J Woodcroft, Christopher W Schadt, Basem Al-Shayeb, Xiaoguang Dai, Christopher Mozsary, Scott Hickey, Christine He, John Beaulaurier, Sissel Juul, Rohan Sachdeva, Jillian F Banfield, Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires, Nature Communications, 2024, 15 (1), pp.5414. ⟨10.1038/s41467-024-49548-8⟩.
• 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
  Nußbaum P, Kureisaite-Ciziene D, Bellini D, van der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV, Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division., Nat Microbiol 2024 Mar; 9(3): 698-711.
• 2024
  Anjou C, Lotoux A, Zhukova A, Royer M, Caulat LC, Capuzzo E, Morvan C, Martin-Verstraete I, The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia., PLoS Pathog 2024 Feb; 20(2): e1012001.
• 2023
  Shrestha S, Taib N, Gribaldo S, Shen A, Diversification of division mechanisms in endospore-forming bacteria revealed by analyses of peptidoglycan synthesis in Clostridioides difficile., Nat Commun 2023 Dec; 14(1): 7975.
• 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
  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
  Zhukova A, Dunn D, Gascuel O, Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK., 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.
• 2023
  Hannah Frost, Julien Guglielmini, Sebastian Duchêne, Jake Lacey, Martina Sanderson-Smith, Andrew Steer, Mark Walker, Anne Botteaux, Mark Davies, Pierre Smeesters, Promiscuous evolution of Group A Streptococcal M and M-like proteins, Microbiology, 2023, 169 (1), pp.001280. ⟨10.1099/mic.0.001280⟩.
• 2023
  Bratuleanu BE, Răileanu C, Bennouna A, Chretien D, Bigot T, Guardado-Calvo P, Savuta G, Moutailler S, Eloit M, Temmam S, Diversity of Viruses in Ixodes ricinus in Europe including Novel and Potential Arboviruses., Transbound Emerg Dis 2023 ; 2023(): 6661723.
• 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
  Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, Eloit M, Bat coronaviruses related to SARS-CoV-2 and infectious for human cells., Nature 2022 Apr; 604(7905): 330-336.
• 2022
  Bratuleanu BE, Temmam S, Munier S, Chrétien D, Bigot T, van der Werf S, Savuta G, Eloit M, Detection of Phenuiviridae, Chuviridae Members, and a Novel Quaranjavirus in Hard Ticks From Danube Delta., Front Vet Sci 2022 ; 9(): 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.