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Mainguy, Jean; Lemane, Téo; Médigue, Claudine; Calteau, Alexandra; Vallenet, David
PanGBank: a database of pangenome graphs for comparative microbial genomics Proceedings Article
In: EAGS 2026-International Environmental and Agronomical Genomics symposium, 2026.
@inproceedings{mainguy2026pangbank,
title = {PanGBank: a database of pangenome graphs for comparative microbial genomics},
author = {Jean Mainguy and Téo Lemane and Claudine Médigue and Alexandra Calteau and David Vallenet},
year = {2026},
date = {2026-01-01},
booktitle = {EAGS 2026-International Environmental and Agronomical Genomics symposium},
keywords = {},
pubstate = {published},
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Poubanne, Florent; Darii, Ekaterina; Mariage, Aline; Elisée, Eddy; Sirvain, Peggy; Hassan, Camille; Rivollier, Julie; Fossey-Jouenne, Aurélie; Perret, Alain; Méheust, Raphaël; others,
Functional convergence in Z-DNA biosynthesis highlighted by the characterization of nucleotide metabolism enzymes in bacteriophages Journal Article
In: Nucleic Acids Research, vol. 54, no. 4, pp. gkag079, 2026.
@article{poubanne2026functional,
title = {Functional convergence in Z-DNA biosynthesis highlighted by the characterization of nucleotide metabolism enzymes in bacteriophages},
author = {Florent Poubanne and Ekaterina Darii and Aline Mariage and Eddy Elisée and Peggy Sirvain and Camille Hassan and Julie Rivollier and Aurélie Fossey-Jouenne and Alain Perret and Raphaël Méheust and others},
year = {2026},
date = {2026-01-01},
journal = {Nucleic Acids Research},
volume = {54},
number = {4},
pages = {gkag079},
publisher = {Oxford University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bolzoni, Romain; Monteil, Caroline L; Alonso, Béatrice; Bergot, Marine; Chevrier, Daniel M; Godon, Christian; Menguy, Nicolas; Fouteau, Stephanie; Cunha, Violette Da; Skouri-Panet, Fériel; others,
Magnetoreception in a freshwater ciliate arises from endosymbiosis Journal Article
In: Nature Communications, 2026.
@article{bolzoni2026magnetoreception,
title = {Magnetoreception in a freshwater ciliate arises from endosymbiosis},
author = {Romain Bolzoni and Caroline L Monteil and Béatrice Alonso and Marine Bergot and Daniel M Chevrier and Christian Godon and Nicolas Menguy and Stephanie Fouteau and Violette Da Cunha and Fériel Skouri-Panet and others},
year = {2026},
date = {2026-01-01},
journal = {Nature Communications},
publisher = {Nature Publishing Group UK London},
keywords = {},
pubstate = {published},
tppubtype = {article}
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Novak, Lukas VF; Jiang, Lijing; Hemon, Marie; Fernandez, Marilina; Russo, Léa; Wang, Shasha; Shao, Zongze; Cunha, Violette Da; Alain, Karine
Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin Journal Article
In: The ISME Journal, pp. wrag042, 2026.
@article{novak2026sulfur,
title = {Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin},
author = {Lukas VF Novak and Lijing Jiang and Marie Hemon and Marilina Fernandez and Léa Russo and Shasha Wang and Zongze Shao and Violette Da Cunha and Karine Alain},
year = {2026},
date = {2026-01-01},
journal = {The ISME Journal},
pages = {wrag042},
publisher = {Oxford University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
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Royer, Guilhem; Chau, Françoise; Vallenet, David; Denamur, Erick; Colibafi,; groups, Septicoli; group, Colocoli; group, Coliville
Identification of specific metabolic capacities associated with major extraintestinal pathogenic Escherichia coli lineages Journal Article
In: Journal of Bacteriology, pp. e00421–25, 2026.
@article{royer2026identification,
title = {Identification of specific metabolic capacities associated with major extraintestinal pathogenic Escherichia coli lineages},
author = {Guilhem Royer and Françoise Chau and David Vallenet and Erick Denamur and Colibafi and Septicoli groups and Colocoli group and Coliville group},
year = {2026},
date = {2026-01-01},
journal = {Journal of Bacteriology},
pages = {e00421–25},
publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
keywords = {},
pubstate = {published},
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2025
Mangin, Camille C; Benzerara, Karim; Bergot, Marine; Menguy, Nicolas; Alonso, Béatrice; Fouteau, Stéphanie; Méheust, Raphaël; Chevrier, Daniel M; Godon, Christian; Turrini, Elsa; others,
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate Journal Article
In: The ISME Journal, vol. 19, no. 1, pp. wrae260, 2025.
@article{mangin2025magnetotactic,
title = {Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate},
author = {Camille C Mangin and Karim Benzerara and Marine Bergot and Nicolas Menguy and Béatrice Alonso and Stéphanie Fouteau and Raphaël Méheust and Daniel M Chevrier and Christian Godon and Elsa Turrini and others},
year = {2025},
date = {2025-01-01},
journal = {The ISME Journal},
volume = {19},
number = {1},
pages = {wrae260},
publisher = {Oxford University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
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Lopez, Pierre; Fradet, Benjamin; Coffion, Lucie; Bernardet, Jean-François; Saulnier, Denis; Duchaud, Eric
Tenacibaculum platacis sp. nov., Tenacibaculum vairaonense sp. nov. and Tenacibaculum polynesiense sp. nov. isolated from batfish (Platax orbicularis) in Tahiti Island, French Polynesia Journal Article
In: International Journal of Systematic and Evolutionary Microbiology, vol. 75, no. 1, pp. 006605, 2025.
@article{lopez2025tenacibaculum,
title = {Tenacibaculum platacis sp. nov., Tenacibaculum vairaonense sp. nov. and Tenacibaculum polynesiense sp. nov. isolated from batfish (Platax orbicularis) in Tahiti Island, French Polynesia},
author = {Pierre Lopez and Benjamin Fradet and Lucie Coffion and Jean-François Bernardet and Denis Saulnier and Eric Duchaud},
year = {2025},
date = {2025-01-01},
journal = {International Journal of Systematic and Evolutionary Microbiology},
volume = {75},
number = {1},
pages = {006605},
publisher = {Microbiology Society},
keywords = {},
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Bailly, Thomas; Elisée, Eddy; Vallenet, David
ASMC: investigating the amino acid diversity of enzyme active sites Journal Article
In: Bioinformatics, vol. 41, no. 6, pp. btaf307, 2025.
@article{bailly2025asmc,
title = {ASMC: investigating the amino acid diversity of enzyme active sites},
author = {Thomas Bailly and Eddy Elisée and David Vallenet},
year = {2025},
date = {2025-01-01},
journal = {Bioinformatics},
volume = {41},
number = {6},
pages = {btaf307},
publisher = {Oxford University Press},
keywords = {},
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Bartoli, Manon; Pradel, Nathalie; Fouteau, Stéphanie; Rouy, Zoé; Cruaud, Corinne; Nadalig, Thierry; Vallenet, David; Oliveira, Pedro H; Hirschler-Réa, Agnès
Complete genome sequence of Hyphomicrobium sp. strain 1Nfss2. 1 from marine sediments of the Berre lagoon, France Journal Article
In: Microbiology Resource Announcements, vol. 14, no. 8, pp. e00254–25, 2025.
@article{bartoli2025complete,
title = {Complete genome sequence of Hyphomicrobium sp. strain 1Nfss2. 1 from marine sediments of the Berre lagoon, France},
author = {Manon Bartoli and Nathalie Pradel and Stéphanie Fouteau and Zoé Rouy and Corinne Cruaud and Thierry Nadalig and David Vallenet and Pedro H Oliveira and Agnès Hirschler-Réa},
year = {2025},
date = {2025-01-01},
journal = {Microbiology Resource Announcements},
volume = {14},
number = {8},
pages = {e00254–25},
publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
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Pradel, Manon Bartoli Stéphanie Fouteau Nathalie
Complete genome sequence of Nitratireductor aquimarinus strain MNA2.1 isolated from sediments of the Berre lagoon, France Journal Article
In: ASM Journals, 2025.
@article{nathalie2025complete,
title = {Complete genome sequence of Nitratireductor aquimarinus strain MNA2.1 isolated from sediments of the Berre lagoon, France},
author = {Manon Bartoli Stéphanie Fouteau Nathalie Pradel},
year = {2025},
date = {2025-01-01},
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Finn, Robert D; Balech, Bachir; Burgin, Josephine; Chua, Physilia; Corre, Erwan; Cox, Cymon J; Donati, Claudio; Santos, Vitor Martins Dos; Fosso, Bruno; Hancock, John; others,
Establishing the ELIXIR Microbiome Community Journal Article
In: F1000Research, vol. 13, pp. ELIXIR–50, 2025.
@article{finn2025establishing,
title = {Establishing the ELIXIR Microbiome Community},
author = {Robert D Finn and Bachir Balech and Josephine Burgin and Physilia Chua and Erwan Corre and Cymon J Cox and Claudio Donati and Vitor Martins Dos Santos and Bruno Fosso and John Hancock and others},
year = {2025},
date = {2025-01-01},
journal = {F1000Research},
volume = {13},
pages = {ELIXIR–50},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Turrini, Elsa CA; Godon, Christian; Bergot, Marine; Alonso, Béatrice; Lambert, Sascha; Gachon, Emilie; Menguy, Nicolas; Fouteau, Stéphanie; Klumpp, Stefan; Lefèvre, Christopher T; others,
Giant multicellular magnetotactic prokaryotes in marine sediments Journal Article
In: The ISME Journal, vol. 20, no. 1, pp. wrag017, 2025.
@article{turrini2025giant,
title = {Giant multicellular magnetotactic prokaryotes in marine sediments},
author = {Elsa CA Turrini and Christian Godon and Marine Bergot and Béatrice Alonso and Sascha Lambert and Emilie Gachon and Nicolas Menguy and Stéphanie Fouteau and Stefan Klumpp and Christopher T Lefèvre and others},
year = {2025},
date = {2025-01-01},
journal = {The ISME Journal},
volume = {20},
number = {1},
pages = {wrag017},
publisher = {Oxford University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2024
Little, Alexander S; Younker, Isaac T; Schechter, Matthew S; Bernardino, Paola Nol; Méheust, Raphaël; Stemczynski, Joshua; Scorza, Kaylie; Mullowney, Michael W; Sharan, Deepti; Waligurski, Emily; others,
Dietary-and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration Journal Article
In: Nature microbiology, vol. 9, no. 1, pp. 55–69, 2024.
@article{little2024dietary,
title = {Dietary-and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration},
author = {Alexander S Little and Isaac T Younker and Matthew S Schechter and Paola Nol Bernardino and Raphaël Méheust and Joshua Stemczynski and Kaylie Scorza and Michael W Mullowney and Deepti Sharan and Emily Waligurski and others},
year = {2024},
date = {2024-01-01},
journal = {Nature microbiology},
volume = {9},
number = {1},
pages = {55–69},
publisher = {Nature Publishing Group UK London},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Barbe, Valérie; Jacquin, Justine; Bouzon, Madeleine; Wolinski, Adèle; Derippe, Gabrielle; Cheng, Jingguang; Cruaud, Corinne; Roche, David; Fouteau, Stéphanie; Petit, Jean-Louis; others,
Bioplastic degradation and assimilation processes by a novel bacterium isolated from the marine plastisphere Journal Article
In: Journal of Hazardous Materials, vol. 466, pp. 133573, 2024.
@article{barbe2024bioplastic,
title = {Bioplastic degradation and assimilation processes by a novel bacterium isolated from the marine plastisphere},
author = {Valérie Barbe and Justine Jacquin and Madeleine Bouzon and Adèle Wolinski and Gabrielle Derippe and Jingguang Cheng and Corinne Cruaud and David Roche and Stéphanie Fouteau and Jean-Louis Petit and others},
year = {2024},
date = {2024-01-01},
journal = {Journal of Hazardous Materials},
volume = {466},
pages = {133573},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Arnoux, Jérôme; Bonifati, Angela; Calteau, Alexandra; Dumbrava, Stefania; Gautreau, Guillaume
Integrating Complex Pangenome Graphs Proceedings Article
In: 2024 IEEE 40th International Conference on Data Engineering Workshops (ICDEW), pp. 350–354, IEEE 2024.
@inproceedings{arnoux2024integrating,
title = {Integrating Complex Pangenome Graphs},
author = {Jérôme Arnoux and Angela Bonifati and Alexandra Calteau and Stefania Dumbrava and Guillaume Gautreau},
year = {2024},
date = {2024-01-01},
booktitle = {2024 IEEE 40th International Conference on Data Engineering Workshops (ICDEW)},
pages = {350–354},
organization = {IEEE},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
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Elisée, Eddy; Ducrot, Laurine; Méheust, Raphaël; Bastard, Karine; Fossey-Jouenne, Aurélie; Grogan, Gideon; Pelletier, Eric; Petit, Jean-Louis; Stam, Mark; Berardinis, Véronique; others,
A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening Journal Article
In: Nature Communications, vol. 15, no. 1, pp. 4933, 2024.
@article{elisee2024refined,
title = {A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening},
author = {Eddy Elisée and Laurine Ducrot and Raphaël Méheust and Karine Bastard and Aurélie Fossey-Jouenne and Gideon Grogan and Eric Pelletier and Jean-Louis Petit and Mark Stam and Véronique Berardinis and others},
year = {2024},
date = {2024-01-01},
journal = {Nature Communications},
volume = {15},
number = {1},
pages = {4933},
publisher = {Nature Publishing Group UK London},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huang, Shuo; Méheust, Raphaël; Barquera, Blanca; Light, Samuel H.
Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer Journal Article
In: mSystems, vol. 9, no. 8, pp. e00375–24, 2024.
@article{huang2024versatile,
title = {Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer},
author = {Shuo Huang and Raphaël Méheust and Blanca Barquera and Samuel H. Light},
year = {2024},
date = {2024-01-01},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e00375–24},
publisher = {ASM Journals},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2023
Roche, David; Calteau, Alexandra; Vallenet, David
Analyzing Prokaryotic Transcriptomics in the Light of Genome Data with the MicroScope Platform Book Section
In: Microbial Environmental Genomics (MEG), pp. 241–270, Springer, 2023.
@incollection{roche2023analyzing,
title = {Analyzing Prokaryotic Transcriptomics in the Light of Genome Data with the MicroScope Platform},
author = {David Roche and Alexandra Calteau and David Vallenet},
year = {2023},
date = {2023-01-01},
booktitle = {Microbial Environmental Genomics (MEG)},
pages = {241–270},
publisher = {Springer},
keywords = {},
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Dziuba, MV; Paulus, A; Schramm, L; Awal, RP; Pósfai, M; Monteil, CL; Fouteau, S; Uebe, R; Schüler, D
Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium Journal Article
In: The ISME Journal, vol. 17, no. 3, pp. 326–339, 2023.
@article{dziuba2023silent,
title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium},
author = {MV Dziuba and A Paulus and L Schramm and RP Awal and M Pósfai and CL Monteil and S Fouteau and R Uebe and D Schüler},
year = {2023},
date = {2023-01-01},
journal = {The ISME Journal},
volume = {17},
number = {3},
pages = {326–339},
publisher = {Nature Publishing Group UK London},
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Jabeur, Rania; Guyon, Virginie; Toth, Szabolcs; Pereira, Adriano E; Huynh, Man P; Selmani, Zakia; Boland, Erin; Bosio, Mickael; Beuf, Laurent; Clark, Pete; others,
A novel binary pesticidal protein from Chryseobacterium arthrosphaerae controls western corn rootworm by a different mode of action to existing commercial pesticidal proteins Journal Article
In: Plos one, vol. 18, no. 2, pp. e0267220, 2023.
@article{jabeur2023novel,
title = {A novel binary pesticidal protein from Chryseobacterium arthrosphaerae controls western corn rootworm by a different mode of action to existing commercial pesticidal proteins},
author = {Rania Jabeur and Virginie Guyon and Szabolcs Toth and Adriano E Pereira and Man P Huynh and Zakia Selmani and Erin Boland and Mickael Bosio and Laurent Beuf and Pete Clark and others},
year = {2023},
date = {2023-01-01},
journal = {Plos one},
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publisher = {Public Library of Science San Francisco, CA USA},
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L'Haridon, Stéphane; Goulaouic, Steven; John, Emily St; Fouteau, Stephanie; Reysenbach, Anna-Louise
Methanocaldococcus lauensis sp. nov., a novel deep-sea hydrothermal vent hyperthermophilic methanogen Journal Article
In: International Journal of Systematic and Evolutionary Microbiology, vol. 73, no. 1, pp. 005646, 2023.
@article{l2023methanocaldococcus,
title = {Methanocaldococcus lauensis sp. nov., a novel deep-sea hydrothermal vent hyperthermophilic methanogen},
author = {Stéphane L'Haridon and Steven Goulaouic and Emily St John and Stephanie Fouteau and Anna-Louise Reysenbach},
year = {2023},
date = {2023-01-01},
journal = {International Journal of Systematic and Evolutionary Microbiology},
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Daugeron, Marie-Claire; Missoury, Sophia; Cunha, Violette Da; Lazar, Noureddine; Collinet, Bruno; Tilbeurgh, Herman; Basta, Tamara
A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea Journal Article
In: Nature Communications, vol. 14, no. 1, pp. 526, 2023.
@article{daugeron2023paralog,
title = {A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea},
author = {Marie-Claire Daugeron and Sophia Missoury and Violette Da Cunha and Noureddine Lazar and Bruno Collinet and Herman Tilbeurgh and Tamara Basta},
year = {2023},
date = {2023-01-01},
journal = {Nature Communications},
volume = {14},
number = {1},
pages = {526},
publisher = {Nature Publishing Group UK London},
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Stam, Mark; Lelièvre, Pernelle; Hoebeke, Mark; Corre, Erwan; Barbeyron, Tristan; Michel, Gurvan
SulfAtlas, the sulfatase database: state of the art and new developments Journal Article
In: Nucleic Acids Research, vol. 51, no. D1, pp. D647–D653, 2023.
@article{stam2023sulfatlas,
title = {SulfAtlas, the sulfatase database: state of the art and new developments},
author = {Mark Stam and Pernelle Lelièvre and Mark Hoebeke and Erwan Corre and Tristan Barbeyron and Gurvan Michel},
year = {2023},
date = {2023-01-01},
journal = {Nucleic Acids Research},
volume = {51},
number = {D1},
pages = {D647–D653},
publisher = {Oxford University Press},
keywords = {},
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Fossey-Jouenne, Aurélie; Ducrot, Laurine; Jongkind, Ewald PJ; Elisée, Eddy; Zaparucha, Anne; Grogan, Gideon; Paul, Caroline E; Vergne-Vaxelaire, Carine
Native amine dehydrogenases can catalyze the direct reduction of carbonyl compounds to alcohols in the absence of ammonia Journal Article
In: Frontiers in Catalysis, vol. 3, pp. 1105948, 2023.
@article{fossey2023native,
title = {Native amine dehydrogenases can catalyze the direct reduction of carbonyl compounds to alcohols in the absence of ammonia},
author = {Aurélie Fossey-Jouenne and Laurine Ducrot and Ewald PJ Jongkind and Eddy Elisée and Anne Zaparucha and Gideon Grogan and Caroline E Paul and Carine Vergne-Vaxelaire},
year = {2023},
date = {2023-01-01},
journal = {Frontiers in Catalysis},
volume = {3},
pages = {1105948},
publisher = {Frontiers Media SA},
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pubstate = {published},
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Rivera-Lugo, Rafael; Huang, Shuo; Lee, Frank; Méheust, Raphaël; Iavarone, Anthony T; Sidebottom, Ashley M; Oldfield, Eric; Portnoy, Daniel A; Light, Samuel H
Distinct energy-coupling factor transporter subunits enable flavin acquisition and extracytosolic trafficking for extracellular electron transfer in Listeria monocytogenes Journal Article
In: Mbio, vol. 14, no. 1, pp. e03085–22, 2023.
@article{rivera2023distinct,
title = {Distinct energy-coupling factor transporter subunits enable flavin acquisition and extracytosolic trafficking for extracellular electron transfer in Listeria monocytogenes},
author = {Rafael Rivera-Lugo and Shuo Huang and Frank Lee and Raphaël Méheust and Anthony T Iavarone and Ashley M Sidebottom and Eric Oldfield and Daniel A Portnoy and Samuel H Light},
year = {2023},
date = {2023-01-01},
journal = {Mbio},
volume = {14},
number = {1},
pages = {e03085–22},
publisher = {Am Soc Microbiol},
keywords = {},
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}
Bremer, Erhard; Calteau, Alexandra; Danchin, Antoine; Harwood, Colin; Helmann, John D; Médigue, Claudine; Palsson, Bernhard O; Sekowska, Agnieszka; Vallenet, David; Zuniga, Abril; others,
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century Journal Article
In: Microbial biotechnology, vol. 16, no. 6, pp. 1203–1231, 2023.
@article{bremer2023model,
title = {A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century},
author = {Erhard Bremer and Alexandra Calteau and Antoine Danchin and Colin Harwood and John D Helmann and Claudine Médigue and Bernhard O Palsson and Agnieszka Sekowska and David Vallenet and Abril Zuniga and others},
year = {2023},
date = {2023-01-01},
journal = {Microbial biotechnology},
volume = {16},
number = {6},
pages = {1203–1231},
publisher = {Wiley Online Library},
keywords = {},
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tppubtype = {article}
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de Moura, Ginaini Grazielli Doin; Mouffok, Saida; Gaudu, Nil; Cazalé, Anne-Claire; Milhes, Marine; Bulach, Tabatha; Valière, Sophie; Roche, David; Ferdy, Jean-Baptiste; Masson-Boivin, Catherine; others,
A selective bottleneck during host entry drives the evolution of new legume symbionts Journal Article
In: Molecular Biology and Evolution, vol. 40, no. 5, pp. msad116, 2023.
@article{doin2023selective,
title = {A selective bottleneck during host entry drives the evolution of new legume symbionts},
author = {Ginaini Grazielli Doin de Moura and Saida Mouffok and Nil Gaudu and Anne-Claire Cazalé and Marine Milhes and Tabatha Bulach and Sophie Valière and David Roche and Jean-Baptiste Ferdy and Catherine Masson-Boivin and others},
year = {2023},
date = {2023-01-01},
journal = {Molecular Biology and Evolution},
volume = {40},
number = {5},
pages = {msad116},
publisher = {Oxford University Press US},
keywords = {},
pubstate = {published},
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}
Royer, Guilhem; Clermont, Olivier; Marin, Julie; Condamine, Bénédicte; Dion, Sara; Blanquart, François; Galardini, Marco; Denamur, Erick
Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence Journal Article
In: Nature Communications, vol. 14, no. 1, pp. 3667, 2023.
@article{royer2023epistatic,
title = {Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence},
author = {Guilhem Royer and Olivier Clermont and Julie Marin and Bénédicte Condamine and Sara Dion and François Blanquart and Marco Galardini and Erick Denamur},
year = {2023},
date = {2023-01-01},
journal = {Nature Communications},
volume = {14},
number = {1},
pages = {3667},
publisher = {Nature Publishing Group UK London},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2022
Royer, Guilhem; Clermont, Olivier; Condamine, Bénédicte; Mercier-Darty, Mélanie; Laouénan, Cédric; Lefort, Agnès; Denamur, Erick; Lastours, Victoire
O-Antigen Targeted Vaccines Against Escherichia coli May Be Useful in Reducing Morbidity, Mortality, and Antimicrobial Resistance Journal Article
In: Clinical Infectious Diseases, vol. 74, no. 2, pp. 364–366, 2022.
@article{royer2022antigen,
title = {O-Antigen Targeted Vaccines Against Escherichia coli May Be Useful in Reducing Morbidity, Mortality, and Antimicrobial Resistance},
author = {Guilhem Royer and Olivier Clermont and Bénédicte Condamine and Mélanie Mercier-Darty and Cédric Laouénan and Agnès Lefort and Erick Denamur and Victoire Lastours},
year = {2022},
date = {2022-01-01},
journal = {Clinical Infectious Diseases},
volume = {74},
number = {2},
pages = {364–366},
publisher = {Oxford University Press US},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Denamur, Erick; Condamine, Bénédicte; Esposito-Farèse, Marina; Royer, Guilhem; Clermont, Olivier; Laouenan, Cédric; Lefort, Agnès; Lastours, Victoire; Galardini, Marco; COLIBAFI,; others,
Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome Journal Article
In: PLoS Genetics, vol. 18, no. 3, pp. e1010112, 2022.
@article{denamur2022genome,
title = {Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome},
author = {Erick Denamur and Bénédicte Condamine and Marina Esposito-Farèse and Guilhem Royer and Olivier Clermont and Cédric Laouenan and Agnès Lefort and Victoire Lastours and Marco Galardini and COLIBAFI and others},
year = {2022},
date = {2022-01-01},
journal = {PLoS Genetics},
volume = {18},
number = {3},
pages = {e1010112},
publisher = {Public Library of Science San Francisco, CA USA},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Surgers, Laure; Chiarabini, Thibault; Royer, Guilhem; Rougier, Hayette; Mercier-Darty, Mélanie; Decré, Dominique; Valin, Nadia; Woerther, Paul-Louis; Decousser, Jean-Winoc; Girard, Pierre-Marie; others,
Evidence of Sexual Transmission of Extended-Spectrum β-Lactamase–Producing Enterobacterales: A Cross-sectional and Prospective Study Journal Article
In: Clinical Infectious Diseases, vol. 75, no. 9, pp. 1556–1564, 2022.
@article{surgers2022evidence,
title = {Evidence of Sexual Transmission of Extended-Spectrum β-Lactamase–Producing Enterobacterales: A Cross-sectional and Prospective Study},
author = {Laure Surgers and Thibault Chiarabini and Guilhem Royer and Hayette Rougier and Mélanie Mercier-Darty and Dominique Decré and Nadia Valin and Paul-Louis Woerther and Jean-Winoc Decousser and Pierre-Marie Girard and others},
year = {2022},
date = {2022-01-01},
journal = {Clinical Infectious Diseases},
volume = {75},
number = {9},
pages = {1556–1564},
publisher = {Oxford University Press US},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Royer, Guilhem; de la Rosa, Jose-Manuel Ortiz; Vuillemin, Xavier; Lacombe, Béatrice; Chau, Françoise; Clermont, Olivier; Mercier-Darty, Mélanie; Decousser, Jean-Winoc; Ricard, Jean-Damien; Nordmann, Patrice; others,
Reduced chlorhexidine susceptibility is associated with tetracycline resistance tet genes in clinical isolates of Escherichia coli Journal Article
In: Antimicrobial Agents and Chemotherapy, vol. 66, no. 3, pp. e01972–21, 2022.
@article{royer2022reduced,
title = {Reduced chlorhexidine susceptibility is associated with tetracycline resistance tet genes in clinical isolates of Escherichia coli},
author = {Guilhem Royer and Jose-Manuel Ortiz de la Rosa and Xavier Vuillemin and Béatrice Lacombe and Françoise Chau and Olivier Clermont and Mélanie Mercier-Darty and Jean-Winoc Decousser and Jean-Damien Ricard and Patrice Nordmann and others},
year = {2022},
date = {2022-01-01},
journal = {Antimicrobial Agents and Chemotherapy},
volume = {66},
number = {3},
pages = {e01972–21},
publisher = {Am Soc Microbiol},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Delmas, Valérie A; Perchat, Nadia; Monet, Oriane; Fouré, Marion; Darii, Ekatarina; Roche, David; Dubois, Ivan; Pateau, Emilie; Perret, Alain; Döring, Volker; others,
Genetic and biocatalytic basis of formate dependent growth of Escherichia coli strains evolved in continuous culture Journal Article
In: Metabolic Engineering, vol. 72, pp. 200–214, 2022.
@article{delmas2022genetic,
title = {Genetic and biocatalytic basis of formate dependent growth of Escherichia coli strains evolved in continuous culture},
author = {Valérie A Delmas and Nadia Perchat and Oriane Monet and Marion Fouré and Ekatarina Darii and David Roche and Ivan Dubois and Emilie Pateau and Alain Perret and Volker Döring and others},
year = {2022},
date = {2022-01-01},
journal = {Metabolic Engineering},
volume = {72},
pages = {200–214},
publisher = {Academic Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Perchat, Nadia; Dubois, Christelle; Mor-Gautier, Rémi; Duquesne, Sophie; Lechaplais, Christophe; Roche, David; Fouteau, Stéphanie; Darii, Ekaterina; Perret, Alain
Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes Journal Article
In: Journal of Biological Chemistry, vol. 298, no. 7, 2022.
@article{perchat2022characterization,
title = {Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes},
author = {Nadia Perchat and Christelle Dubois and Rémi Mor-Gautier and Sophie Duquesne and Christophe Lechaplais and David Roche and Stéphanie Fouteau and Ekaterina Darii and Alain Perret},
year = {2022},
date = {2022-01-01},
journal = {Journal of Biological Chemistry},
volume = {298},
number = {7},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Monteil, Caroline L; Vallenet, David; Schüler, Dirk; Lefevre, Christopher T
Magnetosome proteins belong to universal protein families involved in many cell processes Journal Article
In: Proceedings of the National Academy of Sciences, vol. 119, no. 39, pp. e2208648119, 2022.
@article{monteil2022magnetosome,
title = {Magnetosome proteins belong to universal protein families involved in many cell processes},
author = {Caroline L Monteil and David Vallenet and Dirk Schüler and Christopher T Lefevre},
year = {2022},
date = {2022-01-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {119},
number = {39},
pages = {e2208648119},
publisher = {National Acad Sciences},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Crécy-Lagard, Valérie; de Hegedus, Rocio Amorin; Arighi, Cecilia; Babor, Jill; Bateman, Alex; Blaby, Ian; Blaby-Haas, Crysten; Bridge, Alan J; Burley, Stephen K; Cleveland, Stacey; others,
A roadmap for the functional annotation of protein families: a community perspective Journal Article
In: Database, vol. 2022, 2022.
@article{de2022roadmap,
title = {A roadmap for the functional annotation of protein families: a community perspective},
author = {Valérie Crécy-Lagard and Rocio Amorin de Hegedus and Cecilia Arighi and Jill Babor and Alex Bateman and Ian Blaby and Crysten Blaby-Haas and Alan J Bridge and Stephen K Burley and Stacey Cleveland and others},
year = {2022},
date = {2022-01-01},
journal = {Database},
volume = {2022},
publisher = {Oxford Academic},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fouteau, Stéphanie; Van, Vuong Bui; Rouy, Zoé; Beraud, Mélanie; Cruaud, Corinne; Cayol, Jean-Luc; Chifflet, Sandrine; Van, Thuoc Chu; The, Thu Pham; Vallenet, David; others,
Complete Genome Sequence of Tepidibacter sp. Strain 8C15b, Isolated from Bank Sediments of Haiphong Bay, Vietnam Journal Article
In: Microbiology Resource Announcements, vol. 11, no. 7, pp. e00132–22, 2022.
@article{fouteau2022complete,
title = {Complete Genome Sequence of Tepidibacter sp. Strain 8C15b, Isolated from Bank Sediments of Haiphong Bay, Vietnam},
author = {Stéphanie Fouteau and Vuong Bui Van and Zoé Rouy and Mélanie Beraud and Corinne Cruaud and Jean-Luc Cayol and Sandrine Chifflet and Thuoc Chu Van and Thu Pham The and David Vallenet and others},
year = {2022},
date = {2022-01-01},
journal = {Microbiology Resource Announcements},
volume = {11},
number = {7},
pages = {e00132–22},
publisher = {Am Soc Microbiol},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Marin, Julie; Clermont, Olivier; Royer, Guilhem; Mercier-Darty, Mélanie; Decousser, Jean Winoc; Tenaillon, Olivier; Denamur, Erick; Blanquart, François
The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France Journal Article
In: Applied and Environmental Microbiology, vol. 88, no. 15, pp. e00664–22, 2022.
@article{marin2022population,
title = {The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France},
author = {Julie Marin and Olivier Clermont and Guilhem Royer and Mélanie Mercier-Darty and Jean Winoc Decousser and Olivier Tenaillon and Erick Denamur and François Blanquart},
year = {2022},
date = {2022-01-01},
journal = {Applied and Environmental Microbiology},
volume = {88},
number = {15},
pages = {e00664–22},
publisher = {Am Soc Microbiol},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maucourt, Bruno; Roche, David; Chaignaud, Pauline; Vuilleumier, Stéphane; Bringel, Françoise
Genome-wide transcription start sites mapping in Methylorubrum grown with dichloromethane and methanol Journal Article
In: Microorganisms, vol. 10, no. 7, pp. 1301, 2022.
@article{maucourt2022genome,
title = {Genome-wide transcription start sites mapping in Methylorubrum grown with dichloromethane and methanol},
author = {Bruno Maucourt and David Roche and Pauline Chaignaud and Stéphane Vuilleumier and Françoise Bringel},
year = {2022},
date = {2022-01-01},
journal = {Microorganisms},
volume = {10},
number = {7},
pages = {1301},
publisher = {Multidisciplinary Digital Publishing Institute},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ducrot, Laurine; Bennett, Megan; André-Leroux, Gwenaëlle; Elisée, Eddy; Marynberg, Sacha; Fossey-Jouenne, Aurélie; Zaparucha, Anne; Grogan, Gideon; Vergne-Vaxelaire, Carine
Expanding the substrate scope of native amine dehydrogenases through in silico structural exploration and targeted protein engineering Journal Article
In: ChemCatChem, vol. 14, no. 22, pp. e202200880, 2022.
@article{ducrot2022expanding,
title = {Expanding the substrate scope of native amine dehydrogenases through in silico structural exploration and targeted protein engineering},
author = {Laurine Ducrot and Megan Bennett and Gwenaëlle André-Leroux and Eddy Elisée and Sacha Marynberg and Aurélie Fossey-Jouenne and Anne Zaparucha and Gideon Grogan and Carine Vergne-Vaxelaire},
year = {2022},
date = {2022-01-01},
journal = {ChemCatChem},
volume = {14},
number = {22},
pages = {e202200880},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chaignaud, Pauline; Gruffaz, Christelle; Borreca, Adrien; Fouteau, Stéphanie; Kuhn, Lauriane; Masbou, Jérémy; Rouy, Zoé; Hammann, Philippe; Imfeld, Gwenaël; Roche, David; others,
A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source Journal Article
In: Microorganisms, vol. 10, no. 11, pp. 2302, 2022.
@article{chaignaud2022methylotrophic,
title = {A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source},
author = {Pauline Chaignaud and Christelle Gruffaz and Adrien Borreca and Stéphanie Fouteau and Lauriane Kuhn and Jérémy Masbou and Zoé Rouy and Philippe Hammann and Gwenaël Imfeld and David Roche and others},
year = {2022},
date = {2022-01-01},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {2302},
publisher = {MDPI},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Roche, David; Calteau, Alexandra; Vallenet, David
Analyzing Prokaryotic Transcriptomics in the Light of Genome Data with the MicroScope Platform Book Section
In: Microbial Environmental Genomics (MEG), pp. 241–270, Springer US New York, NY, 2022.
@incollection{roche2022analyzing,
title = {Analyzing Prokaryotic Transcriptomics in the Light of Genome Data with the MicroScope Platform},
author = {David Roche and Alexandra Calteau and David Vallenet},
year = {2022},
date = {2022-01-01},
booktitle = {Microbial Environmental Genomics (MEG)},
pages = {241–270},
publisher = {Springer US New York, NY},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2021
Royer, Guilhem; Darty, Mélanie Mercier; Clermont, Olivier; Condamine, Bénédicte; Laouenan, Cédric; Decousser, Jean-Winoc; Vallenet, David; Lefort, Agnès; Lastours, Victoire; Denamur, Erick; others,
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period Journal Article
In: Genome Medicine, vol. 13, no. 1, pp. 77, 2021.
@article{royer2021phylogroup,
title = {Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period},
author = {Guilhem Royer and Mélanie Mercier Darty and Olivier Clermont and Bénédicte Condamine and Cédric Laouenan and Jean-Winoc Decousser and David Vallenet and Agnès Lefort and Victoire Lastours and Erick Denamur and others},
year = {2021},
date = {2021-01-01},
journal = {Genome Medicine},
volume = {13},
number = {1},
pages = {77},
publisher = {BioMed Central London},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Schorn, Michelle A; Verhoeven, Stefan; Ridder, Lars; Huber, Florian; Acharya, Deepa D; Aksenov, Alexander A; Aleti, Gajender; Moghaddam, Jamshid Amiri; Aron, Allegra T; Aziz, Saefuddin; others,
A community resource for paired genomic and metabolomic data mining Journal Article
In: Nature Chemical Biology, vol. 17, no. 4, pp. 363–368, 2021.
@article{schorn2021community,
title = {A community resource for paired genomic and metabolomic data mining},
author = {Michelle A Schorn and Stefan Verhoeven and Lars Ridder and Florian Huber and Deepa D Acharya and Alexander A Aksenov and Gajender Aleti and Jamshid Amiri Moghaddam and Allegra T Aron and Saefuddin Aziz and others},
year = {2021},
date = {2021-01-01},
journal = {Nature Chemical Biology},
volume = {17},
number = {4},
pages = {363–368},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wang, Shi-Zhen; Cruaud, Corinne; Aury, Jean-Marc; Vallenet, David; Poulain, Julie; Vacherie, Benoit; Zaparucha, Anne; Vergne-Vaxelaire, Carine
Complete genome sequences of two pseudomonas species isolated from marine environments of the Pacific Ocean Journal Article
In: Microbiology Resource Announcements, vol. 10, no. 16, pp. 10–1128, 2021.
@article{wang2021complete,
title = {Complete genome sequences of two pseudomonas species isolated from marine environments of the Pacific Ocean},
author = {Shi-Zhen Wang and Corinne Cruaud and Jean-Marc Aury and David Vallenet and Julie Poulain and Benoit Vacherie and Anne Zaparucha and Carine Vergne-Vaxelaire},
year = {2021},
date = {2021-01-01},
journal = {Microbiology Resource Announcements},
volume = {10},
number = {16},
pages = {10–1128},
publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Castelle, Cindy J; Méheust, Raphaël; Jaffe, Alexander L; Seitz, Kiley; Gong, Xianzhe; Baker, Brett J; Banfield, Jillian F
Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea Journal Article
In: Frontiers in microbiology, vol. 12, pp. 1233, 2021.
@article{castelle2021protein,
title = {Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea},
author = {Cindy J Castelle and Raphaël Méheust and Alexander L Jaffe and Kiley Seitz and Xianzhe Gong and Brett J Baker and Jillian F Banfield},
year = {2021},
date = {2021-01-01},
journal = {Frontiers in microbiology},
volume = {12},
pages = {1233},
publisher = {Frontiers},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Méheust, Raphaël; Huang, Shuo; Rivera-Lugo, Rafael; Banfield, Jillian F; Light, Samuel H
Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life Journal Article
In: Elife, vol. 10, pp. e66878, 2021.
@article{meheust2021post,
title = {Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life},
author = {Raphaël Méheust and Shuo Huang and Rafael Rivera-Lugo and Jillian F Banfield and Samuel H Light},
year = {2021},
date = {2021-01-01},
journal = {Elife},
volume = {10},
pages = {e66878},
publisher = {eLife Sciences Publications Limited},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pascucci, Marco; Royer, Guilhem; Adamek, Jakub; Asmar, Mai Al; Aristizabal, David; Blanche, Laetitia; Bezzarga, Amine; Boniface-Chang, Guillaume; Brunner, Alex; Curel, Christian; others,
AI-based mobile application to fight antibiotic resistance Journal Article
In: Nature communications, vol. 12, no. 1, pp. 1–10, 2021.
@article{pascucci2021ai,
title = {AI-based mobile application to fight antibiotic resistance},
author = {Marco Pascucci and Guilhem Royer and Jakub Adamek and Mai Al Asmar and David Aristizabal and Laetitia Blanche and Amine Bezzarga and Guillaume Boniface-Chang and Alex Brunner and Christian Curel and others},
year = {2021},
date = {2021-01-01},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1–10},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Joly, Pierre; Calteau, Alexandra; Wauquier, Aurélie; Dumas, Rémi; Beuvin, Mylène; Vallenet, David; Crovadore, Julien; Cochard, Bastien; Lefort, François; Berthon, Jean-Yves
From Strain Characterization to Field Authorization: Highlights on Bacillus velezensis Strain B25 Beneficial Properties for Plants and Its Activities on Phytopathogenic Fungi Journal Article
In: Microorganisms, vol. 9, no. 9, pp. 1924, 2021.
@article{joly2021strain,
title = {From Strain Characterization to Field Authorization: Highlights on Bacillus velezensis Strain B25 Beneficial Properties for Plants and Its Activities on Phytopathogenic Fungi},
author = {Pierre Joly and Alexandra Calteau and Aurélie Wauquier and Rémi Dumas and Mylène Beuvin and David Vallenet and Julien Crovadore and Bastien Cochard and François Lefort and Jean-Yves Berthon},
year = {2021},
date = {2021-01-01},
journal = {Microorganisms},
volume = {9},
number = {9},
pages = {1924},
publisher = {MDPI},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bazin, Adelme; Medigue, Claudine; Vallenet, David; Calteau, Alexandra
panModule: detecting conserved modules in the variable regions of a pangenome graph Journal Article
In: bioRxiv, pp. 2021–12, 2021.
@article{bazin2021panmodule,
title = {panModule: detecting conserved modules in the variable regions of a pangenome graph},
author = {Adelme Bazin and Claudine Medigue and David Vallenet and Alexandra Calteau},
year = {2021},
date = {2021-01-01},
journal = {bioRxiv},
pages = {2021–12},
publisher = {Cold Spring Harbor Laboratory},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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