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Alexandra CALTEAU

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A model industrial workhorse: $Bacillus\ subtilis$ strain 168 and its genome after a quarter of a century

Erhard Bremer , Alexandra Calteau , Antoine Danchin , Colin Harwood , John D Helmann
Microbial Biotechnology, 2023, 16 (6), pp.1203-1231. ⟨10.1111/1751-7915.14257⟩
Article dans une revue cea-04284953v1
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A community resource for paired genomic and metabolomic data mining

Michelle A. Schorn , Stefan Verhoeven , Lars Ridder , Florian Huber , Deepa D. Acharya
Nature Chemical Biology, 2021, ⟨10.1038/s41589-020-00724-z⟩
Article dans une revue pasteur-03153704v1
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From strain characterization to field authorization: highlights on $Bacillus\ velezensis$ strain B25 beneficial properties for plants and its activities on phytopathogenic fungi

Pierre Joly , Alexandra Calteau , Aurélie Wauquier , Rémi Dumas , Mylène Beuvin
Microorganisms, 2021, 9 (9), pp.e1924. ⟨10.3390/microorganisms9091924⟩
Article dans une revue cea-04284767v1
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau , Adelme Bazin , Mathieu Gachet , Rémi Planel , Laura Burlot
PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩
Article dans une revue hal-03089210v1
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panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , David Vallenet , Alexandra Calteau
Bioinformatics, 2020, 36 (Supplément 2), pp.i651 - i658. ⟨10.1093/bioinformatics/btaa792⟩
Article dans une revue hal-03322363v1
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Physiological and evolutionary implications of tetrameric photosystem I in cyanobacteria

Meng Li , Alexandra Calteau , Dmitry Semchonok , Thomas Witt , Jonathan Nguyen
Nature Plants, 2019, 5 (12), pp.1309-1319. ⟨10.1038/s41477-019-0566-x⟩
Article dans une revue pasteur-03016132v1
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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Paul Amours , Adelme Bazin
Nucleic Acids Research, 2019, 48 (D1), pp.D579-D589. ⟨10.1093/nar/gkz926⟩
Article dans une revue hal-02403170v1
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MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

Claudine Médigue , Alexandra Calteau , Stéphane Cruveiller , Mathieu Gachet , Guillaume Gautreau
Briefings in Bioinformatics, 2019, 20 (4), pp.1071-1084. ⟨10.1093/bib/bbx113⟩
Article dans une revue hal-02626039v1
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A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle

Frédéric Partensky , Christophe Six , Morgane Ratin , Laurence Garczarek , Daniel Vaulot
Scientific Reports, 2018, 8 (1), pp.9142. ⟨10.1038/s41598-018-27542-7⟩
Article dans une revue hal-01805749v1
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Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

Elizabeth Ficko-Blean , Aurelie Prechoux , François Thomas , Tatiana Rochat , Robert Larocque
Nature Communications, 2017, 8, pp.1685. ⟨10.1038/s41467-017-01832-6⟩
Article dans une revue hal-01899178v1
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Rearranged Biosynthetic Gene Cluster and Synthesis of Hassallidin E in Planktothrix serta PCC 8927.

Claire Pancrace , Jouni Jokela , Nathalie Sassoon , Christelle Ganneau , Marie Desnos-Ollivier
ACS Chemical Biology, 2017, 12 (7), pp.1796-1804. ⟨10.1021/acschembio.7b00093⟩
Article dans une revue pasteur-01535773v1
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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle , Rémi Planel , Simon Penel , David Chapulliot , Valérie Barbe
Genome Biology and Evolution, 2017, 9 (12), pp.3413 - 3431. ⟨10.1093/gbe/evx255⟩
Article dans une revue hal-01913841v1
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Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains

Claire Pancrace , Marie-Anne Barny , Reiko Ueoka , Alexandra Calteau , Thibault Scalvenzi
Scientific Reports, 2017, 7, pp.41181. ⟨10.1038/srep41181⟩
Article dans une revue hal-01470599v1
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Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme

Tatiana Rochat , Erina Fujiwara-Nagata , Ségolène Calvez , Inger Dalsgaard , Lone Madsen
Frontiers in Microbiology, 2017, 8, ⟨10.3389/fmicb.2017.01752⟩
Article dans une revue hal-02619160v1
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MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

David Vallenet , Alexandra Calteau , Stéphane Cruveiller , Mathieu Gachet , Aurélie Lajus
Nucleic Acids Research, 2017, 45 (D1), pp.D517-D528. ⟨10.1093/nar/gkw1101⟩
Article dans une revue cea-04320303v1
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A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters

David Goudenège , Marie Agnès Travers , Astrid Lemire , Philippe Haffner , Yannick Labreuche
Environmental Microbiology, 2015, 17 (11), pp.4189-4199. ⟨10.1111/1462-2920.12699⟩
Article dans une revue hal-01444897v1

Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters

Astrid Lemire , David Goudenège , Typhaine Versigny , Bruno Petton , Alexandra Calteau
The International Society of Microbiologial Ecology Journal, 2015, 9 (7), pp.1523-1531. ⟨10.1038/ismej.2014.233⟩
Article dans une revue hal-02083151v1
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Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria.

Alexandra Calteau , David P Fewer , Amel Latifi , Thérèse Coursin , Thierry Laurent
BMC Genomics, 2014, 15, pp.977. ⟨10.1186/1471-2164-15-977⟩
Article dans une revue pasteur-01370484v1

Genome Mining Expands the Chemical Diversity of the Cyanobactin Family to Include Highly Modified Linear Peptides

Niina Leikoski , Liwei Liu , Jouni Jokela , Matti Wahlsten , Muriel Gugger
Chemistry and Biology, 2013, 20 (8), pp.1033 - 1043. ⟨10.1016/j.chembiol.2013.06.015⟩
Article dans une revue pasteur-01388247v1
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Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits

David Goudenège , Yannick Labreuche , Evelyne Krin , Dominique Ansquer , Sophie Mangenot
The International Society of Microbiologial Ecology Journal, 2013, Integrated genomics and post-genomics approaches in microbial ecology, 7 (10), pp.1985-1996. ⟨10.1038/ismej.2013.90⟩
Article dans une revue pasteur-01699814v1
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Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

M. Shih , D. Wu , A. Latifi , S. D. Axen , D. P. Fewer
Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (3), pp.1053 - 1058. ⟨10.1073/pnas.1217107110⟩
Article dans une revue pasteur-01389305v1
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A Tribute to Disorder in the Genome of the Bloom- Forming Freshwater Cyanobacterium Microcystis aeruginosa

Jean-François Humbert , Valérie Barbe , Amel Latifi , Muriel Gugger , Alexandra Calteau
PLoS ONE, 2013, 8 (8), pp.e70747. ⟨10.1371/journal.pone.0070747⟩
Article dans une revue bioemco-00851371v1

Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces

Philippe Normand , Jérome Gury , Petar Pujic , B. Chouaia , E. Crotti
Journal of Bacteriology, 2012, 194 (17), pp.4773-4774. ⟨10.1128/JB.01029-12⟩
Article dans une revue hal-02531835v1
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Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics

P.N. Bertin , A. Heinrich-Salmeron , E. Pelletier , F. Goulhen-Chollet , F. Arsène-Ploetze
The International Society of Microbiologial Ecology Journal, 2011, 5 (11), pp.1735-1747. ⟨10.1038/ismej.2011.51⟩
Article dans une revue hal-01631857v1
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Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.

Florence Wisniewski-Dyé , Kirill Borziak , Gurusahai Khalsa-Moyers , Gladys Alexandre , Leonid O.Sukharnikov
PLoS Genetics, 2011, 7 (12), pp.e1002430. ⟨10.1371/journal.pgen.1002430⟩
Article dans une revue halsde-00724551v1
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Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

Benoît Remenant , Bénédicte Coupat-Goutaland , Alice Guidot , Gilles Cellier , Emmanuel Wicker
BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-379⟩
Article dans une revue hal-02936853v1
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Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

Jean-Claude Ogier , Alexandra Calteau , Steve Forst , Heidi Goodrich-Blair , David Roche
BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-568⟩
Article dans une revue hal-02660280v1

A Module Located at a Chromosomal Integration Hot Spot Is Responsible for the Multidrug Resistance of a Reference Strain from Escherichia coli Clonal Group A

Mathilde Lescat , Alexandra Calteau , Claire Hoede , Valérie Barbe , Marie Touchon
Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩
Article dans une revue hal-03612468v1
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Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Marie Touchon , Claire Hoede , Olivier Tenaillon , Valérie Barbe , Simon Baeriswyl
PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩
Article dans une revue hal-00390293v1

Mutation rate and genome reduction in endosymbiotic and free-living bacteria

Gabriel Marais , A. Calteau , O. Tenaillon
Genetica, 2007, DOI 10.1007/s10709-007-9226-6, pp.357-358
Article dans une revue hal-00434820v1
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Horizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms

Saliou Fall , Anne Mercier , Franck Bertolla , Alexandra Calteau , Laurent Gueguen
PLoS ONE, 2007, 2 (10), pp.e1055-e1066. ⟨10.1371/journal.pone.0001055⟩
Article dans une revue halsde-00182457v1

Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.

A. Calteau , Manolo Gouy , G. Perrière
Journal of Molecular Evolution, 2005, 60 (5), pp.557-65. ⟨10.1007/s00239-004-0094-8⟩
Article dans une revue hal-00427722v1

Exploration and curation of microbial genomes using the MicroScope platform

Alexandra Calteau
Pyrococcus abyssi 20 years, Violette Da Cunha; Patrick Forterre, Sep 2023, Evry-Courcouronnes, France
Communication dans un congrès hal-04370597v1

The MicroScope platform: 20 years of expertise in microbial genomics

Claudine Médigue , Alexandra Calteau , David Vallenet
The 20th MicroScope anniversary, Alexandra Calteau; David Vallenet, Sep 2023, Evry-Courcouronnes, France
Communication dans un congrès hal-04370626v1

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Jean Mainguy , Laura Bry , Quentin Fernandez De Grado , David Vallenet
The local pangenome, Oct 2023, Alicante, Spain
Communication dans un congrès hal-04371302v1

PPanGGOLiN V2: technical enhancement and new features to analyze thousands of prokaryotic genomes

Jean Mainguy , Jérôme Arnoux , Guillaume Gautreau , Adelme Bazin , David Vallenet
The local pangenome, Oct 2023, Alicante, Spain
Communication dans un congrès hal-04371316v1

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Laura Bry , Quentin Fernandez De Grado , David Vallenet , Alexandra Calteau
ISMB/ECCB 2023, ISCB ECCB, Jul 2023, Lyon, France
Communication dans un congrès hal-04371284v1

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , David Vallenet , Alexandra Calteau
JOBIM 2021 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris (virtual), France
Communication dans un congrès hal-04360257v1

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , David Vallenet , Alexandra Calteau
the 19th European Conference on Computational Biology, ECCB 2020, Aug 2020, Barcelona (Virtual), Spain
Communication dans un congrès hal-04360043v1

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

Alexandra Calteau
Séminaire CBIB, Macha Nikolski; Alexis Groppi, Feb 2020, Bordeaux, France
Communication dans un congrès hal-04370609v1

Comparative microbial pangenomics to explore mobilome dynamics

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , Alexandra Calteau , David Vallenet
The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom
Communication dans un congrès hal-04359455v1

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Mylène Beuvin , Laura Burlot
The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom
Communication dans un congrès hal-04358401v1

Unités de plasticité dans le génome de Photorhabdus : des réarrangements chromosomiques à l’échelle du temps du laboratoire à l’évolution des espèces.

Jean-Claude Ogier , Alexandra Calteau , Anne Lanois , Sylvie Pages , David Roche
8. Congrès National de la Société Française de Microbiologie (SFM), Jun 2010, Palais des Congrès, Parc Chanot, Marseille, France
Communication dans un congrès hal-02823581v1
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PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Laura Bry , Quentin Fernandez De Grado , David Vallenet , Alexandra Calteau
ISMB/ECCB 2023, Jul 2023, Lyon, France
Poster de conférence hal-04358457v1

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Alexandra Calteau , David Vallenet
The 2nd FEMS Conference on Microbiology, Jun 2022, Belgrade, Serbia
Poster de conférence hal-04371199v1

MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis

Alexandra Calteau , Mathieu Dubois , Jérôme Arnoux , Lucie Coffion , Stéphanie Fouteau
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, Jul 2022, Rennes, France
Poster de conférence hal-04360324v1

MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis

Alexandra Calteau , Mathieu Dubois , Jérôme Arnoux , Adelme Bazin , Mylène Beuvin
The 2nd FEMS Conference on Microbiology, Jun 2022, Belgrade, Serbia
Poster de conférence hal-04371191v1
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PANORAMA : comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Alexandra Calteau , David Vallenet
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, Jul 2022, Rennes, France
Poster de conférence hal-04371243v1

MicroScope: an Integrated Platform for the Annotation and Exploration of Microbial Gene Functions through Genomic, Pangenomic and Metabolic Comparative Analysis

Alexandra Calteau , Mathieu Dubois , Adelme Bazin , Mylène Beuvin , Stéphanie Fouteau
World Microbe Forum 2021, Jun 2021, Virtual, United States
Poster de conférence hal-04360076v1

MicroScope: an integrated platform for the annotation and axploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

Alexandra Calteau , Mathieu Dubois , Jérôme Arnoux , Adelme Bazin , Mylène Beuvin
JOBIM 2021 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris (virtual), France
Poster de conférence hal-04360241v1

PanFam: a pangenomic workflow for the iterative construction of gene families on thousands of genomes

Jérôme Arnoux , Mylène Beuvin , Adelme Bazin , Alexandra Calteau , David Vallenet
JOBIM 2020 Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier (virtual), France
Poster de conférence hal-04360011v1

PanGBank: exploring GenBank genomes through a resource of pangenome graphs

Paul Amours , Adelme Bazin , Guillaume Gautreau , Mathieu Dubois , Laura Burlot
JOBIM 2020 Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier (virtual), France
Poster de conférence hal-04360000v1

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Paul Amours , Jérôme Arnoux , Adelme Bazin
JOBIM 2020 Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier (virtual), France
Poster de conférence hal-04359963v1
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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Mylène Beuvin , Laura Burlot
JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France
Poster de conférence hal-04358357v1
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Comparative microbial pangenomics to explore mobilome dynamics

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , Alexandra Calteau , David Vallenet
JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France
Poster de conférence hal-04358338v1
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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

Claudine Médigue , Alexandra Calteau , Stéphane Cruveiller , Mathieu Gachet , Guillaume Gautreau
JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France
Poster de conférence hal-04356218v1

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Aurélie Lajus , David Roche
International symposium on environmental and agronomical genomics, Nov 2018, Paris, France
Poster de conférence hal-04357657v1

Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

Jean-Claude Ogier , Alexandra Calteau , Steve Forst , Heidi Goodrich-Blair , David Roche
4. Congress of the FEMS, Jun 2011, Geneva, Suisse. , 2011
Poster de conférence hal-02808493v1

Analyzing prokaryotic transcriptomics in the light of genome data with the MicroScope platform

David Roche , Alexandra Calteau , David Vallenet
Francis Martin; Stephane Uroz. Microbial Environmental Genomics (MEG), 2605, Springer US, pp.241-270, 2022, Methods in Molecular Biology, 978-1-0716-2871-3. ⟨10.1007/978-1-0716-2871-3_13⟩
Chapitre d'ouvrage cea-04286744v1

Genomics of NRPS/PKS Biosynthetic Gene Clusters in Cyanobacteria

Claire Pancrace , Muriel Gugger , Alexandra Calteau
CYANOBACTERIA: OMICS AND MANIPULATION, CAISTER ACADEMIC PRESS, pp.20, 2017, 978-1-910190-55-5; 978-1-910190-56-2
Chapitre d'ouvrage hal-01605637v1

Genomics of NRPS/PKS Biosynthetic Gene Clusters in Cyanobacteria

Claire Pancrace , Muriel Gugger , Alexandra Calteau
Dmitry A. Los. Cyanobacteria: Omics and Manipulation, Caister Academic Press, pp.55-74, 2017, 978-1-910190-55-5 (print) ; 978-1-910190-56-2 (e-book). ⟨10.21775/9781910190555.03⟩
Chapitre d'ouvrage pasteur-03026934v1