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authFullName_s : Martial Marbouty
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instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Lyam Baudry , Nadège Guiglielmoni , Hervé Marie-Nelly , Alexandre Cormier , Martial Marbouty , et al.
Genome Biology, 2020, 21 (1), ⟨10.1186/s13059-020-02041-z⟩
Journal articles pasteur-02873422v1
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Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture

Isabelle Boutet , Homère Alves Monteiro , Lyam Baudry , Takeshi Takeuchi , Eric Bonnivard , et al.
Evolutionary Applications, 2022, 15 (11), pp.1730-1748. ⟨10.1111/eva.13462⟩
Journal articles hal-03896508v1
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Filling annotation gaps in yeast genomes using genome-wide contact maps.

Hervé Marie-Nelly , Martial Marbouty , Axel Cournac , Gianni Liti , Gilles Fischer , et al.
Bioinformatics, 2014, 30 (15), pp.2105-13. ⟨10.1093/bioinformatics/btu162⟩
Journal articles pasteur-01488132v1
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Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori

Sumith Kumar , Christine Schmitt , Olivier Gorgette , Martial Marbouty , Magalie Duchateau , et al.
mBio, 2022, 13 (5), pp.e0163322. ⟨10.1128/mbio.01633-22⟩
Journal articles pasteur-04093078v1
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Spatial reorganization of telomeres in long-lived quiescent cells

Micol Guidi , Myriam Ruault , Martial Marbouty , Isabelle Loïodice , Axel Cournac , et al.
Genome Biology, 2015, 16 (1), pp.206. ⟨10.1186/s13059-015-0766-2⟩
Journal articles hal-01206018v1
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Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder

Lyam Baudry , Martial Marbouty , Hervé Marie-Nelly , Alexandre Cormier , Nadège Guiglielmoni , et al.
Preprints, Working Papers, ... hal-02947625v1
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Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes

Etienne Jourdier , Lyam Baudry , Dante Poggi-Parodi , Yoan Vicq , Romain Koszul , et al.
Biotechnology for Biofuels, 2017, 10 (1), pp.151. ⟨10.1186/s13068-017-0837-6⟩
Journal articles hal-01581813v1
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Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Jérémy Gauthier , Hélène Boulain , Joke J F A van Vugt , Lyam Baudry , Emma Persyn , et al.
Communications Biology, 2021, 4 (1), pp.1-15. ⟨10.1038/s42003-020-01623-8⟩
Journal articles hal-03127732v1
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Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

Kati Böhm , Giacomo Giacomelli , Andreas U. Schmidt , Axel Imhof , Romain Koszul , et al.
Nature Communications, 2020, 11 (1), pp.1485. ⟨10.1038/s41467-020-15238-4⟩
Journal articles pasteur-02612484v1
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Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Jérémy Gauthier , Hélène Boulain , Joke J.F.A. van Vugt , Lyam Baudry , Emma Persyn , et al.
Preprints, Working Papers, ... hal-03090838v1
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Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

Pierrick Moreau , Axel Cournac , Gianna Aurora Palumbo , Martial Marbouty , Shogofa Mortaza , et al.
Nature Communications, 2018, 9 (1), pp.4268. ⟨10.1038/s41467-018-06739-4⟩
Journal articles pasteur-02866759v1
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Purification of G1 daughter cells from different Saccharomycetes species through an optimized centrifugal elutriation procedure.

Martial Marbouty , Caroline Ermont , Bernard Dujon , Guy-Franck Richard , Romain Koszul
Yeast, 2014, 31 (5), pp.159-166. ⟨10.1002/yea.3005⟩
Journal articles pasteur-01420008v1
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Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Paul Simion , Jitendra Narayan , Antoine Houtain , Alessandro Derzelle , Lyam Baudry , et al.
Science Advances , 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩
Journal articles hal-03406292v1
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MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Martial Marbouty , Agnès Thierry , Gael A. Millot , Romain Koszul
eLife, 2021, 10, pp.e60608. ⟨10.7554/eLife.60608⟩
Journal articles pasteur-03369735v1
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Normalization of a chromosomal contact map

Axel Cournac , Hervé Marie-Nelly , Martial Marbouty , Romain Koszul , Julien Mozziconacci
BMC Genomics, 2012, 13 (1), pp.436. ⟨10.1186/1471-2164-13-436⟩
Journal articles pasteur-00769663v1

Metagenomes Binning Using Proximity-Ligation Data

Martial Marbouty , Romain Koszul
Hi-C Data Analysis, 2301, Springer US, pp.163-181, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1390-0_8⟩
Book sections pasteur-03369745v1
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Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.

Martial Marbouty , Antoine Le gall , Diego I Cattoni , Axel Cournac , Alan Koh , et al.
Molecular Cell, 2015, 59 (4), pp.588-602. ⟨10.1016/j.molcel.2015.07.020⟩
Journal articles pasteur-01419993v1

Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota

Théo Foutel-Rodier , Agnès Thierry , Romain Koszul , Martial Marbouty
High-Density Sequencing Applications in Microbial Molecular Genetics, 612, pp.183-195, 2018, Methods in Enzymology, 978-0-12-815993-4. ⟨10.1016/bs.mie.2018.08.001⟩
Book sections pasteur-02866616v1
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Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria

Quentin Lamy-Besnier , Amaury Bignaud , Julian R Garneau , Marie Titecat , Devon E Conti , et al.
Microbiome, 2023, 11 (1), pp.111. ⟨10.1186/s40168-023-01541-x⟩
Journal articles pasteur-04158849v1
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High-quality genome (re)assembly using chromosomal contact data

Hervé Marie-Nelly , Martial Marbouty , Axel Cournac , Jean-François Flot , Gianni Liti , et al.
Nature Communications, 2014, 5, pp.5695. ⟨10.1038/ncomms6695⟩
Journal articles hal-01138788v1
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Closed and high quality bacterial genomes of the Oligo Mouse Microbiota community

Quentin Lamy-Besnier , Romain Koszul , Laurent Debarbieux , Martial Marbouty
Microbiology Resource Announcements, 2021, 10 (17), pp.e01396-20. ⟨10.1128/MRA.01396-20⟩
Journal articles pasteur-03204821v1
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Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast.

Maya Spichal , Alice Brion , Sébastien Herbert , Axel Cournac , Martial Marbouty , et al.
Journal of Cell Science, 2016, 129 (4), pp.681-92. ⟨10.1242/jcs.175745⟩
Journal articles pasteur-01419905v1
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Generation and Analysis of Chromosomal Contact Maps of Yeast Species.

Axel Cournac , Martial Marbouty , Julien Mozziconacci , Romain Koszul
Methods in Molecular Biology, 2016, Yeast Functional Genomics, 1361, pp.227-45. ⟨10.1007/978-1-4939-3079-1_13⟩
Journal articles pasteur-01419912v1
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Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

Martial Marbouty , Lyam Baudry , Axel Cournac , Romain Koszul
Science Advances , 2017, 3 (2), pp.e1602105. ⟨10.1126/sciadv.1602105⟩
Journal articles pasteur-02866658v1

Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

Virginia S. Lioy , Axel Cournac , Martial Marbouty , Stéphane Duigou , Julien Mozziconacci , et al.
Cell, 2018, 172 (4), pp.771--783.e18. ⟨10.1016/j.cell.2017.12.027⟩
Journal articles hal-02180787v1
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High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome

Julian R. Garneau , Véronique Legrand , Martial Marbouty , Maximilian O. Press , Dean R. Vik , et al.
Scientific Reports, 2021, 11 (1), pp.18319. ⟨10.1038/s41598-021-97867-3⟩
Journal articles pasteur-03369740v1
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Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data.

Martial Marbouty , Romain Koszul
Trends in Genetics, 2015, 31 (12), pp.673-82. ⟨10.1016/j.tig.2015.10.003⟩
Journal articles pasteur-01419974v1
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Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

Martial Marbouty , Axel Cournac , Jean-François Flot , Hervé Marie-Nelly , Julien Mozziconacci , et al.
eLife, 2014, 3, pp.e03318. ⟨10.7554/eLife.03318⟩
Journal articles hal-01316684v1
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Genome-wide replication landscape of Candida glabrata.

Stéphane Descorps-Declère , Cyril Saguez , Axel Cournac , Martial Marbouty , Thomas Rolland , et al.
BMC Biology, 2015, 13, pp.69. ⟨10.1186/s12915-015-0177-6⟩
Journal articles pasteur-01370696v1
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MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries

Lyam Baudry , Théo Foutel-Rodier , Agnès Thierry , Romain Koszul , Martial Marbouty
Frontiers in Genetics, 2019, 10, pp.753. ⟨10.3389/fgene.2019.00753⟩
Journal articles pasteur-02866613v1