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Generating High-Resolution Hi-C Contact Maps of Bacteria

 Agnès Thierry , Charlotte Cockram
Hi-C Data Analysis, 2301, Springer US, pp.183-195, 2021, Methods in Molecular Biology, 978-1-0716-1390-0. ⟨10.1007/978-1-0716-1390-0_9⟩
Chapitre d'ouvrage pasteur-03686079v1
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Genome-wide chromatin and expression datasets of various pathogenic ascomycetes

 Sébastien Bloyer , Romain Koszul
2022, pp.100014. ⟨10.24072/pci.genomics.100014⟩
Autre publication hal-03722802v1
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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⟩
Article dans une revue pasteur-02866658v1
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Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution.

 Julien Mozziconacci , Romain Koszul
Genome Biology, 2015, 16 (1), pp.169. ⟨10.1186/s13059-015-0744-8⟩
Article dans une revue pasteur-01420328v1
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3D genome reconstruction from chromosomal contacts

 Annick Lesne , Julien Riposo , Paul Roger , Axel Cournac , Julien Mozziconacci
Nature Methods, 2014, 11, pp.1141-1143. ⟨10.1038/NMETH.3104⟩
Article dans une revue hal-02324120v1

Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops

 Nathalie Bastié , Christophe Chapard , Lise Dauban , Olivier Gadal , Frederic Beckouet , et al.
Nature Structural and Molecular Biology, 2022, 29 (6), pp.575-585. ⟨10.1038/s41594-022-00780-0⟩
Article dans une revue hal-03697578v1

Effect of nuclear architecture on the efficiency of double-strand break repair

 Neta Agmon , Batia Liefshitz , Christophe Zimmer , Emmanuelle Fabre , Martin Kupiec
Nature Cell Biology, 2013, 15 (6), pp.694-699. ⟨10.1038/ncb2745⟩
Article dans une revue pasteur-02446715v1
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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⟩
Article dans une revue pasteur-03369740v1

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⟩
Article dans une revue hal-02180787v1
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MatP local enrichment delays segregation independently of tetramer formation and septal anchoring in Vibrio cholerae

 Elena Espinosa , Jihane Challita , Jean-Michel Desfontaines , Christophe Possoz , Marie-Eve Val , et al.
2024
Pré-publication, Document de travail hal-04781720v1
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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⟩
Article dans une revue 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⟩
Article dans une revue pasteur-01419905v1
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Beyond the bounds of evolution: Synthetic chromosomes… How and what for?

 Romain Koszul
Comptes Rendus Biologies, 2016, 339 (7-8), pp.324-8. ⟨10.1016/j.crvi.2016.05.007⟩
Article dans une revue pasteur-01419924v1
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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⟩
Article dans une revue hal-01138788v1
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Nucleosome positioning on large tandem DNA repeats of the ’601’ sequence engineered in Saccharomyces cerevisiae

 Astrid Lancrey , Alexandra Joubert , Evelyne Duvernois-Berthet , Etienne Routhier , Saurabh Raj , et al.
Journal of Molecular Biology, 2022, ⟨10.1016/j.jmb.2022.167497⟩
Article dans une revue hal-03343705v2
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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⟩
Article dans une revue pasteur-01419912v1
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3D organization of synthetic and scrambled chromosomes

 Guillaume Mercy , Julien Mozziconacci , Vittore F Scolari , Kun Yang , Guanghou Zhao , et al.
Science, 2017, 355 (6329), pp.eaaf4597. ⟨10.1126/science.aaf4597⟩
Article dans une revue pasteur-01523221v1

Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal

 Juliette Guitard , Pernille Andersen , Caroline Ermont , Sédami Gnidehou , Nadine Fievet , et al.
Malaria Journal, 2010, 9 (1), pp.165. ⟨10.1186/1475-2875-9-165⟩
Article dans une revue hal-03962282v1
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Computer vision for pattern detection in chromosome contact maps

 Cyril Matthey-Doret , Lyam Baudry , Axel Breuer , Rémi Montagne , Nadège Guiglielmoni , et al.
Nature Communications, 2020, 11 (1), pp.5795. ⟨10.1038/s41467-020-19562-7⟩
Article dans une revue pasteur-03263561v1

A single microfluidic device for multi-omics analysis sample preparation

 Yann Verdier , Ravi Kumar Ranjith Kumar , Iman Haddad , Martial Marbouty , Joelle Vinh
39TH FRENCH DAYS OF MASS SPECTROMETRY, Société Française de Spectrométrie de Masse, Sep 2023, Marseille, France
Communication dans un congrès hal-04228697v1
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Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

 Jean-François Flot , Boris Hespeels , Xiang Li , Benjamin Noel , Irina Arkhipova , et al.
Nature, 2013, 500 (7463), pp.453-457. ⟨10.1038/nature12326⟩
Article dans une revue hal-01282538v1
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Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C

 Héloise Muller , Vittore F Scolari , Nicolas Agier , Aurele Piazza , Agnès Thierry , et al.
Molecular Systems Biology, 2018, 14 (7), pp.e8293. ⟨10.15252/msb.20188293⟩
Article dans une revue hal-01890095v1

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⟩
Chapitre d'ouvrage pasteur-03369745v1
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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⟩
Article dans une revue pasteur-04158849v1
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Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer

 Vittore F Scolari , Guillaume Mercy , Romain Koszul , Annick Lesne , Julien Mozziconacci
Physical Review Letters, 2018, 121 (5), pp.057801. ⟨10.1103/PhysRevLett.121.057801⟩
Article dans une revue hal-01992814v1
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Exogenous chromosomes reveal how sequence composition drives chromatin assembly, activity, folding and compartmentalization

 Christophe Chapard , Léa Meneu , Jacques Serizay , Alex Westbrook , Etienne Routhier , et al.
2023
Pré-publication, Document de travail hal-04278801v1
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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⟩
Article dans une revue pasteur-01419993v1
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Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes

 Amaury Bignaud , Charlotte Cockram , Céline Borde , Justine Groseille , Eric Allemand , et al.
Nature Structural and Molecular Biology, 2024, ⟨10.1038/s41594-023-01178-2⟩
Article dans une revue hal-04468362v1
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Generation of gene-level resolution chromosome contact maps in bacteria and archaea

 Charlotte Cockram , Agnès Thierry , Romain Koszul
STAR Protocols, 2021, 2 (2), pp.100512. ⟨10.1016/j.xpro.2021.100512⟩
Article dans une revue pasteur-03376845v1

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⟩
Chapitre d'ouvrage pasteur-02866616v1
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