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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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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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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

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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Sir3 mediates long-range chromosome interactions in budding yeast

Myriam Ruault , Vittore F Scolari , Luciana Lazar-Stefanita , Antoine Hocher , Isabelle Loïodice , et al.
Genome Research, 2021, 31 (3), pp.411-425. ⟨10.1101/gr.267872.120⟩
Article dans une revue hal-03169421v1
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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⟩
Article dans une revue pasteur-02866759v1
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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⟩
Article dans une revue 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⟩
Article dans une revue pasteur-03369735v1
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A predictive computational model of the dynamic 3D interphase yeast nucleus.

Hua Wong , Hervé Marie-Nelly , Sébastien Herbert , Pascal Carrivain , Hervé Blanc , et al.
Current Biology - CB, 2012, 22 (20), pp.1881-1890. ⟨10.1016/j.cub.2012.07.069⟩
Article dans une revue pasteur-01420017v1

Sister chromatid cohesion halts DNA loop expansion

Nathalie Bastié , Christophe Chapard , Axel Cournac , Sanae Nejmi , Henri Mboumba , et al.
Molecular Cell, 2024, 84 (6), pp.1139-1148.e5. ⟨10.1016/j.molcel.2024.02.004⟩
Article dans une revue pasteur-04603601v1
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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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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
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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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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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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
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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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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
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Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri

Sylvain Legrand , Asma Saifudeen , Hélène Bordelet , Julien Vernerey , Arnaud Guille , et al.
2023
Pré-publication, Document de travail hal-04300727v1
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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⟩
Article dans une revue pasteur-02612484v1
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Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome

Brenna Conin , Ingrid Billault-Chaumartin , Hafez El Sayyed , Nicole Quenech'Du , Charlotte Cockram , et al.
Nucleic Acids Research, 2022, 50 (5), pp.2635-2650. ⟨10.1093/nar/gkac105⟩
Article dans une revue pasteur-03689317v1
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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

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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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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The silencing factor Sir3 is a molecular bridge that sticks together distant loci

Myriam Ruault , Vittore F Scolari , Luciana Lazar-Stefanita , Antoine Hocher , Isabelle Loïodice , et al.
2020
Pré-publication, Document de travail hal-03013702v1
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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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Kinetics of the Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response and Serological Estimation of Time Since Infection

Stéphane Pelleau , Tom Woudenberg , Jason Rosado , Françoise Donnadieu , Laura Garcia , et al.
Journal of Infectious Diseases, 2021, 224 (9), pp.1489-1499. ⟨10.1093/infdis/jiab375⟩
Article dans une revue pasteur-03319587v2
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Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study

Jason Rosado , Stéphane Pelleau , Charlotte A. Cockram , Sarah Hélène Merkling , Narimane Nekkab , et al.
The Lancet Microbe, 2021, 2 (2), pp.e60-e69. ⟨10.1016/S2666-5247(20)30197-X⟩
Article dans une revue hal-03128905v1
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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⟩
Article dans une revue pasteur-01488132v1
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Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis

Thomas Guerin , Claire Béneut , Natalja Barinova , Virginia López , Luciana Lazar-Stefanita , et al.
Molecular Cell, 2019, 75 (1), pp.131-144.e3. ⟨10.1016/j.molcel.2019.05.021⟩
Article dans une revue pasteur-02866762v1