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Investigating the functional architecture of microbial genomes with synthetic approaches


Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study

Author(s): Jason Rosado, Stéphane Pelleau, Charlotte Cockram, Sarah Hélène Merkling, Narimane Nekkab, Caroline Demeret, Annalisa Meola, Solen Kerneis, Benjamin Terrier, Samira Fafi-Kremer, Jerome de Seze, Timothée Bruel, François Dejardin, Stéphane Petres, Rhea Longley, Arnaud Fontanet, Marija Backovic, Ivo Mueller, Michael T White
Published in: The Lancet Microbe, Issue 2/2, 2021, Page(s) e60-e69, ISSN 2666-5247
Publisher: Elsevier
DOI: 10.1016/s2666-5247(20)30197-x

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Author(s): Martial Marbouty, Agnès Thierry, Gaël A Millot, Romain Koszul
Published in: eLife, Issue 10, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.60608

Computer vision for pattern detection in chromosome contact maps

Author(s): Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Rémi Montagne, Nadège Guiglielmoni, Vittore Scolari, Etienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar Oriol, Adrien Méot, Laurent Politis, Antoine Vigouroux, Pierrick Moreau, Romain Koszul, Axel Cournac
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts

Author(s): Luciana Lazar-Stefanita; Jingchuan Luo; Remi Montagne; Agnes Thierry; Xiaoji Sun; Guillaume Mercy; Julien Mozziconacci; Romain Koszul; Jef D. Boeke
Published in: Cell Genomics, Issue 1, 2022, ISSN 2666-979X
Publisher: Elsevier
DOI: 10.1016/j.xgen.2022.100163

Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization

Author(s): Charlotte Cockram, Agnès Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul
Published in: Molecular Cell, 2020, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2020.12.013

FACT mediates cohesin function on chromatin

Author(s): Jonay Garcia-Luis, Luciana Lazar-Stefanita, Pilar Gutierrez-Escribano, Agnes Thierry, Axel Cournac, Alicia García, Sara González, Mar Sánchez, Adam Jarmuz, Alex Montoya, Marian Dore, Holger Kramer, Mohammad M. Karimi, Francisco Antequera, Romain Koszul, Luis Aragon
Published in: Nature Structural & Molecular Biology, Issue 26/10, 2019, Page(s) 970-979, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-019-0307-x

Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria

Author(s): Quentin, Lamy-Besnier; Amaury, Bignaud; Julian R, Garneau; Marie, Titecat; Devon E, Conti; Alexandra, Von Strempel; Marc, Monot; Bärbel, Stecher; Romain, Koszul; Laurent, Debarbieux; Martial, Marbouty
Published in: Microbiome, Issue 7, 2023, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-023-01541-x

Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C

Author(s): Héloïse Muller, Vittore F Scolari, Nicolas Agier, Aurèle Piazza, Agnès Thierry, Guillaume Mercy, Stéphane Descorps‐Declere, Luciana Lazar‐Stefanita, Olivier Espeli, Bertrand Llorente, Gilles Fischer, Julien Mozziconacci, Romain Koszul
Published in: Molecular Systems Biology, Issue 14/7, 2018, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20188293

Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners

Author(s): Lise Dauban, Rémi Montagne, Agnès Thierry, Luciana Lazar-Stefanita, Nathalie Bastié, Olivier Gadal, Axel Cournac, Romain Koszul, Frédéric Beckouët
Published in: Molecular Cell, Issue 77/6, 2020, Page(s) 1279-1293.e4, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2020.01.019

Serpentine: a flexible 2D binning method for differential Hi-C analysis

Author(s): Lyam Baudry, Gaël A Millot, Agnes Thierry, Romain Koszul, Vittore F Scolari
Published in: Bioinformatics, Issue 36/12, 2020, Page(s) 3645-3651, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa249

Sir3 mediates long-range chromosome interactions in budding yeast

Author(s): Myriam Ruault, Vittore F. Scolari, Luciana Lazar-Stefanita, Antoine Hocher, Isabelle Loïodice, Romain Koszul, Angela Taddei
Published in: Genome Research, Issue 31/3, 2021, Page(s) 411-425, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.267872.120

Insights in bacterial genome folding

Author(s): Fares Osam Yáñez-Cuna; Romain Koszul
Published in: Current Opinion in Structural Biology, Issue 2, 2023, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/

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

Author(s): Nathalie Bastié, Christophe Chapard, Lise Dauban, Olivier Gadal, Frederic Beckouёt, Romain Koszul
Published in: Biorxiv, 2021
Publisher: Biorxiv
DOI: 10.1101/2021.04.21.440823

Genomic contacts reveal the control of sister chromosome decatenation in E. coli

Author(s): Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Charlotte Cockram, Romain Koszul, Olivier Espeli
Published in: Biorxiv, 2021
Publisher: Biorxiv
DOI: 10.1101/2021.05.17.444411

Cohesin regulates homology search during recombinational DNA repair

Author(s): Aurèle Piazza, Hélène Bordelet, Agnès Dumont, Agnès Thierry, Jérôme Savocco, Fabien Girard, Romain Koszul
Published in: Biorxiv, 2020
Publisher: Biorxiv
DOI: 10.1101/2020.12.17.423195

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