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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
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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

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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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⟩
Article dans une revue pasteur-01420008v1
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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
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Investigating chromosome dynamics through Hi-C assembly

 Lyam Baudry
Quantitative Methods [q-bio.QM]. Sorbonne Université, 2019. English. ⟨NNT : 2019SORUS026⟩
Thèse tel-02935877v1
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Tethering of molecular parasites on inactive chromatin in eukaryote nucleus

 Fabien Girard
Genomics [q-bio.GN]. Sorbonne Université, 2023. English. ⟨NNT : 2023SORUS661⟩
Thèse tel-04524712v1
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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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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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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

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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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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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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L'organisation 3D des chromosomes synthétiques de levure

 Guillaume Mercy
Génomique, Transcriptomique et Protéomique [q-bio.GN]. Sorbonne Université, 2018. Français. ⟨NNT : 2018SORUS034⟩
Thèse tel-02111002v1
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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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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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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

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
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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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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
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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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The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

 Axel Cournac , Romain Koszul , Julien Mozziconacci
Nucleic Acids Research, 2016, 44 (1), pp.245-255. ⟨10.1093/nar/gkv1292⟩
Article dans une revue hal-01294687v1
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Serpentine: a flexible 2D binning method for differential Hi-C analysis

 Lyam Baudry , Gaël A Millot , Agnès Thierry , Romain Koszul , Vittore F Scolari
Bioinformatics, 2020, ⟨10.1093/bioinformatics/btaa249⟩
Article dans une revue pasteur-02612482v1
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Serological signatures of SARS-CoV-2 infection: Implications for antibody-based diagnostics

 Jason Rosado , Stéphane Pelleau , Charlotte Cockram , Sarah Hélène Merkling , Narimane Nekkab , et al.
2020
Pré-publication, Document de travail pasteur-02569149v2
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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.
2020
Pré-publication, Document de travail hal-03090838v1
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Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts

 Luciana Lazar-Stefanita , Jingchuan Luo , Remi Montagne , Agnes Thierry , Xiaoji Sun , et al.
Cell Genomics, 2022, 2 (8), pp.100163. ⟨10.1016/j.xgen.2022.100163⟩
Article dans une revue hal-03930009v1
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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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