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Unscheduled origin building in S-phase upon tight CDK1 inhibition suppresses CFS instability

Olivier Brison , Stefano Gnan , Dana Azar , Mélanie Schmidt , Stéphane Koundrioukoff et al.
2021
Preprints, Working Papers, ... hal-03443067v1
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Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer

Ming-Jun Shi , Xiang-Yu Meng , Jacqueline Fontugne , Chun-Long Chen , François Radvanyi et al.
Genome Medicine, 2020, 12 (1), ⟨10.1186/s13073-020-00781-y⟩
Journal articles hal-03015020v1
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Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome

Arijita Chakraborty , Piroon Jenjaroenpun , Jing Li , Sami El Hilali , Andrew Mcculley et al.
Cell Reports, 2020, 32 (12), pp.108179. ⟨10.1016/j.celrep.2020.108179⟩
Journal articles hal-03015043v1
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Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide

Olivier Brison , Sami El-Hilali , Dana Azar , Stéphane Koundrioukoff , Mélanie Schmidt et al.
Nature Communications, 2019, 10, pp.5693. ⟨10.1038/s41467-019-13674-5⟩
Journal articles hal-02430920v1

Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes.

Chun-Long Chen , Aurélien Rappailles , Lauranne Duquenne , Maxime Huvet , Guillaume Guilbaud et al.
Genome Research, 2010, 20 (4), pp.447-57. ⟨10.1101/gr.098947.109⟩
Journal articles ensl-00517756v1

Linking the DNA strand asymmetry to the spatio-temporal replication program I. About the role of the replication fork polarity in genome evolution

A. Baker , H. Julienne , C. L. Chen , B. Audit , Y. d'Aubenton-Carafa et al.
European Physical Journal E: Soft matter and biological physics, 2012, 35 (9), pp.25. ⟨10.1140/epje/i2012-12092-y⟩
Journal articles hal-01557082v1

Genome-Wide Evolutionary Analysis of the Non-Coding RNA Genes and Non-Coding DNA of Paramecium tetraurelia.

Chen C.L. , H. Zhou , Liao J.Y. , Qu L.H. , Laurence Amar et al.
RNA, 2009, 15(4), pp.503-14
Journal articles hal-00413942v1
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Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication

Weitao Wang , Kyle Klein , Karel Proesmans , Hongbo Yang , Claire Marchal et al.
2021
Preprints, Working Papers, ... hal-03014247v1
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APOBEC-mediated Mutagenesis as a Likely Cause of FGFR3 S249C Mutation Over-representation in Bladder Cancer

Ming-Jun Shi , Xiang-Yu Meng , Philippe Lamy , A. Rouf Banday , Jie Yang et al.
European Urology, 2019, 76 (1), pp.9-13. ⟨10.1016/j.eururo.2019.03.032⟩
Journal articles hal-02369388v1

From the chromatin interaction network to the organization of the human genome into replication N/U-domains

Rasha E Boulos , Hanna Julienne , Antoine Baker , Chun-Long Chen , Nataliya Petryk et al.
New Journal of Physics, 2014, 16 (11), pp.115014. ⟨10.1088/1367-2630/16/11/115014⟩
Journal articles cea-01120311v1
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Replication landscape of the human genome

Nataliya Petryk , Malik Kahli , Yves d'Aubenton-Carafa , Yan Jaszczyszyn , Yimin Shen et al.
Nature Communications, 2016, 7, ⟨10.1038/ncomms10208⟩
Journal articles hal-01412672v1

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Sabeeha S Merchant , Simon E Prochnik , Olivier Vallon , Elizabeth H Harris , Steven J Karpowicz et al.
Science, 2007, 318 (5848), pp.245-50. ⟨10.1126/science.1143609⟩
Journal articles hal-00198837v1

Linking the DNA strand asymmetry to the spatio-temporal replication program II. Accounting for neighbor-dependent substitution rates

A. Baker , C. L. Chen , H. Julienne , B. Audit , Y. d'Aubenton-Carafa et al.
European Physical Journal E: Soft matter and biological physics, 2012, 35 (11), pp.12. ⟨10.1140/epje/i2012-12123-9⟩
Journal articles hal-01557084v1
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Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

Guillaume Guilbaud , Aurélien Rappailles , Antoine Baker , Chun-Long Chen , Alain Arneodo et al.
PLoS Computational Biology, 2011, 7 (12), pp.e1002322. ⟨10.1371/journal.pcbi.1002322⟩
Journal articles inserm-00691534v1
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Editorial: DNA Replication Stress and Cell Fate

Lin Deng , Chun-Long Chen , Yuanliang Zhai , Yunzhou Dong , Huiqiang Lou et al.
Frontiers in Cell and Developmental Biology, 2021, 9, ⟨10.3389/fcell.2021.778486⟩
Journal articles hal-03426812v1
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Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

Alexy Promonet , Ismaël Padioleau , Yaqun Liu , Lionel A. Sanz , Anna Biernacka et al.
Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-020-17858-2⟩
Journal articles hal-02931000v1
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Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation.

Aurore Sanchez , Céline Adam , Felix Rauh , Yann Duroc , Lepakshi Ranjha et al.
Proceedings of the National Academy of Sciences of the United States of America, 2020, ⟨10.1073/pnas.2013012117⟩
Journal articles hal-03020386v1

Biomimetic water channels: general discussion

Marc Baaden , Mihail Barboiu , Roslyn Bill , Chun-Long Chen , Jeffery Davis et al.
Faraday Discussions, 2018, 209, pp.205 - 229. ⟨10.1039/C8FD90020E⟩
Journal articles hal-01926861v1
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OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Yaqun Liu , Xia Wu , Yves D’aubenton-Carafa , Claude Thermes , Chun-Long Chen et al.
2022
Preprints, Working Papers, ... hal-03840939v1
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Kronos scRT: a uniform framework for single-cell replication timing analysis

Stefano Gnan , Joseph M Josephides , Xia Wu , Manuela Spagnuolo , Dalila Saulebekova et al.
Nature Communications, 2022, 13 (1), pp.2329. ⟨10.1038/s41467-022-30043-x⟩
Journal articles hal-03840947v1
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Cohesin-mediated loop anchors confine the locations of human replication origins

Daniel J Emerson , Peiyao A Zhao , Ashley L Cook , R. Jordan Barnett , Kyle N Klein et al.
Nature, 2022, 606 (7915), pp.812 - 819. ⟨10.1038/s41586-022-04803-0⟩
Journal articles hal-03840949v1
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GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium

Stefano Gnan , Mélody Matelot , Marion Weiman , Olivier Arnaiz , Frédéric Guérin et al.
Genome Research, 2022, pp.699-709. ⟨10.1101/2021.08.05.455221⟩
Journal articles hal-03400776v1
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The impact of transcription-mediated replication stress on genome instability and human disease

Stefano Gnan , Yaqun Liu , Manuela Spagnuolo , Chun-Long Chen
Genome Instability & Disease, 2020, 1 (5), pp.207-234. ⟨10.1007/s42764-020-00021-y⟩
Journal articles hal-03015011v1
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Kronos scRT: a uniform framework for single-cell replication timing analysis

Stefano Gnan , Joseph M Josephides , Xia Wu , Manuela Spagnuolo , Dalila Saulebekova et al.
2021
Preprints, Working Papers, ... hal-03436209v1
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DNA molecular combing-based replication fork directionality profiling

Marion Blin , Laurent Lacroix , Nataliya Petryk , Yan Jaszczyszyn , Chun-Long Chen et al.
Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab219⟩
Journal articles hal-03195930v1
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DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands

Zhiming Li , Xu Hua , Albert Serra-Cardona , Xiaowei Xu , Songlin Gan et al.
Science Advances , 2020, 6 (35), pp.eabb5820. ⟨10.1126/sciadv.abb5820⟩
Journal articles hal-03015005v1
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Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm

Benjamin Audit , Antoine Baker , Chun-Long Chen , Aurélien Rappailles , Guillaume Guilbaud et al.
Nature Protocols, 2013, 8 (1), pp.98-110. ⟨10.1038/nprot.2012.145⟩
Journal articles hal-01557077v1
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Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines.

Antoine Baker , Benjamin Audit , Chun-Long Chen , Benoit Moindrot , Antoine Leleu et al.
PLoS Computational Biology, 2012, 8 (4), pp.e1002443. ⟨10.1371/journal.pcbi.1002443⟩
Journal articles inserm-00706043v1

Replication-Associated Mutational Asymmetry in the Human Genome

C. L. Chen , L. Duquenne , B. Audit , G. Guilbaud , A. Rappailles et al.
Molecular Biology and Evolution, 2011, 28 (8), pp.2327-2337. ⟨10.1093/molbev/msr056⟩
Journal articles hal-01557088v1

From Simple Bacterial and Archaeal Replicons to Replication N/U-Domains

Olivier Hyrien , Aurélien Rappailles , Guillaume Guilbaud , Antoine Baker , Chun-Long Chen et al.
Journal of Molecular Biology, 2013, 425 (23), pp.4673-4689. ⟨10.1016/j.jmb.2013.09.021⟩
Journal articles hal-01557075v1