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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

Deciphering regulatory networks of the fish pathogen Flavobacterium psychrophilum by primary transcriptome mapping

Tatiana Rochat , Cyprien Guerin , Erwin van Dijk , Brigitte Kerouault , Bogdan Mirauta et al.
4. International Conference on Flavobacterium - Flavobacterium 2015, Oct 2015, Auburn, United States
Conference papers hal-01535372v1
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DNA physical properties determine nucleosome occupancy from yeast to fly.

Vincent Miele , Cédric Vaillant , Yves d'Aubenton-Carafa , Claude Thermes , Thierry Grange et al.
Nucleic Acids Research, 2008, 36 (11), pp.3746-56. ⟨10.1093/nar/gkn262⟩
Journal articles hal-00319296v1

Caractérisation des éléments actifs dans des cellules souches neurales in vivo par recherche de marques chromatiniennes p300

Rosaria Esposito , Delphine Naquin , Aurélie Heuzé , Yan Jaszczyszyn , Claude Thermes et al.
Journées d’Animation des Crédits Incitatifs du Département de Physiologie Animale et Systèmes d’Elevage (JACI Phase 2016), Apr 2016, Tours, France. , 115 p., 2016, Crédits Incitatifs financés entre 2011 et 2014
Conference poster hal-02742145v1

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq

Maxime Wery , Marc Descrimes , Claude Thermes , Daniel Gautheret , Antonin Morillon et al.
Methods, 2013, 63 (1), pp.25-31. ⟨10.1016/j.ymeth.2013.03.009⟩
Journal articles hal-02349844v1

Deciphering regulatory networks of the salmonid fish pathogen flavobacterium psychrophilum by primary transcriptome mapping

Tatiana Rochat , Cyprien Guerin , Erwin van Dijk , Brigitte Kerouault , Claude Thermes et al.
6. Congress of European Microbiologist FEMS 2015, Jun 2015, Maastricht, Netherlands
Conference papers hal-01204480v1
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What can we learn with wavelets about DNA sequences?

Alain Arneodo , Yves d'Aubenton-Carafa , Benjamin Audit , Emmanuel Bacry , Jean-François Muzy et al.
Physica A: Statistical Mechanics and its Applications, 1998, 249 (1-4), pp.439-448. ⟨10.1016/s0378-4371(97)00504-9⟩
Journal articles hal-01557120v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise et al.
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Journal articles hal-00647725v1
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Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen

Cyprien Guérin , Bo-Hyung Lee , Benjamin Fradet , Erwin van Dijk , Bogdan Mirauta et al.
ISME Communications, 2021, 1 (1), ⟨10.1038/s43705-021-00029-9⟩
Journal articles hal-03356343v1
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Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses.

Besma Ben Amor , Sonia Wirth , Francisco Merchan , Philippe Laporte , Yves d'Aubenton-Carafa et al.
Genome Research, 2009, 19 (1), pp.57-69. ⟨10.1101/gr.080275.108⟩
Journal articles hal-00736193v1

Large replication skew domains delimit GC-poor gene deserts in human

Lamia Zaghloul , Guénola Drillon , Rasha E. Boulos , Françoise Argoul , Claude Thermes et al.
Computational Biology and Chemistry, 2014, 53 (A), pp.13. ⟨10.1016/j.compbiolchem.2014.08.020⟩
Journal articles ensl-01141382v1

Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts

Judith Hirsch , Vincent Lefort , Marion Vankersschaver , Adnane Boualem , Antoine Lucas et al.
Plant Physiology, 2006, 140 (4), pp.1192-1204. ⟨10.1104/pp.105.073817⟩
Journal articles hal-00118293v1
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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.
Preprints, Working Papers, ... hal-03443067v1

DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons

Lucile Marion-Poll , Jean-Pierre Roussarie , Lieng Taing , Cloelia Dard-Dascot , Nicolas Servant et al.
Communications Biology, 2022, 5 (1), pp.1321. ⟨10.1038/s42003-022-04269-w⟩
Journal articles hal-03939291v1

Expression of GFRα1 receptor splicing variants with different biochemical properties is modulated during kidney development

Nicolas Charlet-Berguerand , Hervé Le Hir , Mariarosaria Incoronato , Umberto Di Porzio , Yanbin Yu et al.
Cellular Signalling, 2004, 16 (12), pp.1425-1434. ⟨10.1016/j.cellsig.2004.05.006⟩
Journal articles istex hal-03339582v1
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Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

Julien Fumey , Hélène Hinaux , Céline Noirot , Claude Thermes , Sylvie Rétaux et al.
BMC Evolutionary Biology, 2018, 18 (1), pp.43. ⟨10.1186/s12862-018-1156-7⟩
Journal articles hal-01828523v1

Nucleoid organization in the radioresistant bacterium Deinococcus radiodurans.

Fanny Marie Passot , Hong Ha Nguyen , Cloelia Dard-Dascot , Claude Thermes , Pascale Servant et al.
Molecular Microbiology, 2015, pp.759-74. ⟨10.1111/mmi.13064⟩
Journal articles hal-01464688v1

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

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Erwin L. van Dijk , Evangelia Eleftheriou , Claude Thermes
Journal of visualized experiments : JoVE, 2019, 151, ⟨10.3791/60056⟩
Journal articles hal-02307637v1
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Systematic comparison of small RNA library preparation protocols for next-generation sequencing

Cloelia Dard-Dascot , Delphine Naquin , Yves d'Aubenton-Carafa , Karine Alix , Claude Thermes et al.
BMC Genomics, 2018, 19, pp.1-16. ⟨10.1186/s12864-018-4491-6⟩
Journal articles hal-02621630v1
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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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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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OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Yaqun Liu , Xia Wu , Yves D’aubenton-Carafa , Claude Thermes , Chun-Long Chen et al.
Preprints, Working Papers, ... hal-03840939v1

The evolution of the temporal program of genome replication

Nicolas Agier , Stéphane Delmas , Qing Zhang , Aubin Fleiss , Yan Jaszczyszyn et al.
Nature Communications, 2018, 9 (1), pp.2199. ⟨10.1038/s41467-018-04628-4⟩
Journal articles hal-02175123v1

The Third Revolution in Sequencing Technology

Erwin L. Van Dijk , Yan Jaszczyszyn , Delphine Naquin , Claude Thermes
Trends in Genetics, 2018, 34 (9), pp.666--681. ⟨10.1016/j.tig.2018.05.008⟩
Journal articles hal-02184812v1

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

Post-embryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-type Gene Expression Profile.

Emilie Dambroise , Matthieu Simion , Thomas Bourquard , Stéphanie Bouffard , Barbara Rizzi et al.
Stem Cells / Stem Cells (Miamisburg), 2017, 35 (6), pp.1505-1518. ⟨10.1002/stem.2588⟩
Journal articles hal-01490733v1

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
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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
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Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Maxime Policarpo , Julien Fumey , Philippe Lafargeas , Delphine Naquin , Claude Thermes et al.
Molecular Biology and Evolution, 2021, 38 (2), pp.589-605. ⟨10.1093/molbev/msaa249⟩
Journal articles hal-02968373v1