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Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide.

Brison O, El-Hilali S, Azar D, Koundrioukoff S, Schmidt M, Nähse V, Jaszczyszyn Y, Lachages AM, Dutrillaux B, Thermes C, Debatisse M, Chen CL.

Nat Commun. 2019 Dec 13;10(1):5693. doi: 10.1038/s41467-019-13674-5.


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

van Dijk EL, Eleftheriou E, Thermes C.

J Vis Exp. 2019 Sep 16;(151). doi: 10.3791/60056.


The Third Revolution in Sequencing Technology.

van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C.

Trends Genet. 2018 Sep;34(9):666-681. doi: 10.1016/j.tig.2018.05.008. Epub 2018 Jun 22. Review.


The evolution of the temporal program of genome replication.

Agier N, Delmas S, Zhang Q, Fleiss A, Jaszczyszyn Y, van Dijk E, Thermes C, Weigt M, Cosentino-Lagomarsino M, Fischer G.

Nat Commun. 2018 Jun 6;9(1):2199. doi: 10.1038/s41467-018-04628-4.


Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252.

Naquin D, Panozzo C, Dujardin G, van Dijk E, d'Aubenton-Carafa Y, Thermes C.

Genome Announc. 2018 Apr 26;6(17). pii: e00219-18. doi: 10.1128/genomeA.00219-18.


Evidence for late Pleistocene origin of Astyanax mexicanus cavefish.

Fumey J, Hinaux H, Noirot C, Thermes C, Rétaux S, Casane D.

BMC Evol Biol. 2018 Apr 18;18(1):43. doi: 10.1186/s12862-018-1156-7.


Systematic comparison of small RNA library preparation protocols for next-generation sequencing.

Dard-Dascot C, Naquin D, d'Aubenton-Carafa Y, Alix K, Thermes C, van Dijk E.

BMC Genomics. 2018 Feb 5;19(1):118. doi: 10.1186/s12864-018-4491-6.


Postembryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-Type Gene Expression Profile.

Dambroise E, Simion M, Bourquard T, Bouffard S, Rizzi B, Jaszczyszyn Y, Bourge M, Affaticati P, Heuzé A, Jouralet J, Edouard J, Brown S, Thermes C, Poupon A, Reiter E, Sohm F, Bourrat F, Joly JS.

Stem Cells. 2017 Jun;35(6):1505-1518. doi: 10.1002/stem.2588. Epub 2017 Mar 14.


Replication landscape of the human genome.

Petryk N, Kahli M, d'Aubenton-Carafa Y, Jaszczyszyn Y, Shen Y, Silvain M, Thermes C, Chen CL, Hyrien O.

Nat Commun. 2016 Jan 11;7:10208. doi: 10.1038/ncomms10208.


Nucleoid organization in the radioresistant bacterium Deinococcus radiodurans.

Passot FM, Nguyen HH, Dard-Dascot C, Thermes C, Servant P, Espéli O, Sommer S.

Mol Microbiol. 2015 Aug;97(4):759-74. doi: 10.1111/mmi.13064. Epub 2015 Jun 25.


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

Zaghloul L, Drillon G, Boulos RE, Argoul F, Thermes C, Arneodo A, Audit B.

Comput Biol Chem. 2014 Dec;53 Pt A:153-65. doi: 10.1016/j.compbiolchem.2014.08.020. Epub 2014 Aug 27.


Ten years of next-generation sequencing technology.

van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C.

Trends Genet. 2014 Sep;30(9):418-26. doi: 10.1016/j.tig.2014.07.001. Epub 2014 Aug 6. Review.


CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.

Naquin D, d'Aubenton-Carafa Y, Thermes C, Silvain M.

BMC Bioinformatics. 2014 Jun 18;15:198. doi: 10.1186/1471-2105-15-198.


Library preparation methods for next-generation sequencing: tone down the bias.

van Dijk EL, Jaszczyszyn Y, Thermes C.

Exp Cell Res. 2014 Mar 10;322(1):12-20. doi: 10.1016/j.yexcr.2014.01.008. Epub 2014 Jan 15. Review.


From simple bacterial and archaeal replicons to replication N/U-domains.

Hyrien O, Rappailles A, Guilbaud G, Baker A, Chen CL, Goldar A, Petryk N, Kahli M, Ma E, d'Aubenton-Carafa Y, Audit B, Thermes C, Arneodo A.

J Mol Biol. 2013 Nov 29;425(23):4673-89. doi: 10.1016/j.jmb.2013.09.021. Epub 2013 Oct 3. Review.


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

Wery M, Descrimes M, Thermes C, Gautheret D, Morillon A.

Methods. 2013 Sep 1;63(1):25-31. doi: 10.1016/j.ymeth.2013.03.009. Epub 2013 Mar 21.


Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm.

Audit B, Baker A, Chen CL, Rappailles A, Guilbaud G, Julienne H, Goldar A, d'Aubenton-Carafa Y, Hyrien O, Thermes C, Arneodo A.

Nat Protoc. 2013 Jan;8(1):98-110. doi: 10.1038/nprot.2012.145. Epub 2012 Dec 13.


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

Baker A, Chen CL, Julienne H, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Eur Phys J E Soft Matter. 2012 Nov;35(11):123. doi: 10.1140/epje/i2012-12123-9. Epub 2012 Nov 27.


Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

Audit B, Zaghloul L, Baker A, Arneodo A, Chen CL, d'Aubenton-Carafa Y, Thermes C.

Subcell Biochem. 2013;61:57-80. doi: 10.1007/978-94-007-4525-4_3. Review.


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

Baker A, Julienne H, Chen CL, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Eur Phys J E Soft Matter. 2012 Sep;35(9):92. Epub 2012 Sep 26.


3D chromatin conformation correlates with replication timing and is conserved in resting cells.

Moindrot B, Audit B, Klous P, Baker A, Thermes C, de Laat W, Bouvet P, Mongelard F, Arneodo A.

Nucleic Acids Res. 2012 Oct;40(19):9470-81. doi: 10.1093/nar/gks736. Epub 2012 Aug 8.


BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

Allali J, Saule C, Chauve C, d'Aubenton-Carafa Y, Denise A, Drevet C, Ferraro P, Gautheret D, Herrbach C, Leclerc F, de Monte A, Ouangraoua A, Sagot MF, Termier M, Thermes C, Touzet H.

Adv Bioinformatics. 2012;2012:893048. doi: 10.1155/2012/893048. Epub 2012 May 23.


Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines.

Baker A, Audit B, Chen CL, Moindrot B, Leleu A, Guilbaud G, Rappailles A, Vaillant C, Goldar A, Mongelard F, d'Aubenton-Carafa Y, Hyrien O, Thermes C, Arneodo A.

PLoS Comput Biol. 2012;8(4):e1002443. doi: 10.1371/journal.pcbi.1002443. Epub 2012 Apr 5.


Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

Guilbaud G, Rappailles A, Baker A, Chen CL, Arneodo A, Goldar A, d'Aubenton-Carafa Y, Thermes C, Audit B, Hyrien O.

PLoS Comput Biol. 2011 Dec;7(12):e1002322. doi: 10.1371/journal.pcbi.1002322. Epub 2011 Dec 29.


Tight protein-DNA interactions favor gene silencing.

Dubarry M, Loïodice I, Chen CL, Thermes C, Taddei A.

Genes Dev. 2011 Jul 1;25(13):1365-70. doi: 10.1101/gad.611011.


XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.

van Dijk EL, Chen CL, d'Aubenton-Carafa Y, Gourvennec S, Kwapisz M, Roche V, Bertrand C, Silvain M, Legoix-Né P, Loeillet S, Nicolas A, Thermes C, Morillon A.

Nature. 2011 Jun 22;475(7354):114-7. doi: 10.1038/nature10118.


Replication-associated mutational asymmetry in the human genome.

Chen CL, Duquenne L, Audit B, Guilbaud G, Rappailles A, Baker A, Huvet M, d'Aubenton-Carafa Y, Hyrien O, Arneodo A, Thermes C.

Mol Biol Evol. 2011 Aug;28(8):2327-37. doi: 10.1093/molbev/msr056. Epub 2011 Mar 2.


Evolution of Hox gene clusters in gnathostomes: insights from a survey of a shark (Scyliorhinus canicula) transcriptome.

Oulion S, Debiais-Thibaud M, d'Aubenton-Carafa Y, Thermes C, Da Silva C, Bernard-Samain S, Gavory F, Wincker P, Mazan S, Casane D.

Mol Biol Evol. 2010 Dec;27(12):2829-38. doi: 10.1093/molbev/msq172. Epub 2010 Jul 8.


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

Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d'Aubenton-Carafa Y, Arneodo A, Hyrien O, Thermes C.

Genome Res. 2010 Apr;20(4):447-57. doi: 10.1101/gr.098947.109. Epub 2010 Jan 26.


Thermodynamics of intragenic nucleosome ordering.

Chevereau G, Palmeira L, Thermes C, Arneodo A, Vaillant C.

Phys Rev Lett. 2009 Oct 30;103(18):188103. Epub 2009 Oct 30.


A novel strategy of transcription regulation by intragenic nucleosome ordering.

Vaillant C, Palmeira L, Chevereau G, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Genome Res. 2010 Jan;20(1):59-67. doi: 10.1101/gr.096644.109. Epub 2009 Oct 26.


Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells.

Audit B, Zaghloul L, Vaillant C, Chevereau G, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Nucleic Acids Res. 2009 Oct;37(18):6064-75. doi: 10.1093/nar/gkp631. Epub 2009 Aug 10.


Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses.

Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M.

Genome Res. 2009 Jan;19(1):57-69. doi: 10.1101/gr.080275.108. Epub 2008 Nov 7.


DNA physical properties determine nucleosome occupancy from yeast to fly.

Miele V, Vaillant C, d'Aubenton-Carafa Y, Thermes C, Grange T.

Nucleic Acids Res. 2008 Jun;36(11):3746-56. doi: 10.1093/nar/gkn262. Epub 2008 May 17.


DNA replication timing data corroborate in silico human replication origin predictions.

Audit B, Nicolay S, Huvet M, Touchon M, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Phys Rev Lett. 2007 Dec 14;99(24):248102. Epub 2007 Dec 12.


The Dogfish Scyliorhinus canicula: A Reference in Jawed Vertebrates.

Coolen M, Menuet A, Chassoux D, Compagnucci C, Henry S, Lévèque L, Da Silva C, Gavory F, Samain S, Wincker P, Thermes C, D'Aubenton-Carafa Y, Rodriguez-Moldes I, Naylor G, Depew M, Sourdaine P, Mazan S.

CSH Protoc. 2008 Dec 1;2008:pdb.emo111. doi: 10.1101/pdb.emo111.


Human gene organization driven by the coordination of replication and transcription.

Huvet M, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Arneodo A, Thermes C.

Genome Res. 2007 Sep;17(9):1278-85. Epub 2007 Aug 3.


Bifractality of human DNA strand-asymmetry profiles results from transcription.

Nicolay S, Brodie Of Brodie EB, Touchon M, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Mar;75(3 Pt 1):032902. Epub 2007 Mar 12.


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

Hirsch J, Lefort V, Vankersschaver M, Boualem A, Lucas A, Thermes C, d'Aubenton-Carafa Y, Crespi M.

Plant Physiol. 2006 Apr;140(4):1192-204. Epub 2006 Feb 24.


Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorder.

Vaillant C, Audit B, Thermes C, Arnéodo A.

Eur Phys J E Soft Matter. 2006 Mar;19(3):263-77. Epub 2006 Feb 14.


Analysing grouping of nucleotides in DNA sequences using lumped processes constructed from Markov chains.

Guédon Y, d'Aubenton-Carafa Y, Thermes C.

J Math Biol. 2006 Mar;52(3):343-72. Epub 2006 Feb 7.


From DNA sequence analysis to modeling replication in the human genome.

Brodie Of Brodie EB, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Phys Rev Lett. 2005 Jun 24;94(24):248103. Epub 2005 Jun 23.


Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins.

Touchon M, Nicolay S, Audit B, Brodie of Brodie EB, d'Aubenton-Carafa Y, Arneodo A, Thermes C.

Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9836-41. Epub 2005 Jun 28.


Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation?

Nicolay S, Argoul F, Touchon M, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Phys Rev Lett. 2004 Sep 3;93(10):108101. Epub 2004 Aug 31.


Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes.

Touchon M, Arneodo A, d'Aubenton-Carafa Y, Thermes C.

Nucleic Acids Res. 2004 Sep 23;32(17):4969-78. Print 2004.


Expression of GFRalpha1 receptor splicing variants with different biochemical properties is modulated during kidney development.

Charlet-Berguerand N, Le Hir H, Incoronato M, di Porzio U, Yu Y, Jing S, de Franciscis V, Thermes C.

Cell Signal. 2004 Dec;16(12):1425-34.


Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences.

Audit B, Vaillant C, Arnéodo A, d'Aubenton-Carafa Y, Thermes C.

J Biol Phys. 2004 Mar;30(1):33-81. doi: 10.1023/B:JOBP.0000016438.86794.8e.


Transcription-coupled TA and GC strand asymmetries in the human genome.

Touchon M, Nicolay S, Arneodo A, d'Aubenton-Carafa Y, Thermes C.

FEBS Lett. 2003 Dec 18;555(3):579-82.


Influence of the sequence on elastic properties of long DNA chains.

Vaillant C, Audit B, Thermes C, Arnéodo A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):032901. Epub 2003 Mar 11.


Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium.

Raux E, Leech HK, Beck R, Schubert HL, Santander PJ, Roessner CA, Scott AI, Martens JH, Jahn D, Thermes C, Rambach A, Warren MJ.

Biochem J. 2003 Mar 1;370(Pt 2):505-16.

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