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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.


Human genome replication proceeds through four chromatin states.

Julienne H, Zoufir A, Audit B, Arneodo A.

PLoS Comput Biol. 2013;9(10):e1003233. doi: 10.1371/journal.pcbi.1003233. Epub 2013 Oct 10.


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.


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.


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.


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.


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.


Ubiquitous human 'master' origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers.

Drillon G, Audit B, Argoul F, Arneodo A.

J Phys Condens Matter. 2015 Feb 18;27(6):064102. doi: 10.1088/0953-8984/27/6/064102. Epub 2015 Jan 7.


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.


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.


Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features.

Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M.

Genome Res. 2011 Sep;21(9):1438-49. doi: 10.1101/gr.121830.111. Epub 2011 Jul 12.


[Regulation of DNA replication timing].

Kolesnikova TD.

Mol Biol (Mosk). 2013 Jan-Feb;47(1):12-37. Review. Russian.


Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments.

Sadoni N, Langer S, Fauth C, Bernardi G, Cremer T, Turner BM, Zink D.

J Cell Biol. 1999 Sep 20;146(6):1211-26.


Inferring the spatiotemporal DNA replication program from noisy data.

Baker A, Bechhoefer J.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Mar;89(3):032703. Epub 2014 Mar 6.


Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins.

Mesner LD, Valsakumar V, Cieslik M, Pickin R, Hamlin JL, Bekiranov S.

Genome Res. 2013 Nov;23(11):1774-88. doi: 10.1101/gr.155218.113. Epub 2013 Jul 16.


Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.


Eukaryotic DNA replication.

Zannis-Hadjopoulos M, Price GB.

J Cell Biochem. 1999;Suppl 32-33:1-14. Review.


Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

Farkash-Amar S, David Y, Polten A, Hezroni H, Eldar YC, Meshorer E, Yakhini Z, Simon I.

PLoS One. 2012;7(11):e48986. doi: 10.1371/journal.pone.0048986. Epub 2012 Nov 7.


General and specific replication profiles are detected in normal human cells by genome-wide and single-locus molecular combing.

Palumbo E, Tosoni E, Russo A.

Exp Cell Res. 2013 Dec 10;319(20):3081-93. doi: 10.1016/j.yexcr.2013.10.001. Epub 2013 Oct 12.


DNA replication origins: from sequence specificity to epigenetics.

Méchali M.

Nat Rev Genet. 2001 Aug;2(8):640-5. Review.


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