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Items: 1 to 20 of 59

1.

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.

2.

CTCF-mediated functional chromatin interactome in pluripotent cells.

Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL.

Nat Genet. 2011 Jun 19;43(7):630-8. doi: 10.1038/ng.857. Erratum in: Nat Genet. 2011 Aug;43(8):815.

3.

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.

PMID:
21368316
4.

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription.

Mesner LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, Bekiranov S.

Genome Res. 2011 Mar;21(3):377-89. doi: 10.1101/gr.111328.110. Epub 2010 Dec 20. Erratum in: Genome Res. 2011 Sep;21(9):1561.

5.

Eukaryotic DNA replication origins: many choices for appropriate answers.

Méchali M.

Nat Rev Mol Cell Biol. 2010 Oct;11(10):728-38. doi: 10.1038/nrm2976. Review.

PMID:
20861881
6.

Evaluating genome-scale approaches to eukaryotic DNA replication.

Gilbert DM.

Nat Rev Genet. 2010 Oct;11(10):673-84. doi: 10.1038/nrg2830. Epub 2010 Sep 1. Review.

7.

Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing.

Yang SC, Rhind N, Bechhoefer J.

Mol Syst Biol. 2010 Aug 24;6:404. doi: 10.1038/msb.2010.61.

8.

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.

Yaffe E, Farkash-Amar S, Polten A, Yakhini Z, Tanay A, Simon I.

PLoS Genet. 2010 Jul 1;6(7):e1001011. doi: 10.1371/journal.pgen.1001011.

9.

Mathematical modelling of whole chromosome replication.

de Moura AP, Retkute R, Hawkins M, Nieduszynski CA.

Nucleic Acids Res. 2010 Sep;38(17):5623-33. doi: 10.1093/nar/gkq343. Epub 2010 May 10.

10.

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types.

Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM.

Genome Res. 2010 Jun;20(6):761-70. doi: 10.1101/gr.099655.109. Epub 2010 Apr 29.

11.

Cell type specificity of chromatin organization mediated by CTCF and cohesin.

Hou C, Dale R, Dean A.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3651-6. doi: 10.1073/pnas.0912087107. Epub 2010 Feb 2.

12.

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.

13.

Does CTCF mediate between nuclear organization and gene expression?

Ohlsson R, Lobanenkov V, Klenova E.

Bioessays. 2010 Jan;32(1):37-50. doi: 10.1002/bies.200900118. Review.

PMID:
20020479
14.

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA.

Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. doi: 10.1073/pnas.0912402107. Epub 2009 Dec 4.

15.

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis.

Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM.

Genome Res. 2010 Feb;20(2):155-69. doi: 10.1101/gr.099796.109. Epub 2009 Dec 1.

16.

A winding road to origin discovery.

Hamlin JL, Mesner LD, Dijkwel PA.

Chromosome Res. 2010 Jan;18(1):45-61. doi: 10.1007/s10577-009-9089-z.

17.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

18.

Predictable dynamic program of timing of DNA replication in human cells.

Desprat R, Thierry-Mieg D, Lailler N, Lajugie J, Schildkraut C, Thierry-Mieg J, Bouhassira EE.

Genome Res. 2009 Dec;19(12):2288-99. doi: 10.1101/gr.094060.109. Epub 2009 Sep 18.

19.

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.

20.

CTCF: master weaver of the genome.

Phillips JE, Corces VG.

Cell. 2009 Jun 26;137(7):1194-211. doi: 10.1016/j.cell.2009.06.001. Review.

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