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Temporal profile of replication of human chromosomes.

Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A.

Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24. Epub 2005 Apr 21.


Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection.

Karnani N, Taylor CM, Malhotra A, Dutta A.

Mol Biol Cell. 2010 Feb 1;21(3):393-404. doi: 10.1091/mbc.E09-08-0707. Epub 2009 Dec 2.


Identification of higher-order functional domains in the human ENCODE regions.

Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA.

Genome Res. 2007 Jun;17(6):917-27.


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.


Histone H3 Thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae.

Baker SP, Phillips J, Anderson S, Qiu Q, Shabanowitz J, Smith MM, Yates JR 3rd, Hunt DF, Grant PA.

Nat Cell Biol. 2010 Mar;12(3):294-8. doi: 10.1038/ncb2030. Epub 2010 Feb 7.


Possible role of H1 histone in replication timing.

Flickinger RA.

Dev Growth Differ. 2015 Jan;57(1):1-9. doi: 10.1111/dgd.12190. Epub 2014 Dec 14. Review.


Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.

Lee TJ, Pascuzzi PE, Settlage SB, Shultz RW, Tanurdzic M, Rabinowicz PD, Menges M, Zheng P, Main D, Murray JA, Sosinski B, Allen GC, Martienssen RA, Hanley-Bowdoin L, Vaughn MW, Thompson WF.

PLoS Genet. 2010 Jun 10;6(6):e1000982. doi: 10.1371/journal.pgen.1000982.


Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.

Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):886-97. Epub 2006 Nov 21.


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.


Phosphorylation of MLL by ATR is required for execution of mammalian S-phase checkpoint.

Liu H, Takeda S, Kumar R, Westergard TD, Brown EJ, Pandita TK, Cheng EH, Hsieh JJ.

Nature. 2010 Sep 16;467(7313):343-6. doi: 10.1038/nature09350. Epub 2010 Sep 5.


S-phase-dependent p50/NF-кB1 phosphorylation in response to ATR and replication stress acts to maintain genomic stability.

Crawley CD, Kang S, Bernal GM, Wahlstrom JS, Voce DJ, Cahill KE, Garofalo A, Raleigh DR, Weichselbaum RR, Yamini B.

Cell Cycle. 2015;14(4):566-76. doi: 10.4161/15384101.2014.991166.


Dynamic changes in chromatin structure through post-translational modifications of histone H3 during replication origin activation.

Rampakakis E, Di Paola D, Chan MK, Zannis-Hadjopoulos M.

J Cell Biochem. 2009 Oct 1;108(2):400-7. doi: 10.1002/jcb.22266.


Microarray analysis of DNA replication timing.

Karnani N, Taylor CM, Dutta A.

Methods Mol Biol. 2009;556:191-203. doi: 10.1007/978-1-60327-192-9_14.


ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

Hon G, Ren B, Wang W.

PLoS Comput Biol. 2008 Oct;4(10):e1000201. doi: 10.1371/journal.pcbi.1000201. Epub 2008 Oct 17.


Shifts in replication timing actively affect histone acetylation during nucleosome reassembly.

Lande-Diner L, Zhang J, Cedar H.

Mol Cell. 2009 Jun 26;34(6):767-74. doi: 10.1016/j.molcel.2009.05.027.


Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos.

Lindeman LC, Winata CL, Aanes H, Mathavan S, Alestrom P, Collas P.

Int J Dev Biol. 2010;54(5):803-13. doi: 10.1387/ijdb.103081ll.


Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells.

Schiavone D, Guilbaud G, Murat P, Papadopoulou C, Sarkies P, Prioleau MN, Balasubramanian S, Sale JE.

EMBO J. 2014 Nov 3;33(21):2507-20. doi: 10.15252/embj.201488398. Epub 2014 Sep 4.


The landscape of histone modifications across 1% of the human genome in five human cell lines.

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I.

Genome Res. 2007 Jun;17(6):691-707.

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