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Complex correlations: replication timing and mutational landscapes during cancer and genome evolution.

Sima J, Gilbert DM.

Curr Opin Genet Dev. 2014 Apr;25:93-100. doi: 10.1016/j.gde.2013.11.022. Epub 2014 Mar 2. Review.


DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes.

De S, Michor F.

Nat Biotechnol. 2011 Nov 20;29(12):1103-8. doi: 10.1038/nbt.2030.


Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.

Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM.

Genome Res. 2013 May;23(5):762-76. doi: 10.1101/gr.143677.112. Epub 2013 Feb 14.


Differential relationship of DNA replication timing to different forms of human mutation and variation.

Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA.

Am J Hum Genet. 2012 Dec 7;91(6):1033-40. doi: 10.1016/j.ajhg.2012.10.018. Epub 2012 Nov 21.


DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes.

Woo YH, Li WH.

Nat Commun. 2012;3:1004. doi: 10.1038/ncomms1982.


Diverse mechanisms of somatic structural variations in human cancer genomes.

Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ.

Cell. 2013 May 9;153(4):919-29. doi: 10.1016/j.cell.2013.04.010. Erratum in: Cell. 2014 Jun 19;157(7):1736.


The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming.

Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ, Lerou PH.

Cell Rep. 2014 Apr 10;7(1):70-8. doi: 10.1016/j.celrep.2014.03.007. Epub 2014 Mar 27.


Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes.

Pedersen BS, De S.

Nucleic Acids Res. 2013 Sep;41(16):7615-24. doi: 10.1093/nar/gkt552. Epub 2013 Jun 22.


Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data.

Luo H, Li J, Eshaghi M, Liu J, Karuturi RK.

BMC Bioinformatics. 2010 May 13;11:247. doi: 10.1186/1471-2105-11-247.


Break-induced replication: functions and molecular mechanism.

Malkova A, Ira G.

Curr Opin Genet Dev. 2013 Jun;23(3):271-9. doi: 10.1016/j.gde.2013.05.007. Epub 2013 Jun 18. Review.


Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins.

Kunnev D, Freeland A, Qin M, Leach RW, Wang J, Shenoy RM, Pruitt SC.

Genome Res. 2015 Apr;25(4):558-69. doi: 10.1101/gr.176099.114. Epub 2015 Mar 11.


Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data.

Zhang J, Zhang S, Wang Y, Zhang XS.

BMC Syst Biol. 2013;7 Suppl 2:S4. doi: 10.1186/1752-0509-7-S2-S4. Epub 2013 Oct 14.


Differential DNA mismatch repair underlies mutation rate variation across the human genome.

Supek F, Lehner B.

Nature. 2015 May 7;521(7550):81-4. doi: 10.1038/nature14173. Epub 2015 Feb 23.


Late-replicating domains have higher divergence and diversity in Drosophila melanogaster.

Weber CC, Pink CJ, Hurst LD.

Mol Biol Evol. 2012 Feb;29(2):873-82. doi: 10.1093/molbev/msr265. Epub 2011 Oct 31.


The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells.

Jørgensen HF, Azuara V, Amoils S, Spivakov M, Terry A, Nesterova T, Cobb BS, Ramsahoye B, Merkenschlager M, Fisher AG.

Genome Biol. 2007;8(8):R169.


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.


DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability.

Donley N, Thayer MJ.

Semin Cancer Biol. 2013 Apr;23(2):80-9. doi: 10.1016/j.semcancer.2013.01.001. Epub 2013 Jan 14. Review.


Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures.

Seplyarskiy VB, Bazykin GA, Soldatov RA.

Mol Biol Evol. 2015 Dec;32(12):3158-72. doi: 10.1093/molbev/msv184. Epub 2015 Sep 15.


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