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Items: 18

1.

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.

Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM.

Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27.

PMID:
30595451
2.

RT States: systematic annotation of the human genome using cell type-specific replication timing programs.

Poulet A, Li B, Dubos T, Rivera-Mulia JC, Gilbert DM, Qin ZS.

Bioinformatics. 2018 Nov 22. doi: 10.1093/bioinformatics/bty957. [Epub ahead of print]

PMID:
30475980
3.

Integrative detection and analysis of structural variation in cancer genomes.

Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Oct;50(10):1388-1398. doi: 10.1038/s41588-018-0195-8. Epub 2018 Sep 10.

4.

Cellular senescence induces replication stress with almost no affect on DNA replication timing.

Rivera-Mulia JC, Schwerer H, Besnard E, Desprat R, Trevilla-Garcia C, Sima J, Bensadoun P, Zouaoui A, Gilbert DM, Lemaitre JM.

Cell Cycle. 2018;17(13):1667-1681. doi: 10.1080/15384101.2018.1491235. Epub 2018 Aug 21.

PMID:
29963964
5.

Allele-specific control of replication timing and genome organization during development.

Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM.

Genome Res. 2018 Jun;28(6):800-811. doi: 10.1101/gr.232561.117. Epub 2018 May 7.

6.

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

Marchal C, Sasaki T, Vera D, Wilson K, Sima J, Rivera-Mulia JC, Trevilla-García C, Nogues C, Nafie E, Gilbert DM.

Nat Protoc. 2018 May;13(5):819-839. doi: 10.1038/nprot.2017.148. Epub 2018 Mar 29.

7.

Replication Domains: Genome Compartmentalization into Functional Replication Units.

Zhao PA, Rivera-Mulia JC, Gilbert DM.

Adv Exp Med Biol. 2017;1042:229-257. doi: 10.1007/978-981-10-6955-0_11. Review.

PMID:
29357061
8.

DNA replication timing alterations identify common markers between distinct progeroid diseases.

Rivera-Mulia JC, Desprat R, Trevilla-Garcia C, Cornacchia D, Schwerer H, Sasaki T, Sima J, Fells T, Studer L, Lemaitre JM, Gilbert DM.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10972-E10980. doi: 10.1073/pnas.1711613114. Epub 2017 Dec 1.

9.

Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia.

Sasaki T, Rivera-Mulia JC, Vera D, Zimmerman J, Das S, Padget M, Nakamichi N, Chang BH, Tyner J, Druker BJ, Weng AP, Civin CI, Eaves CJ, Gilbert DM.

Exp Hematol. 2017 Jul;51:71-82.e3. doi: 10.1016/j.exphem.2017.04.004. Epub 2017 Apr 19.

10.

The Set of Structural DNA-Nuclear Matrix Interactions in Neurons Is Cell-Type Specific and Rather Independent of Functional Constraints.

Silva-Santiago E, Rivera-Mulia JC, Aranda-Anzaldo A.

J Cell Biochem. 2017 Aug;118(8):2151-2160. doi: 10.1002/jcb.25852. Epub 2017 Apr 18.

PMID:
27996173
11.

Replicating Large Genomes: Divide and Conquer.

Rivera-Mulia JC, Gilbert DM.

Mol Cell. 2016 Jun 2;62(5):756-65. doi: 10.1016/j.molcel.2016.05.007. Review.

12.

Replication timing and transcriptional control: beyond cause and effect-part III.

Rivera-Mulia JC, Gilbert DM.

Curr Opin Cell Biol. 2016 Jun;40:168-178. doi: 10.1016/j.ceb.2016.03.022. Epub 2016 Apr 23. Review.

13.

Large-Scale Chromatin Structure-Function Relationships during the Cell Cycle and Development: Insights from Replication Timing.

Dileep V, Rivera-Mulia JC, Sima J, Gilbert DM.

Cold Spring Harb Symp Quant Biol. 2015;80:53-63. doi: 10.1101/sqb.2015.80.027284. Epub 2015 Nov 20. Review.

PMID:
26590169
14.

Computing interaction probabilities in signaling networks.

Gabr H, Rivera-Mulia JC, Gilbert DM, Kahveci T.

EURASIP J Bioinform Syst Biol. 2015 Nov 11;2015(1):10. eCollection 2015 Dec.

15.

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.

Rivera-Mulia JC, Buckley Q, Sasaki T, Zimmerman J, Didier RA, Nazor K, Loring JF, Lian Z, Weissman S, Robins AJ, Schulz TC, Menendez L, Kulik MJ, Dalton S, Gabr H, Kahveci T, Gilbert DM.

Genome Res. 2015 Aug;25(8):1091-103. doi: 10.1101/gr.187989.114. Epub 2015 Jun 8.

16.

Copy number variation is a fundamental aspect of the placental genome.

Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC.

PLoS Genet. 2014 May 1;10(5):e1004290. doi: 10.1371/journal.pgen.1004290. eCollection 2014 May.

17.

DNA moves sequentially towards the nuclear matrix during DNA replication in vivo.

Rivera-Mulia JC, Hernández-Muñoz R, Martínez F, Aranda-Anzaldo A.

BMC Cell Biol. 2011 Jan 19;12:3. doi: 10.1186/1471-2121-12-3.

18.

Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach.

Rivera-Mulia JC, Aranda-Anzaldo A.

DNA Res. 2010 Feb;17(1):23-35. doi: 10.1093/dnares/dsp027. Epub 2010 Jan 4.

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