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Items: 1 to 50 of 151

1.

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.

PMID:
29735606
2.

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.

PMID:
29599440
3.

Single-cell replication profiling to measure stochastic variation in mammalian replication timing.

Dileep V, Gilbert DM.

Nat Commun. 2018 Jan 30;9(1):427. doi: 10.1038/s41467-017-02800-w.

4.

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.

PMID:
29357061
5.

Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors.

Sima J, Bartlett DA, Gordon MR, Gilbert DM.

Nucleic Acids Res. 2018 Feb 28;46(4):1810-1820. doi: 10.1093/nar/gkx1265.

6.

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.

7.

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.

PMID:
28433605
8.

Unearthing worm replication origins.

Sasaki T, Gilbert DM.

Nat Struct Mol Biol. 2017 Mar 3;24(3):195-196. doi: 10.1038/nsmb.3385. No abstract available.

PMID:
28257138
9.

Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification.

Wilson KA, Elefanty AG, Stanley EG, Gilbert DM.

Cell Cycle. 2016 Sep 16;15(18):2464-75. doi: 10.1080/15384101.2016.1203492. Epub 2016 Jul 19.

10.

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.

11.

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.

12.

Influence of ATM-Mediated DNA Damage Response on Genomic Variation in Human Induced Pluripotent Stem Cells.

Lu J, Li H, Baccei A, Sasaki T, Gilbert DM, Lerou PH.

Stem Cells Dev. 2016 May 1;25(9):740-7. doi: 10.1089/scd.2015.0393. Epub 2016 Apr 11.

13.

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.

Foti R, Gnan S, Cornacchia D, Dileep V, Bulut-Karslioglu A, Diehl S, Buness A, Klein FA, Huber W, Johnstone E, Loos R, Bertone P, Gilbert DM, Manke T, Jenuwein T, Buonomo SC.

Mol Cell. 2016 Jan 21;61(2):260-73. doi: 10.1016/j.molcel.2015.12.001. Epub 2015 Dec 24.

14.

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
15.

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.

16.

Precise repair of mPing excision sites is facilitated by target site duplication derived microhomology.

Gilbert DM, Bridges MC, Strother AE, Burckhalter CE, Burnette JM 3rd, Hancock CN.

Mob DNA. 2015 Sep 7;6:15. doi: 10.1186/s13100-015-0046-4. eCollection 2015.

17.

Three Dimensional Organization of the Nucleus: adding DNA sequences to the big picture.

Gilbert DM, Fraser P.

Genome Biol. 2015 Aug 29;16:181. doi: 10.1186/s13059-015-0751-9. No abstract available.

18.

Many paths lead chromatin to the nuclear periphery.

Gordon MR, Pope BD, Sima J, Gilbert DM.

Bioessays. 2015 Aug;37(8):862-6. doi: 10.1002/bies.201500034. Epub 2015 Jun 8. Review.

19.

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.

20.

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program.

Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM.

Genome Res. 2015 Aug;25(8):1104-13. doi: 10.1101/gr.183699.114. Epub 2015 May 20.

21.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS.

Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12.

22.

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.

23.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

24.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

25.

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.

26.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

27.

Genetics: Up and down in Down's syndrome.

Pope BD, Gilbert DM.

Nature. 2014 Apr 17;508(7496):323-4. doi: 10.1038/508323a. No abstract available.

PMID:
24740061
28.

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.

29.

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.

30.

Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains.

Takebayashi S, Lei I, Ryba T, Sasaki T, Dileep V, Battaglia D, Gao X, Fang P, Fan Y, Esteban MA, Tang J, Crabtree GR, Wang Z, Gilbert DM.

Epigenetics Chromatin. 2013 Dec 13;6(1):42. doi: 10.1186/1756-8935-6-42.

31.

DNA replication timing.

Rhind N, Gilbert DM.

Cold Spring Harb Perspect Biol. 2013 Aug 1;5(8):a010132. doi: 10.1101/cshperspect.a010132. Review.

32.

Low-cost fabrication of centimetre-scale periodic arrays of single plasmid DNA molecules.

Kirkland B, Wang Z, Zhang P, Takebayashi S, Lenhert S, Gilbert DM, Guan J.

Lab Chip. 2013 Sep 7;13(17):3367-72. doi: 10.1039/c3lc50562f. Epub 2013 Jul 4.

33.

The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture.

Pope BD, Gilbert DM.

J Mol Biol. 2013 Nov 29;425(23):4690-5. doi: 10.1016/j.jmb.2013.04.014. Epub 2013 Apr 17. Review.

34.

SnapShot: Replication timing.

Pope BD, Aparicio OM, Gilbert DM.

Cell. 2013 Mar 14;152(6):1390-1390.e1. doi: 10.1016/j.cell.2013.02.038. No abstract available.

35.

Development of a single-cell array for large-scale DNA fluorescence in situ hybridization.

Liu Y, Kirkland B, Shirley J, Wang Z, Zhang P, Stembridge J, Wong W, Takebayashi S, Gilbert DM, Lenhert S, Guan J.

Lab Chip. 2013 Apr 7;13(7):1316-24. doi: 10.1039/c2lc40364a.

36.

A trial of scheduled deep brain stimulation for Tourette syndrome: moving away from continuous deep brain stimulation paradigms.

Okun MS, Foote KD, Wu SS, Ward HE, Bowers D, Rodriguez RL, Malaty IA, Goodman WK, Gilbert DM, Walker HC, Mink JW, Merritt S, Morishita T, Sanchez JC.

JAMA Neurol. 2013 Jan;70(1):85-94. doi: 10.1001/jamaneurol.2013.580.

PMID:
23044532
37.

Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding.

Takebayashi S, Ryba T, Gilbert DM.

Nucleus. 2012 Nov-Dec;3(6):500-7. doi: 10.4161/nucl.22318. Epub 2012 Sep 28.

38.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

39.

Replication origins run (ultra) deep.

Gilbert DM.

Nat Struct Mol Biol. 2012 Aug;19(8):740-2. doi: 10.1038/nsmb.2352. No abstract available.

PMID:
22864361
40.

Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells.

Cornacchia D, Dileep V, Quivy JP, Foti R, Tili F, Santarella-Mellwig R, Antony C, Almouzni G, Gilbert DM, Buonomo SB.

EMBO J. 2012 Sep 12;31(18):3678-90. doi: 10.1038/emboj.2012.214. Epub 2012 Jul 31.

41.

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding.

Takebayashi S, Dileep V, Ryba T, Dennis JH, Gilbert DM.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12574-9. doi: 10.1073/pnas.1207185109. Epub 2012 Jul 17.

42.

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.

Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M.

Mol Cell. 2012 Jul 27;47(2):203-14. doi: 10.1016/j.molcel.2012.06.010. Epub 2012 Jul 12.

43.

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse.

Pope BD, Chandra T, Buckley Q, Hoare M, Ryba T, Wiseman FK, Kuta A, Wilson MD, Odom DT, Gilbert DM.

Hum Mol Genet. 2012 Oct 1;21(19):4162-70. doi: 10.1093/hmg/dds232. Epub 2012 Jun 26.

44.

Genome-wide analysis of replication timing in mammalian cells: troubleshooting problems encountered when comparing different cell types.

Dileep V, Didier R, Gilbert DM.

Methods. 2012 Jun;57(2):165-9. doi: 10.1016/j.ymeth.2012.05.009. Epub 2012 Jun 6.

45.

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia.

Ryba T, Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM.

Genome Res. 2012 Oct;22(10):1833-44. doi: 10.1101/gr.138511.112. Epub 2012 May 24.

46.

Productive hepatitis C virus infection of stem cell-derived hepatocytes reveals a critical transition to viral permissiveness during differentiation.

Wu X, Robotham JM, Lee E, Dalton S, Kneteman NM, Gilbert DM, Tang H.

PLoS Pathog. 2012;8(4):e1002617. doi: 10.1371/journal.ppat.1002617. Epub 2012 Apr 5.

47.

Microfluidic extraction and stretching of chromosomal DNA from single cell nuclei for DNA fluorescence in situ hybridization.

Wang X, Takebayashi S, Bernardin E, Gilbert DM, Chella R, Guan J.

Biomed Microdevices. 2012 Jun;14(3):443-51. doi: 10.1007/s10544-011-9621-8.

48.

DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy.

Pope BD, Tsumagari K, Battaglia D, Ryba T, Hiratani I, Ehrlich M, Gilbert DM.

PLoS One. 2011;6(11):e27413. doi: 10.1371/journal.pone.0027413. Epub 2011 Nov 11. Erratum in: PLoS One. 2012;7(1):doi/10.1371/annotation/4fc6a867-640c-4454-ac3b-eb8a386d0ec4.

49.

Replication timing: a fingerprint for cell identity and pluripotency.

Ryba T, Hiratani I, Sasaki T, Battaglia D, Kulik M, Zhang J, Dalton S, Gilbert DM.

PLoS Comput Biol. 2011 Oct;7(10):e1002225. doi: 10.1371/journal.pcbi.1002225. Epub 2011 Oct 20.

50.

Evidence for a mammalian late-G1 phase inhibitor of replication licensing distinct from geminin or Cdk activity.

Sasaki T, Li A, Gillespie PJ, Blow JJ, Gilbert DM.

Nucleus. 2011 Sep-Oct;2(5):455-64. doi: 10.4161/nucl.2.5.17859. Epub 2011 Sep 1.

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