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Items: 42

1.

Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins.

Zhang H, Petrie MV, He Y, Peace JM, Chiolo IE, Aparicio OM.

Elife. 2019 May 14;8. pii: e45512. doi: 10.7554/eLife.45512.

2.

Identification of Fkh1 and Fkh2 binding site variants associated with dynamically bound DNA elements including replication origins.

Ostrow AZ, Aparicio OM.

Nucleus. 2017 Nov 2;8(6):600-604. doi: 10.1080/19491034.2017.1380139. Epub 2017 Nov 13.

3.

Quantitative Bromodeoxyuridine Immunoprecipitation Analyzed by High-Throughput Sequencing (qBrdU-Seq or QBU).

Haye-Bertolozzi JE, Aparicio OM.

Methods Mol Biol. 2018;1672:209-225. doi: 10.1007/978-1-4939-7306-4_16.

PMID:
29043627
4.

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data.

Liu Z, Lou H, Xie K, Wang H, Chen N, Aparicio OM, Zhang MQ, Jiang R, Chen T.

Nat Commun. 2017 Jun 19;8(1):22. doi: 10.1038/s41467-017-00039-z.

5.

Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae.

Ostrow AZ, Kalhor R, Gan Y, Villwock SK, Linke C, Barberis M, Chen L, Aparicio OM.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2411-E2419. doi: 10.1073/pnas.1612422114. Epub 2017 Mar 6.

6.

Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase.

Peace JM, Villwock SK, Zeytounian JL, Gan Y, Aparicio OM.

Genome Res. 2016 Mar;26(3):365-75. doi: 10.1101/gr.196857.115. Epub 2016 Jan 4.

7.

ChIP-Seq to Analyze the Binding of Replication Proteins to Chromatin.

Ostrow AZ, Viggiani CJ, Aparicio JG, Aparicio OM.

Methods Mol Biol. 2015;1300:155-68. doi: 10.1007/978-1-4939-2596-4_11.

PMID:
25916712
8.

Two-dimensional agarose gel electrophoresis for analysis of DNA replication.

Villwock SK, Aparicio OM.

Methods Mol Biol. 2014;1205:329-40. doi: 10.1007/978-1-4939-1363-3_19.

PMID:
25213253
9.

Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome.

Peace JM, Ter-Zakarian A, Aparicio OM.

PLoS One. 2014 May 30;9(5):e98501. doi: 10.1371/journal.pone.0098501. eCollection 2014.

10.

Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics.

Ostrow AZ, Nellimoottil T, Knott SR, Fox CA, Tavaré S, Aparicio OM.

PLoS One. 2014 Feb 4;9(2):e87647. doi: 10.1371/journal.pone.0087647. eCollection 2014.

11.

The level of origin firing inversely affects the rate of replication fork progression.

Zhong Y, Nellimoottil T, Peace JM, Knott SR, Villwock SK, Yee JM, Jancuska JM, Rege S, Tecklenburg M, Sclafani RA, Tavaré S, Aparicio OM.

J Cell Biol. 2013 Apr 29;201(3):373-83. doi: 10.1083/jcb.201208060.

12.

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.

13.

Location, location, location: it's all in the timing for replication origins.

Aparicio OM.

Genes Dev. 2013 Jan 15;27(2):117-28. doi: 10.1101/gad.209999.112. Review.

14.

Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.

Knott SR, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM.

Cell. 2012 Jan 20;148(1-2):99-111. doi: 10.1016/j.cell.2011.12.012.

15.

Genome-wide analysis of DNA synthesis by BrdU immunoprecipitation on tiling microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae.

Viggiani CJ, Knott SR, Aparicio OM.

Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5385. doi: 10.1101/pdb.prot5385. No abstract available.

PMID:
20150148
16.

Strategies for analyzing highly enriched IP-chip datasets.

Knott SR, Viggiani CJ, Aparicio OM, Tavaré S.

BMC Bioinformatics. 2009 Sep 22;10:305. doi: 10.1186/1471-2105-10-305.

17.

To promote and protect: coordinating DNA replication and transcription for genome stability.

Knott SR, Viggiani CJ, Aparicio OM.

Epigenetics. 2009 Aug 16;4(6):362-5. Epub 2009 Aug 3. Review.

PMID:
19736523
18.

DNA polymerase epsilon, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator.

Dhillon N, Raab J, Guzzo J, Szyjka SJ, Gangadharan S, Aparicio OM, Andrews B, Kamakaka RT.

EMBO J. 2009 Sep 2;28(17):2583-600. doi: 10.1038/emboj.2009.198. Epub 2009 Jul 23.

19.

ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays.

Viggiani CJ, Aparicio JG, Aparicio OM.

Methods Mol Biol. 2009;521:255-78. doi: 10.1007/978-1-60327-815-7_14.

PMID:
19563111
21.

Yeast telomere capping protein Stn1 overrides DNA replication control through the S phase checkpoint.

Gasparyan HJ, Xu L, Petreaca RC, Rex AE, Small VY, Bhogal NS, Julius JA, Warsi TH, Bachant J, Aparicio OM, Nugent CI.

Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2206-11. doi: 10.1073/pnas.0812605106. Epub 2009 Jan 26.

22.

Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae.

Szyjka SJ, Aparicio JG, Viggiani CJ, Knott S, Xu W, Tavaré S, Aparicio OM.

Genes Dev. 2008 Jul 15;22(14):1906-20. doi: 10.1101/gad.1660408.

23.

Identification of Clb2 residues required for Swe1 regulation of Clb2-Cdc28 in Saccharomyces cerevisiae.

Hu F, Gan Y, Aparicio OM.

Genetics. 2008 Jun;179(2):863-74. doi: 10.1534/genetics.108.086611.

24.

Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage.

O'Neill BM, Szyjka SJ, Lis ET, Bailey AO, Yates JR 3rd, Aparicio OM, Romesberg FE.

Proc Natl Acad Sci U S A. 2007 May 29;104(22):9290-5. Epub 2007 May 21.

25.
27.

Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae.

Gibson DG, Bell SP, Aparicio OM.

Genes Cells. 2006 Jun;11(6):557-73. Erratum in: Genes Cells. 2006 Aug;11(8):969.

28.

H2A.Z functions to regulate progression through the cell cycle.

Dhillon N, Oki M, Szyjka SJ, Aparicio OM, Kamakaka RT.

Mol Cell Biol. 2006 Jan;26(2):489-501.

29.

Mrc1 is required for normal progression of replication forks throughout chromatin in S. cerevisiae.

Szyjka SJ, Viggiani CJ, Aparicio OM.

Mol Cell. 2005 Sep 2;19(5):691-7.

30.
31.

Functional annotation and network reconstruction through cross-platform integration of microarray data.

Zhou XJ, Kao MC, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH.

Nat Biotechnol. 2005 Feb;23(2):238-43. Epub 2005 Jan 16.

PMID:
15654329
32.
33.
34.

Tackling an essential problem in functional proteomics of Saccharomyces cerevisiae.

Aparicio OM.

Genome Biol. 2003;4(10):230. Epub 2003 Sep 24. Review.

35.

Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins.

Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, Young RA, Bell SP, Aparicio OM.

Science. 2001 Dec 14;294(5550):2357-60.

36.

Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication.

Aparicio OM, Stout AM, Bell SP.

Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9130-5.

38.
39.

Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage.

Renauld H, Aparicio OM, Zierath PD, Billington BL, Chhablani SK, Gottschling DE.

Genes Dev. 1993 Jul;7(7A):1133-45.

40.

Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae.

Aparicio OM, Billington BL, Gottschling DE.

Cell. 1991 Sep 20;66(6):1279-87.

PMID:
1913809
41.

Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription.

Gottschling DE, Aparicio OM, Billington BL, Zakian VA.

Cell. 1990 Nov 16;63(4):751-62.

PMID:
2225075
42.

Overproduction and identification of the ftsQ gene product, an essential cell division protein in Escherichia coli K-12.

Storts DR, Aparicio OM, Schoemaker JM, Markovitz A.

J Bacteriol. 1989 Aug;171(8):4290-7.

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