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Prediction of Saccharomyces cerevisiae replication origins
Adam M Breier, Sourav Chatterji, Nicholas R Cozzarelli
Genome Biol. 2004; 5(4): R22. Published online 2004 March 4.
PMCID:
PMC395781
Abstract Full Text PDF–411K Supplementary Material

Is Cited by the Following 33 Articles in this Archive:

New insights into replication origin characteristics in metazoans
Christelle Cayrou, Philippe Coulombe, Aurore Puy, Stéphanie Rialle, Noam Kaplan, Eran Segal, Marcel Méchali
Cell Cycle. 2012 February 15; 11(4): 658–667. Published online 2012 February 15. doi: 10.4161/cc.11.4.19097
PMCID:
PMC3318102
Abstract Full Text PDF–2.4M
Novel features of ARS selection in budding yeast Lachancea kluyveri
Ivan Liachko, Emi Tanaka, Katherine Cox, Shau Chee Claire Chung, Lu Yang, Arael Seher, Lindsay Hallas, Eugene Cha, Gina Kang, Heather Pace, Jasmine Barrow, Maki Inada, Bik-Kwoon Tye, Uri Keich
BMC Genomics. 2011; 12: 633. Published online 2011 December 28. doi: 10.1186/1471-2164-12-633
PMCID:
PMC3306766
Abstract Full Text PDF–2.5M Supplementary Material
Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
Christelle Cayrou, Philippe Coulombe, Alice Vigneron, Slavica Stanojcic, Olivier Ganier, Isabelle Peiffer, Eric Rivals, Aurore Puy, Sabine Laurent-Chabalier, Romain Desprat, Marcel Méchali
Genome Res. 2011 September; 21(9): 1438–1449. doi: 10.1101/gr.121830.111
PMCID:
PMC3166829
Abstract Full Text PDF–3.3M
Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences
Manuel S. Valenzuela, Yidong Chen, Sean Davis, Fan Yang, Robert L. Walker, Sven Bilke, John Lueders, Melvenia M. Martin, Mirit I. Aladjem, Pierre P. Massion, Paul S. Meltzer
PLoS One. 2011; 6(5): e17308. Published online 2011 May 13. doi: 10.1371/journal.pone.0017308
PMCID:
PMC3094316
Abstract Full Text PDF–2.1M Supplementary Material
High-resolution analysis of four efficient yeast replication origins reveals new insights into the ORC and putative MCM binding elements
FuJung Chang, Caitlin D. May, Timothy Hoggard, Jeremy Miller, Catherine A. Fox, Michael Weinreich
Nucleic Acids Res. 2011 August; 39(15): 6523–6535. Published online 2011 May 9. doi: 10.1093/nar/gkr301
PMCID:
PMC3159467
Abstract Full Text PDF–1.6M Supplementary Material
Defining the replication program through the chromatin landscape
Queying Ding, David M. MacAlpine
Crit Rev Biochem Mol Biol. Author manuscript; available in PMC 2012 April 1.
Published in final edited form as: Crit Rev Biochem Mol Biol. 2011 April; 46(2): 165–179. doi: 10.3109/10409238.2011.560139
PMCID:
PMC3074350
Abstract Full Text PDF–665K
Nuclear Mitochondrial DNA Activates Replication in Saccharomyces cerevisiae
Laurent Chatre, Miria Ricchetti
PLoS One. 2011; 6(3): e17235. Published online 2011 March 8. doi: 10.1371/journal.pone.0017235
PMCID:
PMC3050842
Abstract Full Text PDF–1.0M Supplementary Material
Chromatin signatures of the Drosophila replication program
Matthew L. Eaton, Joseph A. Prinz, Heather K. MacAlpine, George Tretyakov, Peter V. Kharchenko, David M. MacAlpine
Genome Res. 2011 February; 21(2): 164–174. doi: 10.1101/gr.116038.110
PMCID:
PMC3032920
Abstract Full Text PDF–874K
Evaluating genome-scale approaches to eukaryotic DNA replication
David M. Gilbert
Nat Rev Genet. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Nat Rev Genet. 2010 October; 11(10): 673–684. Published online 2010 September 1. doi: 10.1038/nrg2830
PMCID:
PMC2962615
Abstract Full Text PDF–418K
A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome
Ivan Liachko, Anand Bhaskar, Chanmi Lee, Shau Chee Claire Chung, Bik-Kwoon Tye, Uri Keich
PLoS Genet. 2010 May; 6(5): e1000946. Published online 2010 May 13. doi: 10.1371/journal.pgen.1000946
PMCID:
PMC2869322
Abstract Full Text PDF–1.8M Supplementary Material
Conserved nucleosome positioning defines replication origins
Matthew L. Eaton, Kyriaki Galani, Sukhyun Kang, Stephen P. Bell, David M. MacAlpine
Genes Dev. 2010 April 15; 24(8): 748–753. doi: 10.1101/gad.1913210
PMCID:
PMC2854390
Abstract Full Text PDF–630K
Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe
Cristina Cotobal, Mónica Segurado, Francisco Antequera
EMBO J. 2010 March 3; 29(5): 934–942. Published online 2010 January 21. doi: 10.1038/emboj.2009.411
PMCID:
PMC2837175
Abstract Full Text PDF–1.1M Supplementary Material
An ensemble model of competitive multi-factor binding of the genome
Todd Wasson, Alexander J. Hartemink
Genome Res. 2009 November; 19(11): 2101–2112. doi: 10.1101/gr.093450.109
PMCID:
PMC2775586
Abstract Full Text PDF–1.3M
The right half of the Escherichia coli replication origin is not essential for viability, but facilitates multi-forked replication
Nicholas Stepankiw, Akihiro Kaidow, Erik Boye, David Bates
Mol Microbiol. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: Mol Microbiol. 2009 October; 74(2): 467–479. Published online 2009 September 8. doi: 10.1111/j.1365-2958.2009.06877.x
PMCID:
PMC2967437
Abstract Full Text PDF–1.3M Supplementary Material
Subtelomeric ACS-containing Proto-silencers Act as Antisilencers in Replication Factors Mutants in Saccharomyces cerevisiae
Muhammad Attiq Rehman, Dongliang Wang, Genevieve Fourel, Eric Gilson, Krassimir Yankulov
Mol Biol Cell. 2009 January 15; 20(2): 631–641. doi: 10.1091/mbc.E08-01-0099
PMCID:
PMC2626567
Abstract Full Text PDF–612K Supplementary Material
Multiple Mechanisms Contribute to Schizosaccharomyces pombe Origin Recognition Complex-DNA Interactions
Christopher R. Houchens, Wenyan Lu, Ray-Yuan Chuang, Mark G. Frattini, Alex Fuller, Pam Simancek, Thomas J. Kelly
J Biol Chem. 2008 October 31; 283(44): 30216–30224. doi: 10.1074/jbc.M802649200
PMCID:
PMC2573090
Abstract Full Text
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast
Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato, Bik K Tye
BMC Bioinformatics. 2008; 9: 372. Published online 2008 September 12. doi: 10.1186/1471-2105-9-372
PMCID:
PMC2566582
Abstract Full Text PDF–301K
Analysis of Chromosome III Replicators Reveals an Unusual Structure for the ARS318 Silencer Origin and a Conserved WTW Sequence within the Origin Recognition Complex Binding Site
FuJung Chang, James F. Theis, Jeremy Miller, Conrad A. Nieduszynski, Carol S. Newlon, Michael Weinreich
Mol Cell Biol. 2008 August; 28(16): 5071–5081. Published online 2008 June 23. doi: 10.1128/MCB.00206-08
PMCID:
PMC2519699
Abstract Full Text PDF–2.1M Supplementary Material
AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions
David SH Chew, Ming-Ying Leung, Kwok Pui Choi
BMC Bioinformatics. 2007; 8: 163. Published online 2007 May 21. doi: 10.1186/1471-2105-8-163
PMCID:
PMC1904460
Abstract Full Text PDF–382K
Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae
Weihong Xu, Jennifer G Aparicio, Oscar M Aparicio, Simon Tavaré
BMC Genomics. 2006; 7: 276. Published online 2006 October 26. doi: 10.1186/1471-2164-7-276
PMCID:
PMC1657020
Abstract Full Text PDF–1.6M Supplementary Material
The spatial arrangement of ORC binding modules determines the functionality of replication origins in budding yeast
Yung-Tsi Bolon, Anja-Katrin Bielinsky
Nucleic Acids Res. 2006 October; 34(18): 5069–5080. Published online 2006 September 19. doi: 10.1093/nar/gkl661
PMCID:
PMC1635292
Abstract Full Text PDF–491K
Genome-Wide Hierarchy of Replication Origin Usage in Saccharomyces cerevisiae
Justin J Donato, Shau Chee C Chung, Bik K Tye
PLoS Genet. 2006 September; 2(9): e141. Prepublished online 2006 July 25. Published online 2006 September 8. doi: 10.1371/journal.pgen.0020141
PMCID:
PMC1560401
Abstract Full Text PDF–325K Supplementary Material
Asymmetric Positioning of Nucleosomes and Directional Establishment of Transcriptionally Silent Chromatin by Saccharomyces cerevisiae Silencers
Yanfei Zou, Qun Yu, Xin Bi
Mol Cell Biol. 2006 October; 26(20): 7806–7819. Published online 2006 August 14. doi: 10.1128/MCB.01197-06
PMCID:
PMC1636860
Abstract Full Text PDF–661K
Genome-wide identification of replication origins in yeast by comparative genomics
Conrad A. Nieduszynski, Yvonne Knox, Anne D. Donaldson
Genes Dev. 2006 July 15; 20(14): 1874–1879. doi: 10.1101/gad.385306
PMCID:
PMC1522085
Abstract Full Text PDF–437K
Genome-wide Analysis of Re-replication Reveals Inhibitory Controls That Target Multiple Stages of Replication Initiation
Robyn E. Tanny, David M. MacAlpine, Hannah G. Blitzblau, Stephen P. Bell
Mol Biol Cell. 2006 May; 17(5): 2415–2423. doi: 10.1091/mbc.E05-11-1037
PMCID:
PMC1446079
Abstract Full Text PDF–1.6M Supplementary Material
Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses
David S. H. Chew, Kwok Pui Choi, Ming-Ying Leung
Nucleic Acids Res. 2005; 33(15): e134. Published online 2005 September 1. doi: 10.1093/nar/gni135
PMCID:
PMC1197138
Abstract Full Text PDF–282K
Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression
Horst Irlbacher, Jacqueline Franke, Thomas Manke, Martin Vingron, Ann E. Ehrenhofer-Murray
Genes Dev. 2005 August 1; 19(15): 1811–1822. doi: 10.1101/gad.334805
PMCID:
PMC1182343
Abstract Full Text PDF–391K
Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins
Prashanth Ak, Craig J Benham
PLoS Comput Biol. 2005 June; 1(1): e7. Published online 2005 June 24. doi: 10.1371/journal.pcbi.0010007
PMCID:
PMC1183513
Abstract Full Text PDF–238K Supplementary Material
Identification of cis-Acting Elements That Mediate the Replication and Maintenance of Human Papillomavirus Type 16 Genomes in Saccharomyces cerevisiae
Kitai Kim, Peter C. Angeletti, Elizabeth C. Hassebroek, Paul F. Lambert
J Virol. 2005 May; 79(10): 5933–5942. doi: 10.1128/JVI.79.10.5933-5942.2005
PMCID:
PMC1091711
Abstract Full Text PDF–594K
Independence of replisomes in Escherichia coli chromosomal replication
Adam M. Breier, Heinz-Ulrich G. Weier, Nicholas R. Cozzarelli
Proc Natl Acad Sci U S A. 2005 March 15; 102(11): 3942–3947. Published online 2005 February 28. doi: 10.1073/pnas.0500812102
PMCID:
PMC552787
Abstract Full Text PDF–613K Supplementary Material
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