Studies that cite OriDB

72. Asymmetry indices for analysis and prediction of replication origins in eukaryotic genomes.

Marie-Claude Marsolier-Kergoat

PLoS ONE (2012), 7(9):e45050

71. Inferring where and when replication initiates from genome-wide replication timing data.

A Baker, B Audit, S C-H Yang, J Bechhoefer, A Arneodo

Phys. Rev. Lett. (2012), 108(26):268101

70. Conservation of replication timing reveals global and local regulation of replication origin activity.

Carolin A Müller, Conrad A Nieduszynski

Genome Res. (2012), 22(10):1953-62

69. Maintaining replication origins in the face of genomic change.

Sara C Di Rienzi, Kimberly C Lindstrom, Tobias Mann, William S Noble, M K Raghuraman, Bonita J Brewer

Genome Res. (2012), 22(10):1940-52

68. Functional centromeres determine the activation time of pericentric origins of DNA replication in Saccharomyces cerevisiae.

Thomas J Pohl, Bonita J Brewer, M K Raghuraman

PLoS Genet. (2012), 8(5):e1002677

67. DNA in 3R: Repair, Replication, and Recombination.

Frédéric Coin, Bernardo Reina-San-Martin, Giuseppina Giglia-Mari, Mark Berneburg

Mol Biol Int (2012), 2012(0):658579

66. Genome-wide identification and characterization of replication origins by deep sequencing.

Jia Xu, Yoshimi Yanagisawa, Alexander M Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, Nicholas Rhind

Genome Biol. (2012), 13(4):R27

65. Structure, replication efficiency and fragility of yeast ARS elements.

Manoj K Dhar, Shelly Sehgal, Sanjana Kaul

Res. Microbiol. (2012), 163(4):243-53

64. DeOri: a database of eukaryotic DNA replication origins.

Feng Gao, Hao Luo, Chun-Ting Zhang

Bioinformatics (2012), 28(11):1551-2

63. Prediction of replication origins by calculating DNA structural properties.

Wei Chen, Pengmian Feng, Hao Lin

FEBS Lett. (2012), 586(6):934-8

62. Forced binding of the origin of replication complex to chromosomal sites in Drosophila S2 cells creates an origin of replication.

Gilles Crevel, Sue Cotterill

J. Cell. Sci. (2012), 125(0):965-72

61. Intrinsic coupling of lagging-strand synthesis to chromatin assembly.

Duncan J Smith, Iestyn Whitehouse

Nature (2012), 483(7390):434-8

60. Optimal placement of origins for DNA replication.

Jens Karschau, J Julian Blow, Alessandro P S de Moura

Phys. Rev. Lett. (2012), 108(5):058101

59. Origin association of sld3, sld7, and cdc45 proteins is a key step for determination of origin-firing timing.

Seiji Tanaka, Ryuichiro Nakato, Yuki Katou, Katsuhiko Shirahige, Hiroyuki Araki

Curr. Biol. (2011), 21(24):2055-63

58. OriDB, the DNA replication origin database updated and extended.

Cheuk C Siow, Sian R Nieduszynska, Carolin A Müller, Conrad A Nieduszynski

Nucleic Acids Res. (2011), 40(Database issue):D682-6

57. Databases and bioinformatics tools for the study of DNA repair.

Kaja Milanowska, Kristian Rother, Janusz M Bujnicki

Mol Biol Int (2011), 2011(0):475718

56. Do replication forks control late origin firing in Saccharomyces cerevisiae?

Emilie Ma, Olivier Hyrien, Arach Goldar

Nucleic Acids Res. (2011), 40(5):2010-9

55. Comparative analysis of the molecular mechanisms controlling the initiation of chromosomal DNA replication in yeast and in mammalian cells.

Elena Sacco, Md Mehedi Hasan, Lilia Alberghina, Marco Vanoni

Biotechnol. Adv. (2011), 30(1):73-98

54. DNA replication induces compositional biases in yeast.

Marie-Claude Marsolier-Kergoat, Arach Goldar

Mol. Biol. Evol. (2011), 29(3):893-904

53. Dynamics of DNA replication in yeast.

Renata Retkute, Conrad A Nieduszynski, Alessandro de Moura

Phys. Rev. Lett. (2011), 107(6):068103

52. Initiation of DNA replication: functional and evolutionary aspects.

John A Bryant, Stephen J Aves

Ann. Bot. (2011), 107(7):1119-26

51. The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation.

Hui-Yong Lian, E Douglas Robertson, Shin-ichiro Hiraga, Gina M Alvino, David Collingwood, Heather J McCune, Akila Sridhar, Bonita J Brewer, M K Raghuraman, Anne D Donaldson

Mol. Biol. Cell (2011), 22(10):1753-65

50. Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae.

Laurent Chatre, Miria Ricchetti

PLoS ONE (2011), 6(3):e17235

49. Nucleosomes in the neighborhood: new roles for chromatin modifications in replication origin control.

Elizabeth Suzanne Dorn, Jeanette Gowen Cook

Epigenetics (2011), 6(5):552-9

48. From sequence to function: Insights from natural variation in budding yeasts.

Conrad A Nieduszynski, Gianni Liti

Biochim. Biophys. Acta (2011), 1810(10):959-66

47. Replication origins and timing of temporal replication in budding yeast: how to solve the conundrum?

Matteo Barberis, Thomas W Spiesser, Edda Klipp

Curr. Genomics (2010), 11(3):199-211

46. Analysis of replication profiles reveals key role of RFC-Ctf18 in yeast replication stress response.

Laure Crabbé, Aubin Thomas, Véronique Pantesco, John De Vos, Philippe Pasero, Armelle Lengronne

Nat. Struct. Mol. Biol. (2010), 17(11):1391-7

45. Relicensing of transcriptionally inactivated replication origins in budding yeast.

Marko Lõoke, Jüri Reimand, Tiina Sedman, Juhan Sedman, Lari Järvinen, Signe Värv, Kadri Peil, Kersti Kristjuhan, Jaak Vilo, Arnold Kristjuhan

J. Biol. Chem. (2010), 285(51):40004-11

44. Genome-wide model for the normal eukaryotic DNA replication fork.

Andres A Larrea, Scott A Lujan, Stephanie A Nick McElhinny, Piotr A Mieczkowski, Michael A Resnick, Dmitry A Gordenin, Thomas A Kunkel

Proc. Natl. Acad. Sci. U.S.A. (2010), 107(41):17674-9

43. Gene-specific RNA polymerase II phosphorylation and the CTD code.

Hyunmin Kim, Benjamin Erickson, Weifei Luo, David Seward, Joel H Graber, David D Pollock, Paul C Megee, David L Bentley

Nat. Struct. Mol. Biol. (2010), 17(10):1279-86

42. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure.

Nicolas M Berbenetz, Corey Nislow, Grant W Brown

PLoS Genet. (2010), 6(9):

41. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing.

Scott Cheng-Hsin Yang, Nicholas Rhind, John Bechhoefer

Mol. Syst. Biol. (2010), 6(0):404

40. Confidently estimating the number of DNA replication origins.

Anand Bhaskar, Uri Keich

Stat Appl Genet Mol Biol (2010), 9(1):Article28

39. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

John A Capra, Katrin Paeschke, Mona Singh, Virginia A Zakian

PLoS Comput. Biol. (2010), 6(7):e1000861

38. Replication stress checkpoint signaling controls tRNA gene transcription.

Vesna C Nguyen, Brett W Clelland, Darren J Hockman, Sonya L Kujat-Choy, Holly E Mewhort, Michael C Schultz

Nat. Struct. Mol. Biol. (2010), 17(8):976-81

37. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin.

Philipp Müller, Sookhee Park, Erika Shor, Dana J Huebert, Christopher L Warren, Aseem Z Ansari, Michael Weinreich, Matthew L Eaton, David M MacAlpine, Catherine A Fox

Genes Dev. (2010), 24(13):1418-33

36. 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), 6(5):e1000946

35. Mathematical modelling of whole chromosome replication.

Alessandro P S de Moura, Renata Retkute, Michelle Hawkins, Conrad A Nieduszynski

Nucleic Acids Res. (2010), 38(17):5623-33

34. Fragile genomic sites are associated with origins of replication.

Sara C Di Rienzi, David Collingwood, M K Raghuraman, Bonita J Brewer

Genome Biol Evol (2009), 1(0):350-63

33. GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.

Matthew D Sekedat, David Fenyö, Richard S Rogers, Alan J Tackett, John D Aitchison, Brian T Chait

Mol. Syst. Biol. (2010), 6(0):353

32. Mathematical modelling of eukaryotic DNA replication.

Olivier Hyrien, Arach Goldar

Chromosome Res. (2010), 18(1):147-61

31. Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX.

Rachel K Szilard, Pierre-Etienne Jacques, Louise Laramée, Benjamin Cheng, Sarah Galicia, Alain R Bataille, ManTek Yeung, Megan Mendez, Maxime Bergeron, François Robert, Daniel Durocher

Nat. Struct. Mol. Biol. (2010), 17(3):299-305

30. Defining replication origin efficiency using DNA fiber assays.

Sandie Tuduri, Hélène Tourrière, Philippe Pasero

Chromosome Res. (2010), 18(1):91-102

29. The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication.

Erika Shor, Christopher L Warren, Joshua Tietjen, Zhonggang Hou, Ulrika Müller, Ilaria Alborelli, Florence H Gohard, Adrian I Yemm, Lev Borisov, James R Broach, Michael Weinreich, Conrad A Nieduszynski, Aseem Z Ansari, Catherine A Fox

PLoS Genet. (2009), 5(12):e1000755

28. Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression.

Larsson Omberg, Joel R Meyerson, Kayta Kobayashi, Lucy S Drury, John F X Diffley, Orly Alter

Mol. Syst. Biol. (2009), 5(0):312

27. Strategies for analyzing highly enriched IP-chip datasets.

Simon R V Knott, Christopher J Viggiani, Oscar M Aparicio, Simon Tavaré

BMC Bioinformatics (2009), 10(0):305

26. The S-phase checkpoint is required to respond to R-loops accumulated in THO mutants.

Belén Gómez-González, Irene Felipe-Abrio, Andrés Aguilera

Mol. Cell. Biol. (2009), 29(19):5203-13

25. Hidden chromosome symmetry: in silico transformation reveals symmetry in 2D DNA walk trajectories of 671 chromosomes.

Maria S Poptsova, Sergei A Larionov, Eugeny V Ryadchenko, Sergei D Rybalko, Ilya A Zakharov, Alexander Loskutov

PLoS ONE (2009), 4(7):e6396

24. Detection of replication origins using comparative genomics and recombinational ARS assay.

Conrad A Nieduszynski, Anne D Donaldson

Methods Mol. Biol. (2009), 521(0):295-313

23. H3 k36 methylation helps determine the timing of cdc45 association with replication origins.

Fiona Pryde, Devanshi Jain, Alastair Kerr, Rebecca Curley, Francesca Romana Mariotti, Maria Vogelauer

PLoS ONE (2009), 4(6):e5882

22. Physical signals for protein-DNA recognition.

Xiao-Qin Cao, Jia Zeng, Hong Yan

Phys Biol (2009), 6(3):036012

21. The impact of nucleosome positioning on the organization of replication origins in eukaryotes.

Shanye Yin, Wenjun Deng, Landian Hu, Xiangyin Kong

Biochem. Biophys. Res. Commun. (2009), 385(3):363-8

20. Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.

Jonathan L Gordon, Kevin P Byrne, Kenneth H Wolfe

PLoS Genet. (2009), 5(5):e1000485

19. Factoring local sequence composition in motif significance analysis.

Patrick Ng, Uri Keich

Genome Inform (2008), 21(0):15-26

18. Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae.

Simon R V Knott, Christopher J Viggiani, Simon Tavaré, Oscar M Aparicio

Genes Dev. (2009), 23(9):1077-90

17. A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae.

T W Spiesser, E Klipp, Matteo Barberis

Mol. Genet. Genomics (2009), 282(1):25-35

16. The functional role of S/MARs in episomal vectors as defined by the stress-induced destabilization profile of the vector sequences.

Aristeidis Giannakopoulos, Eleana F Stavrou, Ioannis Zarkadis, Nicholas Zoumbos, Adrian J Thrasher, Aglaia Athanassiadou

J. Mol. Biol. (2009), 387(5):1239-49

15. Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair.

Hyun-Min Kim, Vidhya Narayanan, Piotr A Mieczkowski, Thomas D Petes, Maria M Krasilnikova, Sergei M Mirkin, Kirill S Lobachev

EMBO J. (2008), 27(21):2896-906

14. The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae.

Heather J McCune, Laura S Danielson, Gina M Alvino, David Collingwood, Jeffrey J Delrow, Walton L Fangman, Bonita J Brewer, M K Raghuraman

Genetics (2008), 180(4):1833-47

13. 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(0):372

12. Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating-type switching in Saccharomyces cerevisiae.

Amy M Lyndaker, Tamara Goldfarb, Eric Alani

Genetics (2008), 179(4):1807-21

11. 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), 28(16):5071-81

10. Division of labor at the eukaryotic replication fork.

Stephanie A Nick McElhinny, Dmitry A Gordenin, Carrie M Stith, Peter M J Burgers, Thomas A Kunkel

Mol. Cell (2008), 30(2):137-44

9. ATP-dependent chromatin remodeling shapes the DNA replication landscape.

Jack A Vincent, Tracey J Kwong, Toshio Tsukiyama

Nat. Struct. Mol. Biol. (2008), 15(5):477-84

8. Ino80 chromatin remodeling complex promotes recovery of stalled replication forks.

Kenji Shimada, Yukako Oma, Thomas Schleker, Kazuto Kugou, Kunihiro Ohta, Masahiko Harata, Susan M Gasser

Curr. Biol. (2008), 18(8):566-75

7. Chromosome evolution with naked eye: palindromic context of the life origin.

Sergei Larionov, Alexander Loskutov, Eugeny Ryadchenko

Chaos (2008), 18(1):013105

6. Regulation of rtt107 recruitment to stalled DNA replication forks by the cullin rtt101 and the rtt109 acetyltransferase.

Tania M Roberts, Iram Waris Zaidi, Jessica A Vaisica, Matthias Peter, Grant W Brown

Mol. Biol. Cell (2007), 19(1):171-80

5. Identification of mutations that decrease the stability of a fragment of Saccharomyces cerevisiae chromosome III lacking efficient replicators.

James F Theis, Ann Dershowitz, Carmela Irene, Clelia Maciariello, Michael L Tobin, Giordano Liberi, Sahba Tabrizifard, Malgorzata Korus, Lucia Fabiani, Carol S Newlon

Genetics (2007), 177(3):1445-58

4. Cell cycle regulation of DNA replication.

R A Sclafani, T M Holzen

Annu. Rev. Genet. (2007), 41(0):237-80

3. Enhanced expression of EGFP gene in CHSE-214 cells by an ARS element from mud loach (Misgurnus mizolepis).

Moo-Sang Kim, Hak-Seob Lim, Sang Jung Ahn, Yong-Kee Jeong, Chul Geun Kim, Hyung Ho Lee

Plasmid (2007), 58(3):228-39

2. Linear derivatives of Saccharomyces cerevisiae chromosome III can be maintained in the absence of autonomously replicating sequence elements.

Ann Dershowitz, Marylynn Snyder, Mohammed Sbia, Joan H Skurnick, Loke Y Ong, Carol S Newlon

Mol. Cell. Biol. (2007), 27(13):4652-63

1. 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(0):276