Cite Us

Please either cite the URL (www.replicationdomain.org) or the following manuscript that describes the creation and usage of this web site:

Nodin Weddington*, Alexander Stuy*, Ichiro Hiratani*, Tyrone Ryba, Tomoki Yokochi, and David M. Gilbert, "ReplicationDomain: a visualization tool and comparative database for genome-wide replication-timing data," BMC Bioinformatics (2008) 9:530

Publication on Biomedcentral

Here are the papers describing the data sets displayed in the public domain:

MOUSE

Lu J, Li F, Murphy CS, Davidson MW, Gilbert DM. G2 phase chromatin lacks determinants of replication timing. J Cell Biol. 2010;189(6):967-80. PMID: 20530209

Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 2010;20(2):155-69. PMID: 19952138

Yokochi T, Poduch K, Ryba T, Lu J, Hiratani I, Tachibana M, Shinkai Y, Gilbert DM. G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc Natl Acad Sci USA. 2009;106(46):19363-8. PMID: 19889976

Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schübeler D, Gilbert DM. Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation. PLoS Biol. 2008;6(10):e245. PMID: 18842067

Local Publication

DROSOPHILA

Schwaiger M, Kohler H, Oakeley EJ, Stadler MB, Schübeler D. Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome. Genome Res. 2010;20(6):771-80. PMID: 20435908

Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schübeler D. Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev. 2009;23(5):589-601. PMID: 19270159

HUMAN

Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 2010;20(6):761-70. PMID: 20430782

Pope BD, Tsumagari K, Battaglia D, Ryba T, Hiratani I, Ehrlich M, Gilbert DM. DNA Replication Timing Is Maintained Genome-Wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy. PLoS ONE 2011;6(11):e27413. PMID: 22096571

Ryba T, Hiratani I, Sasaki T, Battaglia D, Kulik M, Zhang J, Dalton S, Gilbert DM. Replication Timing: A Fingerprint for Cell Identity and Pluripotency. PLoS Comput Biol. 2011;7(10):e1002225. PMID: 22028635

PROTOCOL

Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM. Genome-scale analysis of replication timing: from bench to bioinformatics. Nat Protoc. 2011;6(6):870-95. PMID: 21637205

Local Publication

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