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 Jun 14;189(6):967-80. Epub 2010 Jun 7.

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 Feb;20(2):155-69. Epub 2009 Dec 1.

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 U S A. 2009 Nov 17;106(46):19363-8.

Ichiro Hiratani, Tyrone Ryba, Mari Itoh, Tomoki Yokochi, Michaela Schwaiger, Chia-Wei Chang, Yung Lyou, Tim M. Townes, Dirk Sch\xfcbeler, David M. Gilbert, "Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation," PLoS Biology (2008) 6:e245

Publication on www.plosbiology.org

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: 771-780. 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) 23:589-601.

HUMAN

Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz T, Robins A, Dalton S, Gilbert DM. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 2010 20: 155-169. PMID: 20430782

PROTOCOL