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Shang WH, Hori T, Martins NM, Toyoda A, Misu S, Monma N, Hiratani I, Maeshima K, Ikeo K, Fujiyama A, Kimura H, Earnshaw WC, Fukagawa T.
Chromosome engineering allows the efficient isolation of vertebrate neocentromeres.
Developmental Cell 24:635-648 (2013)
[PubMed] [Developmental Cell] [ReplicationDomain]

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 6:e27413 (2011)
[PubMed] [PLoS One] [ReplicationDomain] [PDF]

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 Computational Biology 7:e1002225 (2011)
[PubMed] [PLoS Computational Biology] [ReplicationDomain] [PDF]

Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM.
Genome-scale analysis of replication timing: from bench to bioinformatics.
Nature Protocols 6:870-895 (2011)
[PubMed] [Nature Protocols] [PMC version PDF]

Hiratani I, Gilbert DM.
Autosomal lyonization of replication domains during early mammalian development. In: The Cell Biology of Stem Cells. Landes Bioscience and Springer (edited by Eran Meshorer and Kathrin Plath).
Advances in Experimental Medicine and Biology 695:41-58 (2010) [Review]
[PubMed] [Advances in Experimental Medicine and Biology] [PDF]

Gilbert DM, Takebayashi SI, Ryba T, Lu J, Pope BD, Wilson KA, Hiratani I.
Space and time in the nucleus: developmental control of replication timing and chromosome architecture.
Cold Spring Harbor Symposia on Quantitative Biology 75:143-153 (2010) [Review]
[PubMed] [Cold Spring Harbor Symposia on Quantitative Biology]

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 Research 20:761-770 (2010)
[PubMed] [Genome Research] [ReplicationDomain] [PDF]

Pope BD, Hiratani I, Gilbert DM.
Domain-wide regulation of DNA replication timing during mammalian development.
Chromosome Research 18:127-136 (2010) [Review]
[PubMed] [Chromosome Research] [PMC version PDF]

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 Research 20:155-169 (2010)
[PubMed] [Genome Research] [ReplicationDomain] [PDF]

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.
Proceedings of the National Academy of Sciences USA 106:19363-19368 (2009)
[PubMed] [Proceedings of the National Academy of Sciences USA] [ReplicationDomain] [PDF]

Hiratani I, Takebayashi S, Lu J, Gilbert DM.
Replication timing and transcriptional control: beyond cause and effect. Part II.
Current Opinion in Genetics & Development 19:142-149 (2009) [Review]
[PubMed] [Current Opinion in Genetics & Development] [PMC version PDF]

Hiratani I, Gilbert DM.
Replication timing as an epigenetic mark.
Epigenetics 4:93-97 (2009) [Review]
[PubMed] [Epigenetics] [PDF]

Weddington N*, Stuy A*, Hiratani I*, Ryba T, Yokochi T, Gilbert DM. (*Equal Contributions)
ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data.
BMC Bioinformatics 9:530 (2008)
[PubMed] [BMC Bioinformatics] [ReplicationDomain] [PDF]

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 Biology 6:e245 (2008)
[PubMed] [PLoS Biology] [Faculty of 1000] [ReplicationDomain] [PDF]

Hiratani I, Leskovar A, Gilbert DM.
Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores.
Proceedings of the National Academy of Sciences USA 101:16861-16866 (2004)
[PubMed] [Proceedings of the National Academy of Sciences USA] [PDF]

Hiratani I, Yamamoto N, Mochizuki T, Ohmori SY, Taira M.
Selective degradation of excess Ldb1 by Rnf12/RLIM confers proper Ldb1 expression levels and Xlim-1/Ldb1 stoichiometry in Xenopus organizer functions.
Development 130:4161-4175 (2003)
[PubMed] [Development] [PDF]

Hikasa H, Shibata M, Hiratani I, Taira M.
The Xenopus receptor tyrosine kinase Xror2 modulates morphogenetic movements of the axial mesoderm and neuroectoderm via Wnt signaling.
Development 129:5227-5239 (2002)
[PubMed] [Development] [PDF]

Hiratani I, Mochizuki T, Tochimoto N, Taira M.
Functional domains of the LIM homeodomain protein Xlim-1 involved in negative regulation, transactivation, and axis formation in Xenopus embryos.

Developmental Biology 229:456-467 (2001)
[PubMed] [Developmental Biology] [PDF]

Tsuji T, Sato A, Hiratani I, Taira M, Saigo K, Kojima T.
Requirements of Lim1, a Drosophila LIM-homeobox gene, for normal leg and antennal development.
Development 127:4315-4323 (2000)
[PubMed] [Development] [PDF]

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