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

FISH Finder: a high-throughput tool for analyzing FISH images. - James W. Shirley; Sereyvathana Ty; Shin-ichiro Takebayashi; Xiuwen Liu; David M. Gilbert (Bioinform., 2011)

Replication Timing: A Fingerprint for Cell Identity and Pluripotency. - Tyrone Ryba; Ichiro Hiratani; Takayo Sasaki; Dana Battaglia; Michael Kulik; Jinfeng Zhang; Stephen Dalton; David M. Gilbert (PLoS Comput. Biol., 2011)

Topologically associating domains are stable units of replication-timing regulation Open. - Benjamin D. Pope; Tyrone Ryba; Vishnu Dileep; Feng Yue; Wei-Sheng Wu; Olgert Denas; Daniel L. Vera; Yanli Wang; R. Scott Hansen; Theresa K. Canfield; Robert E. Thurman; Yong Cheng; et al. (Nat., 2014)

Computing interaction probabilities in signaling networks. - Haitham Gabr; Juan Carlos Rivera-Mulia; David M. Gilbert; Tamer Kahveci (EURASIP J. Bioinform. Syst. Biol., 2015)

Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. - Yang Yang 094; Quanquan Gu; Takayo Sasaki; Julianna Crivello; Rachel O'Neill; David M. Gilbert; Jian Ma 004 (RECOMB, 2018)

RT States: systematic annotation of the human genome using cell type-specific replication timing programs. - Axel Poulet; Ben Li; Tristan Dubos; Juan Carlos Rivera-Mulia; David M. Gilbert; Zhaohui S. Qin (Bioinform., 2019)

Statistical Comparisons Of Chromosomal Shape Populations. - Carlos J. Soto 002; Peiyao A. Zhao; Kyle N. Klein; David M. Gilbert; Anuj Srivastava (ISBI, 2021)