Predicting Human Nucleosome Occupancy from Primary Sequence. - Shobhit Gupta; Jonathan H. Dennis; Robert E. Thurman; Robert E. Kingston; John A. Stamatoyannopoulos; William Stafford Noble (PLoS Comput. Biol., 2008)

A computational exploration of gene regulation by nucleosome position. - Justin A. Fincher; Gary S. Tyson; Jonathan H. Dennis (BCB, 2010)

DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoost. - Yu Zhang; Xiuwen Liu; Justin A. Fincher; Jonathan H. Dennis (BCB, 2010)

Joint clustering and alignment for nucleosome occupancy analysis. - Teng L. Liu; Yu Zhang; Jonathan H. Dennis (BIBM Workshops, 2012)

One-base-pair localization of nucleosomes. - Xiuwen Liu; Yu Zhang; Teng L. Liu; Jonathan H. Dennis (BIBM Workshops, 2012)

Quantitative models for statistical nucleosome occupancy prediction. - Yu Zhang; Xiuwen Liu; Jonathan H. Dennis (BIBM Workshops, 2012)

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)

iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. - Senthil B. Girimurugan; Yuhang Liu; Pei-Yau Lung; Daniel L. Vera; Jonathan H. Dennis; Hank W. Bass; Jinfeng Zhang (BMC Bioinform., 2018)