BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. - Tien-ho Lin; Pradipta Ray; Geir Kjetil Sandve; Selen Uguroglu; Eric P. Xing (RECOMB, 2008)

CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing. - Pradipta Ray; Suyash Shringarpure; Mladen Kolar; Eric P. Xing (PLoS Comput. Biol., 2008)

DISCOVER: a feature-based discriminative method for motif search in complex genomes. - Wenjie Fu 002; Pradipta Ray; Eric P. Xing (Bioinform., 2009)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. - Milos Pavlovic; Pradipta Ray; Kristina Pavlovic; Aaron Kotamarti; Min Chen 014; Michael Q. Zhang (Bioinform., 2017)