AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization. - Daniel Newkirk; Jacob Biesinger; Alvin Chon; Kyoko Yokomori; Xiaohui Xie (J. Comput. Biol., 2011)

Discovering and mapping chromatin states using a tree hidden Markov model. - Jacob Biesinger; Yuanfeng Wang; Xiaohui Xie (BMC Bioinform., 2013)