A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation. - Yuncong Geng; Christopher Herrick Bohrer; Nicolás Yehya; Hunter Hendrix; Lior I. Shachaf; Jian Liu; Jie Xiao; Elijah Roberts (PLoS Comput. Biol., 2022)

Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM. - Lior I. Shachaf; Elijah Roberts; Patrick Cahan; Jie Xiao (BMC Bioinform., 2023)