CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations. - Quentin R. Johnson; Richard J. Lindsay; Tongye Shen (J. Comput. Chem., 2018)

Regulatory Mechanics of Constitutive Androstane Receptors: Basal and Ligand-Directed Actions. - Bill Pham; Avery Bancroft Arons; Jeremy G. Vincent; Elias J. Fernandez; Tongye Shen (J. Chem. Inf. Model., 2019)

Inferring chromosome radial organization from Hi-C data. - Priyojit Das; Tongye Shen; Rachel Patton McCord (BMC Bioinform., 2020)

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment. - Priyojit Das; Tongye Shen; Rachel Patton McCord (PLoS Comput. Biol., 2022)