RNApasta: a tool for analysis of RNA structural alignments. - Russell L. Malmberg; Timothy I. Shaw; Liming Cai (Int. J. Bioinform. Res. Appl., 2010)

Analyzing Modular RNA Structure reveals Low Global Structural Entropy in microRNA Sequence. - Timothy I. Shaw; Amir Manzour; Yingfeng Wang; Russell L. Malmberg; Liming Cai (J. Bioinform. Comput. Biol., 2011)

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds. - Yingfeng Wang; Amir Manzour; Pooya Shareghi; Timothy I. Shaw; Ying-Wai Li; Russell L. Malmberg; Liming Cai (BMC Bioinform., 2012)

STRAW: Species TRee Analysis Web server. - Timothy I. Shaw; Zheng Ruan; Travis C. Glenn; Liang Liu (Nucleic Acids Res., 2013)

HIV N-linked glycosylation site analyzer and its further usage in anchored alignment. - Timothy I. Shaw; Ming Zhang (Nucleic Acids Res., 2013)

PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. - Alyssa N. Obermayer; Darwin Chang; Gabrielle Nobles; Mingxiang Teng; Aik Choon Tan; Xuefeng Wang; Y. Ann Chen; Steven Eschrich; Paulo C. Rodriguez; G. Daniel Grass; Soheil Meshinchi; Ahmad Tarhini; et al. (BMC Bioinform., 2023)

An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. - Xiang Liu; Nancy Gillis; Chang Jiang; Anthony McCofie; Timothy I. Shaw; Aik Choon Tan; Bo Zhao; Lixin Wan; Derek R. Duckett; Mingxiang Teng (PLoS Comput. Biol., 2024)