GBshape: a genome browser database for DNA shape annotations. - Tsu-Pei Chiu; Lin Yang; Tianyin Zhou; Bradley J. Main; Stephen C. J. Parker; Sergey V. Nuzhdin; Thomas D. Tullius; Remo Rohs (Nucleic Acids Res., 2015)

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. - Tsu-Pei Chiu; Federico Comoglio; Tianyin Zhou; Lin Yang; Renato Paro; Remo Rohs (Bioinform., 2016)

TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. - Tsu-Pei Chiu; Beibei Xin; Nicholas Markarian; Yingfei Wang; Remo Rohs (Nucleic Acids Res., 2020)

Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics. - Brendon H. Cooper; Tsu-Pei Chiu; Remo Rohs (Bioinform., 2022)