Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians. - Heinz Sklenar; Daniel Wüstner; Remo Rohs (J. Comput. Chem., 2006)

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. - Tianyin Zhou; Lin Yang; Yan Lu 003; Iris Dror; Ana Carolina Dantas Machado; Tahereh Ghane; Rosa Di Felice; Remo Rohs (Nucleic Acids Res., 2013)

NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. - Lin Yang; Tianyin Zhou; Iris Dror; Anthony Mathelier; Wyeth W. Wasserman; Raluca Gordân; Remo Rohs (Nucleic Acids Res., 2014)

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)

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. - Wenxiu Ma; Lin Yang; Remo Rohs; William Stafford Noble (Bioinform., 2017)

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. - Jared M. Sagendorf; Helen M. Berman; Remo Rohs (Nucleic Acids Res., 2017)

Deep Graph Embedding for Ranking Optimization in E-commerce. - Chen Chu; Zhao Li 007; Beibei Xin; Fengchao Peng; Chuanren Liu; Remo Rohs; Qiong Luo 001; Jingren Zhou 001 (CIKM, 2018)

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)

DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes. - Jared M. Sagendorf; Nicholas Markarian; Helen M. Berman; 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)

Structure-Based Drug Design with a Deep Hierarchical Generative Model. - Jesse A. Weller; Remo Rohs (J. Chem. Inf. Model., 2024)