RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. - Matan Drory Retwitzer; Maya Polishchuk; Elena Churkin; Ilona Kifer; Zohar Yakhini; Danny Barash (Nucleic Acids Res., 2015)

incaRNAfbinv: a web server for the fragment-based design of RNA sequences. - Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Nucleic Acids Res., 2016)

Design of RNAs: comparing programs for inverse RNA folding. - Alexander Churkin; Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Briefings Bioinform., 2018)

RiboD: a comprehensive database for prokaryotic riboswitches. - Sumit Mukherjee; Sukhen Das Mandal; Nikita Gupta; Matan Drory Retwitzer; Danny Barash; Supratim Sengupta (Bioinform., 2019)

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. - Matan Drory Retwitzer; Vladimir Reinharz; Alexander Churkin; Yann Ponty; Jérôme Waldispühl; Danny Barash (Bioinform., 2020)

A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding. - Sumit Mukherjee; Matan Drory Retwitzer; Sara M. Hubbell; Michelle M. Meyer; Danny Barash (Briefings Bioinform., 2023)