Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs. - Assaf Avihoo; Nir Dromi; Danny Barash (CSB, 2004)

Temperature and Mutation Switches in the Secondary Structure of Small RNAs. - Assaf Avihoo; Danny Barash (CSB Workshops, 2005)

An image processing approach to computing distances between RNA secondary structures dot plots. - Tor Ivry; Shahar Michal; Assaf Avihoo; Guillermo Sapiro; Danny Barash (Algorithms Mol. Biol., 2009)

RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. - Assaf Avihoo; Alexander Churkin; Danny Barash (BMC Bioinform., 2011)

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. - Lina Weinbrand; Assaf Avihoo; Danny Barash (Bioinform., 2013)