Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding. - Joshua S. Martin; Katrina Simmons; Alain Laederach (Algorithms, 2009)

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation. - Justin Ritz; Joshua S. Martin; Alain Laederach (PLoS Comput. Biol., 2013)

Describing the Structural Diversity within an RNA's Ensemble. - Joshua S. Martin (Entropy, 2014)

HUGIn: Hi-C Unifying Genomic Interrogator. - Joshua S. Martin; Zheng Xu 010; Alex P. Reiner; Karen L. Mohlke; Patrick F. Sullivan; Bing Ren; Ming Hu 001; Yun Li (Bioinform., 2017)