XRate: a fast prototyping, training and annotation tool for phylo-grammars. - Peter S. Klosterman; Andrew V. Uzilov; Yuri R. Bendaña; Robert K. Bradley; Sharon Chao; Carolin Kosiol; Nick Goldman; Ian H. Holmes (BMC Bioinform., 2006)

Transducers: an emerging probabilistic framework for modeling indels on trees. - Robert K. Bradley; Ian H. Holmes (Bioinform., 2007)

Specific alignment of structured RNA: stochastic grammars and sequence annealing. - Robert K. Bradley; Lior Pachter; Ian H. Holmes (Bioinform., 2008)

Evolutionary Triplet Models of Structured RNA. - Robert K. Bradley; Ian H. Holmes (PLoS Comput. Biol., 2009)

Fast Statistical Alignment. - Robert K. Bradley; Adam Roberts; Michael E. Smoot; Sudeep Juvekar; Jaeyoung Do; Colin N. Dewey; Ian H. Holmes; Lior Pachter (PLoS Comput. Biol., 2009)