Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes. - Christopher A. Lavender; Robert J. Gorelick; Kevin M. Weeks (PLoS Comput. Biol., 2015)

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA. - Christopher A. Lavender; Ronny Lorenz; Ge Zhang; Rita Tamayo; Ivo L. Hofacker; Kevin M. Weeks (PLoS Comput. Biol., 2015)

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper. - Thomas W. Christy; Catherine A. Giannetti; Alain Laederach; Kevin M. Weeks (PLoS Comput. Biol., 2021)