Constrained RNA Structural Alignment: Algorithms and Application to Motif Detection in the Untranslated Regions of Trypanosoma brucei mRNAs. - Mugdha Khaladkar; Vivian Bellofatto; Jason Tsong-Li Wang; Vandanaben Patel; Marvin K. Nakayama (BIBE, 2007)

Detecting conserved secondary structures in RNA molecules using constrained structural alignment. - Mugdha Khaladkar; Vandanaben Patel; Vivian Bellofatto; Jeffrey Wilusz; Jason Tsong-Li Wang (Comput. Biol. Chem., 2008)

On Comparing Two Structured RNA Multiple alignments. - Vandanaben Patel; Jason T. L. Wang; Shefali Setia; Anurag Verma; Charles D. Warden; Kaizhong Zhang (J. Bioinform. Comput. Biol., 2010)