QNet: A Tool for Querying Protein Interaction Networks. - Banu Dost; Tomer Shlomi; Nitin Gupta 002; Eytan Ruppin; Vineet Bafna; Roded Sharan (J. Comput. Biol., 2008)

Structural Alignment of Pseudoknotted RNA. - Buhm Han; Banu Dost; Vineet Bafna; Shaojie Zhang 001 (J. Comput. Biol., 2008)

Shared Peptides in Mass Spectrometry Based Protein Quantification. - Banu Dost; Nuno Bandeira; Xiangqian Li; Zhouxin Shen; Steve Briggs; Vineet Bafna (RECOMB, 2009)

Optimization algorithms for biological data. - Banu Dost (2010)

TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. - Banu Dost; Chunlei Wu; Andrew I. Su; Vineet Bafna (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. - Banu Dost; Nuno Bandeira; Xiangqian Li; Zhouxin Shen; Steve Briggs; Vineet Bafna (J. Comput. Biol., 2012)