Improved database searches for orthologous sequences by conditioning on outgroup sequences. - Philip J. Cotter; Daniel R. Caffrey; Denis C. Shields (Bioinform., 2002)

Wrapping up BLAST and other applications for use on Unix clusters. - Karsten Hokamp; Denis C. Shields; Kenneth H. Wolfe; Daniel R. Caffrey (Bioinform., 2003)

PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments. - Daniel R. Caffrey; Paul H. Dana; Vidhya Mathur; Marco Ocano; Eun-Jong Hong; Yaoyu E. Wang; Shyamal Somaroo; Brian E. Caffrey; Shobha Potluri; Enoch S. Huang (BMC Bioinform., 2007)

Prediction of specificity-determining residues for small-molecule kinase inhibitors. - Daniel R. Caffrey; Elizabeth A. Lunney; Deborah J. Moshinsky (BMC Bioinform., 2008)