ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. - Wenjie Deng; David C. Nickle; Gerald H. Learn; Brandon Maust; James I. Mullins (Bioinform., 2007)

Coping with Viral Diversity in HIV Vaccine Design. - David C. Nickle; Morgane Rolland; Mark A. Jensen; Sergei L. Kosakovsky Pond; Wenjie Deng; Mark Seligman; David Heckerman; James I. Mullins; Nebojsa Jojic (PLoS Comput. Biol., 2007)

Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. - David C. Nickle; Nebojsa Jojic; David Heckerman; Vladimir Jojic; Darko Kirovski; Morgane Rolland; Sergei L. Kosakovsky Pond; James I. Mullins (PLoS Comput. Biol., 2008)

Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information. - Kai Wang 063; Jeremy A. Horst; Gong Cheng; David C. Nickle; Ram Samudrala (PLoS Comput. Biol., 2008)