Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions. - Nela Zavaljevski; Fred J. Stevens; Jaques Reifman (Bioinform., 2002)

Fold-specific substitution matrices for protein classification. - R. B. Vilim; R. M. Cunningham; B. Lu; P. Kheradpour; Fred J. Stevens (Bioinform., 2004)

Classifying noisy protein sequence data: a case study of immunoglobulin light chains. - Chenggang Yu; Nela Zavaljevski; Fred J. Stevens; Kelly Yackovich; Jaques Reifman (ISMB (Supplement of Bioinformatics), 2005)

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. - Chenggang Yu; Nela Zavaljevski; Valmik Desai; Seth Johnson; Fred J. Stevens; Jaques Reifman (BMC Bioinform., 2008)