Less is more: towards an optimal universal description of protein folds. - Joseph D. Szustakowski; Simon Kasif; Zhiping Weng (ECCB/JBI, 2005)

Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks. - Qicheng Ma; Gung-Wei Chirn; Richard Cai; Joseph D. Szustakowski; N. R. Nirmala (BMC Bioinform., 2005)

Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation. - Daniel M. Kemp; N. R. Nirmala; Joseph D. Szustakowski (Bioinform., 2007)

Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles. - Qicheng Ma; Gung-Wei Chirn; Joseph D. Szustakowski; Adel Bakhtiarova; Penelope A. Kosinski; Daniel M. Kemp; Nanguneri Nirmala (BioData Min., 2008)

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data. - Ting Gong; Joseph D. Szustakowski (Bioinform., 2013)