Zujun Shentu, Mohammad Hasan, Chris Bystroff, Mohammed J. Zaki Context Shapes: Efficient Complementary Shape Matching for Protein- Protein Docking, accepted for publication in Proteins: Structure, Function and Bioinformatics (forthcoming; in production).

Bystroff C. & Krogh A. (2006) Hidden Markov Models for Prediction of Protein Features, in Protein Structure Prediction: Methods and Protocols 2 nd Ed (Zaki, Bystroff, eds.) (to appear)

Huang Y-M & Bystroff C. (2006). Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions. Bioinformatics 22(4):413-420

Yuan X & Bystroff C. (2005). Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins. Bioinformatics 21(7):1010-1019

Bystroff C, Shao Y & Yuan X. (2004). Five heirarchical levels of sequence-structure correlation in proteins. Applied Bioinformatics 3(2):97-104

Zaki MJ, Nadimpally V, Bardhan D, & Bystroff C. (2004). Predicting Protein Folding Pathways. Bioinformatics 20 Suppl. 1, i387-i393. abstract PDF

Hou Y, Hsu W, Lee ML & Bystroff C. (2004). Remote Homology Detection Using Local Sequence-structure Correlations. Proteins 57(3):518-30.