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).

Zaki, Mohammed J.; Sequeira, Karlton. Data mining in computational biology. Handbook of Computational Molecular Biology (2006), 38/1-38/26.

Zhang Yongqiang; Zaki, Mohammed J EXMOTIF: efficient structured motif extraction. Algorithms for molecular biology : AMB (2006), 1 21.

Zhang Yongqiang; Zaki, Mohammed J SMOTIF: efficient structured pattern and profile motif search. Algorithms for molecular biology : AMB (2006), 1 22.

Zaki, M.J. (2005) "Efficiently Mining Frequent Embedded Unordered Trees." Fundamenta Informaticae, 65, 1-20.

Zaki M.J.; Parimi, N.; De, N.; Gao, F.; Phoophakdee, B.; Urban, J.; Chaoji, V.; Al Hasan, M.; Salem, S. (2005) "Towards Generic Pattern Mining" Proceedings of the International Conference on Formal Concept Anaysis, 1-20

Zaki, M.J. (2001) "SPADE: An Efficient Algorithm for Mining Frequent Sequences" Machine Learning Journal, special issue on Unsupervised Learning (Doug Fisher, ed.), 42(1/2), 31-60.

Zaki, M.J. (2000) "Scalable Algorithms for Association Mining" EEE Transactions on Knowledge and Data Engineering, 12(3), 372-390.