Refereed Journals:

Mark Berjanskii, Yongjie Liang, Jianjun Zhou, Peter Tang, Paul Stothard, You Zhou, Joseph Cruz, Cam MacDonell, Guohui Lin, Paul Lu and David S. Wishart. "PROSESS: a protein structure evaluation suite and server" Nucleic Acids Research, Web server issue, 38(suppl 2): W633-640, 2010.

Mark Berjanskii, Peter Tang, Jack Liang, Joseph A. Cruz, Jianjun Zhou, You Zhou, Edward Bassett, Cam MacDonell, Paul Lu, Guohui Lin, and David S. Wishart. "GeNMR: a web server for rapid NMR-based protein structure determination" Nucleic Acids Research, Web server issue, 37(suppl 2): W670 - W677, 2009.

Jianjun Zhou, Joerg Sander, Zhipeng Cai, Lusheng Wang, Guohui Lin. "Finding the Nearest Neighbors in Biological Databases Using Less Distance Computations" IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7(4): 669-680, 2010.

David S. Wishart, David Arndt, Mark Berjanskii, Peter Tang, Jianjun Zhou and Guohui Lin. "CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data", Nucleic Acids Research, Web server issue, 36(suppl 2): W496 - W502, 2008.

Yi Shi, Jianjun Zhou, David Arndt, David S Wishart and Guohui Lin. "Protein contact order prediction from primary sequences", BMC Bioinformatics, 2008.

D. S. Wishart, D. Arndt, M. Berjanskii, A. C. Guo, Y. Shi, S. Shrivastava, J. Zhou, Y. Zhu, and G. Lin. "PPT-DB: The Protein Property Prediction and Testing Database", Nucleic Acids Research,Database issue, 36(suppl 1): D222-D229, 2008.

Jianjun Zhou, Joerg Sander, and Guohui Lin, "Efficient Composite Pattern Finding From Monad Patterns". International Journal on Bioinformatics Research and Applications. 3:86-99, 2007.

G. Robertson, M. Bilenky, K. Lin, A. He, W. Yuen, M. Dagpinar, R. Varhol, K. Teague, O. L. Griffith, X. Zhang, Y. Pan, M. Hassel, M. C. Sleumer, W. Pan, E. D. Pleasance, M. Chuang, H. Hao, Y. Y. Li, N. Robertson, C. Fjell, B. Li, S. B. Montgomery, T. Astakhova, J. Zhou, J. Sander, A. S. Siddiqui, and S. J. M. Jones,"cisRED: a database system for genome-scale computational discovery of regulatory elements", Nucleic Acids Research, Database issue, 34(suppl 1): D68-D73, 2006.

Jianjun Zhou, Martin Müller,"Solving systems of difference constraints incrementally with bidirectional search", Algorithmica, 39:255-274, 2004.

Jianjun Zhou, Martin Müller,"Depth-first discovery algorithm for incremental topological sorting of directed acyclic graphs", Information Processing Letters, Vol 88/4, pp 195-200, 2003.

Jianjun Zhou, Rihua Zhang, Xiaoping Chen. "A Decision Algorithm Based on Lm4c". Mini-Micro Systems, Vol 22, pp 1254-1257, China, 2001.

Refereed Conferences:

Jianjun Zhou, Joerg Sander. "Speedup Clustering with Hierarchical Ranking". Proceedings of the Sixth International Conference on Data Mining.(ICDM'06), pp 1205-1210, 2006. Long version in Chapter 3 of my PhD thesis.

Jianjun Zhou, Joerg Sander. "Data Bubbles for Non-Vector Data: Speeding-up Hierarchical Clustering in Arbitrary Metric Spaces". Proceeding of the 29^th International Conference on Very Large Data Bases (VLDB-03), pp 452-463, 2003.

PhD Thesis:

Jianjun Zhou. "Efficiently Searching and Mining Biological Sequence and Structure Data". University of Alberta, 2009.