The Bioinformatics Center at Rensselaer and Wadsworth. Research -- Data Mining


	*The Bioinformatics Center at Rensselaer and Wadsworth*

Gene Expression

Nucleic Acids Folding

Protein Structure
Prediction

Molecular Simulations

Drug Design

Mitochondrial Structure

Data Mining

Nanotechnology

Directed Evolution

	Data Mining	--Home >> Research >> Gene Expression >> Nucleic Acids Folding >> Protein Structure Prediction >> Molecular Simulations >> Drug Design >> Mitochondrial Structure >> Data Mining >> Nanotechnology >> Directed Evolution

Data Mining: Analytical and Management Tools for Protein Structure Prediction and Design

Involved Researchers: Professor Mohammed Zaki in collaboration with Professor Chris Bystroff

Introduction: Bioinformatics is the science of storing, extracting, organizing, analyzing, and interpreting biological data. Its importance has increased with the technology of DNA sequencing, microarrays, as well as the widespread understanding that genes and proteins act in networks. This in turn renders high performance data analysis tools to this task.
Data mining is the process of automatic discovery of patterns, changes, associations and anomalies in massive databases.

Researchers
Introduction
Course
Publications of general interest
Prof. Zaki's publications

Prof. Zaki designs efficient, scalable, and parallel algorithms for various data mining techniques and he is specially interested in developing novel data mining techniques for bioinformatics.

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Course: Prof. Zaki teaches a course in Data Mining in the Fall Semester. Click here for course syllabus.

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Publications of general interest:

Article: Decoding the Protein Language

2D Contact Map for Protein 2igd from Protein Data Bank, and its 3D Structure

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Prof.'s Zaki publications in Data Mining:

Book: Large-Scale Parallel Data Mining

Journal articles:

• Jason Wang, Mohammed J. Zaki, Hannu Toivonen, Dennis Shasha (editors), Data Mining in Bioinformatics, Springer London Ltd., to appear late 2003 (collection of invited chapters).

• Mohammed J. Zaki, Mining Data in Bioinformatics, to appear in Nong Ye (ed.), Handbook of Data Mining, Lawrence Earlbaum Associates, 2003.

• Mohammed J. Zaki, Shan Jin and Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions, to appear in IEEE Transactions on Systems, Man and Cybernetics, special issue on Bioengineering and Bioinformatics, N. Boubakis (ed.), 2003.

• Mohammed J. Zaki, Hannu T.T. Toivonen, and Jason T.L. Wang (editors), Proceedings of the 2nd BIOKDD Workshop on Data Mining in Bioinformatics (with SIGKDD02), ACM Press, July 2002.

• Jingjing Hu, Xioalan Shen, Yu Shao, Chris Bystroff, Mohammed J. Zaki, Mining Protein Contact Maps, 2nd BIOKDD Workshop on Data Mining in Bioinformatics, Edmonton, Canada, July 2002.

• Yu Shao, Malik Magdon-Ismail, Danial Freedman, Srinivas Akella, Mohammed Zaki, Chris Bystroff, Compression of Protein Conformational Space (Poster), in 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB02), Washington, DC, April 2002.

• Mohammed J. Zaki, Hannu T.T. Toivonen, and Jason T.L. Wang (editors), Proceedings of the 1st BIOKDD Workshop on Data Mining in Bioinformatics (with SIGKDD01), San Francisco, CA, August 2001.

• Mohammed J. Zaki, Shan Jin, Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions, in IEEE International Symposium on Bioinformatics and Biomedical Engineering, pp 168-175, Washington, DC, November 2000.

• Vineet Gupta, Srinivasan Parthasarathy, Mohammed J. Zaki, Arithmetic and Logic Operations with DNA, 3rd DIMACS Workshop on DNA Based Computers, Philadelphia, Pennsylvania, June 1997.

For complete list of Prof. Zaki's publications, please follow this link.

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