Research Projects

The CSE Bioinformatics Research Group, a branch of the CSE Bioinformatics, Database, Data Mining and Multimedia Group at University at Buffalo, is led by Dr. Aidong Zhang. The group is pursuing active research in the areas of protein-protein interaction network analysis, microarray data analysis and high dimensional data visualization.

The materials published below are partially based upon work supported by the National Science Foundation under Grants No. 0101244 and No. 0234895. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Publications

2007
  • Young-Rae Cho, Xian Xu, Woochang Hwang and Aidong Zhang Feature Extraction from Microarray Expression Data by Integration of Semantic Knowledge In Proceedings of IEEE 6th International Conference on Machine Learning and Applications (ICMLA 2007), 13-15 December 2007, Cincinnati, OH.
  • Young-Rae Cho, Woochang Hwang and Aidong Zhang Assessing Reliability of Protein-Protein Interactions by Semantic Data Integration In Proceedings of IEEE 7th International Conference on Data Mining ICDM 2007, Workshop on Mining and Management of Biological Data (MMBD 2007), 28 October 2007, Omaha, NE.
  • Woochang Hwang, Taehyong Kim, Young-Rae Cho, Aidong Zhang and Murali Ramanathan SIGN: Reliable Protein Interaction Identification by Integrating the Similarity in GO and the Similarity in Protein Interaction Networks In Proceedings of IEEE 7th Symposium on Bioinformatics and Bioengineering (BIBE 2007), 14-17 October 2007, Boston, MA.
  • Young-Rae Cho, Woochang Hwang and Aidong Zhang Optimizing Flow-based Modularization by Iterative Centroid Search in Protein Interaction Networks In Proceedings of IEEE 7th Symposium on Bioinformatics and Bioengineering (BIBE 2007), 14-17 October 2007, Boston, MA.
  • P. Chanda, A. Zhang, D. Brazeau, L. Sucheston, Jo L Freudenheim, C. Ambrosone, M. Ramanathan, Information Theoretic Metrics for Visualizing Gene Environment Interactions, the American Society of Human Genetics, November 2007.
  • Young-Rae Cho, Woochang Hwang, Murali Ramanathan and Aidong Zhang Semantic Integration to Identify Overlapping Functional Modules in Protein Interaction Networks BMC Bioinformatics, Vol. 8(265), July 2007
  • Young-Rae Cho, Woochang Hwang and Aidong Zhang Modularization of Protein Interaction Networks by Incorporating Gene Ontology Annotations In Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2006), 1-5 April 2007, Honolulu, Hawaii.
  • Chuan Lin, Young-Rae Cho, Woochang Hwang, Pengjun Pei, and Aidong Zhang Clustering Methods in Protein-Protein Interaction Networks in the book "Knowledge Discovery in Bioinformatics: Techniques, Methods and Application", edited by Drs. Xianhua Hu and Yi Pan, Wiley, 2007.
  • Pengjun Pei and Aidong Zhang A "Seed-Refine" Algorithm for Detecting Protein Complexes from Protein Interaction Data IEEE Transactions on Nanobioscience, Vol. 6(1), March 2007
    2006
  • K. Bhasi, L. Zhang, D. Brazeau, A. Zhang, and M. Ramanathan, Information-Theoretic Identification of Predictive SNPs and Supervised Visualization of Genome-wide Association Studies, Nucleic Acids Research, Vol. 34, No. 14, pp. e101, September 2006.
  • Aidong Zhang Advanced Analysis of Gene Expression Microarray Data World Scientific Publishing Co., Inc. 2006
  • Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan A Novel Functional Module Detection Algorithm for Protein-Protein Interaction Networks Algorithms for Molecular Biology, Vol. 1(24), December 2006
  • Young-Rae Cho, Woochang Hwang and Aidong Zhang Identification of Overlapping Functional Modules in Protein Interaction Networks: Information Flow-based Approach In Proceedings of IEEE 6th International Conference on Data Mining ICDM 2006, Workshop on Data Mining in Bioinformatics (DMB 2006), 18 December 2006, Hong Kong.
  • Chuan Lin, Daxin Ziang and Aidong Zhang Prediction of Protein Function Using Common-Neighbors in Protein-Protein Interaction Networks In Proceedings of IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE 2006), 16-18 October 2006, Washington DC.
  • Young-Rae Cho, Woochang Hwang and Aidong Zhang Efficient Modularization of Weighted Protein Interaction Networks using k-Hop Graph Reduction In Proceedings of IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE 2006), 16-18 October 2006, Washington DC.
  • Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan Signal Transduction Model Based Functional Module Detection Algorithm for Protein-Protein Interaction Networks In Proceedings of 6th SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2006), 20 August 2006, Philadelphia, PA.
  • Young-Rae Cho, Woochang Hwang, Aidong Zhang and Murali Ramanathan Assessing Hierarchical Modularity in Protein Interaction Networks (Poster Abstract) In Proceedings of LSS Computational Systems Bioinformatics Conference (CSB 2006), 14-18 August 2006, Stanford, CA.
  • Xian Xu and Aidong Zhang Boost Feature Subset Selection: A New Gene Selection Algorithm for Microarray Dataset In Computational Science ICCS 2006: 6th International Conference, 2006 International Workshop on Bioinformatics Research and Applications, University of Reading, UK May 2006
  • Pengjun Pei and Aidong Zhang Towards Detecting Protein Complexes from Protein Interaction Data In Computational Science ICCS 2006: 6th International Conference, 2006 International Workshop on Bioinformatics Research and Applications, University of Reading, UK May 2006
    2005
  • Pengjun Pei, Aidong Zhang A Two-Step Approach for Clustering Proteins Based on Protein Interaction Profile In Proceedings of IEEE 5th Symposium on Bioinformatics and Bioengineering (BIBE 2005), Minneapolis, MN, Oct 2005:201-209
  • Pengjun Pei, Aidong Zhang A Topological Measurement for Weighted Protein Interaction Network In Proceedings of 4th International IEEE Computer Society Computational Systems Bioinformatics Conference (CSB 2005), 8-11 August 2005, Stanford, CA, USA:268-278
  • Xian Xu and Aidong Zhang Virtual Gene: Using Correlations Between Genes to Select Informative Genes on Microarray Datasets In LNCS Transactions on Computational Systems Biology II, LNBI 3680, page 138-152, 2005
  • Xian Xu and Aidong Zhang Selecting Informative Genes from Microarray Dataset by Incorporating Gene Ontology In Proceedings of IEEE 5th Symposium on Bioinformatics and Bioengineering (BIBE 2005), Minneapolis, MN, Oct 2005
  • Daxin Jiang, Jian Pei and Aidong Zhang A General Approach to Mining Quality Pattern-Based Clusters from Microarray Data In Proceedings of 10th International Conference of Database Systems for Advanced Applications (DASFAA 2005).
  • Daxin Jiang, Jian Pei and Aidong Zhang An Interactive Approach to Mining Gene Expression Data In IEEE Transactions on Knowledge and Data Engineering (TKDE).
  • Xian Xu and Aidong Zhang Virtual Gene: A Gene Selection Algorithm for Sample Classification on Microarray Datasets In Computational Science ICCS 2005: 5th International Conference, 2005 International Workshop on Bioinformatics Research and Applications, Atlanta, GA, May 2005
  • Liangjiang Wang, Aidong Zhang and Murali Ramanathan BioStar Models of Clinical and Genomic Data for Biomedical Data Warehouse Design In International Journal of Bioinformatics Research and Applications (IJBRA), 2005, Vol. 1, No.1, pp. 63-80.
    2004
  • Daxin Jiang, Jian Pei, Murali Ramanathan, Chun Tang, and Aidong Zhang. Mining Coherent Gene Clusters from Gene-Sample-Time Microarray Data (Runner-up for Best Application Paper Award). In Proceedings of the 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'04), August 22 - 25, Seattle, WA, USA.
  • Daxin Jiang, Jian Pei, and Aidong Zhang. GPX: Interactive Mining of Gene Expression Data (demo paper). In Proceedings of the 30th International Conference on Very Large Data Bases (VLDB'04), August 30 - September 3, Toronto, ON, Canada.
  • Murali Ramanathan, Li Zhang, and Aidong Zhang. VizStruct: A Multidimension Visualization Algorithm for Gene Expression. (2004) in Advanced Methods of Pharmacokinetic & Pharmacodynamic Systems Analysis Volume III, Kluwer Academic Press, Norwell, MA. pp197--207.
  • Kavitha Bhasi, Li Zhang, Aidong Zhang, and Murali Ramanathan. Applications of VizStruct, A Novel Multi-dimensional Visualization Technique, in Pharmacokinetics, Pharmacodynamics and harmacogenomics. Pharmaceutical Research. 21(5): 777-781 (2004).
  • Chun Tang, Aidong Zhang, and Murali Ramanathan. ESPD: A Pattern Detection Model Underlying Gene Expression Profiles. Bioinformatics. Vol. 20(6): pp 829-838, April (2004).
  • Chun Tang and Aidong Zhang. Interrelated Two-way Clustering and Its Application on Gene Expression Data. International Journal on Artificial Intelligence Tools (Special Issue).
  • Daxin Jiang, Chun Tang, and Aidong Zhang. Cluster Analysis for Gene Expression Data: A Survey. In IEEE Transactions on Knowledge and Data Engineering (TKDE).
  • Daxing Jiang, Jian Pei and Aidong Zhang. Towards Interactive Exploration of Gene Expression Patterns. ACM SIGKDD Explorations (Special Issue on Microarray Data Analysis), Volume 6, Issue 1, 2004.
  • Li Zhang, Aidong Zhang, and Murali Ramanathan: VizStruct: Exploratory Visualization for Gene Expression Profiling. Bioinformatics. 20(1): 85-92 (2004).

    2003
  • Chun Tang and Aidong Zhang. Mining Multiple Phenotype Structures Underlying Gene Expression Profiles. In Proceedings of 12th ACM International Conference on Information and Knowledge Management (CIKM 2003), New Orleans, Louisiana, November 2003.
  • Li Zhang, Aidong Zhang, and Murali Ramanathan: Enhanced Visualization of Time Series through Higher Fourier Harmonics. In proceeding of BIOKDD 2003, 3rd Workshop on Data Mining in Bioinformatics, in conjunction with 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2003), Washington, DC. August 2003.
  • Chun Tang, Aidong Zhang and Jian Pei. Mining Phenotypes and Informative Genes from Gene Expression Data. In Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2003), Washington, DC, August 2003.
  • Daxing Jiang, Jian Pei and Aidong Zhang. "Interactive Exploration of Coherent Patterns in Time-Series Gene Expression Data". In Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2003), Washington, DC, USA, August 24-27, 2003.
  • Li Zhang, Aidong Zhang, Murali Ramanathan: Fourier Harmonic Approach for Visualizing Temporal Patterns of Gene Expression Data. In proceeding of IEEE Computer Society Bioinformatics Conference (CSB 2003). Stanford, CA, August 2003, pp137-147.
  • Daxin Jiang , Jian Pei, and Aidong Zhang. DHC: A Density-based Hierarchical Clustering Method for Time Series Gene Expression Data. 3rd IEEE Symposium on Bio-informatics and Bio-engineering (BIBE 2003), Washington D.C., March 2003
  • Li Zhang, Chun Tang, Yuqing Song, Aidong Zhang, Murali Ramanathan: VizCluster and its Application on Classifying Gene Expression Data. Distributed and Parallel Databases. 13(1): 73-97 (2003).

    2002
  • Chun Tang and Aidong Zhang. An Iterative Strategy for Pattern Discovery in Multi-dimensional Data Sets. 11th International Conference on Information and Knowledge Management (CIKM 2002). McLean, VA. November 2002.
  • Li Zhang, Aidong Zhang and Murali Ramanathan. Visualized Classification of Multiple Sample Types. BIOKDD 2002, 2nd Workshop on Data Mining in Bioinformatics, in conjunction with 8th ACM SIGKDD (KDD 2003), July 2002, Edmonton, Alberta, Canada.
  • Chun Tang, Li Zhang, Aidong Zhang, Murali Ramanathan: Interrelated Clustering: An Approach for Gene Expression Data Analysis. Computational Biology and Genome Informatics 2003: pp 183-206 (invited chapter).
  • Li Zhang, Chun Tang, Yong Shi, Yuqing Song, and Aidong Zhang, Murali Ramanathan. VizCluster: An Interactive Visualization Approach to Cluster Analysis and Its Application on Microarray Data. Second SIAM International Conference on Data Mining. Arlington, VA. April 2002.
  • Chun Tang, Li Zhang, and Aidong Zhang. Interactive Visualization and Analysis for Gene Expression Data. 2002 IEEE. Published in the Proceedings of the Hawaii International Conference on System Sciences. Big Island, HI. January 2002.

    2001
  • Chun Tang, Li Zhang, and Aidong Zhang, Murali Ramanathan. Interrelated Two-way CLustering: An Unsupervised Approach for Gene Expression Data Analysis. Proc. of 2nd IEEE International Symposium on Bioinformatics and Bioengineering. Bethesda, MD. November 2001.
  • Shumei Jiang, Chun Tang, Li Zhang and Aidong Zhang, Murali Ramanathan. A Maximum Entropy Approach to Classifying Gene Array Data Sets. Proc. of Workshop on Data mining for genomics, First SIAM International Conference on Data Mining. Chicago, IL. April 2001.


    Toolkits

    VizStruct: Exploratory Visualization for Gene Expression Profiling

    Automatic Phenotype Mining from Gene Expression Profiles

    GPX: Interactive Mining of Gene Expression Data


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    Last Modified: 8/15/2004