Buffalo Center for 
      Biomedical Computing
   
  BCBC Home
  BCBC Mission
  BCBC Activities
  BCBC Projects
  BCBC Seminars
  BCBC Symposia
  BCBC People
  BCBC Resources
  BCBC Publication
  Useful Links
   
 
   

Publications

2010

  • Taehyong Kim, Murali Ramanathan, and Aidong Zhang. BoneNET: A Network Model of Bone Microstructure and Dynamics. International Journal of Data Mining and Bioinformatics (IJDMB)
  • Taehyong Kim, Woo-Chang Hwang, Aidong Zhang, and Murali Ramanathan. Computational Framework for Microstructural Bone Dynamics Model and Its Evaluation. IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2010)
  • Taehyong Kim, Murali Ramanathan, and Aidong Zhang. Graph-based Approach on Computational Model of Bone Microstructure. ACM Workshop on Graph Theoretic Approaches for Biological Network Analysis (IWBNA 2010), in conjunction with ACM International Conference Bioinformatics and Computational Biology (ACM-BCB), 2010
  • Brendan J. Gilbert, Raj Sharman, Manish Gupta, H.R. Rao, Shambhu Upadhyaya, Kenneth P. Mortensen, Esq. Content-sensitive, Temporally Adaptive Metadata. 11th Annual New York State Cyber Security Conference, Albany, NY, June 2008, pp. 47-52. (Best Paper Award)
  • Ankur Bansal, Tingting Chen and Sheng Zhong. Privacy preserving Back-propagation neural network learning over arbitrarily partitioned data. Neural Computing & Applications, 2010
  • Tingting Chen, and Sheng Zhong. Emergency Access Authorization for Personally Controlled Online Health Care Data. Journal of Medical Systems, 2010
  • Sunu Mathew, Hung Q. Ngo and Shambhu Upadhyaya. A Data-Centric Approach to Insider Attack Detection in Database Systems. In International Symposium on Recent Advances in Intrusion Detection (RAID), 2010
  • Haricharan Rengamani, Shambhu Upadhyaya, and H. Raghav Rao. Protecting senior citizens from cyber security attacks in the e-health scenario: an international perspective. The Annual Cyber Security and Information Intelligence Research Workshop [CSIIRW], 2010
    2009

  • Young-Rae Cho, Lei Shi and Aidong Zhang. flowNet: Flow-based approach for efficient analysis of complex biological networks. In Proceedings of IEEE International Conference on Data Mining (ICDM 2009), December 6-9, 2009, Miami, FL
  • Young-Rae Cho and Aidong Zhang. Restructuring protein interaction networks to reveal structural hubs and functional organizations. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), November 1-4, 2009, Washington DC
  • Lei Shi, Young-Rae Cho and Aidong Zhang. ANN based protein function prediction using integrated protein-protein interaction data. In Proceedings of International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS 2009), August 3-5 2009, Shanghai, China
  • Young-Rae Cho, Aidong Zhang and Xian Xu. Semantic similarity based feature extraction from microarray expression data. International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 3(3):333-345, July 2009
  • Taehyong Kim, Woo-Chang Hwang, Aidong Zhang, Murali Ramanathan, and Surajit Sen. Damage isolation via strategic self-destruction: A case study in 2D random networks. Europhysics Letters (EPL), 86:24002, April 2009
  • Abhijith Kashyap, Vagelis Hristidis, Michalis Petropoulos, and Sotiria Tavoulari. BioNav: Effective Navigation on Query Results of Biomedical Databases. Proceedings of the 25th International Conference on Data Engineering, ICDE 2009, March 29 2009 - April 2 2009, Shanghai, China 2009
  • Sheng Zhong, Zhiqiang Yang, and Tingting Chen. k-Anonymous data collection. Information Sciences 179 (2009) 2948?2963
  • Tingting Chen and Sheng Zhong. Privacy Preserving Back-Propagation Neural Network Learning. IEEE Transactions on Neural Networks, 2009
  • Abhijith Kashyap, Vagelis Hristidis, Michalis Petropoulos, and Sotiria Tavoulari. Exploring biomedical databases with BioNav. Proceedings of the 35th SIGMOD international conference on Management of data, 2009
    2008

  • Taehyong Kim, Woo-Chang Hwang, Aidong Zhang, Surajit Sen, and Murali Ramanathan. Multi-Agent Model: Containment Strategy on Avian Influenza (AI) in South Korea. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), November 3-5 2008, Philadelphia, PA
  • Young-Rae Cho and Aidong Zhang. Discovering frequent patterns of functional associations in protein interaction networks for function prediction. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), November 3-5 2008, Philadelphia, PA
  • Young-Rae Cho, Lei Shi and Aidong Zhang. Functional module detection by functional flow pattern minining in potein interaction networks. BMC Bioinformatics, Vol. 9(Suppl 10):O1, October 2008
  • P. Chanda, A. Zhang and M. Ramanathan. A novel information theoretic method for detecting gene-gene and gene-environment interactions in complex diseases. In Proceedings of IEEE 8th Symposium on Bioinformatics and Bioengineering (BIBE 2008), 8-10 October 2008, Athens, Greece.
  • Young-Rae Cho, Lei Shi, Murali Ramanathan and Aidong Zhang A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge BMC Bioinformatics, Vol. 9:382, September 2008
  • Woochang Hwang, Taehyong Kim, Murali Ramanathan and Aidong Zhang. Bridging Centrality: Graph Mining from Element Level to Group Level. In Proceedings of ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2008), August 24-27, Las Vegas, NV
  • Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. CASCADE: a novel quasi all path-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics, Vol. 9:64, January 2008
  • Sunu Matthew, Shambhu Upadhyaya, Duc Ha, Hung Q. Ngo. Insider Abuse Comprehension through Capability Acquisition Graphs. in Proceedings of the The 11th International Conference on Information Fusion (FUSION 2008), June 30--July 03, 2008. Cologne, Germany
    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

  • 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.
  • 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.
  • 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
  • Zhiqiang Yang, Sheng Zhong, and Rebecca N. Wright. Privacy-Preserving Queries on Encrypted Data. Lecture Notes in Computer Science, 2006
    2005

  • Pengjun Pei and 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 and 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.
  • Anusha Iyer, and Hung Q. Ngo. Towards a Theory of Insider Threat Assessment. Proceedings of the 2005 International Conference on Dependable Systems and Networks
    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).
  • Raj Sharman, Himabindu Challapalli, Raghav H. Rao and Shambhu Upadhyaya. A Framework for a Secure Federated Patient Healthcare System. Lecture Notes in Computer Science, 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.