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. 1218393, No. 1016929, 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.

NSF Bioinformatics Project

Publications

2017

  • Vishrawas Gopalakrishnan and Aidong Zhang. On Emerging Use-Cases & Techniques in Large Networked Data in Biomedical and Social Media Domain (To Appear). Big Data and Computational Intelligence in Networking
  • 2016

  • Qiuling Suo, Hongfei Xue, Jing Gao and Aidong Zhang. Risk factor analysis based on deep learning models. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM BCB, 2016
  • Xiaowei Jia, Xiaoyi Li, Nan Du, Yuan Zhang, Vishrawas Gopalakrishnan, Guangxu Xun and Aidong Zhang. Influence based Analysis of Community Consistency in Dynamic Networks. The 2016 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2016
  • Xiaowei Jia, Xiaoyi Li, Kang Li, Vishrawas Gopalakrishnan, Guangxu Xun and Aidong Zhang. Collaborative Restricted Boltzmann Machine for Social Event Recommendation. The 2016 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2016
  • Guangxu Xun, Vishrawas Gopalakrishnan, Fenglong Ma, Yaliang Li, Jing Gao, and Aidong Zhang. Topic Discovery for Short Texts Using Word Embeddings (To Appear). IEEE International Conference on Data Mining series, ICDM, 2016
  • Guangxu Xun, Xiaowei Jia, Vishrawas Gopalakrishnan, Aidong Zhang. A Survey on Context Learning. In IEEE Transactions on Knowledge and Data Engineering, TKDE, 2016
  • Guangxu Xun, Xiaowei Jia, Aidong Zhang. Detecting Epileptic Seizures with Electroencephalogram via a Context-Learning Model. BMC Medical Informatics and Decision Making 16. Suppl 2 2016
  • Vishrawas Gopalakrishnan, Kishlay Jha, Aidong Zhang, Wei Jin. Generating Hypothesis: Using Global and Local Features in Graph to Discover New Knowledge from Medical Literature. International Conference on Bioinformatics and Computational Biology, BICoB, 2016
  • 2015

  • Guangxu Xun, Xiaowei Jia, Aidong Zhang. Context-learning based electroencephalogram analysis for epileptic seizure detection. IEEE International Conference on Bioinformatics and Biomedicine, BIBM, 2015
  • Guangxu Xun, Xiaoyi Li, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart, Tiffany R. Walsh, Aidong Zhang. Identifying inorganic material affinity classes for peptide sequences based on context learning . IEEE International Conference on Bioinformatics and Biomedicine, BIBM, 2015
  • Xiaowei Jia, Aosen Wang, Xiaoyi Li, Guangxu Xun, Wenyao Xu, Aidong Zhang. Multi-modal learning for video recommendation based on mobile application usage. IEEE International Conference on Big Data, BigData, 2015
  • Xiaoyi Li, Xiaowei Jia, Guangxu Xun, Aidong Zhang. Improving EEG feature learning via synchronized facial video . IEEE International Conference on Big Data, BigData, 2015
  • Nan Du, Xiaowei Jia, Jing Gao, Vishrawas Gopalakrishnan, and Aidong Zhang. Tracking Temporal Community Strength in Dynamic Networks. IEEE Transactions on Knowledge and Data Engineering, 2015
  • Nan Du, Jing Gao, Liang Ge, Vishrawas Gopalakrishnan, Xiaowei Jia, Kang Li, and Aidong Zhang. Significant Edge Detection in Target Network by Exploring Multiple Auxiliary Networks. The 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2015
  • Kang Li, Jing Gao, Suxin Guo, Nan Du, Aidong Zhang. Functional Node Detection on Linked Data. SIAM International Conference on Data Mining (SDM), 2015
  • 2014

  • Kang Li, Jing Gao, Suxin Guo, Nan Du, Xiaoyi Li, Aidong Zhang. LRBM: A Restricted Boltzmann Machine based Approach for Representation Learning on Linked Data. IEEE International Conference on Data Mining (ICDM), 2014
  • Xiaowei Jia, Nan Du, Jing Gao, Aidong Zhang. Analysis on Community Variational Trend in Dynamic Networks. ACM International Conference on Information and Knowledge Management (CIKM), Shanghai, China, November 3-7, 2014
  • Xiaowei Jia, Kang Li, Xiaoyi Li, and Aidong Zhang. A Novel Semi-supervised Deep Learning Framework for Affective State Recognition on EEG Signals with Two-level Channel Selection. the 14th IEEE International Conference on BioInformatics and BioEngineering (BIBE), Boca Raton, FL, November 10-12, 2014. (Best Student Paper Award)
  • Nan Du, Marc R. Knecht, Mark T. Swihart, Zhenghua Tang, Tiffany R. Walsh and Aidong Zhang. Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-based Model. Special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2014
  • Suxin Guo, Sheng Zhong, Aidong Zhang. Privacy Preserving Calculation of Fisher Criterion Score for Informative Gene Selection. International Conference on Bioinformatics and Bioengineering (BIBE), 2014
  • Hui Li, Aidong Zhang, Lawrence Bone, Cathy Buyea, and Murali Ramanathan, ? A Network Modeling Approach for the Spatial Distribution and Structure of Bone Mineral Content. AAPS journal, 2014
  • Hui Li, Xiaoyi Li, Murali Ramanathan, and Aidong Zhang, ? Prediction and Informative Risk Factor Selection of Bone Diseases. Special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2014
  • Nikhil Londhe, Vishrawas Gopalakrishnan, Aidong Zhang, Hung Q. Ngo and Rohini Srihari? Matching Titles with Cross Title Web-Search Enrichment and Community Detection. VLDB, 2014
    2013

  • Nan Du , Jing Gao and Aidong Zhang. Progression Analysis of Community Strengths in Dynamic Networks. IEEE International Conference on Data Mining, ICDM, 2013
  • Nan Du, Xiaoyi Li, Yuan Zhang and Aidong Zhang. Detecting Mutual Functional Gene Clusters from Multiple Related Diseases. IEEE International Conference on Bioinformatics and Biomedicine, BIBM, 2013
  • Nan Du, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart, Tiffany Walsh and Aidong Zhang. A Framework for Identifying Affinity Classes of Inorganic Materials Binding Peptide Sequences. ACM-BCB, 2013
  • Kang Li, Suxin Guo, Nan Du, Jing Gao and Aidong Zhang. Learning, Analyzing and Predicting Object Roles on Dynamic Networks. IEEE International Conference on Data Mining, ICDM, 2013
  • Kang Li, Xiaoyi Li, Nan Du and Aidong Zhang. Affective State Recognition on EEG using Deep Belief Networks. IEEE International Conference on Bioinformatics and Biomedicine, BIBM, 2013
  • Kang Li, Suxin Guo, Jing Gao and Aidong Zhang. An Ensemble Model for Mobile Devices based Arrhythmias Detection. ACM-BCB, 2013
  • Suxin Guo, Sheng Zhong, Aidong Zhang. A Privacy Preserving Markov Model for Sequence Classification. ACM-BCB, 2013
  • Suxin Guo, Sheng Zhong, Aidong Zhang. Privacy-Preserving Kruskal–Wallis Test. Computer Methods and Programs in Biomedicine, 2013
  • Xiaoyi Li , Nan Du , Hui Li , Kang Li , Jing Gao and Aidong Zhang. A Deep Learning Approach to Link Prediction in Dynamic Networks. SIAM International Conference on Data Mining, SDM, 2013
  • Hui Li, Xiaoyi Li, Murali Ramanathan, Aidong Zhang. A Semi-Supervised Learning Approach to Integrated Salient Risk Features for Bone Diseases. ACM-BCB, 2013
  • Hui Li, Xiaoyi Li, Yuan Zhang, Murali Ramanathan, Aidong Zhang. A generative framework for prediction and informative risk factor selection of bone diseases. IEEE International Conference on Bioinformatics and Biomedicine, BIBM, 2013
  • Liang Ge , Jing Gao, Hung Ngo, Kang Li and Aidong Zhang. On Handling Negative Transfer and Imbalanced Distributions in Multiple Source Transfer Learning. SIAM on Data Mining (SDM), 2013
    2012

  • Vishrawas Gopalakrishnan, Suresh Parthasarathy Iyengar, Rajeev Rastogi, Srinivasan Sengamedu. Matching product titles using web-based enrichment.. ACM international conference on Information and knowledge management (CIKM), 2012
  • Nan Du, Jing Gao, Vishrawas Gopalakrishnan, Aidong Zhang. De-noise biological network from heterogeneous sources via link propagation.. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2012 (This paper is supported by NSF grant award 1016929)
  • Kang Li, Nan Du, Aidong Zhang. A Link Prediction based Unsupervised Rank Aggregation Algorithm for Informative Gene Selection.. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2012 (This paper is supported by NSF grant award 1016929)
  • Hui Li, Xiaoyi Li, Lawrence Bone, Cathy Buyea, Murali Ramanathan and Aidong Zhang. 3D Bone Microarchitecture Modeling and Fracture Risk Prediction. ACM-BCB, 2012
  • Yuan Zhang, Liang Ge, Nan Du, Guoqiang Fan, Kebin Jia, Aidong Zhang. A graph-based cluster ensemble method to detect protein functional modules from multiple information sources. ACM-BCB, 2012
  • Hui Li ; Kang Li ; Taehyong Kim ; Aidong Zhang and Murali Ramanathan. Spatial modeling of bone microarchitecture. Proc. SPIE 8290, Three-Dimensional Image Processing (3DIP) and Applications II
  • Nan Du, Yuan Zhang, Kang Li, Jing Gao, Supriya D. Mahajan, Bindukumar B. Nair, Stanley A. Schwartz, Aidong Zhang. Evolutionary analysis of functional modules in dynamic PPI networks. ACM-BCB, 2012 (This paper is supported by NSF grant award 1016929)
  • Kang Li, Nan Du, Aidong Zhang. Detecting ECG Abnormalities via Transductive Transfer Learning. ACM-BCB, 2012
  • Yuan Zhang, Nan Du, Liang Ge, Kebin Jia, Aidong Zhang. A collective NMF method for detecting protein functional module from multiple data sources. ACM-BCB, 2012
  • Liang Ge , Jing Gao, Xiao Yu, Wei Fan, and Aidong Zhang. Estimating Local Information Trustworthiness via Multi-Source Joint Matrix Factorization. IEEE International Conference on Data Mining (ICDM), 2012 (This paper is supported by NSF grant award 1218393).
  • Liang Ge , Jing Gao, Nan Du and Aidong Zhang. Finding Informative Genes for Prostate Cancer: A General Framework of Integrating Heterogeneous Sources. ACM-BCB, 2012
  • Xiujuan Lei, S. Wu, Liang Ge and Aidong Zhang. Clustering and Overlapping Modules Detection in PPI Network Based on IBFO. Proteomics, 13(2), pp. 278-290. (This paper is supported by NSF grant award 1016929)
  • Liang Ge, and Aidong Zhang. Pseudo Cold Start Link Prediction with Multiple Sources in Social Networks. SIAM on Data Mining (SDM 2012)
    2011

  • Taehyong Kim, Lawrence Bone, Murali Ramanathan, and Aidong Zhang. BoneNET: A Network Model of Bone Microstructure and Dynamics. International Journal of Data Mining and Bioinformatics (IJDMB, in printing)
  • Taehyong Kim, Lawrence Bone, Murali Ramanathan, and Aidong Zhang Mathematical Network Model for Bone Mineral Density(BMD) and Bone Quality Assessment. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2011)
  • Taehyong Kim, Kang Li, Aidong Zhang, Surajit Sen, and Murali Ramanathan. A Computational Model of Mitigating Disease Spread in Spatial Networks. International Journal of Artificial Life Research (IJALR)
  • Liang Ge, Nan Du, Aidong Zhang. Finding Informative Genes from Multiple Microarray Experiments: A Graph-based Consensus Maximization Model. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011): 506-511
  • Xiujuan Lei, Shuang Wu, Liang Ge, Aidong Zhang. Clustering PPI Data Based on Bacteria Foraging Optimization Algorithm. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011): 96-99
  • Nan Du, Supriya D Mahajan, Stanley A. Schwartz, Bindukumar B Nair, Chiu Bin Hsiao and Aidong Zhang. An Artificial fish swarm based supervised gene rank aggregation algorithm for informative genes studies. IASTED Conference on Computational Intelligence and Bioinformatics (IASTED CIB 2011) : 114-121
  • Nan Du, Supriya D Mahajan, Stanley A. Schwartz, Bindukumar B Nair, Chiu Bin Hsiao and Aidong Zhang. Gene Co-AdaBoost: A Semi-Supervised Approach for Classifying Gene Expression Data. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2011) : 531-535
    2010

  • Lei Shi and Aidong Zhang Semi-supervised learning Protein Complexes from Protein Interaction Networks. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010), Hong Kong, Dec. 18-21. 2010
  • Lei Shi, Young-Rae Cho and Aidong Zhang. Prediction of Protein Function from Connectivity of Protein Interaction Networks. International Journal of Computional Bioscience, Vol.1, No.1, 2010
  • Lei Shi, Young-Rae Cho and Aidong Zhang. Functional Flow Simulation Based Analysis of Protein Interaction Network. IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2010),Philadelphia, PA, May 31-Jun 3, 2010
  • Taehyong Kim, Jaehan Koh, Kang Li, Murali Ramanathan, and Aidong Zhang Identification of Critical Location on A Microstructural Bone Network. IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  • Taehyong Kim, Woo-Chang Hwang, Aidong Zhang, Surajit Sen, and Murali Ramanathan Multi-Agent Modeling of the South Korean Avian Influenza Epidemic. BMC Infectious Disease
  • 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
  • Pritam Chanda, Jianmei Yang, Aidong Zhang and Murali Ramanathan. On Mining Statistically Significant Attribute Association Information. SDM 2010: 141-152
    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
    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
    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
    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.
    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



    • Copyright © 2001 CSEBiORG. All rights reserved.
      The State University of New York at Buffalo
      201 Bell Hall, Buffalo, New York 14260
      Last Modified: 8/15/2004