Publications

Publications since the inception of the group on 1/26/2005.

1. Raymond Stallings, Kihoon Yoon, Stephen Kwek and Daijin Ko. The Origin and Imporantance of Chromosome Imbalances in Cander. To appear in Cancer Genetics and Cytogenetics 2007
2. Amitava Karmaker, Mark Doderer and Stephen Kwek. Discovery of Transcription Factors Using Protein Subcellular Localization Prediction and Gene Expression Profile Analysis. To appear in Machine Learning: Models, Technologies and Applications 2007.
3. Mark Doderer, Kihoon Yoon, and Stephen Kwek. Species Independent Protein Localization Prediction for Multicompartmentalized Proteins. To appear in Machine Learning: Models, Technologies and Applications 2007.
4. Amitava Karmaker, Stephen Harris and Stephen Kwek. identification of cis-Regulatory Elements from Cross-Genome Comparison and Gene Expression Profile Analysis. To appear in Biocomputing 2007
5. Amitava Karmaker and Stephen Kwek. An Approach for Analyzing DNA Copy Number Aberrations in Genome Using aCGH Profiles. To appear in Biocomputing 2007
6. Edward Salinas, Amitava Karmaker, Stephen Harris and Stephen Kwek. Identifying Correlations between Genes and Transcription Co-factors using Expression Profile. To appear in Proc. of Conf. on Computational Biology and Genome Informatics 2007.
7. Amitava Karmaker, Stephen Kwek. An Iterative Refinement Approach for Data Cleaning. International Journal of Intelligent Data Analysis (IDA), 2006 (To appear).
8. Mark Doderer, Kihoon Yoon, John Salinas and Stephen Kwek, 2006, Protein Subcellular Localization Prediction using a Hybrid of Similarity search and Error-Correcting Output Code Techniques That Produces Interpretable Results, To appear in In Silico Biology. Manuscript no. isb-2006-0034
9. Amitava Karmaker, Stephen Kwek. A Boosting Approach to remove Class Label Noise. (Extended version). Special issue on "Ensemble Approaches" for the International Journal on Hybrid Intelligent Systems (IJHIS), 2006, published by IOS Press, The Netherlands and Advanced Knowledge International, Australia.
10. Kihoon Yoon and Stephen Kwek, 2005, An Unsupervised Learning Approach to Resolving the Data Imbalanced Issue in Supervised Learning Problems in Functional Genomics. Fifth International Conference on Hybrid Intelligent Systems (HIS'05) pp. 303-308
11. Amitava Karmaker, Stephen Kwek. A Boosting Approach to remove Class Label Noise". Fifth International Conference on Hybrid Intelligent Systems (HIS'05), 2005, pp. 206-211
12. Amitava Karmaker, Stephen Kwek. Incorporating an EM-Approach for Handling Missing Attribute-Values in Decision Tree Induction. Fifth International Conference on Hybrid Intelligent Systems (HIS'05), 2005, pp. 309-314.
13. Kihoon Yoon and Stephen Kwek, A Divide and Conquer Approach for Dealing with Data Imbalanced Problem, with Applications in Functional Genomics. To appear in the proceedings of Hybrid Intelligent Systems 2005.
14. R. Akbani and S. kwek, 2005. Adapting SVM to Predict Translation Initiation Sites in the Human Genome Extended abstract to appear in proceedings of CSB 2005
15. K. Yoon and S. Kwek, 2005, A Filtering Approach to Splice Site Predictions in Human Genes, Advances in Bioinformatics and its Applications Vol 8.
16. D. Dolly, S. Goldman and S. Kwek 2005, Real-Valued Multiple-Instance Learning with Queries, To appear in Journal of Computer and System Science.

1. Kihoon Yoon, Ravi Dashnamoorthy, Mark Doderer, Amy Wiles, Daijin Ko, Stephen Kwek, Alex Bishop. Determining the Off-target Effects within Drosophila Genome-Wide Screen. Keystone Symposium, Systems Biology and Regulatory Networks (X5), Steamboat Springs, Colorado 2007.
2. Amitava Karmaker, Eddie Salinas, Kihoon Yoon, Mark Doderer, Stephen Harris and Stephen Kwek 2007, The Construction of a Human Transcription Subnet Using Tissue-Specific Gene Expression Profile and Cross Genome Comparison, with E2F5 and RELB as case studies. Keystone Symposium, Systems Biology and Regulatory Networks (X5), Steamboat Springs, Colorado 2007.
3. Development of Web-based Bioinformatics Tools to Reveal Relationships between Gene Expression, Gene Function and Anticancer Drug Response. Russell Kruzelock, Wan-Hong Wu, James Courage, Adrienne Lovell, Robert Geller, Keying Ye, Stephen Kwek, Kyriakos Papadopoulos. European Organization for Research and Treatment of Cancer 2006.
4. Kihoon Yoon, Stephen Kwek and Luiz Penelva. A Bioinformatics Approach to Identify Post-transcriptional Regulatory Signals on Untranslated Region (UTRs). Translational Control 2006.
5. K. Yoon, S. Kwek and L. Penalva, 2006, Identifying post-transcriptional regulatory signals on UTR regions of Human mRNAs, Translational control at Cold Spring Harbor Laboratory (CSHL).
6. Kihoon Yoon and Stephen Kwek, 2005, Analysis of human promoters and gene expressions by an integrative approach: constructing an index toward gene expression patterns, 3rd Annual Rocky Mountin Regional Bioinformatics Conference (Rocky'05).
7. Mark Doderer, Stephen Kwek, John Salinas and Kihoon Yoon, 2005, Layered Classification using Homologous Similarity and Error-Correcting Output Coding for Predicting Protein Subcellular Localization, 3rd Annual Rocky Mountain Regional Bioinformatics Conference (Rocky'05).
8. Amitava Karmaker, Kihoon Yoon and Stephen Kwek. A study to identify interactions between transcription factors and non-housekeeping genes to determine expression regulation of cancer genes. Third Annual Rocky Mountain Regional Bioinformatics Conference (Rocky'05).
9. A. Karmaker, K. Yoon and S. Kwek, 2005, Determining transcription factors that trigger non-housekeeping genes of various human tissues, Genome Informatics at Cold Spring Harbor Laboratory (CSHL).
10. K. Yoon and S. Kwek, 2005, An Expectation-Maximization approach for dealing with imbalanced data for human splice site prediction problem, International conference on Intelligent Systems for Molecular Biology (ISMB).
11. M. Doderer, J. Salinas, K. Yoon and S. Kwek, 2005. Using error-correcting output coding for predicting multi-class subcellular localization, International conference on Intelligent Systems for Molecular Biology (ISMB).