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Department of Bioengineering @ UIC
  

 
 
 
 
 

Recent Publications
(Click here for early publications)

 

  • Szilard Asztalos, Peter Gann, Meghan Hayes, Larisa Nonn, Craig Beam, Yang Dai, Elizabeth Wiley, and Debra Tonetti, "Gene expression patterns in the human breast after pregnancy ", Cancer Prevention Research, in press.

  • Cavallari H. Larisa, Vicki L. Groo, Marlos A. Viana, Yang Dai, Shitalben R. Patel, and Thomas D. Stamos, "Circulating aldosterone and mineralocorticoid receptor genotype are predictive of potassium response to spironolactone in heart failure ", Pharmacotherapy, in press.

  • Jonna Frasor, Aisha Weaver, Madhumita Pradhan, Yang Dai, Lance D. Miller, Chin-Yo Lin, and Adina Stanculescu, "Positive Crosstalk between Estrogen Receptor and NFKB in Breast Cancer", Cancer Research, 69(23):8918-8925, 2009. Abstract

  • Peter Larsen and Yang Dai, "Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks", Proceeding of the 5th International Symposium on Bioinformatics Research and Applications (eds. I. Mandoiu, G. Narasimhan, and Y. Zhang), Lecture Notes in Computer Science, Springer Verlag, Vol. 5542 (2009) pp. 40-51. PDF

  • Shantanu Dutt, Yang Dai, Huan Ren, and Joel Fontanarosa, "Selection of Multiple SNPs in Case-Control Association Study Based on a Discretized Network Flow Approach", Proceeding of the First Conference of Bioinformatics and Computational Biology (BICoB 2009), Lecture Notes in Computer Science, Springer Verlag, Vol. 5462, pp.1611-3349, 2009. PDF

  • Yang Dai, Eyad Almasri, Peter Larsen,Guanrao Chen, "Structure Learning of Genetic Regulatory Networks Based on Knowledge Derived from Literature and Microarray Gene Expression Measurements", Book Chapter, Computational Methodologies in Gene Regulatory Networks (S. Das, D. Caragea, W. H. Hsu, S. M. Welch eds.), IGI Global, pp. 289-309, 2009 PDF

  • Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai, "Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data ", Proceeding of the 4th International Symposium on Bioinformatics Research and Applications, Lecture Notes in Bioinformatics, Vol. 4983 (eds.by I.I. Mandoiu, Raj Sunderraman, and A. Zelikovsky), Springer Verlag, pp. 434-443, 2008. PDF

  • Eyad Almasri, Peter Larsen, Guanrao Chen and Yang Dai, "Incorprating Literature Knowledge in Baysian Network for Inferring Gene Networks with Gene Expression Data", Proceeding of the 4th International Symposium on Bioinformatics Research and Applications, Lecture Notes in Bioinformatics, Vol. 4983 (eds. by I.I. Mandoiu, Raj Sunderraman, and A. Zelikovsky), Springer Verlag, pp.184-195, 2008. PDF

  • Guanrao Chen, Peter Larsen, Eyad Almasri,and Yang Dai, "Rank-based edge reconstruction for scale-free genetic regulatory networks", BMC Bioinformatics, 9:75, 2008. PDF

  • Oleksiy Karpenko, Lei Huang and Yang Dai, "A probabilistic meta-predictor for the MHC class II binding peptides ", Immunogenetics, 60:1, pp.25-36, 2008. PDF

  • Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai, "A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments", BMC Bioinformatics, 8:317, 2007. PDF

  • Lei Huang, Oleksiy Karpenko, Naveen Murugan and Yang Dai, "Building a Meta-predictor for MHC Class II-Binding Peptides", Book Chapter, Immunoinformatics: Predicting Immunogenicity In Silico (Flower, D.R. ed.), Humana Press Inc., Totowa, NJ. pp. 355-364, 2007. PDF

  • Zhengdeng Lei and Yang Dai, "Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction", BMC Bioinformatics, 7:491, 2006. PDF

  • Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai, "Correlated discretized expression score: a method for identifying gene interaction networks from time course microarray expression data", Proceedings of the 28th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS) (2006). pp.5842-5845. PDF

  • Guanrao Chen, Peter Larsen, Eyad Almasri and Yang Dai, "Sample scale-free gene regulatory network using gene ontology", Proceedings of the 28th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS) (2006). pp.5523-5526. PDF

  • Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai and Hui Lu, "Improved protein fold assignment using support vector machines", International Journal of Bioinformatics Research and Applications, 1(3):319-334, 2006. PDF

  • Lei Huang and Yang Dai, "Direct prediction of T cell epitopes using SVM with novel sequence encoding schemes", Journal of Bioinformatics and Computational Biology, 4(1):93-107, 2006. PDF

  • Naveen Murugan and Yang Dai, "Prediction of MHC Class II binding peptides based on an iterative learning model", Immunome Research, 1:6, 2005. PDF

  • Zhengdeng Lei and Yang Dai, "An SVM-based system for predicting protein subnuclear localizations", BMC Bioinformatics, 6:291, 2005.PDF

  • J. Balcazar, Y. Dai and O.Watanabe, "Provably fast training algorithms for support vector machines", Theory of Computing Systems, 2005, in press.

  • S. Kuroda, A.S. Virdi, Y. Dai, S, Shott and D. R. Sumner, "Patterns and localization of gene expression during intramembranous bone regeneration in the rat femoral marrow ablation model", Calcified Tissue International, 77(4):212-25, 2005.

  • Zhengdeng Lei and Yang Dai, "A class of new kernels based on a matrix of high-scored pairs of k-peptides and its applications in prediction of protein sub-cellular localization", LNCS Transactions on Computational Systems Biology II, Springer-Verlag, pp.48-58, 2005. PDF

  • Oleksiy Karpenko, Jianming Shi and Yang Dai, "Prediction of MHC class II binders using the ant colony search strategy", Artificial Intelligence in Medicine, Vol. 35, pp.147-156, 2005. PDF

  • Aladino De Ranieri, Amarjit S. Virdi, Shinji Kuroda, S. Shott, Yang Dai and Dale R. Sumner, "Local application of rhTGF-beta2 modulates dynamic gene expression in a rat implant model", Bone, 36(5) pp.931-940, 2005. PDF

  • Zhengdeng Lei and Yang Dai, "A new kernel based on a matrix of high-scored pairs of tri-peptides and its applications in prediction of protein sub-cellular localization", Proc. of International Workshop on Bioinformatics Research and Applications, Lecture Notes in Computer Science (LNCS), Springer-Verlag, Berlin, No.3515, pp.903-910, 2005.PDF

  • Y. Dai, J. M. Shi and W.S. Yang, "Conical partition algorithm for maximizing the sum of several dc ratios", Journal of Global Optimization, Vol.31, pp.253-270, 2005. PDF

  • L. Huang and Y. Dai, "A support vector machine approach for prediction of T cell epitopes", Proc. of the Third Asia-Pacific Bioinformatics Conference (APBC2005), Singapore, Jan. 17-21, 2005. pp.312-328, Imperial College Press. PDF

  • D. Z. Chen, O. Daescu, Y. Dai, N. Katoh, J. Xu and X. Wu, "Efficient algorithms and implementations for optimizing the sum of linear fractional functions, with applications", Journal of Combinatorial Optimization, Vol.9, pp.69-90, 2005. PDF

  • A.S. Virdi, A.D. Ranieri, S. Kuroda, Y. Dai and D.R. Sumner, "Anabolic agents and gene expression around the bone implant interface", Journal of Musculoskeletal & Neuronal Interactions, 4(4), pp.388-389, 2004.

  • R.E. Langlois, A. Diec, Y. Dai and H. Lu, "Kernel based approach for protein fold prediction from Sequence", Proc. of the 26th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS2004) (CD-ROM), 2004.

  • G. Chen and Y. Dai, "A new distance measurement for clustering time-course gene expression data", Proc. of the 26th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS2004) (CD-ROM), 2004.

  • Z. Lei and Y. Dai, "A novel approach for prediction of protein subcellular localization from sequence using fourier analysis and support vector machines", Proc. of 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics, Seattle, August 22, 2004, pp. 11-17. PDF

  • B. Liu, Y. Dai, X. Li, W. S. Lee and P. Yu, "Building text classifiers using positive and unlabeled examples", Proc. of the Third IEEE International Conference on Data Mining(ICDM'03), Melbourne, Florida, November 19-22, 2003, pp.179-188. PDF

  • H-M. Lu, S. Gupta and Y. Dai, "Reduce large diagonals in kernel matrices through semidefinite programming", Proc. of 3rd ACM SIGKDD Workshop on Data Mining in Bioinformatics, 2003, pp.57-62. PDF

  • H-M. Lu, L. Huang and Y. Dai, "Application of support vector regression to Quantitative Structure-Activity Relationships(QSAR)", Proc. of the 5th International Conference on Computational Biology and Genome Informatics, Carey, North Carolina, USA, September 26-30, 2003.

  • L. Huang, H-M. Lu and Y. Dai, "Feature selection of support vector regression for Quantitative Structure-Activity Relationships(QSAR)", Proc. of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '03), Las Vegas, Nevada, June, 2003. PDF
  • Y. Dai, S. Kim and M. Kojima, "Computing all nonsingular solutions of cyclic-n polynomial using polyhedral homotopy continuation methods", Journal of Computational and Applied Mathematics, Vol.152, No.1-2, 2003, pp.83-97. PDF

  • Y. Dai and Mike Landis, "Feature selection in tumor classification using microarray gene expression data", Proc. of International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '02), Las Vegas, Nevada, June 2002. PDF

  • A. Sutou and Y. Dai, "Global optimization approach to unequal sphere packing problems in 3D", Journal of Optimization Theory and Applications, Vol.114, No.3, 2002, pp.671-694. PDF

  • J. Balcazar, Y. Dai and Osamu Watanabe, "Provably fast support vector regression using random sampling", Proc. of SIAM Workshop in Discrete Mathematics and Data Mining, Arlington, VA, April 2002, pp.19-29. PDF

  • Y. Dai and J. M. Shi,"Conical partition algorithm for maximizing the sum of several dc ratios", Proc. of the 5th International Conference on Optimization: Techniques and Applications(ICOTA2001), Hong Kong, 2001, pp. 600-608. ( A detail version of the paper )

  • J. Balcazar, Y. Dai, and O. Watanabe, "Provably fast training algorithms for support vector machines", Proc. of the first IEEE International Conference on Data Mining, IEEE Computer Society, 2001, pp.43--50. PDF

  • J. Balcazar, Y. Dai, and O. Watanabe, "An application of a random sampling technique to primal-form maximal-margin classifiers", Proc. of the 12th International Conference on Algorithmic Learning Theory, Lecture Notes in Artificial Intelligence, LNAI 2225, Springer-Verlag, 2001, pp119-134. PS

  • Y. Dai and N. Katoh, "Generalized LMT-heuristics for several new classes of optimal triangulations", Computational Geometry: Theory and Application 17, 2000, pp.51-68. PDF

  • D. Z. Chen, O. Daescu, Y. Dai, N. Katoh, J. Xu and X. Wu, "Efficient algorithms and implementations for optimizing the sum of linear fractional functions, with applications", Proc. of the 11th Annual SIAM-ACM Symposium on Discrete Algorithms (SODA), San Francisco, 2000, pp.707-716. PS

  • A. Takeda, Y. Dai, M. Kojima and M. Fukuda, "Towards implementations of successive convex relaxation methods for nonconvex quadratic optimization problems", in Approximation and Complexity in Numerical Optimization: Continuous and Discrete Problems, (P. M. Pardalos, Eds), 2000, pp. 489-510, Kluwer Academic Publishers. PS

 
 
 
 
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