Dai Lab - Publications

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	Selected Publications of Yang Dai

Bioinformatics, Data Mining, Machine Learning, Optimizations 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 Bioinformatics, Springer Verlag, in press, 2009. 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 Bioinformatics, Springer Verlag, in press 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, in press. 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. Xelikovsky), Springer Verlag, pp. 434-443, 2008. 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. Xelikovsky), Springer Verlag, pp. 184-195, 2008. PDF Guanrao Chen, Peter Larsen, Eyad Almasri, Yang Dai, Rank-based edge reconstruction for scale-free genetic regulatory networks, BMC Bioinformatics, 9:75, 2008. PDF Oleksiy Karpenko, Lei Huang, 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, 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 L. Huang, O. Karpenko, N. Murugan and Y. Dai, Building a Meta-predictor for MHC Class II Binding Peptides, Book Chapter, Immunoinformatics: Predicting Immunogenicity In Silico, (D. R Flower 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 P. Larsen, E. Almasri, G. Chen and Y. 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 G. Chen, P. Larsen, E. Almasri and Y. 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, Vol. 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 localization," BMC Bioinformatics, vol. 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. PDF 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 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), pp.212-215, 2005. 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," Proceedings 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 M. Kojima, Y. Dai, K. Fujisawa, S. Kim and A. Takeda, "Parallel implementation of polyhedral continuation methods for systems of polynomial equations," Mathematical Software, ICMS2002 (Arjeh M Cohen, Xiao-Shan Gao and Nobuki Takakayama, Editors), World Scientific, Singapore, 2002. 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 Y. Dai and N. Katoh, "On computing new classes of optimal triangulations with angular conditions," Lecture Notes in Computer Science 1449 (1998) pp.15-24, Springer-Verlag. Proc. of 4th Annual International Computing and Combinatorics Conference. PS Y. Dai K. Iwano and N. Katoh, "A new probabilistic evaluation of Karger's randomized algorithm for minimum cut problems," Information Processing Letters 64 (1997) pp.255-261. PDF Y. Dai, "A unified d.c approach to circular separating problems in high dimension," Proc. of Second International Symposium on Operations Research and its Applications Lecture Notes in Operations Research 2 (1996) pp.56-64, World Publishing Corporation. Y. Dai, H. Imai, K. Iwano, N. Katoh, K. Ohtsuka and N. Yoshimura, "A new unified approximate approach to the minimum cut problem and its variants using minimum range cut algorithms," Discrete Applied Mathematics 65 (1996) pp.167-190. PDF Y. Dai, J. M. Shi and Y. Yamamoto, "Global optimization problem with multiple reverse convex constraints and its application to out-of-roundness problem," Journal of the Operations Research Society of Japan 39 (1996) pp. 356-371. Y. Dai, K. Iwano and N. Katoh, "A new approximate algorithm for the minimum k-cut problem by using minimum range k-cut algorithm," Journal of Information and System Society of Japan 114-C (1994) pp.438-443. (in Japanese) Y. Dai and Y. Yamamoto, "A continuous deformation algorithm for variational inequality problems on polytopes," Mathematical Programming 64 (1994) pp.103-122. Y. Dai, H. Imai, K. Iwano and N. Katoh, "How to treat delete requests in semi-online problems," Proceedings of 4th International Symposium, Algorithms and Computation, Lecture Notes in Computer Science 762 (1993) pp.48-57, Springer-Verlag. Y. Dai and Dolf Talman, "Linear stationary point problems on unbounded polyhedra," Mathematics of Operations Research 18 (1993) pp.635-644. Y. Dai, K. Sekitani and Y. Yamamoto, "A variable dimension algorithm with Dantzig-Wolfe decomposition for the structured stationary point problems," ZOR - Methods and Models of Operations Research 36 (1992) pp.23-53. Y. Dai, G. ven der Laan, A.J.J. Talman and Y. Yamamoto, "A simplicial algorithm for the nonlinear stationary point problem on an unbounded polyhedron," SIAM Journal on Optimization 2 (1991) pp.151-165. Y. Dai and Y. Yamamoto, "The path following algorithm for stationary point problems on polyhedral cones," Journal of the Operations Research Society of Japan 30 (1988) pp.181-198. Computational Physics Y. Dai, A. B. Borisov, J. W. Longworth, K. Boyer and C. K. Rhodes, "Quadratic Reciprocity, the Higgs Mass, and Complexity," Journal of Advanced Studies of Contemporary Mathematics, 10 (2) (2005) pp.149-154. Y. Dai, A. B. Borisov, J. W. Longworth, K. Boyer and C. K. Rhodes, "Cryptographic unification of mass and space links neutrino lavour (ne /nm) t ransformations with the cosmological constant L", International Journal of Modern Physics Letters A 18 (2003) pp.4257-4283., Y. Dai, A. B. Borisov, J. W. Longworth K. Boyer and C. K. Rhodes, "Gamma-ray bursts and the particle mass scale," Proc. of 6th of biennial International Conference on Electromagnetics in Advanced Applications (invited talk), Politecnico di Torino, (1999) pp.3-14. Physics A. B. Borisov, J. Davis, X. Y. Song, Y. Koshman, Y. Dai, K. Boyer and C. K. Rhod es, "Saturated multikilovolt x-ray amplification with Xe clusters: single-pulse o bservation of Xe(L) spectral hole burning," Journal of Physics, B, Atomic, Molecular and Optical Physics, 36 (2003) pp. L285-L294. A. B. Borisov, X. Y. Song, F. Frigeni, Y. Koshman, Y. Dai, K. Boyer and C. K . Rhodes, "Ultrabright multikilovolt coherent tunable x-ray source at Lambda~ 2.71-2.93Å," Journal of Physics, B, Atomic, Molecular and Optical Physics, 36 (2003) p p.3433-3455. A. B. Borisov, X. Y. Song, F. Frigeni, Y. Dai, Y. Koshiman, A. A. Shroeder, J. D avis, K. Boyer and C. K. Rhodes, "Ultraviolet-infrared wavelength scalings for strong field induced L-shell emissions from Kr and Xe clusters," Journal of Phsics B : Atomic, Molecular and Optical Physics, 35 (2002) L461-L467. A. B. Borisov, S. Cameron, T. S. Luk, T. Nelson, A. Van Tassle, J. Santoro, W. A . Schroeder, Y. Dai, J. W. Longworth, K. Boyer and C. K. Rhodes, "Bifurcation mode of relativistic and charge-displacement self-channeling," Journal of Physics, B, Atomic, Molecular and Optical Physics 34 (2001) pp.2167-2176. A. B. Borisov, S. Cameron, Y. Dai, J. Davis, T. Nelson, W. A. Schroeder, J. W. Longworth, K. Boyer and C. K. Rhodes, "Dynamics of optimized stable channel formation of intense laser pulses with the relativistic/charge-displacement mechanism," Journal of Physics, B. Atomic, Molecular and Optical Physics, 32 (1999) pp.3511-3525. go back to home
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