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Modeling gene regulation from paired expression and chromatin accessibility data. Proceedings of the National Academy of Sciences. vol. 114 no. 25 E4914-E4923 (2017). A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation. Scientific Report 6, 22656 (2016). NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data. Bioinformatics 31 (20), 3330-3338 (2015). Computational probing protein-protein interactions targeting small molecules. Bioinformatics. 32 (2), 226-234 (2015). A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors. Methods. 83: 3-17 (2015). Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PLoS One 8 (11), e78518 (2013). Network predicting drug's anatomical therapeutic chemical code. Bioinformatics 29 (10), 1317-1324 (2013). ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions. Nucleic Acids Research 41 (4), e53-e53 (2012). Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection. BMC Systems Biology. 6 (1), S15 (2012) A combinatorial model and algorithm for globally searching community structure in complex networks. Journal of Combinatorial Optimization. 23 (4), 425-442 (2012). A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data. Handbook of Research on Computational Methodologies in Gene Regulatory Networks 450-475 (2010). Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res. 38: 5959-5969 (2010). Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res. 37: 5943-5958 (2009). Evaluating protein similarity from coarse structures. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6 (4), 583-593 (2009). A network biology study on circadian rhythm by integrating various omics data. OMICS A Journal of Integrative Biology. 13 (4), 313-324 (2009). Condition specific subnetwork identification using an optimization model. Lecture Notes in Operations Research. 9, 333-340 (2008). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC bioinformatics. 8 (1), 391 (2008). Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics. 22 (19), 2413-2420 (2006). Exploring protein's optimal HP configurations by self-organizing mapping. Journal of bioinformatics and computational biology. 3 (02), 385-400 (2005). A new trust region method for nonlinear equations. Mathematical Methods of Operations Research. 58 (2), 283-298 (2003).