Book Chapters Cui, Y. Bridging Genotype and Phenotype: Causal Pathways from DNA to Complex Traits. In Deng, H.W. (ed), Current Topics in Human Genetics: Studies of Complex Diseases. World Scientific, Singapore, in press. Cui, Y. (2006) Elucidating gene regulatory networks underlying complex phenotypes: Genetical genomics and Bayesian network. In Shannon, F. (ed), Microarrays and Transcription Networks. Landes Bioscience, Georgetown, 114-126. Journal Articles 24. Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L and Cui Y. (2007) An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Human Molecular Genetics 16:1381-1390 23. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW and Cui Y. (2007) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Research. 35: D51-D54. 22. He H, Cai L, Skogerbo G, Deng W, Liu T, Zhu X, Wang Y, Jia D, Zhang Z, Tao Y, Zeng H, Aftab MN, Cui Y, Liu G, Chen R (2006) Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Research 34:2976-2983. 21. Bao L, Wei L, Peirce JL, Homayouni R, Li H, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D and Cui Y. (2006) Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relations. Mammalian Genome 17:575-583. 20. Bao, L. and Cui, Y. (2006) Functional impacts of nonsynonymous single nucleotide polymorphisms: selective constraint and structural environments. FEBS Letters 580: 1231-1234. 19. Li, H., Chen, H., Bao, L., Manly, K.F., Chesler, E.J., Lu, L., Wang, J., Zhou, M., Williams, R.W. and Cui, Y. (2006) Integrative Genetic Analysis of Transcription Modules: Towards Filling the Gap between Genetic Loci and Inherited Traits, Human Molecular Genetics 15: 481-492. 18. Deng, W., Zhu, X., Skogerbo, G., Zhao, Y., Fu, Z., Wang, Y., He, H., Cai, L., Sun, H., Liu, C., Li, B., Bai, B., Wang, J., Jia, D., Sun, S., He, H., Cui, Y., Wang, Y., Bu, D. and Chen, R. (2006) Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Research 16:20-29. 17. Li H, Lu L, Manly KF, Chesler EJ, Bao L, Wang J, Zhou M, Williams RW, Cui Y (2005) Inferring Gene Transcriptional Modulatory Relations: A Genetical Genomics Approach. Human Molecular Genetics 14:1119-1125. 16. Bao L, Zhou M, Cui Y (2005) nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Research 33: W480-W482. 15. Bao L, Cui Y (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information Bioinformatics 21:2185-2190. 14. Li H, Zhou M, Cui Y (2005) Ranking Gene Regulatory Network Models with Microarray Data and Bayesian Network. in Lecture Notes in Computer Science Volume 3327:109 - 118 Springer, Heidelberg. 13. Cui Y, Zhou M, Wong WH (2004) Integrated analysis of microarray data and gene function Information. OMICS: A Journal of Integrative Biology 8: 106-117. 12. Zhou M, Cui Y (2004) GeneInfoViz: constructing and visualizing gene relation networks. In Silico Biology 4:323-332. 11. Qi Z, Cui Y, Fang W, Ling L, Chen RS (2004) Autosomal Similarity Revealed by Eukaryotic Genomic Comparison. Journal of Biological Physics, 30:305-312. 10. Ling L, Wang J, Cui Y, Li W, Chen RS (2002) Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms. Molecular Phylogenetics and Evolution 25: 101-111. 9. Cui Y, Wong WH, Bornberg-Bauer E., Chan HS (2002) Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes, Proceedings of the National Academy of Sciences USA 99:809-814. 8. Cui Y, Wong WH (2000) Multiple sequence information provides protection against mis-specified potential energy function. Physical Review Letters 85:5242-5245. 7. Cui Y, Chen RS, Wong WH (2000) The coevolution of cell senescence and diploid sexual reproduction in unicellular organisms, Proceedings of the National Academy of Sciences 97:3330-3335. 6. Cui Y, Ling LJ, Chen RS, Bai LC, Yuan JG, Qiang BQ (1999) Molecular dynamics simulation of site-directed mutagenesis of HIV type 1 Tat trans-activator. Chinese Science Bulletin 44:708-711. 5. Cui Y, Ling LJ, Chen RS (1998) A fast algorithm for computation of solvent accessible surface area of biomolecules. Acta Biophysica Sinica 14:799-801. 4. Sun ZR, Cui Y, Ling LJ, Guo Q, Chen RS (1998) Molecular dynamics simulation of protein folding with supersecondary structure constraints. Journal of Protein Chemistry 17:765-769. 3. Wong WH, Cui Y, Chen RS (1998) Torsional Relaxation for Biopolymers. Journal of Computational Biology 5:655-665. 2. Cui Y, Chen RS, Wong WH (1998) Molecular dynamic simulation of chaperonin-mediated protein folding. Journal of Protein Chemistry 17:377-380. 1. Cui Y, Chen RS, Wong WH (1998) Protein folding simulation using genetic algorithm and supersecondary structure constraints. Proteins: Structure, Function and Genetics,31:247-257.