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, Page 114-126.

Journal Articles

25. Bao L, Zhou M and Cui Y (2008) CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Research. In press.

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 and 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 KF, Chesler EJ, Lu L, Wang J, Zhou M, Williams RW 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 and Cui Y (2005) Inferring Gene Transcriptional Modulatory Relations: A Genetical Genomics Approach. Human Molecular Genetics 14:1119-1125.

16. Bao L, Zhou M and Cui Y (2005) nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Research 33: W480-W482.

15. Bao L and 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 and 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 and Wong WH (2004) Integrated analysis of microarray data and gene function Information. OMICS: A Journal of Integrative Biology 8: 106-117.

12. Zhou M and 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 and 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 and 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, and 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 and 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 and Wong WH (2000) The coevolution of cell senescence and diploid sexual reproduction in unicellular organisms, Proceedings of the National Academy of Sciences USA 97:3330-3335.

6. Cui Y, Ling LJ, Chen RS, Bai LC, Yuan JG and 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 and 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 and 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 and Chen RS (1998) Torsional Relaxation for Biopolymers. Journal of Computational Biology 5:655-665.

2. Cui Y, Chen RS and Wong WH (1998) Molecular dynamic simulation of chaperonin-mediated protein folding. Journal of Protein Chemistry 17:377-380.

1. Cui Y, Chen RS and Wong WH (1998) Protein folding simulation using genetic algorithm and supersecondary structure constraints. Proteins: Structure, Function and Genetics 31:247-257.