39. Lin L.*, Shen S.*, Jiang P., Sato S., Davidson BL., Xing Y. (2009) (*joint first authors).

38. Shen S., Warzecha CC., Carstens RP., Xing Y. (2009) MADS+: discovery of differential splicing events from Affymetrix exon junction array data. Bioinformatics, in press. [journal] [MADS+ software]

37. Monteys AM., Spengler RM., Wan J., Tecedor L., Lennox KA., Xing Y., Davidson BL. (2009) Structure and activity of putative intronic miRNAs promoters. RNA, in press.

36. Lin CL., Evans V., Shen S., Xing Y., Richter JD. (2009) The nuclear experience of CPEB: implications for RNA processing and translational control. RNA, in press.

35. Lu H., Lin L., Sato S., Xing Y., Lee CJ. (2009) Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS Computational Biology, in press.

34. Borchert GM., Gilmore BL., Spengler RM., Xing Y., Lanier W., Bhattacharya D., Davidson BL. (2009) Adenosine deamination in human transcripts generates novel microRNA binding sites. Human Molecular Genetics. 18:4801-4807. [journal] [pdf]

33. Warzecha CC., Shen S., Xing Y., Carstens RP. (2009) The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biology, in press. [journal]

32. Lin L.*, Liu S.*, Brockway H., Seok J., Jiang P., Wong WH., Xing Y. (2009) Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Research, 12: e90 (*joint first authors). [journal] [pdf] [Supplemental Data] [JETTA software]

31. Lin L., Jiang P., Shen S., Sato S., Davidson BL., Xing Y. (2009) Large-scale analysis of exonized mammalian-wide interspersed repeats (MIRs) in primate genomes. Human Molecular Genetics. 18: 2204-2214 [journal] [pdf]

30. Boudreau R., McBride J., Martins I., Shen S., Xing, Y., Carter B., Davidson, BL. (2009) Non-allele-specific silencing of mutant and wildtype huntingtin demonstrates therapeutic efficacy in Huntington's disease mice. Molecular Therapy. 17:1053-1063 [journal][pdf]

29. Packer, AN., Xing, Y., Harper SQ., Jones, L., Davidson, BL. (2008) The bi-functional microRNA miR-9/miR-9* regulates REST and CoREST and is down-regulated in Huntington's Disease. Journal of Neuroscience. 28: 14341-14346 [journal] [pdf] [This Week in the Journal of Neuroscience].

28. Lin, L., Shen, S., Tye, A., Cai, JJ., Jiang, P., Davidson, BL., Xing, Y. (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genetics. 4(10):e1000225. [journal] [UI news release] [GenomeWeb Daily News] [News and Commentary at Heredity] [Supplemental Data]

27. Kapur, K., Jiang, H., Xing, Y., Wong, WH. (2008) Cross-hybridization modeling on Affymetrix Exon Arrays. Bioinformatics. 24: 2887-2893 [software] [journal] [pdf]

26. Roy, M., Kim, N., Xing, Y., Lee, C. (2008) The effect of intron length on exon creation ratios during evolution of mammalian genomes. RNA. 14: 2261-2273 [journal] [pdf]

25. Xing, Y.*, Stoilov, P., Kapur, K., Han, A., Jiang, H., Shen, S., Black, DL., Wong, WH*. (2008) MADS: a New and Improved Method for Analysis of Differential Alternative Splicing by Exon-tiling Microarrays. RNA.14(8):1470-1479 (* joint corresponding authors). [journal] [pdf] [dataset] [software]

24. Chiao, E, Elezar, M, Xing, Y.,Xiong, A., Kmet, M., Millan, M., Glenn, J., Wong, WH., Baker, J. (2008) Isolation and Transcriptional Profiling of Purified Hepatic Cells Derived from Human Embryonic Stem Cells. Stem Cells, 26(8):2032-2041.. [journal] [pdf]

23. Cahoy, J., Emery, B., Kaushal, A., Foo, L., Zamanian, J., Christopherson, K., Xing, Y., Lubischer, J., Krieg, P., Krupenko, S., Thompson, W. and Barres, B. (2008) A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function. Journal of Neuroscience. 28(1):264-278. [journal] [pdf] [This Week in the Journal of Neuroscience] [faculty of 1000 Must Read]

22. Calarco, JA.*, Xing, Y.*, Caceres, M.*, Calarco, JP., Xiao, X., Pan, Q., Lee, C., Preuss, T. and Blencowe, B. (2007) Global analysis of alternative splicing differences between humans and chimpanzees. Genes and Development. 21:2963-2975. (* joint first authors). [journal] [pdf] [news report] [highlight by Cell]

21. Xing, Y. *, Ouyang, Z., Kapur, K., Scott, MP., Wong, WH*. (2007) Assessing the conservation of mammalian gene expression using high-density Exon Arrays. Molecular Biology and Evolution. 24(6):1-3. (* joint corresponding authors). [journal] [pdf] [dataset]

20. Kapur, K., Xing, Y., Ouyang, Z., Wong, WH. (2007) Exon arrays provide accurate assessments of gene expression. Genome Biology. 8:R82. [journal] [pdf] [software]

19. Xing, Y. (2007) Genomic analysis of alternative splicing in cancers. Frontiers in Biosciences. 12:4034-4041. [journal] [pdf]

18. Parker, DS., Hsiao, RL., Xing, Y., Resch, A., Lee, C. (2007) Solving the problem of trans-genomic query with alignment tables. IEEE Transactions on Computational Biology and Bioinformatics. 2007:1073. [pdf]

17. Lee , JA., Xing, Y., Nguyen, D., Xie, J., Lee, C., Black, DL. (2007) Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements. PLoS Biology. 5(2):e40. [journal] [pdf]

16. Xing, Y., Kapur, K., Wong, WH. (2006) Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE. 1(1):e88. [journal] [pdf] [software]

15. Xing,Y. *#, Yu,T. *, Wu, Y., Roy, M., Kim, J., Lee,C.# (2006) An expectation-maximization algorithm for probabilistic reconstruction of full-length isoforms from splice graphs. Nucleic Acids Research. 34:3150-3160 (# joint corresponding authors; * joint first authors). [journal] [pdf] [source code]

14. Xing,Y., Wang, Q., Lee,C. (2006) Evolutionary divergence of exon flanks: A dissection of mutability and selection. Genetics. 173(3):1787-91. [journal] [pdf]

13. Xing, Y., Lee, C. (2006) Alternative splicing and RNA selection pressure: evolutionary consequences for eukaryotic genomes. Nature Reviews Genetics. 7:499-509. [journal] [pdf]

12. Xing,Y., Lee,C. (2006) Can RNA selection pressure distort the measurement of Ka/Ks? Gene. 370:1-5. [journal] [pdf]

11. Xing,Y., Lee,C. (2005) Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. PLoS Genetics. 1(3):e34. [journal] [pdf]

10. Xing,Y., Lee,C. (2005) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc. Natl. Acad. Sci. U.S.A. 102:13526-13531.[journal] [pdf]

9. Xing,Y., Lee,C. (2005) Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics. 21: 3701-3703. [journal] [pdf]

8. Resch,A., Xing, Y., Alekseyenko, A., Modrek, B., Lee, C. (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Research. 32:1261-9. [journal] [pdf]

7. Xing,Y., Lee,C. (2004) Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends in Genetics. 20:472-5. [journal] [pdf]

6. Resch,A., Xing,Y., Modrek,B.,Gorlick,M., Riley,R., Lee, C. (2004) Assessing the impact of alternative splicing on domain interactions in the human proteome. Journal of Proteome Research. 3:76-83. [journal] [pdf]

5. Xing,Y., Resch,A.,Lee,C. (2004) The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Research. 14(3):426-4. [journal] [pdf] [database]

4. Grasso,C.,Modrek,B.,Xing,Y., Lee,C. (2004) Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs. Pac. Symp. Biocomputing. World Scientific: Singapore 29-41. [pdf]

3. Zewail,A.*, Xie, M.W.*, Xing, Y., Lin, L., Zhang, P.F., Zou, W., Saxe, J.P., and Huang, J. (2003) Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc. Natl. Acad. Sci. U.S.A. 100: 3345-3350. [journal] [pdf]

2. Xing,Y., Xu, Q, Lee,C. (2003) Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Letters. 555(3):572-8. [journal] [pdf]

1. Lee C, Atanelov L, Modrek B, Xing Y. (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Research. 31(1):101-5. [journal] [pdf]