Xing Laboratory of RNA Genomics and Bioinformatics

Publications

Submitted and In Preparation  
  • 53. Yao C., Biesinger J., Wan J., Weng L., Busch A., Xing Y., Xie X., Shi Y. (2012) The Global CstF64-RNA interaction landscape reveals mechanisms for poly(A) site selection and novel functions. Proc. Natl. Acad. Sci. U.S.A., In Revision.
  • 52. Park JW., Tokheim C., Shen S., Xing Y. (2012) Identify differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods in Molecular Biology: Deep Sequencing Data Analysis, Invited Book Chapter, Under Review.

  • 2012  
  • 51. Brown SJ., Stoilov P.+, Xing Y.+ (2012) Chromatin and epigenetic regulation of pre-mRNA processing. Human Molecular Genetics, Invited Review, In Press (+ joint corresponding authors).
  • 50. Ramachandran S., Karp P., Jiang P., Ostedgaard LS., Walz AE., Fisher JT., Keshavjee S., Lennox KA., Jacobi AM., Rose SD., Behlke MA., Welsh MJ.+, Xing Y.+, McCray PB+. (2012) A microRNA network regulates expression and biosynthesis of wild-type and ΔF508 mutant cystic fibrosis transmembrane conductance regulator. Proc. Natl. Acad. Sci. U.S.A., (+ joint corresponding authors). [journal] [news release]
  • 49. Dittmar KA.*, Jiang P.*, Park JW.*, Amirikian K, Wan J., Shen S., Xing Y.+, Carstens RP+. (2012) Genome-wide determination of a broad ESRP-regulated post-transcriptional network by high throughput sequencing. Molecular and Cellular Biology, 32(8):1468-82 (+ joint corresponding authors; * joint first authors). [journal] [dataset]
  • 48. Kim J.*, Zhao K.*, Jiang P.*, Lu ZX., Wang J., Murray JC.+, Xing Y+. (2012) Transcriptome landscape of the human placenta. BMC Genomics, 13:115 (+ joint corresponding authors; * joint first authors). [journal] [dataset]
  • 47. Shen S., Park JW., Huang J, Dittmar KA, Lu ZX., Zhou Q., Carstens RP., Xing Y. (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Research, 40(8): e61. [journal] [MATS software]

  • 2011  
  • 46. Lu ZX., Jiang P., Xing Y. (2011). Genetic variation of pre-mRNA alternative splicing in human populations. Wiley Interdisciplinary Reviews: RNA (WIREs RNA), 3(4):581-92. [journal][pdf]
  • 45. Xu W., Seok J., Mindrinos MN., Schweitzer A., Jiang H., Wilhelmy J., Clark T., Kapur K., Xing Y., Faham M., Storey J., Moldawer LL., Maier RV., Tompkins RG., Wong WH., Davis R., Xiao W., and the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. (2011) A human transcriptome array for high throughput clinical studies. Proc. Natl. Acad. Sci. U.S.A., 108(9):3707-3712. [journal]
  • 44. Shen S.*, Lin L.*, Cai JJ., Jiang P., Kenkel EJ., Stroik MR., Sato S., Davidson BL., Xing Y. (2011) Widespread establishment and regulatory impact of Alu exons in human genes. Proc. Natl. Acad. Sci. U.S.A., 108(7):2837-2842 (*joint first authors). [journal] [news report][UI news release][NIH Biomedical Beat]
  • 43. Lu ZX.*, Jiang P.*, Cai JJ., Xing Y. (2011) Context-dependent robustness to 5' splice site polymorphisms in human populations. Human Molecular Genetics, 20:1084-1096. (*joint first authors). [journal]
  • 42. Liu S.*, Lin L.*, Jiang P., Wang D., Xing Y. (2011) A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Research, 39(2):578-588. (*joint first authors). [journal][dataset]

  • 2010  
  • 41. Warzecha CC., Jiang P., Amirikian, K., Dittmar, KA., Lu, H., Shen, S., Guo, W., Xing Y., Carstens RP. (2010) An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. EMBO J, 29:3286-3300. [journal][editorial][news bite]
  • 40. Lin L.*, Shen S.*, Jiang P., Sato S., Davidson BL., Xing Y. (2010) Evolution of alternative splicing in primate brain transcriptomes. Human Molecular Genetics, 19:2958-2973 (*joint first authors). [journal][pdf]
  • 39. Au KF., Jiang H., Lin L., Xing Y., Wong WH. (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research, 38:4570-4578. [journal] [Genomeweb News]
  • 38. Shen S., Warzecha CC., Carstens RP., Xing Y. (2010) MADS+: discovery of differential splicing events from Affymetrix exon junction array data. Bioinformatics, 26:268-269. [journal] [pdf] [MADS+ software]
  • 37. Monteys AM., Spengler RM., Wan J., Tecedor L., Lennox KA., Xing Y., Davidson BL. (2010) Structure and activity of putative intronic miRNAs promoters. RNA, 16(3):495-505 [journal]
  • 36. Lin CL., Evans V., Shen S., Xing Y., Richter JD. (2010) The nuclear experience of CPEB: implications for RNA processing and translational control. RNA, 16(2):338-348 [journal]

  • 2009  
  • 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, 5(12): e1000608. [journal] [pdf] [Genomeweb Daily News]
  • 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, 6(5):546-563. [journal] [pdf]
  • 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]

  • 2008  
  • 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]

  • 2007  
  • 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]

  • 2006  
  • 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]

  • 2005  
  • 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]

  • 2004  
  • 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]

  • 2003  
  • 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]