Xing Laboratory of RNA Genomics and Bioinformatics

Publications

2017  
  • 88. Park E., Pan Z., Zhang Z., Lin L., Xing Y. (2017) The expanding landscape of alternative splicing variation in human populations. American Journal of Human Genetics, Invited Review, In press.
  • 87. Zhang Z., Xing Y. (2017) CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome. Nucleic Acids Research, 45(16):9260-9271. [journal][software]
  • 86. Zhou H., Molinie B., Daneshvar K., Pondick JV., Wang J., Van Wittenberghe NO., Xing Y., Giallourakis CC., Mullen AC. (2017) Identification and characterization of m6A circular RNA epitranscriptomes. Cell Reports, 20(9):2262-2276. [journal]
  • 85. Park E., Guo J., Shen S., Demirdjian L., Wu YN., Lin L., Xing Y. (2017) Population and allelic variation of A-to-I RNA editing in human transcriptomes. Genome Biology, 18:143. [journal]
  • 84. Wang J., Pan Y., Shen S., Lin L., Xing Y. (2017) rMATS-DVR: rMATS discovery of Differential Variants in RNA. Bioinformatics, 33(14):2216-2217. [journal][software]
  • 2016  
  • 83. Lin L., Park JW., Ramachandran S., Zhang Y., Tseng YT., Shen S., Waldvogel H., Curtis M., Faull R., Troncoso J., Ross C., Davidson BL.+, Xing Y.+ (2016) Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease. Human Molecular Genetics, 25(16):3454-3466. (+ joint corresponding authors). [journal]
  • 82. Molinie B.*, Wang J.*, Lim KS., Hillebrand R., Lu ZX., Van Wittenberghe N., Howard BD., Daneshvar K., Mullen A., Dedon P., Xing Y.+, Giallourakis CC.+ (2016) m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveals the census and complexity of the m6A epitranscriptome. Nature Methods, 13(8):692-8. (+ joint corresponding authors; * joint first authors). [journal] [UCLA news release] [GenomeWeb news story] [News & Views by Nature Methods]
  • 81. Lam MP., Venkatraman V., Xing Y., Lau E., Cao Q., Ng DC., Su AI., Ge J., Van Eyk JE., Ping P. (2016) Data-driven approach to determine popular proteins for targeted proteomics translation of six organ systems. J Proteome Res, 15(11):4126–4134. [journal]
  • 80. Shen S., Wang Y., Wang C., Wu YN., Xing Y. (2016) SURVIV: Survival Analysis of mRNA Isoform Variation. Nature Communications, 7:11548. [journal] [UCLA news release] [GenomeWeb news story]
  • 79. Park JW.+, Chung S., Rouchka E., Tseng YT., Xing Y.+ (2016) rMAPS: RNA map analysis and plotting server for alternative exon regulation. Nucleic Acids Research. 44(W1):W333-8. (+ joint corresponding authors).[journal] [rMAPS web server]
  • 78. Yang Y.*, Park JW.*, Bebee TW., Warzecha CC., Guo Y., Shang X., Xing Y.+, Carstens RP.+ (2016) Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during the epithelial to mesenchymal transition. Molecular and Cellular Biology, 36(11):1704-1719. (+ joint corresponding authors; * joint first authors) [journal]
  • 77. Lin L., Jiang P., Park JW., Wang J., Lu ZX., Lam MP., Ping P., Xing Y. (2016) The contribution of Alu exons to the human proteome. Genome Biology, 17:15. [journal] [Genome Biology Research Highlight: Proteome diversification by genomic parasites]
  • 76. Cieply B.*, Park JW.*, Nakauka-Ddamba A., Bebee TW., Guo Y., Shang X., Lengner CJ., Xing Y.+, Carstens RP.+ (2016) Multiphasic and dynamic changes in alternative splicing during induction of pluripotency are coordinated by numerous RNA binding proteins. Cell Reports, 15, 1–9. (+ joint corresponding authors; * joint first authors). [journal]
  • 75. Ji X.*, Park JW.*, Bahrami-Samani E., Lin L., Duncan-Lewis C., Pherribo G., Xing Y.+, Liebhaber SA.+ (2016) αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome. Nucleic Acids Research, 44 (5): 2283-2297. (+ joint corresponding authors; * joint first authors). [journal]
  • 74. Katrib A., Hsu W., Bui A., Xing Y. (2016) “RADIOTRANSCRIPTOMICS”: A synergy of imaging & transcriptomics in clinical assessment. Quantitative Biology, 4(1): 1–12. [journal]
  • 73. Damianov A., Ying Y., Lin CH., Lee JA., Tran D., Vashisht AA., Bahrami-Samani E., Xing Y., Martin KC., Wohlschlegel JA., Black DL. (2016) Rbfox splicing regulators are recruited to pre-mRNA as part of a novel multi-protein complex, LASR. Cell, 165(3): 606-619.
  • 72. Ruscetti M., Dadashian EL., Guo W., Quach B., Mulholland DJ., Park JW., Tran LM., Kobayashi N., Bianchi-Frias D., Xing Y., Nelson PS., Wu H. (2016) HDAC inhibition impedes epithelial–mesenchymal plasticity and suppresses metastatic, castration-resistant prostate cancer. Oncogene, 35(29):3781-95. [journal]
  • 2015  
  • 71. Lam MP., Venkatraman V., Cao Q., Wang D., Dincer TU., Lau E., Su AI., Xing Y., Ge J., Ping P., Van Eyk JE. (2015) Prioritizing Proteomics Assay Development for Clinical Translation. J Am Coll Cardiol., 14;66(2):202-4. [journal]
  • 70. Stein S.*, Lu ZX.*, Bahrami-Samani E., Park JW., Xing Y. (2015) Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Research, 43 (22): 10612-10622. ( * joint first authors). [journal] [rPGA software]
  • 69. Bebee TW.*, Park JW.*, Sheridan KI., Warzecha CC., Cieply BW., Rohacek AM., Xing Y.+, Carstens RP.+ (2015) The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development, Elife, 4:e08954.(+ joint corresponding authors; * joint first authors). [journal]
  • 68. Wang J.*, Lu ZX.*, Tokheim C., Miller SE., Xing Y. (2015) Species-specific exon loss in human transcriptomes, Molecular Biology and Evolution, 32(2):481-494. (* joint first authors). [journal]
  • 67. Wang J.*, Ma MCJ.*, Mennie AK.*, Pettus JM., Xu Y., Lin L., Traxler MG., Jakoubek J., Atanur SS., Aitman TJ., Xing Y.+, Kwitek AE.+ (2015) Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat, Circulation: Cardiovascular Genetics, 8:316-326. (+ joint corresponding authors; * joint first authors). [journal]
  • 66. Lu ZX.*, Huang Q.*,Park JW.*, Shen S., Lin L., Tokheim C., Henry MD.+, Xing Y.+ (2015) Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization, Molecular Cancer Research, 13(2):305-18. (+ joint corresponding authors; * joint first authors). [journal] [highlight by MCR]
  • 2014  
  • 65. Shen S.*, Park JW.*, Lu ZX., Lin L., Henry MD., Wu YN., Zhou Q., Xing Y. (2014) rMATS: Robust and Flexible Detection of Differential Alternative Splicing from Replicate RNA-Seq Data, Proc. Natl. Acad. Sci. U.S.A., 111(51):E5593-601. (* joint first authors). [journal]
  • 64. Batista PJ.*, Molinie B.*, Wang J.*, Qu K., Zhang J., Li L., Bouley DM., Lujan E., Haddad B., Daneshvar K., Carter AC., Flynn RA., Zhou C., Lim KS., Dedon P., Wernig M., Mullen AC., Xing Y.+, Giallourakis CC.+, Chang HY.+ (2014) m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell, 15(6):707-19. (+ joint corresponding authors; * joint first authors). [journal]
  • 63. Guo R.*, Zheng L.*, Park JW., Lv R., Chen H., Jiao F., Xu W., Mu S., Wen H., Qiu J., Wang Z., Yang P., Wu F., Hui J., Fu X., Shi X., Shi Y., Xing Y.+, Lan F.+, Shi Y.+ (2014) BS69/ZMYND11 Reads and Connects Histone H3.3 Lysine 36 Trimethylation Decorated Chromatin to Regulated Pre-mRNA Processing. Molecular Cell, 56(2):298-310. (+ joint corresponding authors; * joint first authors). [journal]
  • 62. Lackford B., Yao C., Charles GM., Weng L., Zheng X., Choi EA., Xie X., Wan J., Xing Y., Freudenberg JM., Yang P., Jothi R., Hu G., Shi Y. (2014) Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal, EMBO J., 33(8):878-889. [journal]
  • 61. Tokheim C., Park JW., Xing Y. (2014) PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data, Genomics, Proteomics & Bioinformatics, 12(2):105-109. [journal]
  • 60. Boudreau RL., Jiang P., Gilmore BL., Spengler RM., Tirabassi R., Nelson JA., Ross CA., Xing Y.+, Davidson BL.+ (2014) Transcriptome-wide discovery of microRNA binding sites in human brain, Neuron, 81(2):294-305. (+ joint corresponding authors). [journal]
  • 59. McLoughlin HS., Wan J., Spengler RM., Xing Y., Davidson BL. (2014) Human-specific microRNA regulation of FOXO1: implications for microRNA recognition element evolution, Hum. Mol. Genet., 23(10):2593-2603. [journal]
  • 2013  
  • 58. Yao C., Choi EA., Weng L., Xie X., Wan J., Xing Y., Moresco JJ., Tu PG., Yates JR 3rd., Shi Y. (2013) Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing. RNA, 19:1781-1790. [journal]
  • 57. Heinicke LA., Nabet B., Shen S., Jiang P., van Zalen S., Cieply B., Russell JE., Xing Y., Carstens RP. (2013) The RNA Binding Protein RBM38 (RNPC1) Regulates Splicing during Late Erythroid Differentiation. PLoS ONE, 8(10): e78031. [journal]
  • 56. Zhao K., Lu ZX., Park JW., Zhou Q., Xing Y. (2013) GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-Seq data, Genome Biology, 14:R74. [journal] [GLiMMPS software]
  • 55. Park JW., Tokheim C., Shen S., Xing Y. (2013) Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods in Molecular Biology: Deep Sequencing Data Analysis, Invited Book Chapter, 1038:171-179. [book] [PubMed]
  • 54. Ramachandran S., Karp PH., Osterhaus SR., Jiang P., Wohlford-Lenane C., Lennox KA., Jacobi AM., Praekh K., Rose SD., Behlke MA., Xing Y., Welsh MJ., McCray Jr PB. (2013) Post-transcriptional Regulation of CFTR Expression and Function by MicroRNAs. Am. J. Respir. Cell Mol. Biol., 49(4):544-551. [journal]
  • 53. Ji X.*, Wan J.*, Vishnu M., Xing Y.+, Liebhaber SA.+ (2013) The Poly-C Binding Proteins, αCPs, Act as Global Regulators of Alternative Polyadenylation. Molecular and Cellular Biology, 33(13):2560-2573 (+ joint corresponding authors; * joint first authors). [journal]

  • 2012  
  • 52. Yao C., Biesinger J., Wan J., Weng L., Busch A., Xing Y., Xie X., Shi Y. (2012) Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc. Natl. Acad. Sci. U.S.A., 109(46):18773-18778. [journal]
  • 51. Brown SJ., Stoilov P.+, Xing Y.+ (2012) Chromatin and epigenetic regulation of pre-mRNA processing. Human Molecular Genetics, Invited Review, 21(R1):90-96 (+ joint corresponding authors). [journal]
  • 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., 109(33):13362-13367 (+ 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] [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., 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., 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 MW.*, Xing Y., Lin L., Zhang PF., Zou W., Saxe JP., 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]