114. Shen L*, Ma X*, Wang Y*, Wang Z, Zhang Y, Pham HQH, Tao X, Cui Y, Wei J, Lin D, Abeywanada T, Hardikar S, Halabelian L, Smith N, Chen T, Barsyte-Lovejoy D, Qiu S, Xing Y, Yang Y. (2024) Loss-of-function mutation in PRMT9 causes abnormal synapse development by RNA alternative splicing. Nature Communications, 15:2809.

113. Wang Y*, Xie Z*, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. (2024) rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nature Protocols, 19:1083-1104.


112. Wang R, Helbig I, Edmondson AC, Lin L, Xing Y. (2023) Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Briefings in Bioinformatics, 24(5):bbad284.
111. Chen X, Yang HT, Zhang B, Phillips JW, Cheng D, Rigo F, Witte ON, Xing Y, Black DL. (2023) The RNA binding proteins hnRNP H and F regulate splicing of a MYC dependent HRAS exon in prostate cancer cells. PNAS, 120(28):e2220190120.

110. Wang F*, Xu Y*, Wang R*, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y+, Lin L+. (2023) TEQUILA-seq: A versatile and low-cost method for targeted long-read RNA sequencing. Nature Communications, 14:4760.

109. Pan Y*, Phillips JW*, Zhang BD*, Noguchi M*, Kutschera E, McLaughlin J, Nesterenko PA, Mao Z, Bangayan NJ, Wang R, Tran W, Yang HT, Wang Y, Xu Y, Obusan MB, Cheng D, Lee AH, Kadash-Edmondson KE, Champhekar A, Puig-Saus C, Ribas A, Prins RM, Seet CS, Crooks GM, Witte ON, Xing Y. (2023) IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. PNAS, 120(21):e2221116120.

108. Gao Y*, Wang F*, Wang R*, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, and Xing Y. (2023) ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. Science Advances, 9(3):eabq507.


107. Lefaudeux D, Sen S, Jiang K, Hoffmann A, Arriola JGS, Miller N, Cheng Z, Chen E, Mondal S, Spreafico R, Johnson T, Wissink E, Ghosh S, Black D, Lin C-H, Xiao X, Bahn JH, Cass A, Hsiao E, Smale S, Lo H-H, Ernst J, Jaroszewicz A, Pellegrini M, Morselli M, Xing Y, Park E, and Sriram Kosuri. (2022) Kinetics of mRNA nuclear export regulate innate immune response gene expression. Nature Communications, 13(1):7197.

106. Xing Y, Wang R, Davidson BL. (2022) Mis-splicing in Huntington’s disease: harnessing the power of comparative transcriptomics. Trends in Neurosciences, 45(2):91-3. )


105.  Lu C*, Glisovic-Aplenc T*, Bernt KM, Nestler K, Cesare J, Cao L, Lee H, Fazelinia H, Chinwalla A, Xu Y, Shestova O, Xing Y, Gill S, Li M, Garcia B, Aplenc R. (2021) Longitudinal large-scale semiquantitative proteomic data stability across multiple instrument platforms. Journal of Proteome Research, 20(11):5203-11. (*joint first authors)

104. Yeom K-H*, Pan Z*, Lin C-H, Lim H, Xiao W, Xing Y, Black DL. (2021) Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Research, 31(6):1106-19.

103. Park E, Jiang Y, Hao L, Hui J, Xing Y. (2021) Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes. Genome Biology, 22:77.

102. Pan Y, Kadash-Edmondson KE, Wang R, Phillips J, Liu S, Ribas A, Aplenc R, Witte ON, Xing Y. (2021) RNA dysregulation: An expanding source of cancer immunotherapy targets. Trends in Pharmacological Sciences, 42(4):268-82.

101. Xin R*, Gao Y*, Gao Y, Wang R, Kadash-Edmondson KE, Liu B, Wang Y, Lin L, Xing Y. (2021) isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nature Communications, 12:266. (*joint first authors)

100. Gao Y*, Liu Y*, Ma Y, Liu B, Wang Y+, Xing Y+. (2021) abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. Bioinformatics, 37(15):2209-11. (+joint corresponding authors; *joint first authors)


99. Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Pan Z, Stein S, Xie Z, Park E, Wu YN, Xing Y. (2020) Detecting allele-specific alternative splicing from population-scale RNA-seq data. American Journal of Human Genetics, 107:461-72.

98. Zhang Y, Yang H, Kadash-Edmondson K, Pan Y, Pan Z, Davidson BL, Xing Y. (2020) Regional variation of splicing QTLs in human brain. American Journal of Human Genetics, 107:196-210.

97. Annapragada AV, Sikora AG, Bollard CM, Conejo-Garcia JR, Cruz CR, Demehri S, Demetriou M, Demirdjian L, Fong L, Horowitz MM, Hutson A, Kadash-Edmondson K, Kufe D, Lipkin SM, Liu S, McCarthy C, Morgan M, Morris ZA, Pan Y, Pasquini MC, Schoenberger S, Van Allen EM, Vilar E, Xing Y, Zha W, the IOTN Consortium, Odunsi K. (2020) The Cancer Moonshot Immuno-Oncology Translational Network (IOTN): Accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. Journal for ImmunoTherapy of Cancer, 8(1):e000796.

96. Lee S, Sears MJ, Zhang Z, Li H, Salhab I, Krebs P, Xing Y, Nah HD, Williams T, Carstens RP (2020) Cleft lip and cleft palate (CL/P) in Esrp1 KO mice is associated with alterations in epithelial-mesenchymal crosstalk. Development, 147(21):dev187369.

95. Phillips JW*, Pan Y*, Tsai BL, Xie Z, Demirdjian L, Xiao W, Yang HT, Zhang Y, Lin CH, Cheng D, Hu Q, Liu S, Black DL, Witte ON+, Xing Y.+ (2020) Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. PNAS, 117(10):5269-79 (+joint corresponding authors; *joint first authors)

94. Chen H, Gu L, Orellana EA, Wang Y, Guo J, Liu Q, Wang L, Shen Z, Wu H, Gregory RI, Xing Y, Shi Y. (2020) METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing. Cell Research, 30:544-7.


93. Gao Y, Liu B, Wang Y, Xing Y. (2019) TideHunter: Efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics, 35(14):i200-7. [software]

92. Zhang Z*, Pan Z*, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y. (2019) Deep learning-augmented RNA-seq analysis of transcript splicing. Nature Methods, 16:307-10. (*joint first authors)

91. Bahrami-Samani E, Xing Y. (2019) Discovery of allele-specific protein-RNA interactions in human transcriptomes. American Journal of Human Genetics, 104(3):492-502.


90. Qin Z, Stoilov P, Zhang XG+, Xing Y.+ (2018) SEASTAR: Systematic evaluation of alternative transcription start sites in RNA. Nucleic Acids Research, 46(8):e45. (+joint corresponding authors)

89. Zhang Z, Park E, Lin L, Xing Y. (2018) A panoramic view of RNA modifications: Exploring new frontiers. Genome Biology, 19(1):11.

88. Park E, Pan Z, Zhang Z, Lin L, Xing Y. (2018) The expanding landscape of alternative splicing variation in human populations. American Journal of Human Genetics, 102(1):11-26.


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):9260-71.

86. Zhou H, Molinie B, Daneshvar K, Pondick JV, Wang J, Van Wittenberghe NO, Xing Y, Giallourakis CC, Mullen AC. (2017) Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs. Cell Reports, 20(9):2262-76.

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.

84. Wang J, Pan Y, Shen S, Lin L, Xing Y. (2017) rMATS-DVR: rMATS discovery of differential variants in RNA. Bioinformatics, 33(14):2216-7. [software]


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):3454-66. (+joint corresponding authors)

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) [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 Research, 15(11):4126-34.

80. Shen S, Wang Y, Wang C, Wu YN, Xing Y. (2016) SURVIV: Survival analysis of mRNA isoform variation. Nature Communications, 7:11548. [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) [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):1704-19. (+joint corresponding authors; *joint first authors)

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. [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)

75. Ji X*, Park JW*, Bahrami-Samani E, Lin L, Duncan-Lewis C, Pherribo G, Xing Y+, Liebhaber SA+ (2016) aCP 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):2283-7. (+joint corresponding authors; *joint first authors)

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.

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 proteins regulate splicing as part of a large multiprotein complex LASR. Cell, 165(3):606-19.

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.


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 American College of Cardiology, 14;66(2):202-4.

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):10612-22. (*joint first authors). [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)

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):481-94. (*joint first authors)

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, 8:316-26. (+joint corresponding authors; *joint first authors)

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) [highlight by MCR]


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, PNAS, 111(51):E5593-601. (*joint first authors)

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)

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 regulate pre-mRNA processing. Molecular Cell, 56(2):298-310. (+joint corresponding authors; *joint first authors)

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, The EMBO Journal, 33(8):878-89.

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):105-9.

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)

59. McLoughlin HS, Wan J, Spengler RM, Xing Y, Davidson BL. (2014) Human-specific microRNA regulation of FOXO1: Implications for microRNA recognition element evolution, Human Molecular Genetics, 23(10):2593-2603.


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 CstF64t in mammalian mRNA 3′ processing. RNA, 19:1781-90.

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.

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.

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, 1038:171-9. [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. American Journal of Respiratory Cell and Molecular Biology, 49(4):544-51.

53. Ji X*, Wan J*, Vishnu M, Xing Y+, Liebhaber SA.+ (2013) The poly-C binding proteins, aCPs, act as global regulators of alternative polyadenylation. Molecular and Cellular Biology, 33(13):2560-73. (+joint corresponding authors; *joint first authors)


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. PNAS, 109(46):18773-8.

51. Brown SJ, Stoilov P+, Xing Y.+ (2012) Chromatin and epigenetic regulation of pre-mRNA processing. Human Molecular Genetics, Invited Review, 21(R1):90-6. (+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 F508 mutant cystic fibrosis transmembrane conductance regulator. PNAS, 109(33):13362-7. (+joint corresponding authors). [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). [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)

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. [MATS software]


46. Lu ZX, Jiang P, Xing Y. (2011). Genetic variation of pre-mRNA alternative splicing in human populations. Wiley Interdisciplinary Reviews: RNA, 3(4):581-92.

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, the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. (2011) A human transcriptome array for high throughput clinical studies. PNAS, 108(9):3707-12.

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. PNAS, 108(7):2837-42. (*joint first authors). [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, 20:1084-96. (*joint first authors)

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):578-88. (* joint first authors). [dataset]


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. The EMBO Journal, 29:3286-300. [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, 19:2958-73. (*joint first authors)

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, 38:4570-8. [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, 26:268-9.

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.

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):338-48.


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. [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. 18:4801-7.

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):546-63.

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)

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, 18:2204-14.

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, 17:1053-63.


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. J. Neuroscience, 28:14341-6. [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. [UI news release] [GenomeWeb Daily News] [News and Commentary at Heredity]

27. Kapur K, Jiang H, Xing Y, Wong WH. (2008) Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics, 24:2887-93.

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, 14:2261-73.

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):1470-9. (+joint corresponding authors)

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):2032-41.

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. J. Neuroscience, 28(1):264-78. [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, Blencowe B. (2007) Global analysis of alternative splicing differences between humans and chimpanzees. Genes and Development, 21:2963-75. (*joint first authors). [news report]

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)

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

19. Xing Y. (2007) Genomic analysis of alternative splicing in cancers. Frontiers in Biosciences, 12:4034-41.

18. Parker DS, Hsiao RL, Xing Y, Resch A, Lee C. (2007) Solving the problem of trans-genomic query with alignment tables. IEEE Trans. Comput. Biol. Bioinform., 2007:1073.

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.


16. Xing Y, Kapur K, Wong WH. (2006) Probe selection and expression index computation of Affymetrix exon arrays. PLoS ONE, 1(1):e88.

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, 34:3150-60. (+joint corresponding authors; *joint first authors)

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

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

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


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.

10. Xing Y, Lee C. (2005) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. PNAS, 102:13526-31.

9. Xing Y, Lee C. (2005) Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics, 21:3701-3.


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.

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.

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. J. Proteome Research, 3:76-83.

5. Xing Y, Resch A, Lee C. (2004) The multiassembly problem: Reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Research, 14(3):426-34.

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.


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. PNAS, 100:3345-50.

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.

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