| Year |
Citation |
Score |
| 2024 |
Wang Y, Xie Z, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nature Protocols. PMID 38396040 DOI: 10.1038/s41596-023-00944-2 |
0.317 |
|
| 2023 |
Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y, Lin L. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nature Communications. 14: 4760. PMID 37553321 DOI: 10.1038/s41467-023-40083-6 |
0.351 |
|
| 2023 |
Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y. ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. Science Advances. 9: eabq5072. PMID 36662851 DOI: 10.1126/sciadv.abq5072 |
0.334 |
|
| 2021 |
Yeom KH, Pan Z, Lin CH, Lim HY, Xiao W, Xing Y, Black DL. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Research. PMID 33832989 DOI: 10.1101/gr.273904.120 |
0.314 |
|
| 2021 |
Xin R, Gao Y, Gao Y, Wang R, Kadash-Edmondson KE, Liu B, Wang Y, Lin L, Xing Y. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nature Communications. 12: 266. PMID 33436621 DOI: 10.1038/s41467-020-20459-8 |
0.36 |
|
| 2020 |
Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Stein S, Xie Z, Park E, Wu YN, Xing Y. Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data. American Journal of Human Genetics. PMID 32781045 DOI: 10.1016/J.Ajhg.2020.07.005 |
0.409 |
|
| 2020 |
Zhang Y, Yang HT, Kadash-Edmondson K, Pan Y, Pan Z, Davidson BL, Xing Y. Regional Variation of Splicing QTLs in Human Brain. American Journal of Human Genetics. PMID 32589925 DOI: 10.1016/J.Ajhg.2020.06.002 |
0.403 |
|
| 2020 |
Lee S, Sears MJ, Zhang Z, Li H, Salhab I, Krebs P, Xing Y, Nah HD, Williams T, Carstens RP. Cleft lip and cleft palate (CL/P) in KO mice is associated with alterations in epithelial-mesenchymal crosstalk. Development (Cambridge, England). PMID 32253237 DOI: 10.1242/Dev.187369 |
0.326 |
|
| 2020 |
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. Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. Proceedings of the National Academy of Sciences of the United States of America. PMID 32086391 DOI: 10.1073/Pnas.1915975117 |
0.412 |
|
| 2020 |
Chen H, Gu L, Orellana EA, Wang Y, Guo J, Liu Q, Wang L, Shen Z, Wu H, Gregory RI, Xing Y, Shi Y. METTL4 is an snRNA mAm methyltransferase that regulates RNA splicing. Cell Research. PMID 31913360 DOI: 10.1038/S41422-019-0270-4 |
0.362 |
|
| 2019 |
Gao Y, Liu B, Wang Y, Xing Y. TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics (Oxford, England). 35: i200-i207. PMID 31510677 DOI: 10.1093/Bioinformatics/Btz376 |
0.349 |
|
| 2019 |
Zhang Z, Pan Z, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y. Deep-learning augmented RNA-seq analysis of transcript splicing. Nature Methods. 16: 307-310. PMID 30923373 DOI: 10.1038/S41592-019-0351-9 |
0.401 |
|
| 2019 |
Bahrami-Samani E, Xing Y. Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes. American Journal of Human Genetics. 104: 492-502. PMID 30827501 DOI: 10.1016/J.Ajhg.2019.01.018 |
0.424 |
|
| 2018 |
Qin Z, Stoilov P, Zhang X, Xing Y. SEASTAR: systematic evaluation of alternative transcription start sites in RNA. Nucleic Acids Research. PMID 29546410 DOI: 10.1093/Nar/Gky053 |
0.502 |
|
| 2018 |
Zhang Z, Park E, Lin L, Xing Y. A panoramic view of RNA modifications: exploring new frontiers. Genome Biology. 19: 11. PMID 29382368 DOI: 10.1186/S13059-018-1394-4 |
0.321 |
|
| 2018 |
Park E, Pan Z, Zhang Z, Lin L, Xing Y. The Expanding Landscape of Alternative Splicing Variation in Human Populations. American Journal of Human Genetics. 102: 11-26. PMID 29304370 DOI: 10.1016/J.Ajhg.2017.11.002 |
0.421 |
|
| 2017 |
Zhang Z, Xing Y. CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome. Nucleic Acids Research. 45: 9260-9271. PMID 28934506 DOI: 10.1093/Nar/Gkx646 |
0.416 |
|
| 2017 |
Zhou C, Molinie B, Daneshvar K, Pondick JV, Wang J, Van Wittenberghe N, Xing Y, Giallourakis CC, Mullen AC. Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs. Cell Reports. 20: 2262-2276. PMID 28854373 DOI: 10.1016/J.Celrep.2017.08.027 |
0.314 |
|
| 2017 |
Stein S, Bahrami-Samani E, Xing Y. Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants. Methods in Molecular Biology (Clifton, N.J.). 1648: 129-142. PMID 28766294 DOI: 10.1007/978-1-4939-7204-3_10 |
0.442 |
|
| 2017 |
Park E, Guo J, Shen S, Demirdjian L, Wu YN, Lin L, Xing Y. Population and allelic variation of A-to-I RNA editing in human transcriptomes. Genome Biology. 18: 143. PMID 28754146 DOI: 10.1186/S13059-017-1270-7 |
0.352 |
|
| 2017 |
Wang J, Pan Y, Shen S, Lin L, Xing Y. rMATS-DVR: rMATS discovery of Differential Variants in RNA. Bioinformatics (Oxford, England). PMID 28334241 DOI: 10.1093/Bioinformatics/Btx128 |
0.394 |
|
| 2016 |
Zhou R, Park JW, Chun RF, Lisse TS, Garcia AJ, Zavala K, Sea JL, Lu ZX, Xu J, Xing Y, Adams JS, Hewison M. Concerted effects of heterogeneous nuclear ribonucleoprotein C1/C2 to control vitamin D-directed gene transcription and RNA splicing in human bone cells. Nucleic Acids Research. PMID 27672039 DOI: 10.1093/Nar/Gkw851 |
0.362 |
|
| 2016 |
Lin L, Park JW, Ramachandran S, Zhang Y, Tseng YT, Shen S, Waldvogel HJ, Curtis MA, Faull RL, Troncoso JC, Ross CA, Davidson BL, Xing Y. Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease. Human Molecular Genetics. PMID 27378699 DOI: 10.1093/Hmg/Ddw187 |
0.432 |
|
| 2016 |
Molinie B, Wang J, Lim KS, Hillebrand R, Lu ZX, Van Wittenberghe N, Howard BD, Daneshvar K, Mullen AC, Dedon P, Xing Y, Giallourakis CC. m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nature Methods. PMID 27376769 DOI: 10.1038/Nmeth.3898 |
0.329 |
|
| 2016 |
Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P. Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. Journal of Proteome Research. 15: 4126-4134. PMID 27356587 DOI: 10.1021/Acs.Jproteome.6B00095 |
0.346 |
|
| 2016 |
Shen S, Wang Y, Wang C, Wu YN, Xing Y. SURVIV for survival analysis of mRNA isoform variation. Nature Communications. 7: 11548. PMID 27279334 DOI: 10.1038/Ncomms11548 |
0.354 |
|
| 2016 |
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y. rMAPS: RNA map analysis and plotting server for alternative exon regulation. Nucleic Acids Research. PMID 27174931 DOI: 10.1093/Nar/Gkw410 |
0.45 |
|
| 2016 |
Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell. 165: 606-619. PMID 27104978 DOI: 10.1016/J.Cell.2016.03.040 |
0.422 |
|
| 2016 |
Cieply B, Park JW, Nakauka-Ddamba A, Bebee TW, Guo Y, Shang X, Lengner CJ, Xing Y, Carstens RP. Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins. Cell Reports. PMID 27050523 DOI: 10.1016/J.Celrep.2016.03.025 |
0.414 |
|
| 2016 |
Yang Y, Park JW, Bebee TW, Warzecha CC, Guo Y, Shang X, Xing Y, Carstens RP. 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. PMID 27044866 DOI: 10.1128/Mcb.00019-16 |
0.374 |
|
| 2016 |
Ji X, Park JW, Bahrami-Samani E, Lin L, Duncan-Lewis C, Pherribo G, Xing Y, Liebhaber SA. 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. PMID 26896798 DOI: 10.1093/Nar/Gkw088 |
0.417 |
|
| 2016 |
Lin L, Jiang P, Park JW, Wang J, Lu ZX, Lam MP, Ping P, Xing Y. The contribution of Alu exons to the human proteome. Genome Biology. 17: 15. PMID 26821878 DOI: 10.1186/S13059-016-0876-5 |
0.447 |
|
| 2015 |
Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Research. PMID 26578562 DOI: 10.1093/Nar/Gkv1099 |
0.451 |
|
| 2015 |
Brenig B, Duan Y, Xing Y, Ding N, Huang L, Schütz E. Porcine SOX9 Gene Expression Is Influenced by an 18bp Indel in the 5'-Untranslated Region. Plos One. 10: e0139583. PMID 26430891 DOI: 10.1371/journal.pone.0139583 |
0.308 |
|
| 2015 |
Bebee TW, Park JW, Sheridan KI, Warzecha CC, Cieply BW, Rohacek AM, Xing Y, Carstens RP. The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development. Elife. 4. PMID 26371508 DOI: 10.7554/Elife.08954 |
0.356 |
|
| 2015 |
Lam MP, Venkatraman V, Cao Q, Wang D, Dincer TU, Lau E, Su AI, Xing Y, Ge J, Ping P, Van Eyk JE. Prioritizing Proteomics Assay Development for Clinical Translation. Journal of the American College of Cardiology. 66: 202-4. PMID 26160638 DOI: 10.1016/J.Jacc.2015.04.072 |
0.336 |
|
| 2015 |
Wang J, Lu ZX, Tokheim CJ, Miller SE, Xing Y. Species-specific exon loss in human transcriptomes. Molecular Biology and Evolution. 32: 481-94. PMID 25398629 DOI: 10.1093/Molbev/Msu317 |
0.462 |
|
| 2015 |
Lu ZX, Huang Q, Park JW, Shen S, Lin L, Tokheim CJ, Henry MD, Xing Y. Transcriptome-wide landscape of pre-mRNA alternative splicing associated with metastatic colonization. Molecular Cancer Research : McR. 13: 305-18. PMID 25274489 DOI: 10.1158/1541-7786.Mcr-14-0366 |
0.373 |
|
| 2014 |
Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America. 111: E5593-601. PMID 25480548 DOI: 10.1073/Pnas.1419161111 |
0.396 |
|
| 2014 |
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, ... ... Xing Y, et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 15: 707-19. PMID 25456834 DOI: 10.1016/J.Stem.2014.09.019 |
0.355 |
|
| 2014 |
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, ... ... Xing Y, et al. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Molecular Cell. 56: 298-310. PMID 25263594 DOI: 10.1016/J.Molcel.2014.08.022 |
0.376 |
|
| 2014 |
Tokheim C, Park JW, Xing Y. PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data. Genomics, Proteomics & Bioinformatics. 12: 105-9. PMID 24747190 DOI: 10.1016/J.Gpb.2014.04.001 |
0.403 |
|
| 2014 |
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. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. The Embo Journal. 33: 878-89. PMID 24596251 DOI: 10.1002/Embj.201386537 |
0.352 |
|
| 2014 |
Boudreau RL, Jiang P, Gilmore BL, Spengler RM, Tirabassi R, Nelson JA, Ross CA, Xing Y, Davidson BL. Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron. 81: 294-305. PMID 24389009 DOI: 10.1016/J.Neuron.2013.10.062 |
0.302 |
|
| 2014 |
McLoughlin HS, Wan J, Spengler RM, Xing Y, Davidson BL. Human-specific microRNA regulation of FOXO1: implications for microRNA recognition element evolution. Human Molecular Genetics. 23: 2593-603. PMID 24368418 DOI: 10.1093/Hmg/Ddt655 |
0.319 |
|
| 2014 |
Qin Z, Xing Y, Zhang X. A global profiling of alternative splicing exon expression patterns across multiple human tissues with RNA-Seq data F1000research. 5. DOI: 10.7490/F1000Research.1095395.1 |
0.404 |
|
| 2014 |
Shen S, Wu YN, Xing Y. Abstract 4277: Alternative splicing in cancer transcriptomes Cancer Research. 74: 4277-4277. DOI: 10.1158/1538-7445.Am2014-4277 |
0.376 |
|
| 2013 |
Heinicke LA, Nabet B, Shen S, Jiang P, van Zalen S, Cieply B, Russell JE, Xing Y, Carstens RP. The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation. Plos One. 8: e78031. PMID 24250749 DOI: 10.1371/Journal.Pone.0078031 |
0.439 |
|
| 2013 |
Yao C, Choi EA, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, Shi Y. Overlapping and distinct functions of CstF64 and CstF64Ï„ in mammalian mRNA 3' processing. Rna (New York, N.Y.). 19: 1781-90. PMID 24149845 DOI: 10.1261/Rna.042317.113 |
0.363 |
|
| 2013 |
Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome Biology. 14: R74. PMID 23876401 DOI: 10.1186/Gb-2013-14-7-R74 |
0.396 |
|
| 2013 |
Park JW, Tokheim C, Shen S, Xing Y. Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods in Molecular Biology (Clifton, N.J.). 1038: 171-9. PMID 23872975 DOI: 10.1007/978-1-62703-514-9_10 |
0.449 |
|
| 2013 |
Ji X, Wan J, Vishnu M, Xing Y, Liebhaber SA. αCP Poly(C) binding proteins act as global regulators of alternative polyadenylation. Molecular and Cellular Biology. 33: 2560-73. PMID 23629627 DOI: 10.1128/Mcb.01380-12 |
0.464 |
|
| 2012 |
Yao C, Biesinger J, Wan J, Weng L, Xing Y, Xie X, Shi Y. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proceedings of the National Academy of Sciences of the United States of America. 109: 18773-8. PMID 23112178 DOI: 10.1073/Pnas.1211101109 |
0.437 |
|
| 2012 |
Brown SJ, Stoilov P, Xing Y. Chromatin and epigenetic regulation of pre-mRNA processing. Human Molecular Genetics. 21: R90-6. PMID 22936691 DOI: 10.1093/Hmg/Dds353 |
0.375 |
|
| 2012 |
Ramachandran S, Karp PH, Jiang P, Ostedgaard LS, Walz AE, Fisher JT, Keshavjee S, Lennox KA, Jacobi AM, Rose SD, Behlke MA, Welsh MJ, Xing Y, McCray PB. A microRNA network regulates expression and biosynthesis of wild-type and DeltaF508 mutant cystic fibrosis transmembrane conductance regulator. Proceedings of the National Academy of Sciences of the United States of America. 109: 13362-7. PMID 22853952 DOI: 10.1073/Pnas.1210906109 |
0.307 |
|
| 2012 |
Kim J, Zhao K, Jiang P, Lu ZX, Wang J, Murray JC, Xing Y. Transcriptome landscape of the human placenta. Bmc Genomics. 13: 115. PMID 22448651 DOI: 10.1186/1471-2164-13-115 |
0.433 |
|
| 2012 |
Dittmar KA, Jiang P, Park JW, Amirikian K, Wan J, Shen S, Xing Y, Carstens RP. Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Molecular and Cellular Biology. 32: 1468-82. PMID 22354987 DOI: 10.1128/Mcb.06536-11 |
0.51 |
|
| 2012 |
Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Research. 40: e61. PMID 22266656 DOI: 10.1093/Nar/Gkr1291 |
0.444 |
|
| 2012 |
Lu ZX, Jiang P, Xing Y. Genetic variation of pre-mRNA alternative splicing in human populations. Wiley Interdisciplinary Reviews. Rna. 3: 581-92. PMID 22095823 DOI: 10.1002/Wrna.120 |
0.487 |
|
| 2011 |
Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, Wilhelmy J, Clark TA, Kapur K, Xing Y, Faham M, Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, et al. Human transcriptome array for high-throughput clinical studies. Proceedings of the National Academy of Sciences of the United States of America. 108: 3707-12. PMID 21317363 DOI: 10.1073/Pnas.1019753108 |
0.416 |
|
| 2011 |
Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y. Widespread establishment and regulatory impact of Alu exons in human genes. Proceedings of the National Academy of Sciences of the United States of America. 108: 2837-42. PMID 21282640 DOI: 10.1073/Pnas.1012834108 |
0.51 |
|
| 2011 |
Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Human Molecular Genetics. 20: 1084-96. PMID 21224255 DOI: 10.1093/Hmg/Ddq553 |
0.375 |
|
| 2011 |
Liu S, Lin L, Jiang P, Wang D, Xing Y. A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Research. 39: 578-88. PMID 20864445 DOI: 10.1093/Nar/Gkq817 |
0.395 |
|
| 2010 |
Warzecha CC, Jiang P, Amirikian K, Dittmar KA, Lu H, Shen S, Guo W, Xing Y, Carstens RP. An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. The Embo Journal. 29: 3286-300. PMID 20711167 DOI: 10.1038/Emboj.2010.195 |
0.435 |
|
| 2010 |
Lin L, Shen S, Jiang P, Sato S, Davidson BL, Xing Y. Evolution of alternative splicing in primate brain transcriptomes. Human Molecular Genetics. 19: 2958-73. PMID 20460271 DOI: 10.1093/Hmg/Ddq201 |
0.474 |
|
| 2010 |
Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research. 38: 4570-8. PMID 20371516 DOI: 10.1093/Nar/Gkq211 |
0.454 |
|
| 2010 |
Monteys AM, Spengler RM, Wan J, Tecedor L, Lennox KA, Xing Y, Davidson BL. Structure and activity of putative intronic miRNA promoters. Rna (New York, N.Y.). 16: 495-505. PMID 20075166 DOI: 10.1261/Rna.1731910 |
0.302 |
|
| 2010 |
Lin CL, Evans V, Shen S, Xing Y, Richter JD. The nuclear experience of CPEB: implications for RNA processing and translational control. Rna (New York, N.Y.). 16: 338-48. PMID 20040591 DOI: 10.1261/Rna.1779810 |
0.399 |
|
| 2010 |
Shen S, Warzecha CC, Carstens RP, Xing Y. MADS+: discovery of differential splicing events from Affymetrix exon junction array data. Bioinformatics (Oxford, England). 26: 268-9. PMID 19933160 DOI: 10.1093/Bioinformatics/Btp643 |
0.427 |
|
| 2009 |
Lu H, Lin L, Sato S, Xing Y, Lee CJ. Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. Plos Computational Biology. 5: e1000608. PMID 20019791 DOI: 10.1371/Journal.Pcbi.1000608 |
0.615 |
|
| 2009 |
Warzecha CC, Shen S, Xing Y, Carstens RP. The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. Rna Biology. 6: 546-62. PMID 19829082 DOI: 10.4161/Rna.6.5.9606 |
0.459 |
|
| 2009 |
Borchert GM, Gilmore BL, Spengler RM, Xing Y, Lanier W, Bhattacharya D, Davidson BL. Adenosine deamination in human transcripts generates novel microRNA binding sites. Human Molecular Genetics. 18: 4801-7. PMID 19776031 DOI: 10.1093/Hmg/Ddp443 |
0.344 |
|
| 2009 |
Lin L, Liu S, Brockway H, Seok J, Jiang P, Wong WH, Xing Y. Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Research. 37: e90. PMID 19474342 DOI: 10.1093/Nar/Gkp420 |
0.378 |
|
| 2009 |
Lin L, Jiang P, Shen S, Sato S, Davidson BL, Xing Y. Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes. Human Molecular Genetics. 18: 2204-14. PMID 19324900 DOI: 10.1093/Hmg/Ddp152 |
0.373 |
|
| 2008 |
Kapur K, Jiang H, Xing Y, Wong WH. Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics (Oxford, England). 24: 2887-93. PMID 18984598 DOI: 10.1093/Bioinformatics/Btn571 |
0.383 |
|
| 2008 |
Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. Plos Genetics. 4: e1000225. PMID 18841251 DOI: 10.1371/Journal.Pgen.1000225 |
0.44 |
|
| 2008 |
Roy M, Kim N, Xing Y, Lee C. The effect of intron length on exon creation ratios during the evolution of mammalian genomes. Rna (New York, N.Y.). 14: 2261-73. PMID 18796579 DOI: 10.1261/Rna.1024908 |
0.619 |
|
| 2008 |
Parker DS, Hsiao RL, Xing Y, Resch AM, Lee CJ. Solving the problem of Trans-Genomic Query with alignment tables. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 5: 432-47. PMID 18670046 DOI: 10.1109/Tcbb.2007.1073 |
0.761 |
|
| 2008 |
Xing Y, Lee C. Reconstruction of full-length isoforms from splice graphs. Methods in Molecular Biology (Clifton, N.J.). 452: 199-205. PMID 18566766 DOI: 10.1007/978-1-60327-159-2_10 |
0.584 |
|
| 2008 |
Xing Y, Stoilov P, Kapur K, Han A, Jiang H, Shen S, Black DL, Wong WH. MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. Rna (New York, N.Y.). 14: 1470-9. PMID 18566192 DOI: 10.1261/Rna.1070208 |
0.46 |
|
| 2008 |
Chiao E, Elazar M, Xing Y, Xiong A, Kmet M, Millan MT, Glenn JS, Wong WH, Baker J. Isolation and transcriptional profiling of purified hepatic cells derived from human embryonic stem cells. Stem Cells (Dayton, Ohio). 26: 2032-41. PMID 18535157 DOI: 10.1634/Stemcells.2007-0964 |
0.301 |
|
| 2007 |
Xing Y, Lee C. Relating alternative splicing to proteome complexity and genome evolution. Advances in Experimental Medicine and Biology. 623: 36-49. PMID 18380339 DOI: 10.1007/978-0-387-77374-2_3 |
0.59 |
|
| 2007 |
Calarco JA, Xing Y, Cáceres M, Calarco JP, Xiao X, Pan Q, Lee C, Preuss TM, Blencowe BJ. Global analysis of alternative splicing differences between humans and chimpanzees. Genes & Development. 21: 2963-75. PMID 17978102 DOI: 10.1101/Gad.1606907 |
0.576 |
|
| 2007 |
Kapur K, Xing Y, Ouyang Z, Wong WH. Exon arrays provide accurate assessments of gene expression. Genome Biology. 8: R82. PMID 17504534 DOI: 10.1186/Gb-2007-8-5-R82 |
0.336 |
|
| 2007 |
Xing Y. Genomic analysis of RNA alternative splicing in cancers Frontiers in Bioscience. 12: 4034-4041. PMID 17485356 DOI: 10.2741/2369 |
0.469 |
|
| 2007 |
Xing Y, Ouyang Z, Kapur K, Scott MP, Wong WH. Assessing the conservation of mammalian gene expression using high-density exon arrays. Molecular Biology and Evolution. 24: 1283-5. PMID 17387099 DOI: 10.1093/Molbev/Msm061 |
0.38 |
|
| 2007 |
Lee JA, Xing Y, Nguyen D, Xie J, Lee CJ, Black DL. Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. Plos Biology. 5: e40. PMID 17298178 DOI: 10.1371/Journal.Pbio.0050040 |
0.555 |
|
| 2006 |
Xing Y, Kapur K, Wong WH. Probe selection and expression index computation of affymetrix exon arrays Plos One. 1. PMID 17183719 DOI: 10.1371/Journal.Pone.0000088 |
0.368 |
|
| 2006 |
Xing Y, Lee C. Alternative splicing and RNA selection pressure - Evolutionary consequences for eukaryotic genomes Nature Reviews Genetics. 7: 499-509. PMID 16770337 DOI: 10.1038/Nrg1896 |
0.593 |
|
| 2006 |
Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C. An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Research. 34: 3150-60. PMID 16757580 DOI: 10.1093/Nar/Gkl396 |
0.522 |
|
| 2006 |
Xing Y, Wang Q, Lee C. Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics. 173: 1787-91. PMID 16702427 DOI: 10.1534/Genetics.106.057919 |
0.57 |
|
| 2006 |
Xing Y, Lee C. Can RNA selection pressure distort the measurement of Ka / Ks? Gene. 370: 1-5. PMID 16488091 DOI: 10.1016/J.Gene.2005.12.015 |
0.487 |
|
| 2005 |
Xing Y, Lee CJ. Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. Plos Genetics. 1: e34. PMID 16170410 DOI: 10.1371/Journal.Pgen.0010034 |
0.59 |
|
| 2005 |
Xing Y, Lee C. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proceedings of the National Academy of Sciences of the United States of America. 102: 13526-13531. PMID 16157889 DOI: 10.1073/Pnas.0501213102 |
0.56 |
|
| 2005 |
Xing Y, Lee C. Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics (Oxford, England). 21: 3701-3. PMID 16091412 DOI: 10.1093/Bioinformatics/Bti613 |
0.607 |
|
| 2005 |
Xing Y, Lee C. Evidence of functional selection pressure for alternative splicingevents that accelerate evolution of protein subsequences Genome Biology. 6: 8. DOI: 10.1186/Gb-2005-6-5-P8 |
0.564 |
|
| 2004 |
Xing Y, Lee CJ. Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends in Genetics : Tig. 20: 472-5. PMID 15363899 DOI: 10.1016/J.Tig.2004.07.009 |
0.62 |
|
| 2004 |
Resch A, Xing Y, Modrek B, Gorlick M, Riley R, Lee C. Assessing the impact of alternative splicing on domain interactions in the human proteome. Journal of Proteome Research. 3: 76-83. PMID 14998166 DOI: 10.1021/Pr034064V |
0.745 |
|
| 2004 |
Grasso C, Modrek B, Xing Y, Lee C. Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 29-41. PMID 14992490 |
0.78 |
|
| 2004 |
Resch A, Xing Y, Alekseyenko A, Modrek B, Lee C. Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Research. 32: 1261-9. PMID 14982953 DOI: 10.1093/Nar/Gkh284 |
0.772 |
|
| 2004 |
Xing Y, Resch A, Lee C. The multiassembly problems: Reconstructing multiple transcript isoforms from EST fragment mixtures Genome Research. 14: 426-441. PMID 14962984 DOI: 10.1101/Gr.1304504 |
0.798 |
|
| 2004 |
Xing Y, Xu Q, Lee C. Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. Febs Letters. 555: 572-8. PMID 14675776 DOI: 10.1016/s0014-5793(03)01354-1 |
0.526 |
|
| 2004 |
Xing Y, Lee C. Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy Genome Biology. 5: 12. DOI: 10.1186/Gb-2004-5-6-P12 |
0.614 |
|
| 2003 |
Zewail A, Xie MW, Xing Y, Lin L, Fred Zhang P, Zou W, Saxe JP, Huang J. Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin Proceedings of the National Academy of Sciences of the United States of America. 100: 3345-3350. PMID 12615994 DOI: 10.1073/Pnas.0530118100 |
0.321 |
|
| 2003 |
Lee C, Atanelov L, Modrek B, Xing Y. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Research. 31: 101-5. PMID 12519958 DOI: 10.1093/Nar/Gkg029 |
0.804 |
|
| 2003 |
Xing Y, Xu Q, Lee C. Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains Febs Letters. 555: 572-578. DOI: 10.1016/S0014-5793(03)01354-1 |
0.581 |
|
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