rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data S Shen, JW Park, Z Lu, L Lin, MD Henry, YN Wu, Q Zhou, Y Xing Proceedings of the National Academy of Sciences 111 (51), E5593-E5601, 2014 | 2281 | 2014 |
An ESRP‐regulated splicing programme is abrogated during the epithelial–mesenchymal transition CC Warzecha, P Jiang, K Amirikian, KA Dittmar, H Lu, S Shen, W Guo, ... The EMBO journal 29 (19), 3286-3300, 2010 | 418 | 2010 |
Nonallele-specific silencing of mutant and wild-type huntingtin demonstrates therapeutic efficacy in Huntington's disease mice RL Boudreau, JL McBride, I Martins, S Shen, Y Xing, BJ Carter, ... Molecular Therapy 17 (6), 1053-1063, 2009 | 418 | 2009 |
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data S Shen, JW Park, J Huang, KA Dittmar, Z Lu, Q Zhou, RP Carstens, Y Xing Nucleic acids research 40 (8), e61-e61, 2012 | 382 | 2012 |
The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events CC Warzecha, S Shen, Y Xing, RP Carstens RNA biology 6 (5), 546-562, 2009 | 250 | 2009 |
Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing KA Dittmar, P Jiang, JW Park, K Amirikian, J Wan, S Shen, Y Xing, ... Molecular and cellular biology 32 (8), 1468-1482, 2012 | 152 | 2012 |
Widespread establishment and regulatory impact of Alu exons in human genes S Shen, L Lin, JJ Cai, P Jiang, EJ Kenkel, MR Stroik, S Sato, BL Davidson, ... Proceedings of the National Academy of Sciences 108 (7), 2837-2842, 2011 | 152 | 2011 |
Diverse splicing patterns of exonized Alu elements in human tissues L Lin, S Shen, A Tye, JJ Cai, P Jiang, BL Davidson, Y Xing PLoS genetics 4 (10), e1000225, 2008 | 134 | 2008 |
Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease L Lin, JW Park, S Ramachandran, Y Zhang, YT Tseng, S Shen, ... Human molecular genetics 25 (16), 3454-3466, 2016 | 125 | 2016 |
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays Y Xing, P Stoilov, K Kapur, A Han, H Jiang, S Shen, DL Black, WH Wong Rna 14 (8), 1470-1479, 2008 | 119 | 2008 |
SURVIV for survival analysis of mRNA isoform variation S Shen, Y Wang, C Wang, YN Wu, Y Xing Nature communications 7 (1), 11548, 2016 | 107 | 2016 |
Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS JW Park, C Tokheim, S Shen, Y Xing Deep sequencing data analysis, 171-179, 2013 | 85 | 2013 |
Transcriptome-wide landscape of pre-mRNA alternative splicing associated with metastatic colonization Z Lu, Q Huang, JW Park, S Shen, L Lin, CJ Tokheim, MD Henry, Y Xing Molecular Cancer Research 13 (2), 305-318, 2015 | 76 | 2015 |
The nuclear experience of CPEB: implications for RNA processing and translational control CL Lin, V Evans, S Shen, Y Xing, JD Richter Rna 16 (2), 338-348, 2010 | 73 | 2010 |
Evolution of alternative splicing in primate brain transcriptomes L Lin, S Shen, P Jiang, S Sato, BL Davidson, Y Xing Human molecular genetics 19 (15), 2958-2973, 2010 | 65 | 2010 |
Population and allelic variation of A-to-I RNA editing in human transcriptomes E Park, J Guo, S Shen, L Demirdjian, YN Wu, L Lin, Y Xing Genome biology 18, 1-15, 2017 | 56 | 2017 |
The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation LA Heinicke, B Nabet, S Shen, P Jiang, S van Zalen, B Cieply, JE Russell, ... PloS one 8 (10), e78031, 2013 | 48 | 2013 |
MADS+: discovery of differential splicing events from Affymetrix exon junction array data S Shen, CC Warzecha, RP Carstens, Y Xing Bioinformatics 26 (2), 268-269, 2010 | 42 | 2010 |
Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes L Lin, P Jiang, S Shen, S Sato, BL Davidson, Y Xing Human molecular genetics 18 (12), 2204-2214, 2009 | 35 | 2009 |
rMATS-DVR: rMATS discovery of differential variants in RNA J Wang, Y Pan, S Shen, L Lin, Y Xing Bioinformatics 33 (14), 2216-2217, 2017 | 32 | 2017 |