APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data
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Xiaohui Wu | Qingshun Quinn Li | Guoli Ji | Congting Ye | Yuqi Long | Congting Ye | Guoli Ji | Xiaohui Wu | Q. Li | Yuqi Long
[1] A. Hameed,et al. Drought induced programmed cell death and associated changes in antioxidants, proteases, and lipid peroxidation in wheat leaves , 2013, Biologia Plantarum.
[2] E. Wang,et al. Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.
[3] Yong Zeng,et al. Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes , 2015, Briefings Bioinform..
[4] V. Kim,et al. TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. , 2014, Molecular cell.
[5] M. Levine,et al. ELAV links paused Pol II to alternative polyadenylation in the Drosophila nervous system. , 2015, Molecular cell.
[6] Xiaohui Wu,et al. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice , 2014, BMC Genomics.
[7] Liwei Sun,et al. Proteomic Analyses Provide Novel Insights into Plant Growth and Ginsenoside Biosynthesis in Forest Cultivated Panax ginseng (F. Ginseng) , 2016, Front. Plant Sci..
[8] R. Guigó,et al. Modelling and simulating generic RNA-Seq experiments with the flux simulator , 2012, Nucleic acids research.
[9] Xiaohui Wu,et al. PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants , 2016, Front. Plant Sci..
[10] Guoli Ji,et al. Genome-wide dynamics of alternative polyadenylation in rice , 2016, Genome research.
[11] Wei Li,et al. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types , 2014, Nature Communications.
[12] B. Tian,et al. Alternative cleavage and polyadenylation: the long and short of it. , 2013, Trends in biochemical sciences.
[13] E. van Nimwegen,et al. Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells , 2014, Nature Communications.
[14] Hyeshik Chang,et al. Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. , 2016, Molecular cell.
[15] Guoli Ji,et al. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation , 2011, Proceedings of the National Academy of Sciences.
[16] Vicent Pelechano,et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification , 2013, Nucleic acids research.
[17] D. Bartel,et al. Extensive alternative polyadenylation during zebrafish development , 2012, Genome research.
[18] Guoli Ji,et al. Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation , 2008, Nucleic acids research.
[19] Thomas Bonfert,et al. Prediction of Poly(A) Sites by Poly(A) Read Mapping , 2017, PloS one.
[20] Julie L. Yang,et al. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression , 2013, Genes & development.
[21] D. Inzé,et al. Leaf Responses to Mild Drought Stress in Natural Variants of Arabidopsis1[OPEN] , 2015, Plant Physiology.
[22] Yonggui Fu,et al. Evaluation of Two Statistical Methods Provides Insights into the Complex Patterns of Alternative Polyadenylation Site Switching , 2015, PloS one.
[23] K. Nishida,et al. Mechanisms and consequences of alternative polyadenylation. , 2011, Molecules and Cells.
[24] D. Bartel,et al. Widespread Influence of 3′-End Structures on Mammalian mRNA Processing and Stability , 2017, Cell.
[25] B. San Segundo,et al. Overexpression of a Calcium-Dependent Protein Kinase Confers Salt and Drought Tolerance in Rice by Preventing Membrane Lipid Peroxidation1[C][W] , 2014, Plant Physiology.
[26] T. Babak,et al. A quantitative atlas of polyadenylation in five mammals , 2012, Genome research.
[27] G. Yehia,et al. Analysis of alterative cleavage and polyadenylation by 3′ region extraction and deep sequencing , 2012, Nature Methods.
[28] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[29] V. Kim,et al. mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development , 2016, Genes & development.
[30] Jie Li,et al. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals , 2014, Nucleic Acids Res..
[31] Hongzhe Li,et al. A change-point model for identifying 3′UTR switching by next-generation RNA sequencing , 2014, Bioinform..
[32] Stephen J. Benkovic,et al. Corrigendum: RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue , 2014, Nature Communications.
[33] James B. Brown,et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. , 2012, Cell reports.
[34] M. Mangone,et al. Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles , 2015, BMC Biology.
[35] M. Swanson,et al. Global insights into alternative polyadenylation regulation , 2015, RNA biology.
[36] Bin Tian,et al. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes , 2007, Nucleic Acids Res..
[37] John K. Kim,et al. Driving glioblastoma growth by alternative polyadenylation , 2014, Cell Research.
[38] Rick L. Stevens,et al. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource , 2014, Proceedings of the National Academy of Sciences.
[39] Chong-Jian Chen,et al. Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing. , 2011, Genome research.
[40] B. Tian,et al. Alternative polyadenylation of mRNA precursors , 2016, Nature Reviews Molecular Cell Biology.
[41] L. Steinmetz,et al. Alternative polyadenylation diversifies post‐transcriptional regulation by selective RNA–protein interactions , 2014, Molecular Systems Biology.
[42] E. Lai,et al. IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference , 2015, RNA.
[43] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[44] Torsten Seemann,et al. PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome , 2015, RNA.
[45] Anna Tramontano,et al. 3USS: a web server for detecting alternative 3′UTRs from RNA-seq experiments , 2015, Bioinform..
[46] Joseph K. Pickrell,et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing , 2010, Nature.
[47] Inanç Birol,et al. KLEAT: Cleavage Site Analysis of Transcriptomes , 2014, Pacific Symposium on Biocomputing.
[48] Christine Mayr,et al. Alternative 3'UTRs act as scaffolds to regulate membrane protein localization , 2015, Nature.
[49] Ralf Schmidt,et al. A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation , 2015, bioRxiv.
[50] E. Lai,et al. Widespread and extensive lengthening of 3′ UTRs in the mammalian brain , 2013, Genome research.
[51] Sandrine Dudoit,et al. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.
[52] Christine Mayr,et al. Evolution and Biological Roles of Alternative 3'UTRs. , 2016, Trends in cell biology.