DeepSplice: Deep classification of novel splice junctions revealed by RNA-seq
暂无分享,去创建一个
Yi Zhang | Jinze Liu | James N. MacLeod | Xinan Liu | Jinze Liu | J. MacLeod | Yi Zhang | Xinan Liu | Jinze Liu
[1] Marcel H. Schulz,et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.
[2] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[3] Yvan Saeys,et al. SpliceMachine: predicting splice sites from high-dimensional local context representations , 2005, Bioinform..
[4] David Haussler,et al. Improved splice site detection in Genie , 1997, RECOMB '97.
[5] S. Ranade,et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.
[6] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[7] Curie Ahn,et al. Splicing variants of the orphan G-protein-coupled receptor GPR56 regulate the activity of transcription factors associated with tumorigenesis , 2009, Journal of Cancer Research and Clinical Oncology.
[8] Siruo Wang,et al. Human splicing diversity across the Sequence Read Archive , 2016, bioRxiv.
[9] Martín Abadi,et al. TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems , 2016, ArXiv.
[10] Saman K. Halgamuge,et al. Splice site identification using probabilistic parameters and SVM classification , 2006 .
[11] S. Knudsen,et al. Prediction of human mRNA donor and acceptor sites from the DNA sequence. , 1991, Journal of molecular biology.
[12] Emmanuel Dias-Neto,et al. Identification of candidates for tumor‐specific alternative splicing in the thyroid , 2006, Genes, chromosomes & cancer.
[13] V. Solovyev,et al. Analysis of canonical and non-canonical splice sites in mammalian genomes. , 2000, Nucleic acids research.
[14] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[15] Sungroh Yoon,et al. Boosted Categorical Restricted Boltzmann Machine for Computational Prediction of Splice Junctions , 2015, ICML.
[16] Eric T. Wang,et al. Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.
[17] Leonardo Collado-Torres,et al. Rail-RNA: Scalable analysis of RNA-seq splicing and coverage , 2015, bioRxiv.
[18] Serban Nacu,et al. Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..
[19] Bronwen L. Aken,et al. GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.
[20] Jimmy Ba,et al. Adam: A Method for Stochastic Optimization , 2014, ICLR.
[21] Jude W. Shavlik,et al. Training Knowledge-Based Neural Networks to Recognize Genes , 1990, NIPS.
[22] Gunnar Rätsch,et al. Accurate splice site prediction using support vector machines , 2007, BMC Bioinformatics.
[23] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[24] S. Salzberg,et al. GeneSplicer: a new computational method for splice site prediction. , 2001, Nucleic acids research.
[25] J. Huang,et al. An approach of encoding for prediction of splice sites using SVM. , 2006, Biochimie.
[26] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[27] N L Harris,et al. Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project. , 1990, Methods in enzymology.
[28] T. D. Schneider,et al. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. , 1982, Nucleic acids research.