DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
暂无分享,去创建一个
[1] Chuan He,et al. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. , 2016, Trends in genetics : TIG.
[2] Yue Sheng,et al. METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m6A Modification. , 2017, Cell stem cell.
[3] M. Kupiec,et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.
[4] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[5] Chuan He,et al. N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.
[6] Xing Chen,et al. MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome , 2017, Nucleic Acids Res..
[7] Xiaohui S. Xie,et al. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences , 2015, bioRxiv.
[8] F. Liu,et al. m6A modulates haematopoietic stem and progenitor cell specification , 2017, Nature.
[9] Yi Xing,et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. , 2014, Cell stem cell.
[10] Zhengwei Zhu,et al. CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..
[11] Christopher E. Mason,et al. Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome , 2015, Nature Methods.
[12] O. Elemento,et al. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.
[13] J. van Helden,et al. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections , 2016, bioRxiv.
[14] Gideon Rechavi,et al. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing , 2013, Nature Protocols.
[15] Tao Pan,et al. Dynamic RNA Modifications in Gene Expression Regulation , 2017, Cell.
[16] B. Frey,et al. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning , 2015, Nature Biotechnology.
[17] Chuan He,et al. N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis , 2017, Nature Structural &Molecular Biology.
[18] Ning Chen,et al. Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding , 2017, Bioinform..
[19] Guigang Zhang,et al. Deep Learning , 2016, Int. J. Semantic Comput..
[20] Nitish Srivastava,et al. Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..
[21] William Stafford Noble,et al. Quantifying similarity between motifs , 2007, Genome Biology.
[22] Jürgen Schmidhuber,et al. Long Short-Term Memory , 1997, Neural Computation.
[23] O. Troyanskaya,et al. Predicting effects of noncoding variants with deep learning–based sequence model , 2015, Nature Methods.
[24] Nian Liu,et al. N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein , 2017, Nucleic acids research.
[25] Schraga Schwartz,et al. High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis , 2013, Cell.
[26] C. Timpte,et al. Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. , 2002, Nucleic acids research.
[27] Qi Zhou,et al. m(6)A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. , 2015, Cell stem cell.
[28] Beilun Wang,et al. Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks , 2016, PSB.
[29] Geoffrey E. Hinton,et al. Deep Learning , 2015, Nature.
[30] K. Chou,et al. iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition. , 2015, Analytical biochemistry.
[31] Q. Cui,et al. SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features , 2016, Nucleic acids research.
[32] Wei Chen,et al. Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome , 2015, Scientific Reports.
[33] Arne Klungland,et al. A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation , 2015, Genes & development.