MuStARD: Deep Learning for intra- and inter-species scanning of functional genomic patterns
暂无分享,去创建一个
Panagiotis Alexiou | Fotis Plessas | Georgios Georgakilas | Andrea Grioni | Konstantinos G Liakos | Eliska Malanikova
[1] K. Nakai,et al. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. , 2004, Genome research.
[2] Anne E Carpenter,et al. Opportunities and obstacles for deep learning in biology and medicine , 2017, bioRxiv.
[3] P. Baldi,et al. Searching for exotic particles in high-energy physics with deep learning , 2014, Nature Communications.
[4] Jun Liu,et al. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. , 2017, Genome research.
[5] Peter F. Stadler,et al. ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.
[6] Fariza Tahi,et al. miRBoost: boosting support vector machines for microRNA precursor classification , 2015, RNA.
[7] W. Pitts,et al. A Logical Calculus of the Ideas Immanent in Nervous Activity (1943) , 2021, Ideas That Created the Future.
[8] Liang-Hu Qu,et al. snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome , 2006, Nucleic acids research.
[9] Marek Sikora,et al. HuntMi: an efficient and taxon-specific approach in pre-miRNA identification , 2013, BMC Bioinformatics.
[10] K. Pollard,et al. Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.
[11] Ting Chen,et al. Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[12] Fei Li,et al. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine , 2005, BMC Bioinformatics.
[13] Peng Jiang,et al. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features , 2007, Nucleic Acids Res..
[14] Ana Kozomara,et al. miRBase: from microRNA sequences to function , 2018, Nucleic Acids Res..
[15] Yanjun Qi,et al. DeepChrome: deep-learning for predicting gene expression from histone modifications , 2016, Bioinform..
[16] Frederic B. Fitch,et al. McCulloch Warren S. and Pitts Walter. A logical calculus of the ideas immanent in nervous activity. Bulletin of mathematical biophysics , vol. 5 (1943), pp. 115–133. , 1944, Journal of Symbolic Logic.
[17] O. Troyanskaya,et al. Predicting effects of noncoding variants with deep learning–based sequence model , 2015, Nature Methods.
[18] J. V. Moran,et al. Initial sequencing and analysis of the human genome. , 2001, Nature.
[19] L. Lim,et al. An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.
[20] Geoffrey E. Hinton,et al. Deep Learning , 2015, Nature.
[21] Terrence S. Furey,et al. The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..
[22] Ehsan Qasemi,et al. Deep Learning Features in Atmospheric Chemistry: Prediction of Cancer Morbidity Due to Air Pollution , 2017, 2017 International Conference on Computational Science and Computational Intelligence (CSCI).
[23] Vasile Palade,et al. microPred: effective classification of pre-miRNAs for human miRNA gene prediction , 2009, Bioinform..
[24] B. Frey,et al. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning , 2015, Nature Biotechnology.
[25] Ning Chen,et al. DeepEnhancer: Predicting enhancers by convolutional neural networks , 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[26] T. Kiss. Small Nucleolar RNAs An Abundant Group of Noncoding RNAs with Diverse Cellular Functions , 2002, Cell.
[27] Hui Zhou,et al. deepBase: a database for deeply annotating and mining deep sequencing data , 2009, Nucleic Acids Res..
[28] Xiaohui S. Xie,et al. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences , 2015, bioRxiv.
[29] Syed Haider,et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space , 2011, Database J. Biol. Databases Curation.
[30] V. Ambros,et al. An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.
[31] Jan Baumbach,et al. On the performance of pre-microRNA detection algorithms , 2017, Nature Communications.
[32] Vincent J. Henry,et al. OMICtools: an informative directory for multi-omic data analysis , 2014, Database J. Biol. Databases Curation.
[33] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[34] T. Tuschl,et al. New microRNAs from mouse and human. , 2003, RNA.