Spliceator: multi-species splice site prediction using convolutional neural networks
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Olivier Poch | Luc Moulinier | Anne Jeannin-Girardon | Arnaud Kress | Pierre Collet | Nicolas Scalzitti | Romain Orhand | Thomas Weber | Julie Dawn Thompson | J. Thompson | O. Poch | Arnaud Kress | L. Moulinier | Thomas Weber | Nicolas Scalzitti | A. Jeannin-Girardon | P. Collet | Romain Orhand
[1] Ian Korf,et al. Gene finding in novel genomes , 2004, BMC Bioinformatics.
[2] Allison J. Taggart,et al. The effects of structure on pre-mRNA processing and stability. , 2017, Methods.
[3] A. Krainer,et al. Listening to silence and understanding nonsense: exonic mutations that affect splicing , 2002, Nature Reviews Genetics.
[4] Chung-Chin Lu,et al. Prediction of splice sites with dependency graphs and their expanded bayesian networks , 2005, Bioinform..
[5] David Haussler,et al. Improved splice site detection in Genie , 1997, RECOMB '97.
[6] J. Thompson,et al. A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms , 2020, BMC Genomics.
[7] Binhua Tang,et al. Recent Advances of Deep Learning in Bioinformatics and Computational Biology , 2019, Front. Genet..
[8] Yu Li,et al. Deep learning in bioinformatics: Introduction, application, and perspective in the big data era. , 2019, Methods.
[9] Astrid Gall,et al. Ensembl 2020 , 2019, Nucleic Acids Res..
[10] David G. Knowles,et al. Predicting Splicing from Primary Sequence with Deep Learning , 2019, Cell.
[11] L. Feuk,et al. Global and unbiased detection of splice junctions from RNA-seq data , 2010, Genome Biology.
[12] Liran Carmel,et al. Origin and evolution of spliceosomal introns , 2012, Biology Direct.
[13] Wilfried Haerty,et al. Genome-wide discovery of human splicing branchpoints , 2015, Genome research.
[14] Nizamettin Aydin,et al. A novel method for splice sites prediction using sequence component and hidden Markov model , 2016, 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).
[15] Salvatore Rampone,et al. Hs3d, A Dataset Of Homo Sapiens Splice Regions, And Its Extraction Procedure From A Major Public Database , 2002 .
[16] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[17] Wesley De Neve,et al. SpliceRover: interpretable convolutional neural networks for improved splice site prediction , 2018, Bioinform..
[18] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[19] P. Bork,et al. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..
[20] Geoffrey E. Hinton,et al. Deep Learning , 2015, Nature.
[21] Fatih Ozsolak,et al. RNA sequencing: advances, challenges and opportunities , 2011, Nature Reviews Genetics.
[22] S. Karlin,et al. Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.
[23] V. Solovyev,et al. Analysis of canonical and non-canonical splice sites in mammalian genomes. , 2000, Nucleic acids research.
[24] Abramowicz Anna,et al. Splicing mutations in human genetic disorders: examples, detection, and confirmation , 2018, Journal of Applied Genetics.
[25] S. Salzberg,et al. GeneSplicer: a new computational method for splice site prediction. , 2001, Nucleic acids research.
[26] Stephen M. Mount,et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.
[27] Boas Pucker,et al. Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence , 2017, BMC Research Notes.
[28] Steven Salzberg,et al. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..
[29] C. Gooding,et al. A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones , 2006, Genome Biology.
[30] Olivier Poch,et al. OrthoInspector 3.0: open portal for comparative genomics , 2018, Nucleic Acids Res..
[31] Yvan Saeys,et al. SpliceMachine: predicting splice sites from high-dimensional local context representations , 2005, Bioinform..
[32] B. Frey,et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.
[33] Tatsuhiko Naito,et al. Human Splice-Site Prediction with Deep Neural Networks , 2018, J. Comput. Biol..
[34] Deepak Garg,et al. Hybrid Approach Using SVM and MM2 in Splice Site Junction Identification , 2014 .
[35] Boas Pucker,et al. Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites , 2020, Cells.
[36] Britta Hartmann,et al. Genome-wide Analysis of Alternative Pre-mRNA Splicing* , 2008, Journal of Biological Chemistry.
[37] A. Bateman,et al. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases , 2019, Nucleic acids research.
[38] Ghazaleh Khodabandelou,et al. Genome annotation across species using deep convolutional neural networks , 2020, PeerJ Comput. Sci..
[39] Bernard De Baets,et al. Feature subset selection for splice site prediction , 2002, ECCB.
[40] Lefteris Koumakis,et al. Deep learning models in genomics; are we there yet? , 2020, Computational and structural biotechnology journal.
[41] Yvan Saeys,et al. Digging into Acceptor Splice Site Prediction: An Iterative Feature Selection Approach , 2004, PKDD.
[42] Steven L Salzberg,et al. Next-generation genome annotation: we still struggle to get it right , 2019, Genome Biology.
[43] K. Pruitt,et al. P8008 The NCBI Eukaryotic Genome Annotation Pipeline , 2016 .
[44] Ying He,et al. A survey on deep learning in DNA/RNA motif mining , 2020, Briefings Bioinform..
[45] BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database , 2021, NAR genomics and bioinformatics.
[46] A. Gregory Matera,et al. A day in the life of the spliceosome , 2014, Nature Reviews Molecular Cell Biology.
[47] Boas Pucker,et al. Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes , 2018, BMC Genomics.
[48] Demis Hassabis,et al. Improved protein structure prediction using potentials from deep learning , 2020, Nature.
[49] Kinji Ohno,et al. Human branch point consensus sequence is yUnAy , 2008, Nucleic acids research.
[50] M. Yandell,et al. A beginner's guide to eukaryotic genome annotation , 2012, Nature Reviews Genetics.
[51] Ruohan Wang,et al. SpliceFinder: ab initio prediction of splice sites using convolutional neural network , 2019, BMC Bioinformatics.
[52] R. Sachidanandam,et al. Comprehensive splice-site analysis using comparative genomics , 2006, Nucleic acids research.
[53] Nitish Srivastava,et al. Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..
[54] Michael Q. Zhang,et al. RNA landscape of evolution for optimal exon and intron discrimination , 2008, Proceedings of the National Academy of Sciences.
[55] Yuan Yu,et al. TensorFlow: A system for large-scale machine learning , 2016, OSDI.
[56] Geoffrey E. Hinton,et al. ImageNet classification with deep convolutional neural networks , 2012, Commun. ACM.
[57] Gunnar Rätsch,et al. Accurate splice site prediction using support vector machines , 2007, BMC Bioinformatics.
[58] Jiuyong Xie,et al. The matrices and constraints of GT/AG splice sites of more than 1000 species/lineages. , 2018, Gene.
[59] M. Yandell,et al. Genome Annotation and Curation Using MAKER and MAKER‐P , 2014, Current protocols in bioinformatics.
[60] Prabina Kumar Meher,et al. Prediction of donor splice sites using random forest with a new sequence encoding approach , 2016, BioData Mining.
[61] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[62] Peter B. McGarvey,et al. UniProt: the universal protein knowledgebase in 2021 , 2020, Nucleic Acids Res..
[63] Victor V. Solovyev,et al. SpliceDB: database of canonical and non-canonical mammalian splice sites , 2001, Nucleic Acids Res..
[64] Olivier Poch,et al. Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes , 2020, BMC Bioinform..
[65] Yuan Chen,et al. A high-performance approach for predicting donor splice sites based on short window size and imbalanced large samples , 2019, Biology Direct.
[66] Burkhard Morgenstern,et al. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.
[67] Jing Li,et al. Splice sites prediction of Human genome using length-variable Markov model and feature selection , 2010, Expert Syst. Appl..
[68] M. Kilkenny,et al. Data quality: “Garbage in – garbage out” , 2018, Health information management : journal of the Health Information Management Association of Australia.
[69] Carlos González,et al. Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes , 2019, Nucleic acids research.
[70] Mohammed AlQuraishi,et al. AlphaFold at CASP13 , 2019, Bioinform..
[71] Murray Campbell,et al. Deep Blue , 2002, Artif. Intell..
[72] Olivier Poch,et al. PipeAlign: a new toolkit for protein family analysis , 2003, Nucleic Acids Res..
[73] Mario Stanke,et al. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database , 2020, bioRxiv.
[74] Nizamettin Aydin,et al. Splice site identification in human genome using random forest , 2016, Health and Technology.
[75] Shona Murphy,et al. Transcription and splicing: A two‐way street , 2020, Wiley interdisciplinary reviews. RNA.
[76] Jimmy Ba,et al. Adam: A Method for Stochastic Optimization , 2014, ICLR.
[77] Demis Hassabis,et al. Mastering the game of Go with deep neural networks and tree search , 2016, Nature.
[78] Farhad Pourpanah,et al. Recent advances in deep learning , 2020, International Journal of Machine Learning and Cybernetics.
[79] Christopher B. Burge,et al. Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals , 2004, J. Comput. Biol..
[80] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[81] Abhishek Das,et al. Grad-CAM: Visual Explanations from Deep Networks via Gradient-Based Localization , 2016, 2017 IEEE International Conference on Computer Vision (ICCV).
[82] Shuye Tian,et al. Modern deep learning in bioinformatics , 2020, Journal of molecular cell biology.
[83] Felix Stiehler,et al. Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning , 2020, Bioinform..