{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T17:26:04Z","timestamp":1761845164013,"version":"3.37.3"},"reference-count":87,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"6","license":[{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"},{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"funder":[{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","award":["NRF-2017M3C7A1044815"],"award-info":[{"award-number":["NRF-2017M3C7A1044815"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE\/ACM Trans. Comput. Biol. and Bioinf."],"published-print":{"date-parts":[[2021,11,1]]},"DOI":"10.1109\/tcbb.2020.2981335","type":"journal-article","created":{"date-parts":[[2020,3,18]],"date-time":"2020-03-18T21:19:26Z","timestamp":1584566366000},"page":"2526-2534","source":"Crossref","is-referenced-by-count":16,"title":["Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning"],"prefix":"10.1109","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5678-3479","authenticated-orcid":false,"given":"Hilal","family":"Tayara","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1952-0001","authenticated-orcid":false,"given":"Kil To","family":"Chong","sequence":"additional","affiliation":[]}],"member":"263","reference":[{"key":"ref73","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1608"},{"key":"ref72","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2163"},{"key":"ref71","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks697"},{"key":"ref70","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.023"},{"key":"ref76","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2420"},{"key":"ref77","doi-asserted-by":"publisher","DOI":"10.1109\/5.726791"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1016\/j.ab.2019.113364"},{"key":"ref74","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2013.10.062"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2019.2910513"},{"key":"ref75","doi-asserted-by":"publisher","DOI":"10.1101\/gr.082503.108"},{"key":"ref78","doi-asserted-by":"publisher","DOI":"10.1162\/neco.1997.9.8.1735"},{"key":"ref79","doi-asserted-by":"publisher","DOI":"10.3115\/v1\/D14-1179"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00286"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.3390\/genes10080587"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemolab.2019.03.002"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2018.12.034"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4889-1"},{"key":"ref36","article-title":"DeepCpG: Accurate prediction of single-cell DNA methylation states using deep learning","volume":"18","author":"angermueller","year":"2017","journal-title":"Genome Biol"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3547"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"107e","DOI":"10.1093\/nar\/gkw226","article-title":"DanQ: A hybrid convolutional and recurrent deep neural network for quantifying the function of dna sequences","volume":"44","author":"quang","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ref60","article-title":"Protein–rna interactions: new genomic technologies and perspectives","volume":"13","author":"k\u00f6nig","year":"2012","journal-title":"Nature Rev Genetics"},{"key":"ref62","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002484"},{"key":"ref61","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1056"},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2011.09.012"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2018.2886569"},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.1038\/nature07488"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1142\/S0218001499000604"},{"key":"ref65","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1000530"},{"key":"ref66","doi-asserted-by":"publisher","DOI":"10.1038\/nn.2778"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2018.2874208"},{"key":"ref67","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2013.06.029"},{"key":"ref68","doi-asserted-by":"publisher","DOI":"10.4161\/rna.27991"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1101\/gad.3.4.431"},{"key":"ref69","doi-asserted-by":"crossref","DOI":"10.1038\/nsmb.1838","article-title":"iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution","volume":"17","author":"k\u00f6nig","year":"2010","journal-title":"Nature Structural & Molecular Biology"},{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv031"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1109\/TNN.2008.2004370"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.3390\/s18103341"},{"key":"ref21","article-title":"Systematic theory of neural networks for pattern recognition","author":"huang","year":"1996","journal-title":"Publishing House of Electronics Industry"},{"article-title":"Generative and discriminative text classification with recurrent neural networks","year":"2017","author":"yogatama","key":"ref24"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2017.2782260"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.neunet.2017.02.013"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1109\/TSMCB.2012.2192475"},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2864203"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2019.2947461"},{"key":"ref59","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1180"},{"key":"ref58","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr404"},{"key":"ref57","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-07761-0"},{"key":"ref56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0030007"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.112341999"},{"key":"ref54","doi-asserted-by":"publisher","DOI":"10.1101\/gr.10.6.744"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1350"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1126\/science.1081331"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.3791\/2034"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.01184"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2010.12.011"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2014.11.002"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3300"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv023"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-1-r17"},{"key":"ref82","first-page":"807","article-title":"Rectified linear units improve restricted boltzmann machines","author":"nair","year":"2010","journal-title":"Proc 27th Int Conf Mach Learn"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw003"},{"key":"ref81","first-page":"1929","article-title":"Dropout: A simple way to prevent neural networks from overfitting","volume":"15","author":"srivastava","year":"2014","journal-title":"J Mach Learn Res"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.3390\/cells8121635"},{"key":"ref84","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-2-r24"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-123"},{"article-title":"Adam: A method for stochastic optimization","year":"2015","author":"kingma","key":"ref83"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1109\/TPAMI.2017.2699184"},{"key":"ref80","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.112.143370"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M116.772947"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.03.009"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2014.08.004"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3810"},{"key":"ref85","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty222"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1109\/TITB.2009.2018115"},{"key":"ref86","doi-asserted-by":"publisher","DOI":"10.1186\/s13040-017-0155-3"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2819660"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-16-S3-S4"},{"key":"ref87","doi-asserted-by":"publisher","DOI":"10.1038\/nature12311"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1002\/wrna.31"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007227"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1561-8"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2019.2943465"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1101\/gr.247494.118"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.3390\/molecules24224035"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty364"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1261\/rna.070565.119"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0216257"}],"container-title":["IEEE\/ACM Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx7\/8857\/9642421\/09040403.pdf?arnumber=9040403","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T21:27:06Z","timestamp":1646774826000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/9040403\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,1]]},"references-count":87,"journal-issue":{"issue":"6"},"URL":"https:\/\/doi.org\/10.1109\/tcbb.2020.2981335","relation":{},"ISSN":["1545-5963","1557-9964","2374-0043"],"issn-type":[{"type":"print","value":"1545-5963"},{"type":"electronic","value":"1557-9964"},{"type":"electronic","value":"2374-0043"}],"subject":[],"published":{"date-parts":[[2021,11,1]]}}}