{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T21:58:47Z","timestamp":1774475927414,"version":"3.50.1"},"reference-count":49,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"4","license":[{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/OAPA.html"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1636103"],"award-info":[{"award-number":["U1636103"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61876053"],"award-info":[{"award-number":["61876053"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Foundational Research Funding","award":["20170307150024907"],"award-info":[{"award-number":["20170307150024907"]}]},{"name":"Key Technologies Research and Development Program of Shenzhen","award":["JSGG20170817140856618"],"award-info":[{"award-number":["JSGG20170817140856618"]}]},{"name":"HK Polytechnic University","award":["PolyU-RUDD"],"award-info":[{"award-number":["PolyU-RUDD"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE\/ACM Trans. Comput. Biol. and Bioinf."],"published-print":{"date-parts":[[2020,7,1]]},"DOI":"10.1109\/tcbb.2019.2892124","type":"journal-article","created":{"date-parts":[[2019,1,10]],"date-time":"2019-01-10T19:47:58Z","timestamp":1547149678000},"page":"1383-1393","source":"Crossref","is-referenced-by-count":14,"title":["Prediction of TF-Binding Site by Inclusion of Higher Order Position Dependencies"],"prefix":"10.1109","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2145-2976","authenticated-orcid":false,"given":"Jiyun","family":"Zhou","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9092-2476","authenticated-orcid":false,"given":"Qin","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Computing, Hong Kong Polytechnic University, Hung Hom, Hong Kong"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4009-5679","authenticated-orcid":false,"given":"Ruifeng","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8054-9524","authenticated-orcid":false,"given":"Lin","family":"Gui","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China"}]},{"given":"Hongpeng","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China"}]}],"member":"263","reference":[{"key":"ref39","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1109\/TNN.1997.641482","article-title":"The nature of statistical learning theory","volume":"8","author":"vapnik","year":"1997","journal-title":"IEEE Trans Neural Netw"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-6-145"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1093\/nar\/gkq1184","article-title":"NCBI GEO: Archive for functional Genomics data setsupdate","volume":"39","author":"barrett","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.04.043"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.05.009"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1038\/ng1966"},{"key":"ref37","first-page":"4439","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"huynhthu","year":"2010","journal-title":"PLoS ONE"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1126\/science.3287615"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1038\/nature07107"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1038\/nature06008"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-9-S1-S10"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2858806"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1038\/srep27653"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1002\/bies.201600005"},{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(61)80072-7"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1023\/A:1010933404324"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3300"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.07.001"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw226"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3547"},{"key":"ref26","first-page":"78","article-title":"CNNsite: Prediction of DNA-binding residues in proteins using convolutional neural network with sequence features","author":"zhou","year":"2016","journal-title":"Proc IEEE Int Conf Bioinf Biomed"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw255"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm055"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-93"},{"key":"ref40","first-page":"1235","article-title":"Neural networks for pattern recognition","volume":"12","author":"bishop","year":"2001","journal-title":"Agric Eng Int CIGR J Sci Res Dev Manuscr PM"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009722"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003214"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-6-79"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004418"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0846-z"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-1-r7"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0089226"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1246"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2003-5-1-201"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1038\/35054095"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1186\/1475-4924-2-13"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/16.1.16"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.13.2860"},{"key":"ref7","first-page":"83","article-title":"Integrating genomic data to predict transcription factor binding","volume":"16","author":"holloway","year":"2005","journal-title":"Genome Inform"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1176"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.12.2471"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"108d","DOI":"10.1093\/nar\/gkj143","article-title":"TRANSFAC&#x00AE; and its module TRANSCompel&#x00AE;: Transcriptional gene regulation in eukaryotes","volume":"34","author":"matys","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1093\/nar\/gkm955","article-title":"JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update","volume":"36","author":"bryne","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv735"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1080\/07391102.2015.1032554","article-title":"Quantitative modeling of transcription factor binding specificities using DNA shape","volume":"33","author":"tianyin","year":"2015","journal-title":"J Biomolecular Structure Dynamics"},{"key":"ref42","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btg1054","article-title":"Searching for statistically significant regulatory modules","volume":"19","author":"bailey","year":"2003","journal-title":"Bioinf"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg540"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1093\/nar\/gkl224","article-title":"Stubb: A program for discovery and analysis of cis-regulatory modules","volume":"34","author":"sinha","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/nprot.2006.56","article-title":"Locating potential enhancer elements by comparative Genomics using the EEL software","volume":"1","author":"palin","year":"2006","journal-title":"Nature Protocols"}],"container-title":["IEEE\/ACM Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx7\/8857\/9161426\/08607082.pdf?arnumber=8607082","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T20:24:33Z","timestamp":1722457473000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/8607082\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,1]]},"references-count":49,"journal-issue":{"issue":"4"},"URL":"https:\/\/doi.org\/10.1109\/tcbb.2019.2892124","relation":{},"ISSN":["1545-5963","1557-9964","2374-0043"],"issn-type":[{"value":"1545-5963","type":"print"},{"value":"1557-9964","type":"electronic"},{"value":"2374-0043","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,1]]}}}