{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T04:48:02Z","timestamp":1768193282833,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,2,24]],"date-time":"2020-02-24T00:00:00Z","timestamp":1582502400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01LM012806"],"award-info":[{"award-number":["R01LM012806"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention & Research Institute of Texas","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"CPRIT","doi-asserted-by":"publisher","award":["RP180734"],"award-info":[{"award-number":["RP180734"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA N6-methyladenine (6\u2009mA) has recently been found as an essential epigenetic modification, playing its roles in a variety of cellular processes. The abnormal status of DNA 6\u2009mA modification has been reported in cancer and other disease. The annotation of 6\u2009mA marks in genome is the first crucial step to explore the underlying molecular mechanisms including its regulatory roles.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a novel online DNA 6\u2009mA site tool, 6\u2009mA-Finder, by incorporating seven sequence-derived information and three physicochemical-based features through recursive feature elimination strategy. Our multiple cross-validations indicate the promising accuracy and robustness of our model. 6\u2009mA-Finder outperforms its peer tools in general and species-specific 6\u2009mA site prediction, suggesting it can provide a useful resource for further experimental investigation of DNA 6\u2009mA modification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/bioinfo.uth.edu\/6mA_Finder.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa113","type":"journal-article","created":{"date-parts":[[2020,2,14]],"date-time":"2020-02-14T20:12:39Z","timestamp":1581711159000},"page":"3257-3259","source":"Crossref","is-referenced-by-count":47,"title":["6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2086-3893","authenticated-orcid":false,"given":"Haodong","family":"Xu","sequence":"first","affiliation":[{"name":"School of Biomedical Informatics , Center for Precision Health"}]},{"given":"Ruifeng","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics , Center for Precision Health"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4523-4153","authenticated-orcid":false,"given":"Peilin","family":"Jia","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics , Center for Precision Health"}]},{"given":"Zhongming","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics , Center for Precision Health"},{"name":"MD Anderson Cancer Center , UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA"},{"name":"Department of Biomedical Informatics , Vanderbilt University Medical Center, Nashville, TN 37203, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,2,24]]},"reference":[{"key":"2023013112033130200_btaa113-B1","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.omtn.2019.08.011","article-title":"SDM6A: a web-based integrative machine-learning framework for predicting 6mA sites in the rice genome","volume":"18","author":"Basith","year":"2019","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2023013112033130200_btaa113-B2","doi-asserted-by":"crossref","first-page":"2796","DOI":"10.1093\/bioinformatics\/btz015","article-title":"i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome","volume":"35","author":"Chen","year":"2019","journal-title":"Bioinformatics"},{"key":"2023013112033130200_btaa113-B3","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.ygeno.2018.01.005","article-title":"iDNA6mA-PseKNC: identifying DNA N(6)-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC","volume":"111","author":"Feng","year":"2019","journal-title":"Genomics"},{"key":"2023013112033130200_btaa113-B4","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013112033130200_btaa113-B5","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.chemolab.2006.01.007","article-title":"Recursive feature elimination with random forest for PTR-MS analysis of agroindustrial products","volume":"83","author":"Granitto","year":"2006","journal-title":"Chem. Intel. Lab. Syst"},{"key":"2023013112033130200_btaa113-B6","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1016\/j.cell.2015.04.005","article-title":"DNA methylation on N6-adenine in C. elegans","volume":"161","author":"Greer","year":"2015","journal-title":"Cell"},{"key":"2023013112033130200_btaa113-B7","doi-asserted-by":"crossref","first-page":"793","DOI":"10.3389\/fgene.2019.00793","article-title":"iDNA6mA-Rice: a computational tool for detecting N6-methyladenine sites in rice","volume":"10","author":"Lv","year":"2019","journal-title":"Front. Genet"},{"key":"2023013112033130200_btaa113-B8","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1093\/bioinformatics\/btz556","article-title":"MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model","volume":"36","author":"Pian","year":"2020","journal-title":"Bioinformatics"},{"key":"2023013112033130200_btaa113-B9","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nature17640","article-title":"DNA methylation on N6-adenine in mammalian embryonic stem cells","volume":"532","author":"Wu","year":"2016","journal-title":"Nature"},{"key":"2023013112033130200_btaa113-B10","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.molcel.2018.06.015","article-title":"N(6)-methyladenine DNA modification in the human genome","volume":"71","author":"Xiao","year":"2018","journal-title":"Mol. Cell"},{"key":"2023013112033130200_btaa113-B11","first-page":"gkw950","article-title":"MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing","volume":"45","author":"Ye","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013112033130200_btaa113-B12","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1016\/j.cell.2015.04.018","article-title":"N6-methyladenine DNA modification in Drosophila","volume":"161","author":"Zhang","year":"2015","journal-title":"Cell"},{"key":"2023013112033130200_btaa113-B13","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/s41477-018-0214-x","article-title":"Identification and analysis of adenine N 6-methylation sites in the rice genome","volume":"4","author":"Zhou","year":"2018","journal-title":"Nat. Plants"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa113\/32916122\/btaa113.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/10\/3257\/48990962\/bioinformatics_36_10_3257.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/10\/3257\/48990962\/bioinformatics_36_10_3257.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:15:39Z","timestamp":1675199739000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/10\/3257\/5753942"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,2,24]]},"references-count":13,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2020,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa113","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,5,15]]},"published":{"date-parts":[[2020,2,24]]}}}