{"id":"https://openalex.org/W2906996182","doi":"https://doi.org/10.1186/s12859-018-2516-4","title":"DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning","display_name":"DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2906996182","doi":"https://doi.org/10.1186/s12859-018-2516-4","mag":"2906996182","pmid":"https://pubmed.ncbi.nlm.nih.gov/30598068"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2516-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2516-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2516-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2516-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101622790","display_name":"Yiqian Zhang","orcid":"https://orcid.org/0009-0004-6451-8164"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yiqian Zhang","raw_affiliation_strings":["AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan","Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I80188885","display_name":"Nippon Medical School","ror":"https://ror.org/00krab219","country_code":"JP","type":"education","lineage":["https://openalex.org/I80188885"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. mhamada@waseda.jp","Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, 135-0064, Japan. mhamada@waseda.jp","Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. mhamada@waseda.jp","Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan. mhamada@waseda.jp","Institute for Medical-oriented Structural Biology, Waseda University, 2-2, Wakamatsu-cho Shinjuku-ku, Tokyo, 162-8480, Japan. mhamada@waseda.jp","Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. mhamada@waseda.jp","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, 135-0064, Japan. mhamada@waseda.jp","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. mhamada@waseda.jp","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan. mhamada@waseda.jp","institution_ids":["https://openalex.org/I80188885"]},{"raw_affiliation_string":"Institute for Medical-oriented Structural Biology, Waseda University, 2-2, Wakamatsu-cho Shinjuku-ku, Tokyo, 162-8480, Japan. mhamada@waseda.jp","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025857432"],"corresponding_institution_ids":["https://openalex.org/I150744194","https://openalex.org/I73613424","https://openalex.org/I80188885"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":4.2845,"has_fulltext":true,"cited_by_count":159,"citation_normalized_percentile":{"value":0.95701413,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"19","issue":"S19","first_page":"524","last_page":"524"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9778000116348267,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9778000116348267,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.006200000178068876,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13157","display_name":"Cancer-related gene regulation","score":0.003700000001117587,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6477022171020508},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6284416913986206},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.587378978729248},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5648285746574402},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5045686960220337},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4984009265899658},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46609488129615784},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4444625675678253},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.44089236855506897},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4393242299556732},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29444968700408936},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19214007258415222},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13016831874847412}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6477022171020508},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6284416913986206},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.587378978729248},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5648285746574402},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5045686960220337},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4984009265899658},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46609488129615784},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4444625675678253},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.44089236855506897},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4393242299556732},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29444968700408936},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19214007258415222},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13016831874847412},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000241","descriptor_name":"Adenosine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2516-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2516-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2516-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30598068","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30598068","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:56a0eda3344a4235b80f2c7f58baf288","is_oa":true,"landing_page_url":"https://doaj.org/article/56a0eda3344a4235b80f2c7f58baf288","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss S19, Pp 1-11 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5294699","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6311933","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6311933","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6311933","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2516-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2516-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2516-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G156749745","display_name":"Functional classification of long noncoding RNAs based on functional elements and deep learning","funder_award_id":"16H05879","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G1638334167","display_name":null,"funder_award_id":"JP16H05879","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2530989232","display_name":null,"funder_award_id":"JP17K20032, JP16H05879, JP16H01318, and JP16H02484","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G2952512416","display_name":null,"funder_award_id":"JP16H01318","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G32426276","display_name":null,"funder_award_id":"JP16H05879","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G3584406041","display_name":null,"funder_award_id":"JP16H02484","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G4532089706","display_name":null,"funder_award_id":"JP16H02484","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4837072799","display_name":null,"funder_award_id":"JP17K20032","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G541276348","display_name":null,"funder_award_id":"JP17K20032","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8869625558","display_name":null,"funder_award_id":"JP16H01318","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320322638","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2906996182.pdf","grobid_xml":"https://content.openalex.org/works/W2906996182.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W776567260","https://openalex.org/W1019830208","https://openalex.org/W1186776093","https://openalex.org/W1941339056","https://openalex.org/W1970460195","https://openalex.org/W2007429249","https://openalex.org/W2035905956","https://openalex.org/W2054101905","https://openalex.org/W2062821957","https://openalex.org/W2064675550","https://openalex.org/W2065847836","https://openalex.org/W2078964320","https://openalex.org/W2095705004","https://openalex.org/W2103777723","https://openalex.org/W2170747616","https://openalex.org/W2171808845","https://openalex.org/W2180404227","https://openalex.org/W2198606573","https://openalex.org/W2287984595","https://openalex.org/W2314476006","https://openalex.org/W2336509392","https://openalex.org/W2415310056","https://openalex.org/W2589225545","https://openalex.org/W2627064270","https://openalex.org/W2736280136","https://openalex.org/W2751668414","https://openalex.org/W2752985760","https://openalex.org/W2754499625","https://openalex.org/W2758881473","https://openalex.org/W2767731367","https://openalex.org/W2776540408","https://openalex.org/W2919115771","https://openalex.org/W2949152404","https://openalex.org/W2963468488"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W4224241862","https://openalex.org/W2889547007","https://openalex.org/W1510729279","https://openalex.org/W2611989081","https://openalex.org/W2971615643","https://openalex.org/W2076384244","https://openalex.org/W4365452989","https://openalex.org/W2587969176","https://openalex.org/W2106965934"],"abstract_inverted_index":{"BACKGROUND:":[0],"N6-methyladensine":[1],"(m6A)":[2],"is":[3,51,118,192],"a":[4,16,65,138,148,168],"common":[5],"and":[6,38,75,173,177],"abundant":[7],"RNA":[8,28],"methylation":[9],"modification":[10],"found":[11,146],"in":[12,26,120,151],"various":[13],"species.":[14],"As":[15],"type":[17],"of":[18,162],"post-transcriptional":[19],"methylation,":[20],"m6A":[21,46,60,86,132,141,163,187],"plays":[22],"an":[23,34,103],"important":[24],"role":[25],"diverse":[27],"activities":[29],"such":[30],"as":[31,95],"alternative":[32],"splicing,":[33],"interplay":[35],"with":[36],"microRNAs":[37],"translation":[39],"efficiency.":[40],"Although":[41],"existing":[42],"tools":[43],"can":[44],"predict":[45,72,172],"at":[47,88,194],"single-base":[48,89],"resolution,":[49],"it":[50],"still":[52],"challenging":[53],"to":[54,71,97,130,159,171,179,182],"extract":[55],"the":[56,152],"biological":[57,78],"information":[58],"surrounding":[59,77],"sites.":[61,164],"RESULTS:":[62],"We":[63,166],"implemented":[64],"deep":[66,153],"learning":[67,100,154],"framework,":[68],"named":[69],"DeepM6ASeq,":[70],"m6A-containing":[73,111,122,175],"sequences":[74,176],"characterize":[76,174],"features":[79],"based":[80],"on":[81,106],"miCLIP-Seq":[82],"data,":[83,108],"which":[84,109],"detects":[85],"sites":[87],"resolution.":[90],"DeepM6ASeq":[91,128,135],"showed":[92],"better":[93],"performance":[94],"compared":[96],"other":[98],"machine":[99],"classifiers.":[101],"Moreover,":[102],"independent":[104],"test":[105],"m6A-Seq":[107],"identifies":[110,137],"genomic":[112],"regions,":[113],"revealed":[114],"that":[115,147],"our":[116],"model":[117,155],"competitive":[119],"predicting":[121],"sequences.":[123],"The":[124,189],"learned":[125],"motifs":[126],"from":[127],"correspond":[129],"known":[131],"readers.":[133],"Notably,":[134],"also":[136],"newly":[139],"recognized":[140],"reader:":[142],"FMR1.":[143],"Besides,":[144],"we":[145],"saliency":[149],"map":[150],"could":[156],"be":[157],"utilized":[158],"visualize":[160],"locations":[161],"CONCULSION:":[165],"developed":[167],"deep-learning-based":[169],"framework":[170],"hope":[178],"help":[180],"investigators":[181],"gain":[183],"more":[184],"insights":[185],"for":[186],"research.":[188],"source":[190],"code":[191],"available":[193],"https://github.com/rreybeyb/DeepM6ASeq":[195],".":[196]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":34},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2025-10-10T00:00:00"}