{"id":"https://openalex.org/W4410757221","doi":"https://doi.org/10.1093/bib/bbaf235","title":"Machine learning\u2013augmented m6A-Seq analysis without a reference genome","display_name":"Machine learning\u2013augmented m6A-Seq analysis without a reference genome","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410757221","doi":"https://doi.org/10.1093/bib/bbaf235","pmid":"https://pubmed.ncbi.nlm.nih.gov/40415679"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf235","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf235","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf235/63353031/bbaf235.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf235/63353031/bbaf235.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083202469","display_name":"Jing Yang","orcid":"https://orcid.org/0000-0002-6833-8863"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Jing Yang","raw_affiliation_strings":["Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054450357","display_name":"Minggui Song","orcid":"https://orcid.org/0000-0002-4406-3877"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Minggui Song","raw_affiliation_strings":["Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000706151","display_name":"Yifan Bu","orcid":"https://orcid.org/0000-0001-5893-5384"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Yifan Bu","raw_affiliation_strings":["Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106731753","display_name":"Haonan Zhao","orcid":"https://orcid.org/0009-0007-8553-945X"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Haonan Zhao","raw_affiliation_strings":["Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050061521","display_name":"Chenghui Liu","orcid":"https://orcid.org/0000-0001-8375-0242"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Chenghui Liu","raw_affiliation_strings":["Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100458374","display_name":"Ting Zhang","orcid":"https://orcid.org/0000-0003-4229-6332"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ting Zhang","raw_affiliation_strings":["State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111047588","display_name":"Chujun Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chujun Zhang","raw_affiliation_strings":["State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031266962","display_name":"Shutu Xu","orcid":"https://orcid.org/0000-0003-1538-6834"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Shutu Xu","raw_affiliation_strings":["Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","Maize Engineering & Technology Research Centre , College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"Maize Engineering & Technology Research Centre , College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi,","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018556396","display_name":"Chuang Ma","orcid":"https://orcid.org/0000-0001-9612-7898"},"institutions":[{"id":"https://openalex.org/I4210105197","display_name":"Ministry of Agriculture & Farmers Welfare","ror":"https://ror.org/01d1n9n57","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210105197"]},{"id":"https://openalex.org/I4210117091","display_name":"Minist\u00e8re de l'Agriculture et de la Souverainet\u00e9 alimentaire","ror":"https://ror.org/029m96t80","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN","FR","IN"],"is_corresponding":false,"raw_author_name":"Chuang Ma","raw_affiliation_strings":["Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I4210105197","https://openalex.org/I4210117091","https://openalex.org/I89652312"]},{"raw_affiliation_string":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","institution_ids":["https://openalex.org/I89652312"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.2715,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.78302438,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":1.0,"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":1.0,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9901000261306763,"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/computer-science","display_name":"Computer science","score":0.6851721405982971},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.54507976770401},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.524208664894104},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.49434494972229004},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.47271081805229187},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.47224777936935425},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4520329535007477},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4298091232776642},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34390896558761597},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29724282026290894},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15135124325752258},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13315114378929138}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6851721405982971},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.54507976770401},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.524208664894104},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.49434494972229004},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.47271081805229187},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.47224777936935425},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4520329535007477},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4298091232776642},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34390896558761597},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29724282026290894},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15135124325752258},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13315114378929138},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf235","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf235","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf235/63353031/bbaf235.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40415679","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40415679","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:10913962","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12104624","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf235","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf235","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf235/63353031/bbaf235.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2151188511","display_name":null,"funder_award_id":"32470717","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G544903515","display_name":null,"funder_award_id":"Z1090224030","funder_id":"https://openalex.org/F4320334997","funder_display_name":"Chinese Universities Scientific Fund"},{"id":"https://openalex.org/G8303878997","display_name":null,"funder_award_id":"32170681","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320334997","display_name":"Chinese Universities Scientific Fund","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320336350","display_name":"Key Research and Development Projects of Shaanxi Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410757221.pdf","grobid_xml":"https://content.openalex.org/works/W4410757221.grobid-xml"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W1976247738","https://openalex.org/W2011131953","https://openalex.org/W2011657487","https://openalex.org/W2014677321","https://openalex.org/W2035618305","https://openalex.org/W2039725641","https://openalex.org/W2044676948","https://openalex.org/W2050871273","https://openalex.org/W2054101905","https://openalex.org/W2065847836","https://openalex.org/W2067434231","https://openalex.org/W2078964320","https://openalex.org/W2102619694","https://openalex.org/W2108740562","https://openalex.org/W2112888168","https://openalex.org/W2131478115","https://openalex.org/W2152514983","https://openalex.org/W2170551349","https://openalex.org/W2170747616","https://openalex.org/W2180404227","https://openalex.org/W2341599515","https://openalex.org/W2418044989","https://openalex.org/W2432815617","https://openalex.org/W2461624292","https://openalex.org/W2623168030","https://openalex.org/W2752930292","https://openalex.org/W2764301500","https://openalex.org/W2800770690","https://openalex.org/W2886785109","https://openalex.org/W2899065760","https://openalex.org/W2900629010","https://openalex.org/W2947275858","https://openalex.org/W2949841808","https://openalex.org/W2950954328","https://openalex.org/W2951912016","https://openalex.org/W2952110612","https://openalex.org/W2967881004","https://openalex.org/W2972131171","https://openalex.org/W2979684814","https://openalex.org/W2997591727","https://openalex.org/W2998099417","https://openalex.org/W3112628587","https://openalex.org/W3119200243","https://openalex.org/W3133227021","https://openalex.org/W3164595217","https://openalex.org/W3164597438","https://openalex.org/W3165305053","https://openalex.org/W3169862247","https://openalex.org/W3175901821","https://openalex.org/W3181626680","https://openalex.org/W3186661411","https://openalex.org/W3199488319","https://openalex.org/W3202634790","https://openalex.org/W3205328789","https://openalex.org/W3206110491","https://openalex.org/W3216859318","https://openalex.org/W4200564640","https://openalex.org/W4206005991","https://openalex.org/W4206334732","https://openalex.org/W4210795038","https://openalex.org/W4214864012","https://openalex.org/W4220997164","https://openalex.org/W4221083345","https://openalex.org/W4281746310","https://openalex.org/W4313454095","https://openalex.org/W4313454274","https://openalex.org/W4313856397","https://openalex.org/W4367555465","https://openalex.org/W4385897926","https://openalex.org/W4387157510","https://openalex.org/W4387797969","https://openalex.org/W4387966606","https://openalex.org/W4388734245","https://openalex.org/W4391649719","https://openalex.org/W4392508465","https://openalex.org/W4392766984","https://openalex.org/W4394919305","https://openalex.org/W4399363619","https://openalex.org/W4399427787","https://openalex.org/W4402122873","https://openalex.org/W4409387374","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W107105315","https://openalex.org/W1584537303","https://openalex.org/W4388155270","https://openalex.org/W4367156293","https://openalex.org/W2750549761","https://openalex.org/W1872724644","https://openalex.org/W28826848","https://openalex.org/W2122272819","https://openalex.org/W2994151208","https://openalex.org/W2166777687"],"abstract_inverted_index":{"Methylated":[0],"RNA":[1],"m6A":[2,13,67],"immunoprecipitation":[3],"sequencing":[4],"(m6A-Seq)":[5],"is":[6,191],"a":[7,38,52,58,117],"powerful":[8,126],"technique":[9],"for":[10,64,100,184],"investigating":[11],"transcriptome-wide":[12,66],"modification.":[14],"However,":[15],"most":[16],"of":[17,48,61,85,166,186],"the":[18,45,72,138],"existing":[19],"m6A-Seq":[20,49,80,92,181],"protocols":[21],"rely":[22],"on":[23],"reference":[24,53,179],"genomes,":[25],"limiting":[26],"their":[27],"use":[28],"in":[29,51,159],"species":[30],"lacking":[31],"sequenced":[32],"genomes.":[33],"Here,":[34],"we":[35],"introduce":[36],"mlPEA,":[37],"user-friendly,":[39],"multi-functional":[40],"platform":[41],"specifically":[42],"tailored":[43],"to":[44],"streamlined":[46],"processing":[47],"data":[50,93,127,182],"genome-free":[54,180],"manner.":[55],"mlPEA":[56,90,124,141,171,190],"provides":[57],"comprehensive":[59],"collection":[60],"functions":[62,109],"required":[63],"performing":[65],"identification":[68],"and":[69,104,110,129,135,146,169,176],"analysis,":[70],"where":[71],"reference-de":[73],"novo":[74],"assembled":[75],"transcriptome-is":[76],"built":[77],"solely":[78],"using":[79],"data.":[81],"By":[82],"taking":[83],"advantage":[84],"machine":[86],"learning":[87],"(ML)":[88],"algorithms,":[89],"enhances":[91],"analysis":[94,183],"by":[95],"constructing":[96],"robust":[97],"computational":[98],"models":[99,112],"identifying":[101],"high-quality":[102],"transcripts":[103],"high-confidence":[105],"m6A-modified":[106],"regions.":[107],"These":[108],"ML":[111],"have":[113],"been":[114],"integrated":[115],"into":[116],"web-based":[118],"Galaxy":[119],"framework.":[120],"This":[121],"ensures":[122],"that":[123],"has":[125,143,172],"interaction":[128],"visualization":[130],"capabilities,":[131],"with":[132],"flexibility,":[133],"traceability,":[134],"reproducibility":[136],"throughout":[137],"analytical":[139],"process.":[140],"also":[142],"high":[144],"compatibility":[145],"portability":[147],"as":[148],"it":[149],"employs":[150],"advanced":[151],"packaging":[152],"technology,":[153],"dramatically":[154],"simplifying":[155],"its":[156,174],"large-scale":[157],"application":[158],"various":[160,187],"species.":[161],"Validated":[162],"through":[163],"case":[164],"studies":[165],"Arabidopsis,":[167],"maize,":[168],"wheat,":[170],"demonstrated":[173],"utility":[175],"robustness":[177],"regarding":[178],"plants":[185],"genomic":[188],"complexities.":[189],"freely":[192],"available":[193],"via":[194],"GitHub:":[195],"https://github.com/cma2015/mlPEA.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
