{"id":"https://openalex.org/W4406261614","doi":"https://doi.org/10.1109/bibm62325.2024.10822684","title":"Leveraging Machine Learning for Predicting Circadian Transcription in mRNAs and lncRNAs","display_name":"Leveraging Machine Learning for Predicting Circadian Transcription in mRNAs and lncRNAs","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406261614","doi":"https://doi.org/10.1109/bibm62325.2024.10822684","pmid":"https://pubmed.ncbi.nlm.nih.gov/41459404"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822684","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12738177/pdf/nihms-2113662.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044005194","display_name":"Lin Miao","orcid":"https://orcid.org/0000-0002-3866-3104"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Miao","raw_affiliation_strings":["Virginia Tech,Fralin Life Sciences Institute,Department of Biological Sciences,Blacksburg,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech,Fralin Life Sciences Institute,Department of Biological Sciences,Blacksburg,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115840427","display_name":"Krishna Vamsi Dhulipalla","orcid":"https://orcid.org/0009-0001-9769-2343"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krishna Vamsi Dhulipalla","raw_affiliation_strings":["Virginia Tech,Department of Computer Science,Blacksburg,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech,Department of Computer Science,Blacksburg,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113285387","display_name":"Sanchari Kundu","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sanchari Kundu","raw_affiliation_strings":["Virginia Tech,School of Plant and Environmental Sciences,Blacksburg,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech,School of Plant and Environmental Sciences,Blacksburg,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086343551","display_name":"Bokun Zheng","orcid":"https://orcid.org/0000-0001-7333-7016"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bokun Zheng","raw_affiliation_strings":["Virginia Tech,Department of Mechanical Engineering,Blacksburg,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech,Department of Mechanical Engineering,Blacksburg,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089438826","display_name":"Li Song","orcid":"https://orcid.org/0000-0002-4888-6045"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Song Li","raw_affiliation_strings":["Virginia Tech,School of Plant and Environmental Sciences,Blacksburg,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech,School of Plant and Environmental Sciences,Blacksburg,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016672972","display_name":"Shihoko Kojima","orcid":"https://orcid.org/0000-0001-9579-7830"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shihoko Kojima","raw_affiliation_strings":["Virginia Tech,Fralin Life Sciences Institute,Department of Biological Sciences,Blacksburg,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech,Fralin Life Sciences Institute,Department of Biological Sciences,Blacksburg,USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2024","issue":null,"first_page":"6044","last_page":"6048"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9036999940872192,"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"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9036999940872192,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6287062168121338},{"id":"https://openalex.org/keywords/circadian-rhythm","display_name":"Circadian rhythm","score":0.6221733093261719},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5040942430496216},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47690773010253906},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.44174402952194214},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4059154987335205},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30543065071105957},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.19640815258026123}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6287062168121338},{"id":"https://openalex.org/C121446783","wikidata":"https://www.wikidata.org/wiki/Q208353","display_name":"Circadian rhythm","level":2,"score":0.6221733093261719},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5040942430496216},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47690773010253906},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44174402952194214},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4059154987335205},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30543065071105957},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.19640815258026123},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822684","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:41459404","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41459404","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12738177","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12738177/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12738177/pdf/nihms-2113662.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12738177","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12738177/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12738177/pdf/nihms-2113662.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3752218145","display_name":null,"funder_award_id":"R01 GM126223","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406261614.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1973788573","https://openalex.org/W1984912966","https://openalex.org/W1995612990","https://openalex.org/W2009132775","https://openalex.org/W2014677321","https://openalex.org/W2021229976","https://openalex.org/W2054513544","https://openalex.org/W2063946784","https://openalex.org/W2073727170","https://openalex.org/W2103777723","https://openalex.org/W2104290916","https://openalex.org/W2112741367","https://openalex.org/W2119603839","https://openalex.org/W2121847288","https://openalex.org/W2133918896","https://openalex.org/W2137252071","https://openalex.org/W2142735201","https://openalex.org/W2169456326","https://openalex.org/W2198153867","https://openalex.org/W2463616135","https://openalex.org/W2472143021","https://openalex.org/W2479945688","https://openalex.org/W2567503091","https://openalex.org/W2735309017","https://openalex.org/W2765695438","https://openalex.org/W2806373762","https://openalex.org/W2921808728","https://openalex.org/W3026475692","https://openalex.org/W4391527909","https://openalex.org/W6802707855","https://openalex.org/W6853888595"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474"],"abstract_inverted_index":{"The":[0],"circadian":[1],"clock":[2],"is":[3,51,105],"a":[4],"molecular":[5],"timekeeper,":[6],"regulating":[7],"the":[8,18,81,98,102,145],"rhythmic":[9,22,47,72,103,123,140],"expression":[10,154],"of":[11,13,21,31,49,60,125,147],"thousands":[12],"transcripts":[14],"in":[15,80,151],"mammals.":[16],"While":[17],"transcriptional":[19],"regulation":[20],"messenger":[23],"RNAs":[24,34],"(mRNAs)":[25],"has":[26],"been":[27],"extensively":[28],"studied,":[29],"that":[30,97],"long":[32],"non-coding":[33],"(lncRNAs)":[35],"remains":[36],"largely":[37],"unexplored.":[38],"In":[39],"this":[40,63],"study,":[41],"we":[42,65,95,112],"aim":[43],"to":[44,70,116],"investigate":[45],"how":[46],"transcription":[48,73,104,124,142],"lncRNAs":[50,91],"regulated":[52],"by":[53],"comparing":[54],"their":[55],"regulatory":[56,99,136],"mechanisms":[57,100],"with":[58],"those":[59],"mRNAs.":[61],"To":[62],"end,":[64],"applied":[66],"machine":[67,148],"learning":[68,149],"models":[69,85,150],"predict":[71],"patterns":[74,155],"using":[75,156],"k-mer-based":[76],"DNA":[77,119,157],"sequence":[78,158],"features":[79,120],"promoter.":[82],"By":[83],"training":[84],"on":[86,90],"mRNAs":[87,108,127],"and":[88,92,109,128,143],"testing":[89],"vice":[93],"versa,":[94],"demonstrate":[96,144],"governing":[101],"different":[106],"between":[107],"lncRNAs.":[110,129],"Additionally,":[111],"employed":[113],"SHAP":[114],"analysis":[115],"identify":[117],"potential":[118],"critical":[121],"for":[122,139],"both":[126],"Our":[130],"findings":[131],"offer":[132],"valuable":[133],"insights":[134],"into":[135],"elements":[137],"important":[138],"RNA":[141],"utility":[146],"predicting":[152],"gene":[153],"features.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}