{"id":"https://openalex.org/W3157155900","doi":"https://doi.org/10.1093/bib/bbab162","title":"A novel computational framework for genome-scale alternative transcription units prediction","display_name":"A novel computational framework for genome-scale alternative transcription units prediction","publication_year":2021,"publication_date":"2021-04-27","ids":{"openalex":"https://openalex.org/W3157155900","doi":"https://doi.org/10.1093/bib/bbab162","mag":"3157155900","pmid":"https://pubmed.ncbi.nlm.nih.gov/33957668"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab162","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab162","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053486679","display_name":"Qi Wang","orcid":"https://orcid.org/0000-0002-7827-4808"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Wang","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan 250200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan 250200, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075883718","display_name":"Zhaoqian Liu","orcid":"https://orcid.org/0000-0003-0428-3928"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Zhaoqian Liu","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA","School of Mathematics, Shandong University, Jinan 250200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan 250200, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047373431","display_name":"Bo Yan","orcid":"https://orcid.org/0000-0003-0188-1113"},"institutions":[{"id":"https://openalex.org/I115020962","display_name":"New England Biolabs (United States)","ror":"https://ror.org/04ywg3445","country_code":"US","type":"company","lineage":["https://openalex.org/I115020962"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Yan","raw_affiliation_strings":["New England Biolabs Inc., Ipswich, MA 01938, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New England Biolabs Inc., Ipswich, MA 01938, USA","institution_ids":["https://openalex.org/I115020962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027932918","display_name":"Wen\u2010Chi Chou","orcid":"https://orcid.org/0000-0002-0361-4548"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wen-Chi Chou","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064283272","display_name":"Laurence Ettwiller","orcid":"https://orcid.org/0000-0002-3957-6539"},"institutions":[{"id":"https://openalex.org/I115020962","display_name":"New England Biolabs (United States)","ror":"https://ror.org/04ywg3445","country_code":"US","type":"company","lineage":["https://openalex.org/I115020962"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laurence Ettwiller","raw_affiliation_strings":["New England Biolabs Inc., Ipswich, MA 01938, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New England Biolabs Inc., Ipswich, MA 01938, USA","institution_ids":["https://openalex.org/I115020962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qin Ma","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017344694","display_name":"Bingqiang Liu","orcid":"https://orcid.org/0000-0002-5734-1135"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bingqiang Liu","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan 250200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan 250200, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017344694","https://openalex.org/A5022408570"],"corresponding_institution_ids":["https://openalex.org/I154099455","https://openalex.org/I52357470"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03110698,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/gene","display_name":"Gene","score":0.6871606707572937},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6163812279701233},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6047297120094299},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5739895105361938},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.560579240322113},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4604431390762329},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.42987388372421265},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42255210876464844},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.28139153122901917},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.27600908279418945}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6871606707572937},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6163812279701233},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6047297120094299},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5739895105361938},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.560579240322113},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4604431390762329},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.42987388372421265},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42255210876464844},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.28139153122901917},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.27600908279418945},{"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":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab162","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab162","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33957668","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33957668","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3090593387","display_name":null,"funder_award_id":"61772313","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3220252743","display_name":"\u57fa\u4e8e\u56fe\u4e0e\u7ec4\u5408\u4f18\u5316\u7684\u751f\u7269\u6570\u636e\u548c\u7f51\u7edc\u6570\u636e\u6316\u6398\u7b97\u6cd5\u7814\u7a76","funder_award_id":"11931008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4206246871","display_name":null,"funder_award_id":"2018IM020200","funder_id":"https://openalex.org/F4320309618","funder_display_name":"Ministry of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320309618","display_name":"Ministry of Science and Technology","ror":"https://ror.org/02b207r52"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":77,"referenced_works":["https://openalex.org/W637806132","https://openalex.org/W1263422348","https://openalex.org/W1581558601","https://openalex.org/W1866977876","https://openalex.org/W1966786968","https://openalex.org/W1974251842","https://openalex.org/W1974893818","https://openalex.org/W1992204008","https://openalex.org/W1994170056","https://openalex.org/W2011426076","https://openalex.org/W2029112298","https://openalex.org/W2032619610","https://openalex.org/W2033984457","https://openalex.org/W2055109879","https://openalex.org/W2060095084","https://openalex.org/W2062896692","https://openalex.org/W2072361216","https://openalex.org/W2078739770","https://openalex.org/W2089718608","https://openalex.org/W2095691234","https://openalex.org/W2096564217","https://openalex.org/W2096731969","https://openalex.org/W2098849734","https://openalex.org/W2101292724","https://openalex.org/W2102037268","https://openalex.org/W2103441770","https://openalex.org/W2105875994","https://openalex.org/W2109203567","https://openalex.org/W2109295007","https://openalex.org/W2115413658","https://openalex.org/W2116423958","https://openalex.org/W2122683221","https://openalex.org/W2123732476","https://openalex.org/W2132285289","https://openalex.org/W2136132915","https://openalex.org/W2137390416","https://openalex.org/W2138773756","https://openalex.org/W2140091288","https://openalex.org/W2142365163","https://openalex.org/W2146270437","https://openalex.org/W2152571160","https://openalex.org/W2156343210","https://openalex.org/W2159482845","https://openalex.org/W2162190612","https://openalex.org/W2165335121","https://openalex.org/W2294658832","https://openalex.org/W2315132400","https://openalex.org/W2396849069","https://openalex.org/W2432517183","https://openalex.org/W2484808885","https://openalex.org/W2522874168","https://openalex.org/W2593679202","https://openalex.org/W2593769407","https://openalex.org/W2605614082","https://openalex.org/W2740690937","https://openalex.org/W2800593054","https://openalex.org/W2806077419","https://openalex.org/W2809185198","https://openalex.org/W2809500310","https://openalex.org/W2889839407","https://openalex.org/W2900007277","https://openalex.org/W2900645803","https://openalex.org/W2906724057","https://openalex.org/W2950787603","https://openalex.org/W2950827045","https://openalex.org/W2951067234","https://openalex.org/W2960634840","https://openalex.org/W2979921136","https://openalex.org/W2981264952","https://openalex.org/W3040925197","https://openalex.org/W3049760251","https://openalex.org/W4249273120","https://openalex.org/W4294216483","https://openalex.org/W6628043643","https://openalex.org/W6674388619","https://openalex.org/W6727186746","https://openalex.org/W6782185734"],"related_works":["https://openalex.org/W1964572291","https://openalex.org/W4387948744","https://openalex.org/W1987520879","https://openalex.org/W184793361","https://openalex.org/W2352732738","https://openalex.org/W2123060905","https://openalex.org/W2559588208","https://openalex.org/W1923384484","https://openalex.org/W3120676751","https://openalex.org/W2025859988"],"abstract_inverted_index":{"Alternative":[0],"transcription":[1,146,151,237],"units":[2],"(ATUs)":[3],"are":[4,197],"dynamically":[5],"encoded":[6,192],"under":[7,19],"different":[8],"conditions":[9],"and":[10,58,112,150,175,180],"display":[11],"overlapping":[12],"patterns":[13],"(sharing":[14],"one":[15],"or":[16,137,163],"more":[17,198],"genes)":[18],"a":[20,84,108,113,247],"specific":[21],"condition":[22],"in":[23,104,117,193],"bacterial":[24,41],"genomes.":[25],"Genome-scale":[26],"identification":[27],"of":[28,36,55,61,95,97,110,115,135,140,160,178,217,235,239,246],"ATUs":[29,50,103,126,171,196],"is":[30,45],"essential":[31],"for":[32,72],"studying":[33],"the":[34,56,66,98,118,124,133,141,169,194,214,223,233,236,244],"emergence":[35],"human":[37],"diseases":[38],"caused":[39],"by":[40,172,227],"organisms.":[42],"However,":[43],"it":[44],"unrealistic":[46],"to":[47,89,206],"identify":[48],"all":[49,96],"using":[51],"experimental":[52],"techniques":[53],"because":[54],"complexity":[57],"dynamic":[59],"nature":[60],"ATUs.":[62,100,209,219],"Here,":[63],"we":[64],"present":[65],"first-of-its-kind":[67],"computational":[68],"framework,":[69],"named":[70],"SeqATU,":[71],"genome-scale":[73,248],"ATU":[74],"prediction":[75],"based":[76],"on":[77],"next-generation":[78],"RNA-Seq":[79,129],"data.":[80,130],"The":[81,101,185],"framework":[82],"utilizes":[83],"convex":[85],"quadratic":[86],"programming":[87],"model":[88],"seek":[90],"an":[91],"optimum":[92],"expression":[93],"combination":[94],"to-be-identified":[99],"predicted":[102,142,170,218],"Escherichia":[105],"coli":[106],"reached":[107],"precision":[109],"0.77/0.74":[111],"recall":[114],"0.75/0.76":[116],"two":[119,207],"RNA-Sequencing":[120],"datasets":[121],"compared":[122],"with":[123],"benchmarked":[125],"from":[127],"third-generation":[128],"In":[131],"addition,":[132],"proportion":[134],"5'-":[136,162],"3'-end":[138,164],"genes":[139],"ATUs,":[143],"having":[144],"documented":[145],"factor":[147],"binding":[148],"sites":[149],"termination":[152],"sites,":[153],"was":[154],"three":[155],"times":[156],"greater":[157],"than":[158,201],"that":[159,188,203,222],"no":[161],"genes.":[165],"We":[166,220],"further":[167],"evaluated":[168],"Gene":[173],"Ontology":[174],"Kyoto":[176],"Encyclopedia":[177],"Genes":[179],"Genomes":[181],"functional":[182],"enrichment":[183],"analyses.":[184],"results":[186,212],"suggested":[187],"gene":[189],"pairs":[190],"frequently":[191],"same":[195],"functionally":[199],"related":[200],"those":[202],"can":[204],"belong":[205],"distinct":[208],"Overall,":[210],"these":[211],"demonstrated":[213],"high":[215],"reliability":[216],"expect":[221],"new":[224],"insights":[225],"derived":[226],"SeqATU":[228],"will":[229],"not":[230],"only":[231],"improve":[232],"understanding":[234],"mechanism":[238],"bacteria":[240],"but":[241],"also":[242],"guide":[243],"reconstruction":[245],"transcriptional":[249],"regulatory":[250],"network.":[251]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
