{"id":"https://openalex.org/W2344415298","doi":"https://doi.org/10.1109/tcbb.2016.2520919","title":"An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq","display_name":"An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq","publication_year":2016,"publication_date":"2016-01-26","ids":{"openalex":"https://openalex.org/W2344415298","doi":"https://doi.org/10.1109/tcbb.2016.2520919","mag":"2344415298","pmid":"https://pubmed.ncbi.nlm.nih.gov/26829802"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2016.2520919","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2520919","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/8060276/07393555.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/8060276/07393555.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064020510","display_name":"Joseph Azofeifa","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph G. Azofeifa","raw_affiliation_strings":["Department of Computer Science, University of Colorado, Boulder, CO"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047723041","display_name":"Mary A. Allen","orcid":"https://orcid.org/0000-0001-7490-0165"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary A. Allen","raw_affiliation_strings":["BioFrontiers Institute, University of Colorado, Boulder, CO"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioFrontiers Institute, University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002500363","display_name":"Manuel E. Lladser","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manuel E. Lladser","raw_affiliation_strings":["Department of Applied Mathematics, University of Colorado, Boulder, CO"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046467404","display_name":"Robin D. Dowell","orcid":"https://orcid.org/0000-0001-7665-9985"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robin D. Dowell","raw_affiliation_strings":["Department of Molecular, Cellular, and Developmental Biology and the BioFrontiers Institute, University of Colorado, Boulder, CO"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular, and Developmental Biology and the BioFrontiers Institute, University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I188538660"],"apc_list":null,"apc_paid":null,"fwci":1.5377,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.82959664,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"14","issue":"5","first_page":"1070","last_page":"1081"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991999864578247,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991999864578247,"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":0.9983999729156494,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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/transcription","display_name":"Transcription (linguistics)","score":0.6126487255096436},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5986323356628418},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5972379446029663},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5628964900970459},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5083536505699158},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4437265992164612},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4053448438644409},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28988951444625854},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2561127245426178},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21387383341789246},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2127152383327484},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18244314193725586},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.13960564136505127},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12365874648094177}],"concepts":[{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.6126487255096436},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5986323356628418},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5972379446029663},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5628964900970459},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5083536505699158},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4437265992164612},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4053448438644409},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28988951444625854},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2561127245426178},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21387383341789246},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2127152383327484},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18244314193725586},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.13960564136505127},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12365874648094177},{"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":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"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":"D012313","descriptor_name":"RNA","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":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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2016.2520919","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2520919","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/8060276/07393555.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26829802","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26829802","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:5069009","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5667649","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5667649","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5667649","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE/ACM Trans Comput Biol Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1109/tcbb.2016.2520919","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2520919","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/8060276/07393555.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1648166781","display_name":null,"funder_award_id":"ABI DBI-12624L0","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G166213354","display_name":null,"funder_award_id":"T15 LM009451","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G303091578","display_name":null,"funder_award_id":"S10 OD012300","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G363742664","display_name":null,"funder_award_id":"2T15 LM009451","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G414170283","display_name":"IGERT:  Interdisciplinary Quantitative Biology Program","funder_award_id":"1144807","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4210857815","display_name":null,"funder_award_id":"N 2T15 LM009451","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4703209727","display_name":null,"funder_award_id":"DBI-12624L0","funder_id":"https://openalex.org/F4320321785","funder_display_name":"Agro-Biotechnology Institute"},{"id":"https://openalex.org/G5718798143","display_name":null,"funder_award_id":"1S10OD012300","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8097271314","display_name":null,"funder_award_id":"LM009451","funder_id":"https://openalex.org/F4320308537","funder_display_name":"Boettcher Foundation"},{"id":"https://openalex.org/G8747472162","display_name":null,"funder_award_id":"IGERT 1144807","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8791351313","display_name":null,"funder_award_id":"NSF IGERT 1144807","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308537","display_name":"Boettcher Foundation","ror":"https://ror.org/0277pn602"},{"id":"https://openalex.org/F4320311855","display_name":"University of Colorado","ror":"https://ror.org/00jc20583"},{"id":"https://openalex.org/F4320321785","display_name":"Agro-Biotechnology Institute","ror":"https://ror.org/029dygd35"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332538","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2344415298.pdf","grobid_xml":"https://content.openalex.org/works/W2344415298.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1513515886","https://openalex.org/W1524217281","https://openalex.org/W1934019294","https://openalex.org/W1977308882","https://openalex.org/W1978669753","https://openalex.org/W1981974167","https://openalex.org/W1981976602","https://openalex.org/W1982718063","https://openalex.org/W1985621639","https://openalex.org/W1996060670","https://openalex.org/W1997590968","https://openalex.org/W2002179224","https://openalex.org/W2007844697","https://openalex.org/W2008555978","https://openalex.org/W2009126957","https://openalex.org/W2011442948","https://openalex.org/W2014787267","https://openalex.org/W2016015848","https://openalex.org/W2034511309","https://openalex.org/W2037686178","https://openalex.org/W2053256117","https://openalex.org/W2065006553","https://openalex.org/W2066310505","https://openalex.org/W2070494252","https://openalex.org/W2080251115","https://openalex.org/W2089772998","https://openalex.org/W2093900943","https://openalex.org/W2097009498","https://openalex.org/W2098276373","https://openalex.org/W2109962448","https://openalex.org/W2110638928","https://openalex.org/W2111099379","https://openalex.org/W2114040881","https://openalex.org/W2117131162","https://openalex.org/W2118532317","https://openalex.org/W2118671962","https://openalex.org/W2120157855","https://openalex.org/W2121850120","https://openalex.org/W2132257972","https://openalex.org/W2133373613","https://openalex.org/W2136101247","https://openalex.org/W2141225828","https://openalex.org/W2141454371","https://openalex.org/W2152144700","https://openalex.org/W2152239989","https://openalex.org/W2156936974","https://openalex.org/W2164222087","https://openalex.org/W2169714360","https://openalex.org/W2171407623","https://openalex.org/W2259938310","https://openalex.org/W2739999456","https://openalex.org/W6640267182","https://openalex.org/W6652676132"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2251519152"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,20,33,78,109,132],"fast":[3],"and":[4,58,96,125],"simple":[5],"algorithm":[6,115],"to":[7,72,99,119],"detect":[8],"nascent":[9,26],"RNA":[10,49,59],"transcription":[11,146],"in":[12],"global":[13],"nuclear":[14],"run-on":[15],"sequencing":[16],"(GRO-seq).":[17],"GRO-seq":[18,61,129],"is":[19,116],"relatively":[21],"new":[22,79,139],"protocol":[23],"that":[24,68,85],"captures":[25],"transcripts":[27],"from":[28],"actively":[29],"engaged":[30],"polymerase,":[31],"providing":[32],"direct":[34],"read-out":[35],"on":[36],"bona":[37],"fide":[38],"transcription.":[39],"Most":[40],"traditional":[41],"assays,":[42],"such":[43],"as":[44],"RNA-seq,":[45],"measure":[46],"steady":[47],"state":[48],"levels":[50],"which":[51,101],"are":[52,69,106],"affected":[53],"by":[54],"transcription,":[55],"post-transcriptional":[56],"processing,":[57],"stability.":[60],"data,":[62],"however,":[63],"presents":[64],"unique":[65],"analysis":[66],"challenges":[67],"only":[70],"beginning":[71],"be":[73],"addressed.":[74],"Here,":[75],"we":[76],"describe":[77],"algorithm,":[80],"Fast":[81],"Read":[82],"Stitcher":[83],"(FStitch),":[84],"takes":[86],"advantage":[87],"of":[88,103,128,144],"two":[89],"popular":[90],"machine-learning":[91],"techniques,":[92],"hidden":[93],"Markov":[94],"models":[95],"logistic":[97],"regression,":[98],"classify":[100],"regions":[102],"the":[104,145],"genome":[105],"transcribed.":[107],"Given":[108],"small":[110],"user-defined":[111],"training":[112],"set,":[113],"our":[114],"accurate,":[117],"robust":[118],"varying":[120],"read":[121],"depth,":[122],"annotation":[123,136],"agnostic,":[124],"fast.":[126],"Analysis":[127],"data":[130],"without":[131],"priori":[133],"need":[134],"for":[135],"uncovers":[137],"surprising":[138],"insights":[140],"into":[141],"several":[142],"aspects":[143],"process.":[147]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}