{"id":"https://openalex.org/W2053256117","doi":"https://doi.org/10.1145/2649387.2649427","title":"FStitch","display_name":"FStitch","publication_year":2014,"publication_date":"2014-09-20","ids":{"openalex":"https://openalex.org/W2053256117","doi":"https://doi.org/10.1145/2649387.2649427","mag":"2053256117"},"language":"en","primary_location":{"id":"doi:10.1145/2649387.2649427","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2649387.2649427","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/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 Azofeifa","raw_affiliation_strings":["University of Colorado, Boulder, CO","University of Colorado, Boulder, CO,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"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":["University of Colorado, Boulder, CO","University of Colorado, Boulder, CO,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"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 Lladser","raw_affiliation_strings":["University of Colorado, Boulder, CO","University of Colorado, Boulder, CO,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"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 Dowell","raw_affiliation_strings":["University of Colorado, Boulder, CO","University of Colorado, Boulder, CO,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado, Boulder, CO","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"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":null,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"174","last_page":"183"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9984999895095825,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9977999925613403,"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":0.6672725677490234},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.6327166557312012},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.527969241142273},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5151561498641968},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4855930209159851},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44296732544898987},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3785528838634491},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3326285481452942},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15651452541351318}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6672725677490234},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.6327166557312012},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.527969241142273},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5151561498641968},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4855930209159851},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44296732544898987},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3785528838634491},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3326285481452942},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15651452541351318},{"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":1,"locations":[{"id":"doi:10.1145/2649387.2649427","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2649387.2649427","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"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/G8747472162","display_name":null,"funder_award_id":"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/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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1513515886","https://openalex.org/W1934019294","https://openalex.org/W1978669753","https://openalex.org/W1981974167","https://openalex.org/W1981976602","https://openalex.org/W1985621639","https://openalex.org/W1996060670","https://openalex.org/W2002179224","https://openalex.org/W2007844697","https://openalex.org/W2009126957","https://openalex.org/W2011442948","https://openalex.org/W2034511309","https://openalex.org/W2080251115","https://openalex.org/W2089772998","https://openalex.org/W2093900943","https://openalex.org/W2097009498","https://openalex.org/W2109962448","https://openalex.org/W2110638928","https://openalex.org/W2111099379","https://openalex.org/W2118532317","https://openalex.org/W2118671962","https://openalex.org/W2120157855","https://openalex.org/W2121850120","https://openalex.org/W2156936974","https://openalex.org/W2164222087","https://openalex.org/W2169714360","https://openalex.org/W6630856392"],"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/W2364370872","https://openalex.org/W2053269318","https://openalex.org/W2025614924","https://openalex.org/W2625833328"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,20,33,96,111],"fast":[3],"and":[4,58,116,154],"simple":[5],"algorithm":[6,130],"to":[7,70,90,119,148],"detect":[8],"nascent":[9,26],"RNA":[10,49,59],"transcription":[11,77],"in":[12],"global":[13],"nuclear":[14],"run-on":[15],"sequencing":[16],"(GRO-seq).":[17],"GRO-seq":[18,65,79],"is":[19,139],"relatively":[21],"new":[22,97],"protocol":[23],"that":[24,86,103],"captures":[25],"transcripts":[27],"from":[28],"actively":[29],"engaged":[30],"polymerase,":[31],"providing":[32],"direct":[34],"read-out":[35],"on":[36,72,132,142],"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":[51,122],"are":[52,87,127],"affected":[53],"by":[54],"transcription,":[55],"post-transcriptional":[56],"processing,":[57],"stability.":[60],"A":[61],"detailed":[62],"study":[63],"of":[64,75,106,124,135],"data":[66],"has":[67],"the":[68,76,125,133],"potential":[69],"inform":[71],"many":[73],"aspects":[74],"process.":[78],"data,":[80,146],"however,":[81],"presents":[82],"unique":[83],"analysis":[84],"challenges":[85],"only":[88],"beginning":[89],"be":[91],"addressed.":[92],"Here":[93],"we":[94],"describe":[95],"algorithm,":[98],"Fast":[99],"Read":[100],"Stitcher":[101],"(FStitch),":[102],"takes":[104],"advantage":[105],"two":[107],"popular":[108],"machine-learning":[109],"techniques,":[110],"hidden":[112],"Markov":[113],"model":[114],"(HMM)":[115],"logistic":[117],"regression":[118],"robustly":[120],"classify":[121],"regions":[123],"genome":[126],"transcribed.":[128],"Our":[129],"builds":[131],"strengths":[134],"previous":[136],"approaches":[137],"but":[138],"accurate,":[140],"dependent":[141],"very":[143],"little":[144],"training":[145],"robust":[147],"varying":[149],"read":[150],"depth,":[151],"annotation":[152],"agnostic,":[153],"fast.":[155]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2016-06-24T00:00:00"}