{"id":"https://openalex.org/W2096884903","doi":"https://doi.org/10.1093/bioinformatics/btq336","title":"A probabilistic framework for aligning paired-end RNA-seq data","display_name":"A probabilistic framework for aligning paired-end RNA-seq data","publication_year":2010,"publication_date":"2010-06-23","ids":{"openalex":"https://openalex.org/W2096884903","doi":"https://doi.org/10.1093/bioinformatics/btq336","mag":"2096884903"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq336","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq336","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/16/1950/48856230/bioinformatics_26_16_1950.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/16/1950/48856230/bioinformatics_26_16_1950.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101650923","display_name":"Yin Hu","orcid":"https://orcid.org/0000-0003-2258-9787"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yin Hu","raw_affiliation_strings":["1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100437036","display_name":"Kai Wang","orcid":"https://orcid.org/0000-0002-6170-4744"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kai Wang","raw_affiliation_strings":["1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054978528","display_name":"Xiaping He","orcid":"https://orcid.org/0000-0001-9464-7910"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaping He","raw_affiliation_strings":["1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063447892","display_name":"Derek Y. Chiang","orcid":"https://orcid.org/0000-0002-1131-6065"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek Y. Chiang","raw_affiliation_strings":["1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011567934","display_name":"Jan F. Prins","orcid":"https://orcid.org/0000-0003-0853-6099"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jan F. Prins","raw_affiliation_strings":["1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102842945","display_name":"Jinze Liu","orcid":"https://orcid.org/0000-0003-0555-9412"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinze Liu","raw_affiliation_strings":["1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Kentucky, Lexington, KY, 2Department of Genetics and 3Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I143302722"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101650923"],"corresponding_institution_ids":["https://openalex.org/I143302722"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7182,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.83808075,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"26","issue":"16","first_page":"1950","last_page":"1957"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T11482","display_name":"RNA modifications and cancer","score":0.9994999766349792,"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":0.9993000030517578,"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/splice","display_name":"splice","score":0.7563276886940002},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.711485743522644},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.6227551102638245},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6050100922584534},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5913087129592896},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.5785670280456543},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5167550444602966},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.49938249588012695},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41941455006599426},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3717458248138428},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3480961322784424},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.33163172006607056},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2871776819229126},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28506767749786377},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22055599093437195}],"concepts":[{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.7563276886940002},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.711485743522644},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6227551102638245},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6050100922584534},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5913087129592896},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.5785670280456543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5167550444602966},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.49938249588012695},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41941455006599426},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3717458248138428},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3480961322784424},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.33163172006607056},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2871776819229126},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28506767749786377},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22055599093437195}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq336","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq336","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/16/1950/48856230/bioinformatics_26_16_1950.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2161558","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2916723","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq336","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq336","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/16/1950/48856230/bioinformatics_26_16_1950.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096884903.pdf","grobid_xml":"https://content.openalex.org/works/W2096884903.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2049633694","https://openalex.org/W2053742104","https://openalex.org/W2097065948","https://openalex.org/W2112113834","https://openalex.org/W2122789575","https://openalex.org/W2126144698","https://openalex.org/W2158804744","https://openalex.org/W2166422007","https://openalex.org/W2169810552","https://openalex.org/W3129711340"],"related_works":["https://openalex.org/W2068174058","https://openalex.org/W2130439870","https://openalex.org/W2800537687","https://openalex.org/W178291922","https://openalex.org/W2147652847","https://openalex.org/W1976843764","https://openalex.org/W2000278701","https://openalex.org/W3215633333","https://openalex.org/W2001319824","https://openalex.org/W2151954452"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,127,168],"RNA-seq":[3],"paired-end":[4],"read":[5],"(PER)":[6],"protocol":[7,36],"samples":[8],"transcript":[9,47,79,124],"fragments":[10,80],"longer":[11],"than":[12],"the":[13,22,31,34,38,42,57,61,71,74,118,149,154,157,163,171,177,183,213],"sequencing":[14,20],"capability":[15],"of":[16,25,30,45,60,76,92,156,165,170,179,207],"today's":[17],"technology":[18],"by":[19,56,188,221],"just":[21],"two":[23],"ends":[24],"each":[26,46,123],"fragment.":[27,62,125],"Deep":[28],"sampling":[29],"transcriptome":[32],"using":[33,49],"PER":[35,78,83,136,145,198],"presents":[37],"opportunity":[39],"to":[40,69,73,112,131,153],"reconstruct":[41],"unsequenced":[43],"portion":[44],"fragment":[48,146,199],"end":[50,94,158],"reads":[51,159],"from":[52,86,138],"overlapping":[53],"PERs,":[54],"guided":[55],"expected":[58],"length":[59],"Methods:":[63],"A":[64],"probabilistic":[65],"framework":[66],"is":[67],"described":[68],"predict":[70],"alignment":[72,121,147,155,200],"genome":[75],"all":[77,93,113],"in":[81,176,182,212,217],"a":[82],"dataset.":[84],"Starting":[85],"possible":[87],"exonic":[88],"and":[89,116,143,161],"spliced":[90],"alignments":[91],"reads,":[95],"our":[96],"method":[97,108,128],"constructs":[98],"potential":[99],"splicing":[100,196,203],"paths":[101,181],"connecting":[102],"paired":[103],"ends.":[104],"An":[105],"expectation":[106,172],"maximization":[107,173],"assigns":[109,117],"likelihood":[110],"values":[111],"splice":[114,166,184],"junctions":[115],"most":[119],"probable":[120],"for":[122],"Results:":[126],"was":[129,186],"applied":[130],"2":[132],"\u00d7":[133],"35":[134],"bp":[135],"datasets":[137],"cancer":[139],"cell":[140,215],"lines":[141],"MCF-7":[142,214],"SUM-102.":[144],"increased":[148,162],"coverage":[150],"3-fold":[151],"compared":[152],"alone,":[160],"accuracy":[164,169],"detection.":[167],"(EM)":[174],"algorithm":[175],"presence":[178],"alternative":[180,195],"graph":[185],"validated":[187],"qRT\u2013PCR":[189],"experiments":[190],"on":[191],"eight":[192],"exon":[193],"skipping":[194],"events.":[197],"with":[201],"long-range":[202],"confirmed":[204],"8":[205],"out":[206],"10":[208],"fusion":[209],"events":[210],"identified":[211],"line":[216],"an":[218],"earlier":[219],"study":[220],"(Maher":[222],"et":[223],"al.,":[224],"2009).":[225],"Availability:":[226],"Software":[227],"available":[228,238],"at":[229,239],"http://www.netlab.uky.edu/p/bioinfo/MapSplice/PER":[230],"Contact:":[231],"liuj@cs.uky.edu":[232],"Supplementary":[233,235],"information:":[234],"data":[236],"are":[237],"Bioinformatics":[240],"online.":[241]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
