{"id":"https://openalex.org/W2888433179","doi":"https://doi.org/10.1145/3233547.3233589","title":"Towards Selective-Alignment","display_name":"Towards Selective-Alignment","publication_year":2018,"publication_date":"2018-08-15","ids":{"openalex":"https://openalex.org/W2888433179","doi":"https://doi.org/10.1145/3233547.3233589","mag":"2888433179"},"language":"en","primary_location":{"id":"doi:10.1145/3233547.3233589","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3233547.3233589","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3233547.3233589","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3233547.3233589","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040245011","display_name":"Hirak Sarkar","orcid":"https://orcid.org/0000-0003-3636-7384"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hirak Sarkar","raw_affiliation_strings":["Stony Brook University, Stony Brook, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028361756","display_name":"Mohsen Zakeri","orcid":"https://orcid.org/0000-0002-9856-719X"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohsen Zakeri","raw_affiliation_strings":["Stony Brook University, Stony Brook, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037687088","display_name":"Laraib Malik","orcid":"https://orcid.org/0000-0001-8094-0657"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laraib Malik","raw_affiliation_strings":["Stony Brook University, Stony Brook, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014584023","display_name":"Rob Patro","orcid":"https://orcid.org/0000-0001-8463-1675"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Patro","raw_affiliation_strings":["Stony Brook University, Stony Brook, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.4337,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.83699427,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"27","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8780999779701233,"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"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8780999779701233,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7706000208854675,"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/T12162","display_name":"Cellular Automata and Applications","score":0.7588000297546387,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.579875111579895}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.579875111579895}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3233547.3233589","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3233547.3233589","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3233547.3233589","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3233547.3233589","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3233547.3233589","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3233547.3233589","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7699678853","display_name":null,"funder_award_id":"BBSRC-NSF/BIO-156491","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/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888433179.pdf","grobid_xml":"https://content.openalex.org/works/W2888433179.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1828154403","https://openalex.org/W1999574084","https://openalex.org/W2000586119","https://openalex.org/W2064397275","https://openalex.org/W2065128082","https://openalex.org/W2066231767","https://openalex.org/W2095680943","https://openalex.org/W2096441981","https://openalex.org/W2100751585","https://openalex.org/W2102278945","https://openalex.org/W2103441770","https://openalex.org/W2109158187","https://openalex.org/W2110905563","https://openalex.org/W2112113834","https://openalex.org/W2112876600","https://openalex.org/W2121873871","https://openalex.org/W2124985265","https://openalex.org/W2129714591","https://openalex.org/W2133687564","https://openalex.org/W2139747296","https://openalex.org/W2143788241","https://openalex.org/W2151126392","https://openalex.org/W2158874082","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2174938954","https://openalex.org/W2255131131","https://openalex.org/W2323326409","https://openalex.org/W2474973645","https://openalex.org/W2592811885","https://openalex.org/W2734511552","https://openalex.org/W2749927340","https://openalex.org/W2952944477","https://openalex.org/W2953174564","https://openalex.org/W2963629592"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"We":[0,41],"introduce":[1,94],"an":[2],"algorithm":[3,26],"for":[4,119],"selectively":[5],"aligning":[6],"high-throughput":[7],"sequencing":[8],"reads":[9,91,115],"to":[10,28,49,156],"a":[11,43,71,95,185],"transcriptome,":[12],"with":[13,70],"the":[14,30,58,78,87,105,108,124,133,140],"goal":[15],"of":[16,57,60,89,97,113,126,135,142,187],"improving":[17,123,139],"transcript-level":[18,144],"quantification":[19,145],"in":[20,81,138,182],"difficult":[21],"or":[22],"adversarial":[23],"scenarios.":[24],"This":[25,99],"attempts":[27],"bridge":[29],"gap":[31],"between":[32,104],"fast":[33,174],"\\nab":[34],"algorithms":[35],"and":[36,110,189],"more":[37],"traditional":[38],"alignment":[39,137],"procedures.":[40],"adopt":[42],"hybrid":[44],"approach":[45],"that":[46,152,162,173],"is":[47,154,180,190],"able":[48,155],"produce":[50],"accurate":[51],"alignments":[52,172],"while":[53,168],"still":[54],"retaining":[55],"much":[56],"efficiency":[59,125],"non-alignment-based":[61,166],"algorithms.":[62],"To":[63],"achieve":[64],"this,":[65],"we":[66,93,131,150],"combine":[67],"edit-distance-based":[68],"verification":[69],"highly-sensitive":[72],"read":[73],"mapping":[74,160,175],"procedure.":[75],"Additionally,":[76],"unlike":[77],"strategies":[79],"adopted":[80],"most":[82],"aligners":[83],"which":[84],"first":[85],"align":[86],"ends":[88,112],"paired-end":[90,114],"independently,":[92],"notion":[96],"co-mapping.":[98],"procedure":[100],"exploits":[101],"relevant":[102],"information":[103],"\"hits\"":[106],"from":[107,146],"left":[109],"right":[111],"before":[116],"full":[117],"mappings":[118],"each":[120],"are":[121],"generated,":[122],"filtering":[127],"likely-spurious":[128],"alignments.":[129],"Finally,":[130],"demonstrate":[132],"utility":[134],"selective":[136],"accuracy":[141],"efficient":[143],"RNA-seq":[147],"reads.":[148],"Specifically,":[149],"show":[151],"selective-alignment":[153],"resolve":[157],"certain":[158],"complex":[159],"scenarios":[161],"can":[163,177],"confound":[164],"existing":[165],"procedures,":[167],"simultaneously":[169],"eliminating":[170],"spurious":[171],"approaches":[176],"produce.":[178],"Selective-alignment":[179],"implemented":[181],"C++11":[183],"as":[184,192],"part":[186],"Salmon,":[188],"available":[191],"open":[193],"source":[194],"software,":[195],"under":[196],"GPL":[197],"v3,":[198],"at:":[199],"\\hrefhttps://github.com/COMBINE-lab/salmon/tree/selective-alignment":[200],"https://github.com/COMBINE-lab/salmon/tree/selective-alignment":[201]},"counts_by_year":[{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}