{"id":"https://openalex.org/W2749927340","doi":"https://doi.org/10.1145/3107411.3107444","title":"Fleximer","display_name":"Fleximer","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2749927340","doi":"https://doi.org/10.1145/3107411.3107444","mag":"2749927340"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107444","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107444","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","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/A5073504925","display_name":"Chelsea J.\u2010T. Ju","orcid":"https://orcid.org/0000-0001-8674-5318"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chelsea J.-T. Ju","raw_affiliation_strings":["University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101737631","display_name":"Ruirui Li","orcid":"https://orcid.org/0009-0002-4635-6128"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruirui Li","raw_affiliation_strings":["University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043006821","display_name":"Zhengliang L. Wu","orcid":"https://orcid.org/0000-0002-0700-0906"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhengliang Wu","raw_affiliation_strings":["University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048749901","display_name":"Jyun\u2010Yu Jiang","orcid":"https://orcid.org/0000-0002-1753-8099"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jyun-Yu Jiang","raw_affiliation_strings":["University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhao Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhao Yang","raw_affiliation_strings":["University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5073504925"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":null,"apc_paid":null,"fwci":0.7859,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.71675381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"263","last_page":"272"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9922999739646912,"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":0.5248546600341797}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5248546600341797}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107444","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107444","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life below water","score":0.699999988079071,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G131502559","display_name":null,"funder_award_id":"R01GM115833","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5701931726","display_name":null,"funder_award_id":"DBI-1565137,IIS-1313606","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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1972418517","https://openalex.org/W1973996769","https://openalex.org/W2002354456","https://openalex.org/W2021809202","https://openalex.org/W2055770801","https://openalex.org/W2059513841","https://openalex.org/W2065128082","https://openalex.org/W2073921136","https://openalex.org/W2093788424","https://openalex.org/W2099964107","https://openalex.org/W2107079154","https://openalex.org/W2107248520","https://openalex.org/W2110887924","https://openalex.org/W2112876600","https://openalex.org/W2116628377","https://openalex.org/W2121252285","https://openalex.org/W2121873871","https://openalex.org/W2122789575","https://openalex.org/W2126144698","https://openalex.org/W2140729960","https://openalex.org/W2142599475","https://openalex.org/W2143447881","https://openalex.org/W2146749911","https://openalex.org/W2152054335","https://openalex.org/W2163395746","https://openalex.org/W2323326409","https://openalex.org/W2952944477","https://openalex.org/W4230266413"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2093578348","https://openalex.org/W2376932109","https://openalex.org/W2382290278","https://openalex.org/W2049775471","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"The":[0,194],"advent":[1],"of":[2,22,34,41,67,87,97,114,117,125,142,163,188],"RNA-Seq":[3,106],"has":[4],"made":[5],"it":[6],"possible":[7],"to":[8,48,54,72,100,155,183],"quantify":[9],"transcript":[10,24,127,146,208],"expression":[11,38],"on":[12],"a":[13,49,65,74,115,132,151],"large":[14],"scale":[15],"simultaneously.":[16],"This":[17],"technology":[18],"generates":[19],"small":[20],"fragments":[21],"each":[23,98,126],"sequence,":[25],"known":[26],"as":[27,190],"sequencing":[28],"reads.":[29,107],"As":[30],"the":[31,42,85,95,102,122,140,185,205],"first":[32],"step":[33],"data":[35],"analysis":[36,77],"towards":[37],"quantification,":[39],"most":[40],"existing":[43],"methods":[44,68,83],"align":[45],"these":[46],"reads":[47,189],"reference":[50],"genome":[51],"or":[52],"transcriptome":[53],"establish":[55],"their":[56],"origins.":[57],"However,":[58],"read":[59],"alignment":[60],"is":[61,181],"computationally":[62],"costly.":[63],"Recently,":[64],"series":[66],"have":[69],"been":[70],"proposed":[71],"perform":[73],"lightweight":[75],"quantification":[76],"in":[78,131,145,207],"an":[79,160],"alignment-free":[80],"manner.":[81],"These":[82],"utilize":[84],"notion":[86],"k-mers,":[88,179],"which":[89],"are":[90],"short":[91],"consecutive":[92],"sequences":[93],"representing":[94],"signatures":[96,124],"transcript,":[99],"estimate":[101],"relative":[103],"abundance":[104,147,209],"from":[105],"Current":[108],"k-mer":[109],"based":[110],"approaches":[111],"make":[112],"use":[113],"set":[116,162],"fixed":[118,133],"size":[119],"k-mers;":[120],"however,":[121],"true":[123],"may":[128],"not":[129],"exist":[130],"size.":[134],"In":[135],"this":[136],"paper,":[137],"we":[138,174],"demonstrate":[139],"importance":[141],"k-mers":[143,164,196],"selection":[144],"estimation.":[148,210],"We":[149],"propose":[150],"novel":[152],"method,":[153],"Fleximer,":[154],"efficiently":[156],"discover":[157],"and":[158,171,192,201],"select":[159],"optimal":[161],"with":[165,177],"flexible":[166],"lengths.":[167],"Using":[168],"both":[169],"simulated":[170],"real":[172],"datasets,":[173],"show":[175],"that,":[176],"fewer":[178],"Fleximer":[180],"able":[182],"cover":[184],"similar":[186],"amount":[187],"Sailfish":[191],"Kallisto.":[193],"selected":[195],"own":[197],"more":[198],"distinguishing":[199],"features,":[200],"thus":[202],"substantially":[203],"reduce":[204],"errors":[206]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2017-08-31T00:00:00"}
