{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T19:18:14Z","timestamp":1772306294992,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":28,"publisher":"ACM","license":[{"start":{"date-parts":[[2017,8,20]],"date-time":"2017-08-20T00:00:00Z","timestamp":1503187200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1565137,IIS-1313606"],"award-info":[{"award-number":["DBI-1565137,IIS-1313606"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM115833"],"award-info":[{"award-number":["R01GM115833"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2017,8,20]]},"DOI":"10.1145\/3107411.3107444","type":"proceedings-article","created":{"date-parts":[[2017,8,24]],"date-time":"2017-08-24T11:58:11Z","timestamp":1503575891000},"page":"263-272","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Fleximer"],"prefix":"10.1145","author":[{"given":"Chelsea J.-T.","family":"Ju","sequence":"first","affiliation":[{"name":"University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Ruirui","family":"Li","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Zhengliang","family":"Wu","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Jyun-Yu","family":"Jiang","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Zhao","family":"Yang","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, Los Angeles, CA, USA"}]}],"member":"320","published-online":{"date-parts":[[2017,8,20]]},"reference":[{"key":"e_1_3_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1145\/360825.360855"},{"key":"e_1_3_2_1_2_1","doi-asserted-by":"crossref","unstructured":"Kin Fai Au Hui Jiang Lan Lin Yi Xing and Wing Hung Wong. 2010. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic acids research 38 14 (aug 2010) 4570--8.  Kin Fai Au Hui Jiang Lan Lin Yi Xing and Wing Hung Wong. 2010. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic acids research 38 14 (aug 2010) 4570--8.","DOI":"10.1093\/nar\/gkq211"},{"key":"e_1_3_2_1_3_1","volume-title":"Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-94","volume":"5","author":"Bieganski Paul"},{"key":"e_1_3_2_1_4_1","doi-asserted-by":"crossref","unstructured":"Nicolas L Bray Harold Pimentel P\u00e1ll Melsted and Lior Pachter. 2016. Near-optimal probabilistic RNA-seq quantification. Nature biotechnology 34 5 (may 2016) 525--527. arXiv:1505.02710  Nicolas L Bray Harold Pimentel P\u00e1ll Melsted and Lior Pachter. 2016. Near-optimal probabilistic RNA-seq quantification. Nature biotechnology 34 5 (may 2016) 525--527. arXiv:1505.02710","DOI":"10.1038\/nbt.3519"},{"key":"e_1_3_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1010"},{"key":"e_1_3_2_1_6_1","volume-title":"Optimal Suix Tree Construction with Large Alphabets. 38th IEEE Symp. on Foundations of Computer Science","author":"Farach Martin","year":"1997"},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv272"},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"crossref","unstructured":"Manuel Garber Manfred G Grabherr Mitchell Guttman and Cole Trapnell. 2011. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature methods 8 6 (jun 2011) 469--77.  Manuel Garber Manfred G Grabherr Mitchell Guttman and Cole Trapnell. 2011. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature methods 8 6 (jun 2011) 469--77.","DOI":"10.1038\/nmeth.1613"},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.suppl_1.S181"},{"key":"e_1_3_2_1_10_1","first-page":"1","article-title":"Efficient multiple genome alignment","volume":"18","author":"H\u00f6hl Michael","year":"2002","journal-title":"Bioinformatics"},{"key":"e_1_3_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.10.1340"},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1147\/rd.312.0249"},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"crossref","unstructured":"Daehwan Kim Geo Pertea Cole Trapnell Harold Pimentel Ryan Kelley and Steven L Salzberg. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions deletions and gene fusions. Genome biology 14 4 (apr 2013) R36.  Daehwan Kim Geo Pertea Cole Trapnell Harold Pimentel Ryan Kelley and Steven L Salzberg. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions deletions and gene fusions. Genome biology 14 4 (apr 2013) R36.","DOI":"10.1186\/gb-2013-14-4-r36"},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"crossref","unstructured":"Hinanit Koltai and Carmiya Weingarten-Baror. 2008. Speciicity of DNA microarray hybridization: characterization effectors and approaches for data correction. Nucleic acids research 36 7 (apr 2008) 2395--405.  Hinanit Koltai and Carmiya Weingarten-Baror. 2008. Speciicity of DNA microarray hybridization: characterization effectors and approaches for data correction. Nucleic acids research 36 7 (apr 2008) 2395--405.","DOI":"10.1093\/nar\/gkn087"},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/15.5.426"},{"key":"e_1_3_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1145\/321941.321946"},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1137\/S0097539799364092"},{"key":"e_1_3_2_1_18_1","unstructured":"Herve Pag\u00e8s Daniel Bindreither Marc Carlson and Martin Morgan. 2013. SplicingGraphs: Create manipulate visualize splicing graphs and assign RNA-seq reads to them. R package version 1.14.0 (2013).  Herve Pag\u00e8s Daniel Bindreither Marc Carlson and Martin Morgan. 2013. SplicingGraphs: Create manipulate visualize splicing graphs and assign RNA-seq reads to them. R package version 1.14.0 (2013)."},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"crossref","unstructured":"Rob Patro Stephen M Mount and Carl Kingsford. 2014. Sailish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature biotechnology 32 5 (may 2014) 462--4.  Rob Patro Stephen M Mount and Carl Kingsford. 2014. Sailish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature biotechnology 32 5 (may 2014) 462--4.","DOI":"10.1038\/nbt.2862"},{"key":"e_1_3_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1045"},{"key":"e_1_3_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00224-006-1198-x"},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2009.0108"},{"key":"e_1_3_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw277"},{"key":"e_1_3_2_1_24_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01206331"},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl681"},{"key":"e_1_3_2_1_26_1","doi-asserted-by":"crossref","unstructured":"Kai Wang Darshan Singh Zheng Zeng Stephen J Coleman Yan Huang Gleb L Savich Xiaping He Piotr Mieczkowski Sara a Grimm Charles M Perou James N MacLeod Derek Y Chiang Jan F Prins and Jinze Liu. 2010. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic acids research 38 18 (oct 2010) e178.  Kai Wang Darshan Singh Zheng Zeng Stephen J Coleman Yan Huang Gleb L Savich Xiaping He Piotr Mieczkowski Sara a Grimm Charles M Perou James N MacLeod Derek Y Chiang Jan F Prins and Jinze Liu. 2010. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic acids research 38 18 (oct 2010) e178.","DOI":"10.1093\/nar\/gkq622"},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2009.03.016"},{"key":"e_1_3_2_1_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu288"}],"event":{"name":"BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","location":"Boston Massachusetts USA","acronym":"BCB '17","sponsor":["SIGBio ACM Special Interest Group on Bioinformatics"]},"container-title":["Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3107411.3107444","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3107411.3107444","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3107411.3107444","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T03:30:21Z","timestamp":1750217421000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3107411.3107444"}},"subtitle":["Accurate Quantification of RNA-Seq via Variable-Length k-mers"],"short-title":[],"issued":{"date-parts":[[2017,8,20]]},"references-count":28,"alternative-id":["10.1145\/3107411.3107444","10.1145\/3107411"],"URL":"https:\/\/doi.org\/10.1145\/3107411.3107444","relation":{},"subject":[],"published":{"date-parts":[[2017,8,20]]},"assertion":[{"value":"2017-08-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}