{"id":"https://openalex.org/W4232536727","doi":"https://doi.org/10.1109/iccabs.2017.8114315","title":"Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in melilotus","display_name":"Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in melilotus","publication_year":2017,"publication_date":"2017-10-01","ids":{"openalex":"https://openalex.org/W4232536727","doi":"https://doi.org/10.1109/iccabs.2017.8114315"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2017.8114315","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2017.8114315","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"conference-abstract","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/A5103122314","display_name":"Shuhua Fu","orcid":"https://orcid.org/0000-0002-9973-253X"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuhua Fu","raw_affiliation_strings":["Department of Biochemistry &amp; Biophysics, Texas A&amp;M University, College Station, TX 77843, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry &amp; Biophysics, Texas A&amp;M University, College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038551473","display_name":"Peter L. Chang","orcid":"https://orcid.org/0000-0001-7676-7708"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter L. Chang","raw_affiliation_strings":["Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090041632","display_name":"Maren Friesen","orcid":"https://orcid.org/0000-0002-4274-8928"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maren L. Friesen","raw_affiliation_strings":["Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081715002","display_name":"Natasha L. Teakle","orcid":null},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"The University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Natasha L. Teakle","raw_affiliation_strings":["Centre for Ecohydrology, School of Plant Biology (M084), Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Ecohydrology, School of Plant Biology (M084), Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia","institution_ids":["https://openalex.org/I177877127"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039599341","display_name":"Aaron M. Tarone","orcid":"https://orcid.org/0000-0003-0965-7634"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron M. Tarone","raw_affiliation_strings":["Department of Entomology, Texas A&amp;M University, College Station, TX 77843, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Entomology, Texas A&amp;M University, College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107809749","display_name":"Sing\u2010Hoi Sze","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sing-Hoi Sze","raw_affiliation_strings":["Department of Computer Science and Engineering, Department of Biochemistry &amp; Biophysics, Texas A&amp;M University, College Station, TX 77843, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Department of Biochemistry &amp; Biophysics, Texas A&amp;M University, College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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":0.9988999962806702,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.9714999794960022,"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/de-bruijn-graph","display_name":"De Bruijn graph","score":0.872817873954773},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.7594693899154663},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5803060531616211},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5758104920387268},{"id":"https://openalex.org/keywords/de-novo-transcriptome-assembly","display_name":"De novo transcriptome assembly","score":0.4691297709941864},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4500761330127716},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40407681465148926},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39335909485816956},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.36871442198753357},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.31069520115852356},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.30816298723220825},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2790045738220215},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22965297102928162},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1891602873802185},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11781299114227295},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07770437002182007}],"concepts":[{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.872817873954773},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.7594693899154663},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5803060531616211},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5758104920387268},{"id":"https://openalex.org/C50489715","wikidata":"https://www.wikidata.org/wiki/Q5244960","display_name":"De novo transcriptome assembly","level":5,"score":0.4691297709941864},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4500761330127716},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40407681465148926},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39335909485816956},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.36871442198753357},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.31069520115852356},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.30816298723220825},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2790045738220215},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22965297102928162},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1891602873802185},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11781299114227295},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07770437002182007}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2017.8114315","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2017.8114315","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2562683361","https://openalex.org/W3087469195","https://openalex.org/W2354744388","https://openalex.org/W3125399386","https://openalex.org/W2949121831","https://openalex.org/W3215786367","https://openalex.org/W1908987670","https://openalex.org/W2756186577","https://openalex.org/W2735897904","https://openalex.org/W3021160691"],"abstract_inverted_index":{"While":[0],"a":[1,17,47,68,87,189],"popular":[2],"strategy":[3],"in":[4,94,115,135,213],"de":[5,18,36,81,96,117],"novo":[6],"transcriptome":[7],"assembly":[8],"algorithms":[9],"is":[10,28,43,64,175],"to":[11,30,46,50,66,91,102,130,159,163,177,207],"assemble":[12],"the":[13,23,35,77,80,95,105,116,127,136],"reads":[14,142],"by":[15,75,111],"obtaining":[16],"Bruijn":[19,37,82,97,118],"graph":[20,83,98],"that":[21,62,99,172],"represents":[22],"transcriptome,":[24],"an":[25],"additional":[26],"step":[27],"needed":[29],"obtain":[31,51,67],"predicted":[32,58],"transcripts":[33,74,103,162,181,187],"from":[34,79,104,126,143],"graph.":[38],"A":[39],"similarity":[40],"search":[41,78],"algorithm":[42,90,109,151,174,206],"then":[44],"applied":[45],"related":[48,106,128,164],"organism":[49,129],"information":[52,125],"about":[53],"possible":[54,65],"function":[55],"of":[56,72,123,192],"these":[57,133,214],"transcripts.":[59],"We":[60,85,170,194],"observe":[61],"it":[63],"more":[69,179],"complete":[70],"set":[71],"similar":[73,101,161,180],"starting":[76],"directly.":[84],"develop":[86],"heuristic":[88],"extension":[89],"identify":[92,160],"paths":[93,114,134],"are":[100],"organism.":[107],"The":[108],"starts":[110],"enumerating":[112],"short":[113],"graph,":[119],"and":[120,156,188,203,210],"makes":[121],"use":[122],"evolutionary":[124,168],"iteratively":[131],"extend":[132],"most":[137],"promising":[138],"direction.":[139],"By":[140],"extracting":[141],"publicly":[144],"available":[145],"RNA-Seq":[146,197],"libraries,":[147],"we":[148],"apply":[149,204],"our":[150,173,205],"on":[152],"both":[153],"model":[154],"organisms":[155,158,165],"non-model":[157],"with":[166,185],"varying":[167],"distances.":[169],"show":[171],"able":[176],"recover":[178],"than":[182],"existing":[183],"algorithms,":[184],"longer":[186],"better":[190],"resolution":[191],"isoforms.":[193],"construct":[195],"new":[196],"libraries":[198],"for":[199],"two":[200,215],"Melilotas":[201],"species,":[202],"study":[208],"salt":[209],"waterlogging":[211],"tolerance":[212],"species.":[216]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
