{"id":"https://openalex.org/W2973134747","doi":"https://doi.org/10.1145/3307339.3342182","title":"ELITE","display_name":"ELITE","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2973134747","doi":"https://doi.org/10.1145/3307339.3342182","mag":"2973134747"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3342182","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342182","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th 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/A5074552594","display_name":"Anwica Kashfeen","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anwica Kashfeen","raw_affiliation_strings":["University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049295598","display_name":"Harper Fauni","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harper B. Fauni","raw_affiliation_strings":["University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027656240","display_name":"Timothy A. Bell","orcid":"https://orcid.org/0000-0002-9546-6334"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy A. Bell","raw_affiliation_strings":["University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018305231","display_name":"Fernando Pardo\u2010Manuel de Villena","orcid":"https://orcid.org/0000-0002-5738-5795"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fernando Pardo-Manuel de Villena","raw_affiliation_strings":["University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042463953","display_name":"Leonard McMillan","orcid":"https://orcid.org/0000-0002-8453-0847"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonard McMillan","raw_affiliation_strings":["University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2899,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.74628521,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"183","last_page":"189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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/T12858","display_name":"Plant Disease Resistance and Genetics","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6660785675048828},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5717194080352783},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5294173359870911},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4988281726837158},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47603797912597656},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.46376749873161316},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4577014446258545},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4527055621147156},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.4239409863948822},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2602583169937134}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6660785675048828},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5717194080352783},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5294173359870911},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4988281726837158},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47603797912597656},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.46376749873161316},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4577014446258545},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4527055621147156},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.4239409863948822},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2602583169937134},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3307339.3342182","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342182","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1482190741","https://openalex.org/W2007736033","https://openalex.org/W2011016615","https://openalex.org/W2049071198","https://openalex.org/W2055043387","https://openalex.org/W2108234281","https://openalex.org/W2146821392","https://openalex.org/W2161048357","https://openalex.org/W2170687235","https://openalex.org/W2179064901","https://openalex.org/W2210193708","https://openalex.org/W2513006861","https://openalex.org/W2531715486"],"related_works":["https://openalex.org/W2053969879","https://openalex.org/W2082641564","https://openalex.org/W2107333779","https://openalex.org/W3108190435","https://openalex.org/W2790772971","https://openalex.org/W1964419640","https://openalex.org/W1906262170","https://openalex.org/W2921363728","https://openalex.org/W2279684808","https://openalex.org/W3217304749"],"abstract_inverted_index":{"A":[0],"large":[1],"fraction":[2],"of":[3,7,15,51,142,148,154,173],"mammalian":[4],"genome":[5,28,60,72],"consists":[6],"transposable":[8],"elements":[9,12],"(TEs).":[10],"These":[11],"are":[13,21,162],"segments":[14],"DNA":[16],"that":[17,161],"either":[18,57],"move":[19],"or":[20,61],"copied":[22],"from":[23,96],"one":[24],"place":[25],"in":[26,127],"the":[27,94,166],"to":[29,56,89,106,165],"another.":[30],"Such":[31],"movements":[32],"can":[33],"cause":[34],"deleterious":[35],"mutations":[36],"and":[37,80,91,101,119,124,169],"drive":[38],"chromosome":[39],"evolution.":[40],"Existing":[41],"approaches":[42],"search":[43],"for":[44,78],"TE":[45,63],"insertion":[46],"(TEi)":[47],"by":[48],"aligning":[49],"millions":[50],"mostly":[52],"irrelevant":[53],"short":[54],"reads":[55,95],"a":[58,62,69,97,103,121,155,171,178],"reference":[59],"sequence":[64],"library.":[65],"Here":[66],"we":[67,137],"present":[68],"new":[70],"local":[71],"assembly":[73],"based":[74],"pipeline,":[75],"called":[76],"ELITE,":[77],"identifying":[79],"characterizing":[81],"TEi.":[82,129],"ELITE":[83,116,130,149],"uses":[84],"an":[85],"msBWT-based":[86],"data":[87],"structure":[88],"store":[90],"index":[92],"all":[93],"high-throughput":[98],"sequencing":[99],"dataset":[100],"leverages":[102],"sampled":[104],"FM-index":[105],"detect":[107],"TEi":[108,174],"efficiently.":[109],"In":[110],"comparison":[111],"with":[112],"two":[113],"existing":[114],"tools,":[115],"is":[117],"faster":[118],"has":[120],"higher":[122],"precision":[123],"recall":[125],"rate":[126],"predicting":[128],"also":[131],"works":[132],"on":[133],"real":[134],"data,":[135],"which":[136],"validated":[138],"using":[139],"PCR":[140],"assays":[141],"surrounding":[143],"genomic":[144],"context.":[145],"Additional":[146],"features":[147],"include":[150],"finding":[151],"zygosity":[152],"status":[153],"predicted":[156],"TEi,":[157],"discovering":[158],"unannotated":[159],"TEs":[160],"distantly":[163],"related":[164],"target":[167],"one,":[168],"providing":[170],"summary":[172],"sharing":[175],"pattern":[176],"within":[177],"population.":[179]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2019-09-19T00:00:00"}
