{"id":"https://openalex.org/W6944041614","doi":"https://doi.org/10.17615/sxrd-7281","title":"IDENTIFYING AND CHARACTERIZING TRANSPOSABLE ELEMENTS IN THE GENOME","display_name":"IDENTIFYING AND CHARACTERIZING TRANSPOSABLE ELEMENTS IN THE GENOME","publication_year":2022,"publication_date":"2022-05-27","ids":{"openalex":"https://openalex.org/W6944041614","doi":"https://doi.org/10.17615/sxrd-7281"},"language":"en","primary_location":{"id":"doi:10.17615/sxrd-7281","is_oa":true,"landing_page_url":"https://doi.org/10.17615/sxrd-7281","pdf_url":null,"source":{"id":"https://openalex.org/S7407051488","display_name":"UNC Libraries","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"thesis"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.17615/sxrd-7281","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Kashfeen, Anwica","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":true,"raw_author_name":"Kashfeen, Anwica","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.46204005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9401000142097473,"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":0.9401000142097473,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.021800000220537186,"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":0.017500000074505806,"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/genome","display_name":"Genome","score":0.7135000228881836},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.6348999738693237},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.6072999835014343},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5414999723434448},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4708000123500824},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.42899999022483826},{"id":"https://openalex.org/keywords/zygosity","display_name":"Zygosity","score":0.38609999418258667}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7135000228881836},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.6348999738693237},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.6072999835014343},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5638999938964844},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5414999723434448},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.515999972820282},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4708000123500824},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45820000767707825},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.42899999022483826},{"id":"https://openalex.org/C197845989","wikidata":"https://www.wikidata.org/wiki/Q13048280","display_name":"Zygosity","level":2,"score":0.38609999418258667},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.385699987411499},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.3684000074863434},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.367000013589859},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.3612000048160553},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3528999984264374},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.3102000057697296},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.2775000035762787},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2614000141620636},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.260699987411499}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.17615/sxrd-7281","is_oa":true,"landing_page_url":"https://doi.org/10.17615/sxrd-7281","pdf_url":null,"source":{"id":"https://openalex.org/S7407051488","display_name":"UNC Libraries","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"}],"best_oa_location":{"id":"doi:10.17615/sxrd-7281","is_oa":true,"landing_page_url":"https://doi.org/10.17615/sxrd-7281","pdf_url":null,"source":{"id":"https://openalex.org/S7407051488","display_name":"UNC Libraries","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"thesis"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"A":[0],"large":[1],"fraction":[2],"of":[3,7,15,36,57,66,83,142,191,236],"mammalian":[4],"genome":[5,28,92],"consists":[6],"transposable":[8],"elements":[9,12],"(TEs).":[10],"These":[11,214],"are":[13,21,32,40,204],"segments":[14],"DNA":[16],"that":[17,189,203],"either":[18,89],"move":[19],"or":[20,93,224],"copied":[22],"from":[23,165],"one":[24],"place":[25],"in":[26,70,116,206],"the":[27,55,71,140,163,198,233],"to":[29,49,88,136,158,181,220,240],"another.":[30],"TEs":[31,58],"a":[33,90,94,166,207,244],"significant":[34],"source":[35],"genetic":[37],"variation":[38],"and":[39,53,110,128,149,160,170,176],"directly":[41],"responsible":[42],"for":[43,76,184],"many":[44],"diseases.":[45],"It":[46],"is":[47,126,130,135],"difficult":[48],"identify,":[50],"map,":[51],"characterize,":[52],"determine":[54],"zygosity":[56],"using":[59],"current":[60],"high-throughput":[61,167],"short-read":[62],"sequencing":[63,168],"data":[64,156,173],"because":[65],"their":[67],"numerous":[68],"copies":[69],"genome.":[72],"Existing":[73],"approaches":[74],"search":[75,183],"TE":[77,95,143,148,227],"insertion":[78,144],"(TEi)":[79],"by":[80],"aligning":[81],"millions":[82],"mostly":[84],"irrelevant":[85],"short":[86],"reads":[87,164],"reference":[91],"sequence":[96],"library.":[97],"In":[98],"this":[99],"dissertation":[100],"I":[101,152,187],"describe":[102],"two":[103,192],"alignment-free":[104],"novel":[105],"TEi":[106,185],"detection":[107],"algorithms,":[108],"ELITE":[109,125],"Frontier":[111,129],"which":[112,145],"outperform":[113],"existing":[114],"tools":[115],"several":[117],"different":[118],"categories.":[119],"Both":[120],"algorithms":[121],"use":[122,153],"local-genome-assembly":[123],"where":[124],"template-dependent":[127],"template-free.":[131],"The":[132],"key":[133],"idea":[134],"focus":[137],"on":[138,232],"identifying":[139],"boundary":[141],"contains":[146],"partial":[147],"non-TE":[150],"context.":[151],"an":[154],"msBWT-based":[155],"structure":[157],"store":[159],"index":[161],"all":[162,197],"dataset":[169],"leverages":[171],"additional":[172],"structures":[174],"FM-index":[175],"Longest":[177],"Common":[178],"Prefix":[179],"(LCP)":[180],"efficiently":[182],"boundaries.":[186],"show":[188],"combination":[190],"methods":[193,215],"can":[194,216],"identify":[195,221],"nearly":[196],"Endogenous":[199],"RetoVirus":[200],"(ERV)":[201],"insertions":[202],"segregating":[205],"population":[208],"with":[209],"more":[210],"than":[211],"100":[212],"samples.":[213],"also":[217],"be":[218],"used":[219],"very":[222],"recent":[223],"de":[225],"novo":[226],"insertions.":[228],"Moreover,":[229],"characterization":[230],"based":[231],"sharing":[234],"pattern":[235],"ERVis":[237],"allows":[238],"us":[239],"study":[241],"phylogeny":[242],"within":[243],"population.":[245]},"counts_by_year":[],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}