{"id":"https://openalex.org/W4409013692","doi":"https://doi.org/10.1109/bigcomp64353.2025.00021","title":"Assessing the impact of reference genomes on the quality of a reference-guided genome assembly","display_name":"Assessing the impact of reference genomes on the quality of a reference-guided genome assembly","publication_year":2025,"publication_date":"2025-02-09","ids":{"openalex":"https://openalex.org/W4409013692","doi":"https://doi.org/10.1109/bigcomp64353.2025.00021"},"language":"en","primary_location":{"id":"doi:10.1109/bigcomp64353.2025.00021","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bigcomp64353.2025.00021","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Big Data and Smart Computing (BigComp)","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/A5063845970","display_name":"Suyeon Wy","orcid":"https://orcid.org/0000-0003-1461-4815"},"institutions":[{"id":"https://openalex.org/I24062138","display_name":"Konkuk University","ror":"https://ror.org/025h1m602","country_code":"KR","type":"education","lineage":["https://openalex.org/I24062138"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Suyeon Wy","raw_affiliation_strings":["Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I24062138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100383364","display_name":"Junyoung Kim","orcid":"https://orcid.org/0000-0002-4948-6860"},"institutions":[{"id":"https://openalex.org/I24062138","display_name":"Konkuk University","ror":"https://ror.org/025h1m602","country_code":"KR","type":"education","lineage":["https://openalex.org/I24062138"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Junyoung Kim","raw_affiliation_strings":["Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I24062138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063109384","display_name":"Mikang Sim","orcid":"https://orcid.org/0000-0002-8772-7071"},"institutions":[{"id":"https://openalex.org/I24062138","display_name":"Konkuk University","ror":"https://ror.org/025h1m602","country_code":"KR","type":"education","lineage":["https://openalex.org/I24062138"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Mikang Sim","raw_affiliation_strings":["Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I24062138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033232650","display_name":"Daehong Kwon","orcid":"https://orcid.org/0000-0003-2545-0430"},"institutions":[{"id":"https://openalex.org/I24062138","display_name":"Konkuk University","ror":"https://ror.org/025h1m602","country_code":"KR","type":"education","lineage":["https://openalex.org/I24062138"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Daehong Kwon","raw_affiliation_strings":["Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I24062138"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080954876","display_name":"Jaebum Kim","orcid":"https://orcid.org/0000-0002-2287-9760"},"institutions":[{"id":"https://openalex.org/I24062138","display_name":"Konkuk University","ror":"https://ror.org/025h1m602","country_code":"KR","type":"education","lineage":["https://openalex.org/I24062138"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jaebum Kim","raw_affiliation_strings":["Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Konkuk University,Department of Biomedical Science and Engineering,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I24062138"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063845970"],"corresponding_institution_ids":["https://openalex.org/I24062138"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06249873,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"75","last_page":"76"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9312999844551086,"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":0.9312999844551086,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9128000140190125,"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":0.642006516456604},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5685182809829712},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5534899830818176},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.5158559679985046},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4080265760421753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2454570233821869},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17839637398719788},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12436327338218689},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07622978091239929}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.642006516456604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5685182809829712},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5534899830818176},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5158559679985046},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4080265760421753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2454570233821869},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17839637398719788},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12436327338218689},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07622978091239929},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bigcomp64353.2025.00021","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bigcomp64353.2025.00021","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Big Data and Smart Computing (BigComp)","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":9,"referenced_works":["https://openalex.org/W2155628349","https://openalex.org/W2157546065","https://openalex.org/W2173732482","https://openalex.org/W2604308930","https://openalex.org/W2767590279","https://openalex.org/W2928996725","https://openalex.org/W3119817612","https://openalex.org/W4388615740","https://openalex.org/W4388615950"],"related_works":["https://openalex.org/W2921363728","https://openalex.org/W2279684808","https://openalex.org/W3217304749","https://openalex.org/W2066142713","https://openalex.org/W2894932706","https://openalex.org/W2767606877","https://openalex.org/W2582968398","https://openalex.org/W4223446368","https://openalex.org/W4232517363","https://openalex.org/W3214020344"],"abstract_inverted_index":{"Reference-guided":[0],"genome":[1,12,42,58,93,99,119],"assembly":[2,79,100],"uses":[3],"reference":[4,17,69,104],"genomes":[5,18,112],"of":[6,16,23,57,92,107,118],"related":[7,67],"species":[8,70],"to":[9,68,77],"generate":[10],"high-quality":[11],"assemblies.":[13],"The":[14],"selection":[15],"significantly":[19],"influences":[20],"the":[21,45,49,55,78,90,108,115],"quality":[22,56,91,116],"assembly,":[24],"yet":[25],"clear":[26],"guidelines":[27],"are":[28],"lacking.":[29],"In":[30],"this":[31],"study,":[32],"we":[33],"defined":[34],"and":[35,71],"calculated":[36],"35":[37],"genomic":[38,65],"features":[39,52,66],"affecting":[40],"reference-guided":[41,98],"assembly.":[43],"Using":[44],"Select":[46],"K-best":[47],"algorithm,":[48],"top":[50],"20":[51],"associated":[53],"with":[54,128],"assemblies":[59,94,120],"were":[60,121],"selected.":[61],"We":[62,81],"found":[63],"that":[64,88,114],"evolutionary":[72],"distance":[73],"showed":[74],"high":[75],"relevance":[76],"quality.":[80],"also":[82],"implemented":[83],"a":[84,97],"machine":[85],"learning":[86],"model":[87,109],"predicts":[89],"generated":[95],"by":[96],"approach":[101],"using":[102,110],"given":[103],"species.":[105],"Evaluation":[106],"bonobo":[111],"demonstrated":[113],"scores":[117],"well":[122],"predicted":[123],"depending":[124],"on":[125],"reference-outgroup":[126],"pairs":[127],"our":[129],"model.":[130]},"counts_by_year":[],"updated_date":"2025-12-28T23:10:05.387466","created_date":"2025-10-10T00:00:00"}
