{"id":"https://openalex.org/W4387346417","doi":"https://doi.org/10.1145/3584371.3613034","title":"Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis","display_name":"Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis","publication_year":2023,"publication_date":"2023-09-03","ids":{"openalex":"https://openalex.org/W4387346417","doi":"https://doi.org/10.1145/3584371.3613034"},"language":"en","primary_location":{"id":"doi:10.1145/3584371.3613034","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3613034","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613034","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613034","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079733018","display_name":"Kavya Vaddadi","orcid":"https://orcid.org/0000-0001-9020-2666"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Naga Sai Kavya Vaddadi","raw_affiliation_strings":["Johns Hopkins University, Baltimore, USA"],"raw_orcid":"https://orcid.org/0000-0001-9020-2666","affiliations":[{"raw_affiliation_string":"Johns Hopkins University, Baltimore, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000946526","display_name":"Taher Mun","orcid":"https://orcid.org/0000-0002-3588-0883"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taher Mun","raw_affiliation_strings":["Johns Hopkins University, Baltimore, USA"],"raw_orcid":"https://orcid.org/0000-0002-3588-0883","affiliations":[{"raw_affiliation_string":"Johns Hopkins University, Baltimore, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009556658","display_name":"Ben Langmead","orcid":"https://orcid.org/0000-0003-2437-1976"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Langmead","raw_affiliation_strings":["Johns Hopkins University, Baltimore, USA"],"raw_orcid":"https://orcid.org/0000-0003-2437-1976","affiliations":[{"raw_affiliation_string":"Johns Hopkins University, Baltimore, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079733018"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":null,"apc_paid":null,"fwci":0.1499,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59447205,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"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":0.9983999729156494,"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":0.9983999729156494,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9965000152587891,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9959999918937683,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.794775664806366},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.6692485213279724},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6012398600578308},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.558078408241272},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.48268771171569824},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46300461888313293},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.43694227933883667},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.3815267086029053},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20970222353935242},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1651584506034851},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15522724390029907},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09469938278198242}],"concepts":[{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.794775664806366},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.6692485213279724},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6012398600578308},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.558078408241272},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.48268771171569824},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46300461888313293},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.43694227933883667},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.3815267086029053},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20970222353935242},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1651584506034851},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15522724390029907},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09469938278198242}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3584371.3613034","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3613034","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613034","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3584371.3613034","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3613034","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613034","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2241781793","display_name":null,"funder_award_id":"R01HG011392","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387346417.pdf","grobid_xml":"https://content.openalex.org/works/W4387346417.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2950228679","https://openalex.org/W3120295425","https://openalex.org/W3120923229","https://openalex.org/W4372333204"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W2055961818","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549"],"abstract_inverted_index":{"We":[0],"introduce":[1],"the":[2,29,59,77,85],"Impute-first":[3,81],"alignment":[4],"framework":[5,82],"that":[6],"reduces":[7],"reference":[8,35,41,95],"bias":[9,96],"in":[10,64],"genomics":[11],"by":[12],"integrating":[13],"genotype":[14,23],"imputation":[15,24],"with":[16,20],"pangenome":[17,62,92],"alignment.":[18],"Beginning":[19],"genotyping":[21],"and":[22,71,91],"using":[25,76],"a":[26,32,99],"portion":[27],"of":[28,87],"input":[30],"data,":[31],"personalized":[33,40],"diploid":[34],"genome":[36,42],"is":[37,43],"created.":[38],"This":[39],"then":[44],"used":[45],"for":[46],"read":[47],"alignment,":[48],"enhancing":[49],"downstream":[50],"results":[51],"such":[52],"as":[53,74],"variant":[54],"calls.":[55],"Our":[56],"approach":[57],"outperforms":[58],"traditional":[60,88],"graph-based":[61],"references":[63],"variant-calling":[65],"measures,":[66],"exhibiting":[67],"improved":[68],"sensitivity,":[69],"precision,":[70],"overall":[72],"accuracy,":[73],"demonstrated":[75],"HG001":[78],"sample.":[79],"The":[80],"successfully":[83],"merges":[84],"benefits":[86],"reference-based":[89],"methods":[90],"strategies,":[93],"reducing":[94],"while":[97],"maintaining":[98],"low":[100],"computational":[101],"cost.":[102]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
