{"id":"https://openalex.org/W2219104018","doi":"https://doi.org/10.1186/s13015-015-0062-4","title":"HIA: a genome mapper using hybrid index-based sequence alignment","display_name":"HIA: a genome mapper using hybrid index-based sequence alignment","publication_year":2015,"publication_date":"2015-12-01","ids":{"openalex":"https://openalex.org/W2219104018","doi":"https://doi.org/10.1186/s13015-015-0062-4","mag":"2219104018","pmid":"https://pubmed.ncbi.nlm.nih.gov/26702294"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-015-0062-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0062-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0062-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0062-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015974778","display_name":"Jongpill Choi","orcid":"https://orcid.org/0000-0003-2755-1809"},"institutions":[{"id":"https://openalex.org/I4210097010","display_name":"Korea National Institute of Health","ror":"https://ror.org/00qdsfq65","country_code":"KR","type":"government","lineage":["https://openalex.org/I1290491151","https://openalex.org/I2801339556","https://openalex.org/I4210097010"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Jongpill Choi","raw_affiliation_strings":["Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institute of Health, Osong, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institute of Health, Osong, Korea","institution_ids":["https://openalex.org/I4210097010"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041805962","display_name":"Kiejung Park","orcid":null},"institutions":[{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kiejung Park","raw_affiliation_strings":["Biomedical Research Institute, College of Medicine, Hanyang University, Seoul, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Research Institute, College of Medicine, Hanyang University, Seoul, Korea","institution_ids":["https://openalex.org/I4575257"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102821674","display_name":"Seong Beom Cho","orcid":"https://orcid.org/0000-0002-5734-1645"},"institutions":[{"id":"https://openalex.org/I4210097010","display_name":"Korea National Institute of Health","ror":"https://ror.org/00qdsfq65","country_code":"KR","type":"government","lineage":["https://openalex.org/I1290491151","https://openalex.org/I2801339556","https://openalex.org/I4210097010"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seong Beom Cho","raw_affiliation_strings":["Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institute of Health, Osong, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institute of Health, Osong, Korea","institution_ids":["https://openalex.org/I4210097010"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052683529","display_name":"Myungguen Chung","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097010","display_name":"Korea National Institute of Health","ror":"https://ror.org/00qdsfq65","country_code":"KR","type":"government","lineage":["https://openalex.org/I1290491151","https://openalex.org/I2801339556","https://openalex.org/I4210097010"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Myungguen Chung","raw_affiliation_strings":["Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institute of Health, Osong, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institute of Health, Osong, Korea","institution_ids":["https://openalex.org/I4210097010"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5015974778","https://openalex.org/A5052683529"],"corresponding_institution_ids":["https://openalex.org/I4210097010"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":0.0,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.06805496,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"1","first_page":"30","last_page":"30"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9488000273704529,"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":0.9488000273704529,"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/T11269","display_name":"Algorithms and Data Compression","score":0.013000000268220901,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.005900000222027302,"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/substring","display_name":"Substring","score":0.9050679802894592},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.783897876739502},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7681988477706909},{"id":"https://openalex.org/keywords/hash-table","display_name":"Hash table","score":0.6276748776435852},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.596507728099823},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.5630654692649841},{"id":"https://openalex.org/keywords/hash-function","display_name":"Hash function","score":0.5628885626792908},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.5385066270828247},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.48143455386161804},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3650381565093994},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3405224680900574},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.32970255613327026},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.29254084825515747},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.22361046075820923},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17846792936325073},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10107001662254333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09860587120056152}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.9050679802894592},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.783897876739502},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7681988477706909},{"id":"https://openalex.org/C67388219","wikidata":"https://www.wikidata.org/wiki/Q207440","display_name":"Hash table","level":3,"score":0.6276748776435852},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.596507728099823},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.5630654692649841},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.5628885626792908},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.5385066270828247},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.48143455386161804},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3650381565093994},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3405224680900574},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.32970255613327026},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29254084825515747},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.22361046075820923},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17846792936325073},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10107001662254333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09860587120056152},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13015-015-0062-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0062-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0062-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:26702294","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26702294","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4688996","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4688996","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-015-0062-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0062-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0062-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"},{"id":"https://openalex.org/F4320334876","display_name":"Korea National Institute of Health","ror":"https://ror.org/00qdsfq65"},{"id":"https://openalex.org/F4320334882","display_name":"Korea Centers for Disease Control and Prevention","ror":"https://ror.org/056za9j29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2219104018.pdf","grobid_xml":"https://content.openalex.org/works/W2219104018.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1996181407","https://openalex.org/W2024932032","https://openalex.org/W2037113830","https://openalex.org/W2052890777","https://openalex.org/W2074231493","https://openalex.org/W2093931624","https://openalex.org/W2098291606","https://openalex.org/W2103441770","https://openalex.org/W2111217142","https://openalex.org/W2125418992","https://openalex.org/W2139760555","https://openalex.org/W2142619120","https://openalex.org/W2150356570","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2885727518","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W2070949798","https://openalex.org/W1593730394","https://openalex.org/W2124852384","https://openalex.org/W1568850903","https://openalex.org/W4379644220","https://openalex.org/W2736693933","https://openalex.org/W2485439294","https://openalex.org/W3022344494","https://openalex.org/W2560606564","https://openalex.org/W264360214"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1],"number":[2],"of":[3,20,49,56,95,106,170,230,240,250],"alignment":[4,164,186],"tools":[5],"have":[6,37],"been":[7],"developed":[8],"to":[9,13,66,175,183,257],"align":[10],"sequencing":[11,24,255],"reads":[12,256],"the":[14,53,99,128,137,143,162,200,204,211,224,238,258],"human":[15,259],"reference":[16,138,154,191,260],"genome.":[17],"The":[18,89,178],"scale":[19],"information":[21],"from":[22,44],"next-generation":[23],"(NGS)":[25],"experiments,":[26],"however,":[27],"is":[28,64,124,147,173,181,206,246,267],"increasing":[29,54],"rapidly.":[30],"Recent":[31],"studies":[32],"based":[33],"on":[34],"NGS":[35,60,254,276],"technology":[36],"routinely":[38],"produced":[39],"exome":[40],"or":[41,47],"whole-genome":[42],"sequences":[43],"several":[45],"hundreds":[46],"thousands":[48],"samples.":[50],"To":[51],"accommodate":[52],"need":[55],"analyzing":[57],"very":[58,103],"large":[59],"data":[61,272],"sets,":[62],"it":[63],"necessary":[65],"develop":[67],"faster,":[68],"more":[69],"sensitive":[70],"and":[71,84,98,119,155,192,243],"accurate":[72],"mapping":[73,220,231,253],"tools.":[74],"RESULTS:":[75],"HIA":[76,217],"uses":[77],"two":[78],"indices,":[79],"a":[80,85,96,134,148,153,156,168,190,193],"hash":[81,90,117,241],"table":[82,91,118,242],"index":[83,180],"suffix":[86,100,120,129,244],"array":[87,101,121,130,245],"index.":[88],"performs":[92,102],"direct":[93],"lookup":[94,105],"q-gram,":[97],"fast":[104],"variable-length":[107],"strings":[108],"by":[109,275],"exploiting":[110],"binary":[111],"search.":[112],"We":[113,195],"observed":[114],"that":[115,172,197,237],"combining":[116],"(hybrid":[122],"index)":[123],"much":[125,207],"faster":[126,208],"than":[127,209],"method":[131],"for":[132,252,269],"finding":[133],"substring":[135,151],"in":[136,203,219,248],"sequence.":[139,262],"Here,":[140],"we":[141,159],"defined":[142,161],"matching":[144],"region":[145],"(MR)":[146],"longest":[149],"common":[150],"between":[152,189],"read.":[157,194],"And,":[158],"also":[160],"candidate":[163,185],"regions":[165,187,202],"(CARs)":[166,188],"as":[167],"list":[169],"MRs":[171],"close":[174],"each":[176],"other.":[177],"hybrid":[179,239],"used":[182],"find":[184],"found":[196],"aligning":[198,210,270],"only":[199],"unmatched":[201],"CAR":[205],"whole":[212],"CAR.":[213],"In":[214,263],"benchmark":[215],"analysis,":[216],"outperformed":[218],"speed":[221,251],"compared":[222],"with":[223],"other":[225],"aligners,":[226],"without":[227],"significant":[228],"loss":[229],"accuracy.":[232],"CONCLUSIONS:":[233],"Our":[234],"experiments":[235],"show":[236],"useful":[247],"terms":[249],"genome":[261],"conclusion,":[264],"our":[265],"tool":[266],"appropriate":[268],"massive":[271],"sets":[273],"generated":[274],"sequencing.":[277]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
