{"id":"https://openalex.org/W1975667159","doi":"https://doi.org/10.1109/tcbb.2014.2369042","title":"An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length","display_name":"An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length","publication_year":2014,"publication_date":"2014-11-10","ids":{"openalex":"https://openalex.org/W1975667159","doi":"https://doi.org/10.1109/tcbb.2014.2369042","mag":"1975667159","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357316"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2369042","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2369042","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5062385266","display_name":"Ho-Sik Seok","orcid":"https://orcid.org/0000-0002-8258-5369"},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Ho-Sik Seok","raw_affiliation_strings":["School of Computer Science and Engineering, Soongsil University, Seoul, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-8258-5369","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Soongsil University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067462837","display_name":"Tae-Min Song","orcid":"https://orcid.org/0000-0002-2078-4119"},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Taemin Song","raw_affiliation_strings":["School of Computer Science and Engineering, Soongsil University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Soongsil University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039030911","display_name":"Sek Won Kong","orcid":"https://orcid.org/0000-0003-4877-7567"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sek Won Kong","raw_affiliation_strings":["Informatics Program at Boston Children's Hospital, Boston, MA, USA",", Informatics Program at Boston Children's Hospital, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Program at Boston Children's Hospital, Boston, MA, USA","institution_ids":["https://openalex.org/I1288882113"]},{"raw_affiliation_string":", Informatics Program at Boston Children's Hospital, Boston, MA, USA","institution_ids":["https://openalex.org/I1288882113"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048469651","display_name":"Kyu\u2010Baek Hwang","orcid":"https://orcid.org/0000-0003-2652-5326"},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyu-Baek Hwang","raw_affiliation_strings":["School of Computer Science and Engineering, Soongsil University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Soongsil University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.1299,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.49241243,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"4","first_page":"778","last_page":"784"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9973000288009644,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9965999722480774,"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/range","display_name":"Range (aeronautics)","score":0.7760885953903198},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6500189304351807},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5990768074989319},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5497943162918091},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.49874067306518555},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.43891647458076477},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.35058510303497314}],"concepts":[{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.7760885953903198},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6500189304351807},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5990768074989319},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5497943162918091},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.49874067306518555},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.43891647458076477},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35058510303497314},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2014.2369042","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2369042","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26357316","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357316","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1719482465","display_name":null,"funder_award_id":"NRF-2012R1A1A2039822","funder_id":"https://openalex.org/F4320309788","funder_display_name":"Neurosciences Research Foundation"},{"id":"https://openalex.org/G2725772924","display_name":null,"funder_award_id":"P50-MH094267","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320309788","display_name":"Neurosciences Research Foundation","ror":"https://ror.org/05exfab56"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1507039213","https://openalex.org/W1967774221","https://openalex.org/W1971962952","https://openalex.org/W1973950074","https://openalex.org/W1984068087","https://openalex.org/W2012260486","https://openalex.org/W2060842569","https://openalex.org/W2079588819","https://openalex.org/W2099807884","https://openalex.org/W2102619694","https://openalex.org/W2107133912","https://openalex.org/W2119204091","https://openalex.org/W2123056040","https://openalex.org/W2128016314","https://openalex.org/W2128177791","https://openalex.org/W2131478115","https://openalex.org/W2134526812","https://openalex.org/W2135030836","https://openalex.org/W2136672520","https://openalex.org/W2138504341","https://openalex.org/W2141820415","https://openalex.org/W2146481951","https://openalex.org/W2150761237","https://openalex.org/W2259938310","https://openalex.org/W2519244818","https://openalex.org/W2558692177","https://openalex.org/W3145128584","https://openalex.org/W4246219036","https://openalex.org/W6680267820"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W4283209547","https://openalex.org/W4367627632","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2184980933","https://openalex.org/W653452717","https://openalex.org/W2554445088","https://openalex.org/W2335661150","https://openalex.org/W2544423928"],"abstract_inverted_index":{"Efficient":[0],"search":[1,107,169],"algorithms":[2,17],"for":[3,9,18,79,191],"finding":[4],"genomic-range":[5,176],"overlaps":[6,21],"are":[7,148],"essential":[8],"various":[10,175],"bioinformatics":[11],"applications.":[12],"A":[13],"majority":[14],"of":[15,33,42,56,123,154,165],"fast":[16],"searching":[19],"the":[20,52,57,73,85,90,94,120,124,138,145,149,166],"between":[22],"a":[23,27,31,48,63,80,186],"query":[24,82],"range":[25,76,83,88,96,141,168],"(e.g.,":[26,37],"genomic":[28],"variant)":[29],"and":[30,54,84,103,194],"set":[32,97],"N":[34],"reference":[35,58,75,87,95,140],"ranges":[36],"exons)":[38],"has":[39,182],"time":[40,122],"complexity":[41],"O(k":[43],"+":[44],"logN),":[45],"where":[46],"kdenotes":[47],"term":[49],"related":[50],"to":[51,129,137,159],"length":[53,142],"location":[55],"ranges.":[59],"Here,":[60],"we":[61],"present":[62],"simple":[64],"but":[65],"efficient":[66],"algorithm":[67,126,156,181],"that":[68,119,134],"reduces":[69],"k,":[70],"based":[71],"on":[72,174],"maximum":[74,86,139],"length.":[77],"Specifically,":[78],"given":[81],"length,":[89],"proposed":[91,125,180],"method":[92],"divides":[93],"into":[98,185],"three":[99],"subsets:":[100],"always,":[101],"potentially,":[102],"never":[104,114],"overlapping.":[105],"Therefore,":[106],"effort":[108],"can":[109],"be":[110],"reduced":[111],"by":[112],"excluding":[113],"overlapping":[115,131],"subset.":[116],"We":[117],"demonstrate":[118],"running":[121],"is":[127,135,197],"proportional":[128,136],"potentially":[130],"subset":[132],"size,":[133],"if":[143],"all":[144],"other":[146],"conditions":[147],"same.":[150],"Moreover,":[151],"an":[152],"implementation":[153,196],"our":[155],"was":[157],"13.8":[158],"30.0":[160],"percent":[161],"faster":[162],"than":[163],"one":[164],"fastest":[167],"methods":[170],"available":[171,198],"when":[172],"tested":[173],"data":[177],"sets.":[178],"The":[179],"been":[183],"incorporated":[184],"disease-linked":[187],"variant":[188],"prioritization":[189],"pipeline":[190],"WGS":[192],"(http://gnome.tchlab.org)":[193],"its":[195],"at":[199],"http://ml.ssu.ac.kr/gSearch.":[200]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
