{"id":"https://openalex.org/W4412708863","doi":"https://doi.org/10.1093/bib/bbaf379","title":"A comprehensive benchmark of tools for efficient genomic interval querying","display_name":"A comprehensive benchmark of tools for efficient genomic interval querying","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412708863","doi":"https://doi.org/10.1093/bib/bbaf379","pmid":"https://pubmed.ncbi.nlm.nih.gov/40728859"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf379","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf379","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf379/63877186/bbaf379.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf379/63877186/bbaf379.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045313202","display_name":"Richard A Sch\u00e4fer","orcid":"https://orcid.org/0000-0001-9938-1920"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard A Sch\u00e4fer","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611 ,"],"raw_orcid":"https://orcid.org/0000-0001-9938-1920","affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611 ,","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074555821","display_name":"Rendong Yang","orcid":"https://orcid.org/0000-0002-9512-2240"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]},{"id":"https://openalex.org/I4390039227","display_name":"Robert H. Lurie Comprehensive Cancer Center of Northwestern University","ror":"https://ror.org/02p4far57","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4210147348","https://openalex.org/I4390039227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rendong Yang","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611 ,","Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine , Chicago, IL 60611 ,"],"raw_orcid":"https://orcid.org/0000-0002-9512-2240","affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611 ,","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine , Chicago, IL 60611 ,","institution_ids":["https://openalex.org/I4390039227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0875122,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9977999925613403,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9977999925613403,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9904000163078308,"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/T11321","display_name":"Error Correcting Code Techniques","score":0.9898999929428101,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.9387955665588379},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.8356319665908813},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8209410905838013},{"id":"https://openalex.org/keywords/interval","display_name":"Interval (graph theory)","score":0.6404792666435242},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5293681621551514},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.44384899735450745},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.39152705669403076},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34903550148010254},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.26643556356430054}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9387955665588379},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8356319665908813},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8209410905838013},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.6404792666435242},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5293681621551514},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.44384899735450745},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.39152705669403076},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34903550148010254},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26643556356430054},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf379","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf379","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf379/63877186/bbaf379.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40728859","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40728859","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12306436","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12306436","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf379","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf379","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf379/63877186/bbaf379.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4885911906","display_name":null,"funder_award_id":"R35 GM142441","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8310943232","display_name":null,"funder_award_id":"R01 CA259388","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412708863.pdf"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W2102619694","https://openalex.org/W2119451273","https://openalex.org/W2123056040","https://openalex.org/W2128016314","https://openalex.org/W2129785061","https://openalex.org/W2132522861","https://openalex.org/W2142386149","https://openalex.org/W2727352277","https://openalex.org/W2796635314","https://openalex.org/W2918025614","https://openalex.org/W2949231850","https://openalex.org/W3028751898","https://openalex.org/W3088755962","https://openalex.org/W3115683313","https://openalex.org/W3116195356","https://openalex.org/W3163006279","https://openalex.org/W4220920955","https://openalex.org/W4239263507","https://openalex.org/W4386983198","https://openalex.org/W4387948377","https://openalex.org/W4399091503","https://openalex.org/W4406253892","https://openalex.org/W6674733012","https://openalex.org/W6857339572","https://openalex.org/W6869289567"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W4399363378"],"abstract_inverted_index":{"Efficiently":[0],"querying":[1],"genomic":[2,19,49,95],"intervals":[3],"is":[4],"fundamental":[5],"to":[6,11,94,126],"modern":[7],"bioinformatics,":[8],"enabling":[9,124],"researchers":[10,125],"extract":[12],"and":[13,40,66,75,89,108,114,123],"analyze":[14],"specific":[15,105],"regions":[16],"from":[17],"large":[18],"datasets.":[20],"While":[21],"various":[22],"tools":[23,52],"have":[24],"been":[25],"developed":[26],"for":[27,100],"this":[28],"purpose,":[29],"there":[30],"lacks":[31],"a":[32,45],"comprehensive":[33,82],"comparison":[34],"of":[35,48,56,91],"their":[36,128],"performance,":[37,72],"memory":[38,73],"usage,":[39],"practical":[41],"utility.":[42],"We":[43],"present":[44],"systematic":[46],"evaluation":[47],"interval":[50,68,96],"query":[51,76],"using":[53],"simulated":[54],"datasets":[55],"varying":[57],"sizes.":[58],"Our":[59],"benchmarking":[60],"framework,":[61],"segmeter,":[62],"assesses":[63],"both":[64],"basic":[65],"complex":[67],"queries,":[69],"examining":[70],"runtime":[71],"efficiency,":[74],"precision":[77],"across":[78],"different":[79,92],"tools.":[80],"This":[81],"analysis":[83],"provides":[84],"insights":[85],"into":[86],"the":[87],"strengths":[88],"limitations":[90],"approaches":[93],"querying,":[97],"offering":[98],"guidance":[99],"tool":[101],"selection":[102],"based":[103],"on":[104],"use":[106],"cases":[107],"data":[109,117],"requirements.":[110],"The":[111],"segmeter":[112],"framework":[113],"all":[115],"benchmark":[116],"are":[118],"freely":[119],"available,":[120],"facilitating":[121],"reproducibility":[122],"conduct":[127],"own":[129],"comparative":[130],"analyses.":[131]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
