{"id":"https://openalex.org/W4392885742","doi":"https://doi.org/10.1093/bioinformatics/btae150","title":"CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing","display_name":"CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing","publication_year":2024,"publication_date":"2024-03-14","ids":{"openalex":"https://openalex.org/W4392885742","doi":"https://doi.org/10.1093/bioinformatics/btae150","pmid":"https://pubmed.ncbi.nlm.nih.gov/38492564"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae150","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae150/56995286/btae150.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae150/56995286/btae150.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071697234","display_name":"Ali Osman Berk \u015eapc\u0131","orcid":"https://orcid.org/0000-0003-4396-817X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ali Osman Berk \u015eapc\u0131","raw_affiliation_strings":["Bioinformatics and Systems Biology Graduate Program, University of California , San Diego, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Graduate Program, University of California , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040053145","display_name":"Eleonora Rachtman","orcid":"https://orcid.org/0000-0002-6104-5750"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eleonora Rachtman","raw_affiliation_strings":["Bioinformatics and Systems Biology Graduate Program, University of California , San Diego, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Graduate Program, University of California , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087959579","display_name":"Siavash Mirarab","orcid":"https://orcid.org/0000-0001-5410-1518"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siavash Mirarab","raw_affiliation_strings":["Bioinformatics and Systems Biology Graduate Program, University of California , San Diego, CA 92093, United States","Department of Electrical and Computer Engineering, University of California , San Diego, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Graduate Program, University of California , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California , San Diego, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071697234"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":9.0028,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.97024215,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"40","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9966999888420105,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9907000064849854,"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/profiling","display_name":"Profiling (computer programming)","score":0.7611504793167114},{"id":"https://openalex.org/keywords/locality","display_name":"Locality","score":0.6793135404586792},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6624717712402344},{"id":"https://openalex.org/keywords/locality-sensitive-hashing","display_name":"Locality-sensitive hashing","score":0.6491671204566956},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5322399139404297},{"id":"https://openalex.org/keywords/hash-function","display_name":"Hash function","score":0.4987189769744873},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4284136891365051},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2544150948524475},{"id":"https://openalex.org/keywords/hash-table","display_name":"Hash table","score":0.1784433126449585},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.07060962915420532},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.0677187442779541},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06201064586639404}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7611504793167114},{"id":"https://openalex.org/C2779808786","wikidata":"https://www.wikidata.org/wiki/Q6664603","display_name":"Locality","level":2,"score":0.6793135404586792},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6624717712402344},{"id":"https://openalex.org/C74270461","wikidata":"https://www.wikidata.org/wiki/Q1625299","display_name":"Locality-sensitive hashing","level":4,"score":0.6491671204566956},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5322399139404297},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.4987189769744873},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4284136891365051},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2544150948524475},{"id":"https://openalex.org/C67388219","wikidata":"https://www.wikidata.org/wiki/Q207440","display_name":"Hash table","level":3,"score":0.1784433126449585},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07060962915420532},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0677187442779541},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06201064586639404},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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":"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":"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":"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":"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":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae150","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae150/56995286/btae150.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38492564","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38492564","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9sc610cq","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9sc610cq","pdf_url":"https://escholarship.org/content/qt9sc610cq/qt9sc610cq.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Computer applications in the biosciences : CABIOS, vol 40, iss 4","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10985673","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10985673","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10985673/pdf/btae150.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae150","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae150/56995286/btae150.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5661333668","display_name":null,"funder_award_id":"R35GM142725","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320329315","display_name":"Minderoo Foundation","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392885742.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1579534339","https://openalex.org/W1703384511","https://openalex.org/W1822648038","https://openalex.org/W2003347102","https://openalex.org/W2109034006","https://openalex.org/W2124927293","https://openalex.org/W2131026689","https://openalex.org/W2131159440","https://openalex.org/W2135515858","https://openalex.org/W2147783737","https://openalex.org/W2157539385","https://openalex.org/W2170024099","https://openalex.org/W2345658906","https://openalex.org/W2397770138","https://openalex.org/W2404149918","https://openalex.org/W2559993150","https://openalex.org/W2773939681","https://openalex.org/W2897603717","https://openalex.org/W2920716817","https://openalex.org/W2950150251","https://openalex.org/W2951676949","https://openalex.org/W2951934242","https://openalex.org/W2952152744","https://openalex.org/W2968450569","https://openalex.org/W2972246166","https://openalex.org/W2981413553","https://openalex.org/W2990618091","https://openalex.org/W2990925943","https://openalex.org/W2994814458","https://openalex.org/W2995063445","https://openalex.org/W3000238463","https://openalex.org/W3008594856","https://openalex.org/W3019706413","https://openalex.org/W3028280407","https://openalex.org/W3122087892","https://openalex.org/W3193020855","https://openalex.org/W3207897998","https://openalex.org/W4224943843","https://openalex.org/W4225258284","https://openalex.org/W4384079987","https://openalex.org/W4385302437","https://openalex.org/W6855063250"],"related_works":["https://openalex.org/W4287326768","https://openalex.org/W1556451512","https://openalex.org/W2393322642","https://openalex.org/W1555349535","https://openalex.org/W3131198547","https://openalex.org/W1977118386","https://openalex.org/W2144265691","https://openalex.org/W2033383639","https://openalex.org/W3108918257","https://openalex.org/W3016124764"],"abstract_inverted_index":{"CONSULT-II":[0],"is":[1,12],"implemented":[2],"in":[3],"C++,":[4],"and":[5],"the":[6],"software,":[7],"together":[8],"with":[9],"reference":[10],"libraries,":[11],"publicly":[13],"available":[14],"on":[15],"GitHub":[16],"https://github.com/bo1929/CONSULT-II.":[17]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
