{"id":"https://openalex.org/W2950511618","doi":"https://doi.org/10.1093/bioinformatics/bty387","title":"Indexed variation graphs for efficient and accurate resistome profiling","display_name":"Indexed variation graphs for efficient and accurate resistome profiling","publication_year":2018,"publication_date":"2018-05-10","ids":{"openalex":"https://openalex.org/W2950511618","doi":"https://doi.org/10.1093/bioinformatics/bty387","mag":"2950511618","pmid":"https://pubmed.ncbi.nlm.nih.gov/29762644"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty387","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty387","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/21/3601/26146905/bty387.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/21/3601/26146905/bty387.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078257079","display_name":"Will Rowe","orcid":"https://orcid.org/0000-0003-0384-4463"},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]},{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Will P M Rowe","raw_affiliation_strings":["Institute of Integrative Biology, The University of Liverpool, Liverpool, UK","Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK"],"affiliations":[{"raw_affiliation_string":"Institute of Integrative Biology, The University of Liverpool, Liverpool, UK","institution_ids":["https://openalex.org/I146655781"]},{"raw_affiliation_string":"Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK","institution_ids":["https://openalex.org/I2802015276"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052155666","display_name":"Martyn Winn","orcid":"https://orcid.org/0000-0003-0496-6796"},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Martyn D Winn","raw_affiliation_strings":["Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK","institution_ids":["https://openalex.org/I2802015276"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5078257079"],"corresponding_institution_ids":["https://openalex.org/I146655781","https://openalex.org/I2802015276"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":2515,"currency":"EUR","value_usd":2712},"fwci":3.805,"has_fulltext":false,"cited_by_count":80,"citation_normalized_percentile":{"value":0.94587374,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"34","issue":"21","first_page":"3601","last_page":"3608"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9769999980926514,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.975600004196167,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/resistome","display_name":"Resistome","score":0.9441334009170532},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7429561018943787},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.7075663208961487},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5951656103134155},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5461652278900146},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5160279273986816},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47476911544799805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37003087997436523},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3434726893901825},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.29436492919921875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22393015027046204},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16762381792068481},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.14353415369987488}],"concepts":[{"id":"https://openalex.org/C2776666601","wikidata":"https://www.wikidata.org/wiki/Q3457855","display_name":"Resistome","level":5,"score":0.9441334009170532},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7429561018943787},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7075663208961487},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5951656103134155},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5461652278900146},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5160279273986816},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47476911544799805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37003087997436523},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3434726893901825},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29436492919921875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22393015027046204},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16762381792068481},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.14353415369987488},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C132533263","wikidata":"https://www.wikidata.org/wiki/Q2347362","display_name":"Mobile genetic elements","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D001424","descriptor_name":"Bacterial Infections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001424","descriptor_name":"Bacterial Infections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001424","descriptor_name":"Bacterial Infections","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":"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty387","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty387","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/21/3601/26146905/bty387.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:29762644","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29762644","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:europepmc.org:5148404","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6198860","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6198860","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6198860","pdf_url":null,"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"},{"id":"pmh:oai:purl.org/net/epubs:work/40020996","is_oa":false,"landing_page_url":"https://epubs.stfc.ac.uk/work/40020996","pdf_url":null,"source":{"id":"https://openalex.org/S4306400600","display_name":"ePubs (Science and Technology Facilities Council, Research Councils UK)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I162524378","host_organization_name":"Science and Technology Facilities Council","host_organization_lineage":["https://openalex.org/I162524378"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty387","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty387","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/21/3601/26146905/bty387.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4099999964237213}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307856","display_name":"World Health Organization","ror":"https://ror.org/01f80g185"},{"id":"https://openalex.org/F4320312568","display_name":"Public Health Agency of Canada","ror":"https://ror.org/023xf2a37"},{"id":"https://openalex.org/F4320312933","display_name":"Department for Business, Energy and Industrial Strategy, UK Government","ror":"https://ror.org/019ya6433"},{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950511618.pdf","grobid_xml":"https://content.openalex.org/works/W2950511618.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W589619539","https://openalex.org/W1502916507","https://openalex.org/W1579534339","https://openalex.org/W1976436748","https://openalex.org/W1989688741","https://openalex.org/W2008274231","https://openalex.org/W2050820276","https://openalex.org/W2104914423","https://openalex.org/W2118688136","https://openalex.org/W2129264270","https://openalex.org/W2134852597","https://openalex.org/W2152127318","https://openalex.org/W2153325555","https://openalex.org/W2155512447","https://openalex.org/W2155900219","https://openalex.org/W2162494851","https://openalex.org/W2236299009","https://openalex.org/W2261625986","https://openalex.org/W2419548415","https://openalex.org/W2441874462","https://openalex.org/W2460324897","https://openalex.org/W2513506562","https://openalex.org/W2519804289","https://openalex.org/W2519890620","https://openalex.org/W2544493586","https://openalex.org/W2552637961","https://openalex.org/W2557776122","https://openalex.org/W2568214319","https://openalex.org/W2572540562","https://openalex.org/W2581361205","https://openalex.org/W2587351039","https://openalex.org/W2587565766","https://openalex.org/W2602765986","https://openalex.org/W2603734366","https://openalex.org/W2610952444","https://openalex.org/W2615471603","https://openalex.org/W2755500195","https://openalex.org/W2765485035","https://openalex.org/W2765745983","https://openalex.org/W2767051074","https://openalex.org/W2768753541","https://openalex.org/W2773939681","https://openalex.org/W2775648451","https://openalex.org/W2790760775","https://openalex.org/W2949155616","https://openalex.org/W2950150251","https://openalex.org/W2951408331","https://openalex.org/W2952620784","https://openalex.org/W2952839519","https://openalex.org/W2953229963","https://openalex.org/W4297723515","https://openalex.org/W6629956336","https://openalex.org/W6727147013","https://openalex.org/W6731896010","https://openalex.org/W6733498214","https://openalex.org/W6735740338","https://openalex.org/W7008259102"],"related_works":["https://openalex.org/W2325934813","https://openalex.org/W3132280623","https://openalex.org/W2394848516","https://openalex.org/W4394362113","https://openalex.org/W4394432959","https://openalex.org/W4394456278","https://openalex.org/W4394139394","https://openalex.org/W3039769284","https://openalex.org/W4394476261","https://openalex.org/W4394199064"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":3}],"updated_date":"2026-03-29T08:15:47.926485","created_date":"2025-10-10T00:00:00"}
