{"id":"https://openalex.org/W2999354090","doi":"https://doi.org/10.1371/journal.pcbi.1007511","title":"VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning","display_name":"VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning","publication_year":2020,"publication_date":"2020-01-13","ids":{"openalex":"https://openalex.org/W2999354090","doi":"https://doi.org/10.1371/journal.pcbi.1007511","mag":"2999354090","pmid":"https://pubmed.ncbi.nlm.nih.gov/31929521"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007511","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007511","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007511&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007511&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101489993","display_name":"Jiwoong Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiwoong Kim","raw_affiliation_strings":["Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039988163","display_name":"David E. Greenberg","orcid":"https://orcid.org/0000-0002-5101-3106"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David E. Greenberg","raw_affiliation_strings":["Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5101-3106","affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031998020","display_name":"Reed Pifer","orcid":"https://orcid.org/0000-0002-9648-450X"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reed Pifer","raw_affiliation_strings":["Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9648-450X","affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076832561","display_name":"Shuang Jiang","orcid":"https://orcid.org/0000-0002-4675-7143"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuang Jiang","raw_affiliation_strings":["Department of Statistical Science, Southern Methodist University, Dallas, TX, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistical Science, Southern Methodist University, Dallas, TX, United States of America","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009964025","display_name":"Guanghua Xiao","orcid":"https://orcid.org/0000-0001-9387-9883"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guanghua Xiao","raw_affiliation_strings":["Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9387-9883","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080337533","display_name":"Samuel A. Shelburne","orcid":"https://orcid.org/0000-0001-9721-263X"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel A. Shelburne","raw_affiliation_strings":["Department of Infectious Diseases and Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054460729","display_name":"Andrew Y. Koh","orcid":"https://orcid.org/0000-0003-2172-5126"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Koh","raw_affiliation_strings":["Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2172-5126","affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101536657","display_name":"Yang Xie","orcid":"https://orcid.org/0000-0002-6075-3026"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Xie","raw_affiliation_strings":["Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100707493","display_name":"Xiaowei Zhan","orcid":"https://orcid.org/0000-0002-6249-7193"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaowei Zhan","raw_affiliation_strings":["Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6249-7193","affiliations":[{"raw_affiliation_string":"Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5039988163","https://openalex.org/A5100707493"],"corresponding_institution_ids":["https://openalex.org/I867280407"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.6353,"has_fulltext":true,"cited_by_count":74,"citation_normalized_percentile":{"value":0.94836074,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"16","issue":"1","first_page":"e1007511","last_page":"e1007511"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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":0.9970999956130981,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/antibiotic-resistance","display_name":"Antibiotic resistance","score":0.6602949500083923},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5878199338912964},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5603203177452087},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5019686222076416},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.4465331435203552},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3946802318096161},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38294902443885803},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3677688539028168},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34768569469451904},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.25356507301330566},{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.2505875825881958}],"concepts":[{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.6602949500083923},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5878199338912964},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5603203177452087},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5019686222076416},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4465331435203552},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3946802318096161},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38294902443885803},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3677688539028168},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34768569469451904},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.25356507301330566},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.2505875825881958}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007511","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007511","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007511&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:31929521","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31929521","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1007511","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007511","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:e883190d19a34a4e90aed03e1fe73898","is_oa":true,"landing_page_url":"https://doaj.org/article/e883190d19a34a4e90aed03e1fe73898","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 1, p e1007511 (2020)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5981988","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7015433","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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/11593716","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/VAMPr_VAriant_Mapping_and_Prediction_of_antibiotic_resistance_via_explainable_features_and_machine_learning/11593716","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007511","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007511","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007511&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G3789650922","display_name":null,"funder_award_id":"5P30CA142543","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3884107769","display_name":null,"funder_award_id":"RP150596","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G4143021784","display_name":null,"funder_award_id":"5P30CA142543","funder_id":"https://openalex.org/F4320310169","funder_display_name":"University of Texas Southwestern Medical Center"},{"id":"https://openalex.org/G8045388038","display_name":null,"funder_award_id":"RP180319","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G8591465172","display_name":null,"funder_award_id":"1R01GM12647901A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320310169","display_name":"University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2999354090.pdf","grobid_xml":"https://content.openalex.org/works/W2999354090.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1831050183","https://openalex.org/W1926231473","https://openalex.org/W1986708244","https://openalex.org/W1988790447","https://openalex.org/W1998767819","https://openalex.org/W2045204781","https://openalex.org/W2075287054","https://openalex.org/W2103441770","https://openalex.org/W2110065044","https://openalex.org/W2119821739","https://openalex.org/W2120902911","https://openalex.org/W2122825543","https://openalex.org/W2133740160","https://openalex.org/W2134852597","https://openalex.org/W2145514756","https://openalex.org/W2148143831","https://openalex.org/W2154776925","https://openalex.org/W2170747616","https://openalex.org/W2189116376","https://openalex.org/W2295598076","https://openalex.org/W2430356171","https://openalex.org/W2461962987","https://openalex.org/W2551267404","https://openalex.org/W2611339776","https://openalex.org/W2741611011","https://openalex.org/W2758908936","https://openalex.org/W2766658767","https://openalex.org/W2792034759","https://openalex.org/W2803918445","https://openalex.org/W2890300667","https://openalex.org/W2891078715","https://openalex.org/W2898631065","https://openalex.org/W2899068429","https://openalex.org/W2902271181","https://openalex.org/W3102476541","https://openalex.org/W4239510810"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W1840542775","https://openalex.org/W2416830231","https://openalex.org/W3003578468","https://openalex.org/W2336657400","https://openalex.org/W2088351705","https://openalex.org/W179926425","https://openalex.org/W2551532359","https://openalex.org/W4392964369","https://openalex.org/W2086883243"],"abstract_inverted_index":{"Antimicrobial":[0],"resistance":[1,98,178,185],"(AMR)":[2],"is":[3],"an":[4],"increasing":[5],"threat":[6],"to":[7,57,100,129],"public":[8],"health.":[9],"Current":[10],"methods":[11],"of":[12,25,39,47,50,69,77,96,191,202],"determining":[13],"AMR":[14,26,72,131,154,235],"rely":[15],"on":[16,133],"inefficient":[17],"phenotypic":[18,84],"approaches,":[19],"and":[20,65,83,94,124,164,168,183,213,227],"there":[21],"remains":[22],"incomplete":[23],"understanding":[24,76],"mechanisms":[27],"for":[28,43,107,116,145,156,204,234,237,242],"many":[29],"pathogen-antimicrobial":[30],"combinations.":[31],"Given":[32],"the":[33,78,140,188],"rapid,":[34],"ongoing":[35],"increase":[36],"in":[37],"availability":[38],"high-density":[40],"genomic":[41,55],"data":[42,144],"a":[44,88],"diverse":[45],"array":[46],"bacteria,":[48],"development":[49],"algorithms":[51],"that":[52,152],"could":[53,60],"utilize":[54],"information":[56],"predict":[58,130],"phenotype":[59],"both":[61],"be":[62,231],"useful":[63],"clinically":[64],"assist":[66],"with":[67,122,187,240],"discovery":[68],"heretofore":[70],"unrecognized":[71],"pathways.":[73],"To":[74],"facilitate":[75],"connections":[79],"between":[80],"DNA":[81],"variation":[82],"AMR,":[85],"we":[86],"developed":[87],"new":[89],"bioinformatics":[90],"tool,":[91],"variant":[92,162,223],"mapping":[93],"prediction":[95,169,195,228],"antibiotic":[97,177],"(VAMPr),":[99],"(1)":[101],"derive":[102],"gene":[103],"ortholog-based":[104],"sequence":[105],"features":[106],"protein":[108],"variants;":[109],"(2)":[110],"interrogate":[111],"these":[112],"explainable":[113],"gene-level":[114],"variants":[115],"their":[117],"known":[118,175],"or":[119],"novel":[120],"associations":[121],"AMR;":[123],"(3)":[125],"build":[126],"accurate":[127,189],"models":[128,173,196,229],"based":[132],"whole":[134],"genome":[135],"sequencing":[136,143],"data.":[137],"We":[138,159],"curated":[139],"publicly":[141],"available":[142],"3,393":[146],"bacterial":[147],"isolates":[148],"from":[149],"9":[150],"species":[151],"contained":[153],"phenotypes":[155],"29":[157],"antibiotics.":[158],"detected":[160],"14,615":[161],"genotypes":[163],"built":[165],"93":[166],"association":[167,172,226],"models.":[170],"The":[171,194,221],"confirmed":[174],"genetic":[176],"mechanisms,":[179],"such":[180],"as":[181],"blaKPC":[182],"carbapenem":[184],"consistent":[186],"nature":[190],"our":[192],"approach.":[193],"achieved":[197],"high":[198],"accuracies":[199],"(mean":[200],"accuracy":[201],"91.1%":[203],"all":[205],"antibiotic-pathogen":[206],"combinations)":[207],"internally":[208],"through":[209],"nested":[210],"cross":[211],"validation":[212],"were":[214],"also":[215],"validated":[216],"using":[217],"external":[218],"clinical":[219,243],"datasets.":[220],"VAMPr":[222],"detection":[224],"method,":[225],"will":[230],"valuable":[232],"tools":[233],"research":[236],"basic":[238],"scientists":[239],"potential":[241],"applicability.":[244]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":7}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
