{"id":"https://openalex.org/W4416722242","doi":"https://doi.org/10.1186/s12859-025-06294-y","title":"GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes","display_name":"GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes","publication_year":2025,"publication_date":"2025-11-26","ids":{"openalex":"https://openalex.org/W4416722242","doi":"https://doi.org/10.1186/s12859-025-06294-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/41299243"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06294-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06294-y","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06294-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109125285","display_name":"William Wheeler","orcid":null},"institutions":[{"id":"https://openalex.org/I4210110061","display_name":"Information Management Services","ror":"https://ror.org/020k7fn51","country_code":"US","type":"company","lineage":["https://openalex.org/I4210110061"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Wheeler","raw_affiliation_strings":["Information Management Services, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Management Services, Rockville, MD, USA","institution_ids":["https://openalex.org/I4210110061"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083009713","display_name":"Difei Wang","orcid":"https://orcid.org/0000-0002-1118-658X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210165342","display_name":"Department of Health and Human Services","ror":"https://ror.org/05p26gw61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210165342"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Difei Wang","raw_affiliation_strings":["Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Rockville, MD, USA. difei.wang2@nih.gov","Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA. difei.wang2@nih.gov","Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Rockville, MD, USA. difei.wang2@nih.gov","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210130649","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA. difei.wang2@nih.gov","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210165342"]},{"raw_affiliation_string":"Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070318207","display_name":"Isaac Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I919803642","display_name":"American Axle & Manufacturing (United States)","ror":"https://ror.org/00atq5220","country_code":"US","type":"company","lineage":["https://openalex.org/I919803642"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Isaac Zhao","raw_affiliation_strings":["Axle Informatics, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Axle Informatics, Rockville, MD, USA","institution_ids":["https://openalex.org/I919803642"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002187739","display_name":"Filipa F. Vale","orcid":"https://orcid.org/0000-0003-4635-0105"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Filipa F. Vale","raw_affiliation_strings":["BioISI-Instituto de Biossistemas e Ci\u00eancias Integrativas, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisbon, Portugal","BioISI\u2014Instituto de Biossistemas e Ci\u00eancias Integrativas, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioISI-Instituto de Biossistemas e Ci\u00eancias Integrativas, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"BioISI\u2014Instituto de Biossistemas e Ci\u00eancias Integrativas, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048381356","display_name":"Yumi Jin","orcid":"https://orcid.org/0000-0003-2499-8760"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yumi Jin","raw_affiliation_strings":["University of Pennsylvania, Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pennsylvania, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003072430","display_name":"Charles S. Rabkin","orcid":"https://orcid.org/0000-0002-0053-3806"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles S. Rabkin","raw_affiliation_strings":["Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5083009713"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884","https://openalex.org/I4210165342"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2169,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.83922059,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"1","first_page":"308","last_page":"308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10276","display_name":"Helicobacter pylori-related gastroenterology studies","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10276","display_name":"Helicobacter pylori-related gastroenterology studies","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11316","display_name":"Mycobacterium research and diagnosis","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11578","display_name":"Plant Pathogenic Bacteria Studies","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7907999753952026},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.64410001039505},{"id":"https://openalex.org/keywords/helicobacter-pylori","display_name":"Helicobacter pylori","score":0.6097000241279602},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5601000189781189},{"id":"https://openalex.org/keywords/population-stratification","display_name":"Population stratification","score":0.4090999960899353},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.40070000290870667},{"id":"https://openalex.org/keywords/genome-wide-association-study","display_name":"Genome-wide association study","score":0.392300009727478},{"id":"https://openalex.org/keywords/population-genetics","display_name":"Population genetics","score":0.375}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7907999753952026},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7508000135421753},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.64410001039505},{"id":"https://openalex.org/C2776409635","wikidata":"https://www.wikidata.org/wiki/Q180556","display_name":"Helicobacter pylori","level":2,"score":0.6097000241279602},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6079999804496765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5613999962806702},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5601000189781189},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4620000123977661},{"id":"https://openalex.org/C166976648","wikidata":"https://www.wikidata.org/wiki/Q7229824","display_name":"Population stratification","level":5,"score":0.4090999960899353},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.40070000290870667},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.392300009727478},{"id":"https://openalex.org/C85721925","wikidata":"https://www.wikidata.org/wiki/Q31151","display_name":"Population genetics","level":3,"score":0.375},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.37119999527931213},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.36090001463890076},{"id":"https://openalex.org/C75069973","wikidata":"https://www.wikidata.org/wiki/Q913584","display_name":"Genetic genealogy","level":3,"score":0.3479999899864197},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.33820000290870667},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.33239999413490295},{"id":"https://openalex.org/C2983611323","wikidata":"https://www.wikidata.org/wiki/Q7229822","display_name":"Population structure","level":3,"score":0.28690001368522644},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.2777999937534332},{"id":"https://openalex.org/C149737253","wikidata":"https://www.wikidata.org/wiki/Q3240252","display_name":"Polymorphism (computer science)","level":4,"score":0.2669000029563904},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26660001277923584}],"mesh":[{"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":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06294-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06294-y","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41299243","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41299243","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:75cfe37165514bac89cbb03186278995","is_oa":true,"landing_page_url":"https://doaj.org/article/75cfe37165514bac89cbb03186278995","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-17 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12751694","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12751694/","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06294-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06294-y","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1966502880","https://openalex.org/W1977601452","https://openalex.org/W2023749146","https://openalex.org/W2037726252","https://openalex.org/W2044812603","https://openalex.org/W2080873675","https://openalex.org/W2110132014","https://openalex.org/W2113647506","https://openalex.org/W2130550301","https://openalex.org/W2137827639","https://openalex.org/W2141666543","https://openalex.org/W2160378127","https://openalex.org/W2277705055","https://openalex.org/W2486094965","https://openalex.org/W2589064986","https://openalex.org/W2766646173","https://openalex.org/W2809329526","https://openalex.org/W2887652817","https://openalex.org/W2889326414","https://openalex.org/W2946880778","https://openalex.org/W2949236085","https://openalex.org/W2950753995","https://openalex.org/W2953263404","https://openalex.org/W2962593936","https://openalex.org/W3041242936","https://openalex.org/W4254687493","https://openalex.org/W4389546256","https://openalex.org/W4392125218","https://openalex.org/W4403450835","https://openalex.org/W4407119861"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Helicobacter":[1],"pylori":[2,91,101,200],"is":[3,65,174,231],"a":[4,40,194],"highly":[5],"diverse":[6],"gastric":[7],"bacterium":[8],"whose":[9],"genomic":[10],"variation":[11],"both":[12],"reflects":[13],"human":[14,82],"migration":[15],"and":[16,45,62,92,115,140,146,173,181,189,202,225],"complicates":[17],"genome-wide":[18],"association":[19],"studies":[20,221],"(GWAS).":[21],"Its":[22],"1.67":[23],"Mb":[24],"genome":[25],"contains":[26],"~":[27],"143,000":[28,156],"biallelic":[29],"SNPs":[30,142],"with":[31,124,151,237],"minor":[32],"allele":[33],"frequency":[34],">":[35,144,147],"1%,":[36],"making":[37],"population":[38,206],"stratification":[39,207],"major":[41],"confounder.":[42],"Existing":[43],"model-":[44],"distance-based":[46],"methods":[47],"for":[48,86,167,186,197,204],"bacterial":[49,113,205,223],"ancestry":[50,83,171,201],"classification":[51,88],"often":[52],"yield":[53],"inconsistent":[54],"results":[55],"depending":[56],"on":[57,136],"dataset":[58],"composition.":[59],"A":[60],"robust":[61],"generalizable":[63],"framework":[64,185],"needed":[66],"to":[67,131,160,233],"improve":[68],"downstream":[69],"analyses.":[70],"RESULTS:":[71],"We":[72],"developed":[73],"GrafGen,":[74],"an":[75],"open-source":[76],"R":[77],"package":[78,163],"adapted":[79],"from":[80,98,106],"the":[81,87,99,154,218],"tool":[84],"GrafPop,":[85],"of":[89,138,170,215,222],"H.":[90,100,199,245],"prophage":[93,117],"populations.":[94,133],"Using":[95],"reference":[96,239],"data":[97],"Genome":[102],"Project":[103],"(1,011":[104],"genomes":[105],"50":[107],"countries),":[108],"GrafGen":[109,192],"identified":[110],"nine":[111],"distinct":[112],"populations":[114],"four":[116],"groups":[118],"by":[119],"genetic":[120],"distance":[121],"clustering.":[122],"Validation":[123],"255":[125],"GenBank":[126],"sequences":[127],"showed":[128],"consistent":[129],"mapping":[130],"GrafGen-defined":[132],"Classifications":[134],"based":[135],"subsets":[137],"14,300":[139],"1,430":[141],"achieved":[143],"97%":[145],"90%":[148],"concordance,":[149],"respectively,":[150],"those":[152],"using":[153],"full":[155],"SNPs,":[157],"demonstrating":[158],"robustness":[159],"down-sampling.":[161],"The":[162,228],"integrates":[164],"visualization":[165],"tools":[166],"geometric":[168],"interpretation":[169],"structure":[172],"distributed":[175],"via":[176],"Bioconductor":[177],"(v1.4.0,":[178],"nine-population":[179],"reference)":[180],"GitHub":[182],"(v2.0_beta,":[183],"general":[184],"haploid":[187,235],"species":[188],"prophages).":[190],"CONCLUSIONS:":[191],"provides":[193],"reliable":[195],"approach":[196],"classifying":[198],"correcting":[203],"in":[208],"GWAS.":[209],"By":[210],"enabling":[211],"more":[212],"accurate":[213],"inference":[214],"genotype-phenotype":[216],"associations,":[217],"method":[219],"enhances":[220],"genetics":[224],"host-pathogen":[226],"interactions.":[227],"underlying":[229],"algorithm":[230],"extensible":[232],"other":[234],"organisms":[236],"adequate":[238],"data,":[240],"broadening":[241],"its":[242],"relevance":[243],"beyond":[244],"pylori.":[246]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-11-27T00:00:00"}
