{"id":"https://openalex.org/W7204949852","doi":"https://doi.org/10.64898/2026.08.30.748153","title":"Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy","display_name":"Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy","publication_year":2026,"publication_date":"2026-09-01","ids":{"openalex":"https://openalex.org/W7204949852","doi":"https://doi.org/10.64898/2026.08.30.748153"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.30.748153","doi":"https://doi.org/10.64898/2026.08.30.748153","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.30.748153","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.30.748153.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.30.748153.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007784691","display_name":"Sudaraka Mallawaarachchi","orcid":"https://orcid.org/0000-0001-8899-3323","observed_orcids":["https://orcid.org/0000-0001-8899-3323"]},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Sudaraka Mallawaarachchi","raw_affiliation_strings":["Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0001-8899-3323","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210105123"]},{"raw_affiliation_string":"Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016552024","display_name":"Kshitij Tandon","orcid":"https://orcid.org/0000-0003-3022-0808","observed_orcids":["https://orcid.org/0000-0003-3022-0808","https://orcid.org/0009-0005-2855-4632"]},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kshitij Tandon","raw_affiliation_strings":["Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia","Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0003-3022-0808","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210105123"]},{"raw_affiliation_string":"Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046862541","display_name":"Nikhil Rajan","orcid":"https://orcid.org/0000-0002-8982-473X","observed_orcids":["https://orcid.org/0000-0002-8982-473X"]},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nikhil Rajan","raw_affiliation_strings":["Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077090209","display_name":"Vanessa R. Marcelino","orcid":"https://orcid.org/0000-0003-1755-0597","observed_orcids":["https://orcid.org/0000-0003-1755-0597"]},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]},{"id":"https://openalex.org/I4210106702","display_name":"Instituto de Agroqu\u00edmica y Tecnolog\u00eda de Alimentos","ror":"https://ror.org/018m1s709","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210106702"]}],"countries":["AU","ES"],"is_corresponding":false,"raw_author_name":"Vannessa Rossetto Marcelino","raw_affiliation_strings":["Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Valencia, Spain"],"raw_orcid":"https://orcid.org/0000-0003-1755-0597","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210105123"]},{"raw_affiliation_string":"Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Valencia, Spain","institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210106702"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064026461","display_name":"Shahneen Kaur Sandhu","orcid":"https://orcid.org/0000-0002-8660-4475","observed_orcids":["https://orcid.org/0000-0002-8660-4475"]},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Shahneen Sandhu","raw_affiliation_strings":["Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-8660-4475","affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061330101","display_name":"Sammy Bedoui","orcid":"https://orcid.org/0000-0002-7443-0543","observed_orcids":["https://orcid.org/0000-0002-7443-0543"]},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]}],"countries":["AU","DE"],"is_corresponding":false,"raw_author_name":"Sammy Bedoui","raw_affiliation_strings":["Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","Institute of Innate Immunity, University of Bonn, Bonn, North Rhine-Westphalia, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7443-0543","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210105123"]},{"raw_affiliation_string":"Institute of Innate Immunity, University of Bonn, Bonn, North Rhine-Westphalia, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025794832","display_name":"Danielle J. Ingle","orcid":"https://orcid.org/0000-0003-0707-6537","observed_orcids":["https://orcid.org/0000-0003-0707-6537"]},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Danielle J Ingle","raw_affiliation_strings":["Centre for Pathogen Genomics, University of Melbourne, Melbourne, Australia","Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia"],"raw_orcid":"https://orcid.org/0000-0003-0707-6537","affiliations":[{"raw_affiliation_string":"Centre for Pathogen Genomics, University of Melbourne, Melbourne, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210105123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025881431","display_name":"Ashray Gunjur","orcid":"https://orcid.org/0000-0001-9713-1872","observed_orcids":["https://orcid.org/0000-0001-9713-1872"]},"institutions":[{"id":"https://openalex.org/I4210098920","display_name":"Eastern Health","ror":"https://ror.org/00vyyx863","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I4210098920"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ashray Gunjur","raw_affiliation_strings":["Department of Oncology, Eastern Health, Melbourne, Australia","Eastern Health Clinical School, Monash University, Melbourne, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0001-9713-1872","affiliations":[{"raw_affiliation_string":"Department of Oncology, Eastern Health, Melbourne, Australia","institution_ids":["https://openalex.org/I4210098920"]},{"raw_affiliation_string":"Eastern Health Clinical School, Monash University, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I4210098920","https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016112946","display_name":"Gerry Q. Tonkin\u2010Hill","orcid":"https://orcid.org/0000-0003-4397-2224","observed_orcids":["https://orcid.org/0000-0003-4397-2224"]},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Gerry Tonkin-Hill","raw_affiliation_strings":["Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0003-4397-2224","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210105123"]},{"raw_affiliation_string":"Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5007784691"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584","https://openalex.org/I4210105123"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.6157000064849854,"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/T10066","display_name":"Gut microbiota and health","score":0.6157000064849854,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3384000062942505,"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":0.00930000003427267,"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/average-nucleotide-identity","display_name":"average nucleotide identity","score":0.9419999718666077},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.8769999742507935},{"id":"https://openalex.org/keywords/multi-cohort-study","display_name":"multi-cohort study","score":0.7919999957084656},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.8980000019073486},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"colorectal cancer","score":0.9300000071525574},{"id":"https://openalex.org/keywords/adhesin-genes","display_name":"adhesin genes","score":0.8999999761581421},{"id":"https://openalex.org/keywords/microbiome-disease-association","display_name":"microbiome-disease association","score":0.7170000076293945}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7738000154495239},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.7111999988555908},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6342999935150146},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6139000058174133},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.553600013256073},{"id":"https://openalex.org/C122325731","wikidata":"https://www.wikidata.org/wiki/Q3738459","display_name":"Relative species abundance","level":3,"score":0.5139999985694885},{"id":"https://openalex.org/C77077793","wikidata":"https://www.wikidata.org/wiki/Q336019","display_name":"Abundance (ecology)","level":2,"score":0.48559999465942383},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4429999887943268},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4368000030517578},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.435699999332428},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.40939998626708984},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.3986999988555908},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.38280001282691956},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.36329999566078186},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.35920000076293945},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.34549999237060547},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3296999931335449},{"id":"https://openalex.org/C25147867","wikidata":"https://www.wikidata.org/wiki/Q36039","display_name":"Beta diversity","level":3,"score":0.32910001277923584},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.3197000026702881},{"id":"https://openalex.org/C2778355321","wikidata":"https://www.wikidata.org/wiki/Q17079427","display_name":"Identity (music)","level":2,"score":0.311599999666214},{"id":"https://openalex.org/C2992929089","wikidata":"https://www.wikidata.org/wiki/Q748695","display_name":"Genetic similarity","level":4,"score":0.30070000886917114},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.2957000136375427},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29260000586509705},{"id":"https://openalex.org/C23913935","wikidata":"https://www.wikidata.org/wiki/Q2650881","display_name":"Alpha diversity","level":3,"score":0.28700000047683716},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.28299999237060547},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2759000062942505},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.27559998631477356},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.27489998936653137},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.274399995803833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2712000012397766},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.2703000009059906},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.26910001039505005},{"id":"https://openalex.org/C178221405","wikidata":"https://www.wikidata.org/wiki/Q5988338","display_name":"Identity by descent","level":5,"score":0.26649999618530273},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.2644999921321869},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.2639000117778778},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C539455810","wikidata":"https://www.wikidata.org/wiki/Q739734","display_name":"Gut flora","level":2,"score":0.2549000084400177},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.2542000114917755},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2517000138759613}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.30.748153","doi":"https://doi.org/10.64898/2026.08.30.748153","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.30.748153","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.30.748153.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.30.748153","doi":"https://doi.org/10.64898/2026.08.30.748153","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.30.748153","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.30.748153.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8371999859809875,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G342268128","display_name":null,"funder_award_id":"RYC2023\u2010042907\u2010I","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G4437673721","display_name":"Exploiting interactions between microbiota and T cells to improve melanoma immunotherapy ","funder_award_id":"2036149","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":null},{"id":"https://openalex.org/F4320326768","display_name":"Government of Western Australia","ror":"https://ror.org/00wqdbc63"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204949852.pdf","grobid_xml":"https://content.openalex.org/works/W7204949852.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2037299692","https://openalex.org/W4283448571","https://openalex.org/W4413352948"],"related_works":["https://openalex.org/W7161784641","https://openalex.org/W4406135308","https://openalex.org/W3117392845","https://openalex.org/W3079060667","https://openalex.org/W4223640474","https://openalex.org/W2981079979","https://openalex.org/W4402746742","https://openalex.org/W2586360538","https://openalex.org/W3195034766","https://openalex.org/W3194343188"],"abstract_inverted_index":{"Genetic":[0],"variation":[1,45],"among":[2],"microbial":[3,61,180,232],"strains":[4],"of":[5,25,57,141,163,201,223,231],"the":[6,22,35,54,164,220,228],"same":[7],"species":[8,27],"can":[9,66],"profoundly":[10],"influence":[11],"their":[12],"phenotypes,":[13],"ecological":[14],"functions,":[15],"and":[16,37,46,60,96,116,120,166],"impacts":[17],"on":[18,98,216],"human":[19],"health.":[20],"Traditionally,":[21],"relative":[23],"abundance":[24,58],"a":[26,108,142,169],"has":[28],"been":[29],"used":[30],"to":[31,49,93,206],"identify":[32],"associations":[33,153,194],"between":[34],"microbiome":[36],"disease.":[38],"However,":[39],"this":[40],"approach":[41],"overlooks":[42],"intra-species":[43],"genetic":[44],"is":[47,235],"susceptible":[48],"spurious":[50],"correlations":[51],"arising":[52],"from":[53,185],"compositional":[55],"nature":[56],"data":[59],"load.":[62,181,233],"Fast,":[63],"k-mer-based":[64],"algorithms":[65],"now":[67],"accurately":[68],"estimate":[69],"strain-level":[70,85,152,159,193],"Average":[71],"Nucleotide":[72],"Identity":[73],"(ANI)":[74],"in":[75,146,195,204],"metagenomes.":[76],"Despite":[77],"its":[78],"value":[79],"as":[80,237],"an":[81,238],"orthogonal":[82],"metric":[83],"for":[84,134],"analysis,":[86],"existing":[87],"ANI":[88],"association":[89,172],"methods":[90],"are":[91],"limited":[92],"case-control":[94],"designs":[95],"rely":[97],"arbitrary":[99],"identity":[100],"thresholds.":[101,125],"To":[102],"address":[103],"this,":[104],"we":[105],"developed":[106],"StrainSpy,":[107],"statistical":[109],"algorithm":[110],"that":[111,168],"jointly":[112],"captures":[113],"strain":[114],"variations":[115],"replacement":[117],"across":[118,154],"longitudinal":[119,143],"multi-cohort":[121],"studies":[122],"without":[123],"predefined":[124],"In":[126],"simulations,":[127],"StrainSpy":[128,190,234],"achieved":[129],">98%":[130],"sensitivity":[131],"versus":[132],"79%":[133],"comparable":[135],"approaches":[136],"at":[137,241],"similar":[138],"specificity.":[139],"Analysis":[140],"antibiotic":[144],"study":[145],"12":[147],"healthy":[148],"adults":[149],"revealed":[150],"novel":[151,192],"multiple":[155],"species,":[156,165],"including":[157],"reduced":[158,179],"diversity":[160],"despite":[161],"persistence":[162],"showed":[167],"previously":[170],"reported":[171],"with":[173],"E.":[174,196],"coli":[175,197],"was":[176],"driven":[177],"by":[178,199],"Across":[182],"3,414":[183],"metagenomes":[184],"17":[186],"colorectal":[187],"cancer":[188],"cohorts,":[189],"identified":[191],"accompanied":[198],"enrichment":[200],"adhesin":[202],"genes":[203],"addition":[205],"recovering":[207],"well":[208],"established":[209],"associations.":[210],"Importantly,":[211],"machine":[212],"learning":[213],"models":[214],"built":[215],"StrainSpy-selected":[217],"features":[218],"matched":[219],"predictive":[221],"accuracy":[222],"abundance-based":[224],"approaches,":[225],"whilst":[226],"avoiding":[227],"confounding":[229],"effects":[230],"available":[236],"R":[239],"package":[240],"github.com/gtonkinhill/strainspy":[242],".":[243]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-02T00:00:00"}