{"id":"https://openalex.org/W4405427529","doi":"https://doi.org/10.1145/3698587.3701420","title":"Integrated analysis of gut microbiome compositional and genomic alterations reveals strain diversity and actionable biomarkers across multiple colorectal cancer cohorts","display_name":"Integrated analysis of gut microbiome compositional and genomic alterations reveals strain diversity and actionable biomarkers across multiple colorectal cancer cohorts","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405427529","doi":"https://doi.org/10.1145/3698587.3701420"},"language":"en","primary_location":{"id":"doi:10.1145/3698587.3701420","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701420","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101770660","display_name":"Chao Yang","orcid":"https://orcid.org/0000-0001-6518-4574"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Chao Yang","raw_affiliation_strings":["Department of computer science, Hong Kong Baptist University, Hong Kong SAR, China"],"affiliations":[{"raw_affiliation_string":"Department of computer science, Hong Kong Baptist University, Hong Kong SAR, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100426869","display_name":"Jingjing Wang","orcid":"https://orcid.org/0000-0002-5202-9943"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jingjing Wang","raw_affiliation_strings":["Department of computer science, Hong Kong Baptist University, Hong Kong SAR, China"],"affiliations":[{"raw_affiliation_string":"Department of computer science, Hong Kong Baptist University, Hong Kong SAR, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100388624","display_name":"Lu Zhang","orcid":"https://orcid.org/0000-0002-2794-7371"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Lu Zhang","raw_affiliation_strings":["Department of computer science, Hong Kong Baptist University, Hong Kong SAR, China"],"affiliations":[{"raw_affiliation_string":"Department of computer science, Hong Kong Baptist University, Hong Kong SAR, China","institution_ids":["https://openalex.org/I141568987"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101770660"],"corresponding_institution_ids":["https://openalex.org/I141568987"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20682656,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9975000023841858,"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":0.9975000023841858,"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/T10552","display_name":"Colorectal Cancer Screening and Detection","score":0.9829999804496765,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/T10276","display_name":"Helicobacter pylori-related gastroenterology studies","score":0.9120000004768372,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"Colorectal cancer","score":0.7475846409797668},{"id":"https://openalex.org/keywords/gut-microbiome","display_name":"Gut microbiome","score":0.638253927230835},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.6115650534629822},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5122825503349304},{"id":"https://openalex.org/keywords/diversity","display_name":"Diversity (politics)","score":0.47236257791519165},{"id":"https://openalex.org/keywords/strain","display_name":"Strain (injury)","score":0.4546830654144287},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.45184966921806335},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36010944843292236},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.34091857075691223},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3146933317184448},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.2390952706336975}],"concepts":[{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.7475846409797668},{"id":"https://openalex.org/C3019978661","wikidata":"https://www.wikidata.org/wiki/Q739734","display_name":"Gut microbiome","level":3,"score":0.638253927230835},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6115650534629822},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5122825503349304},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.47236257791519165},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.4546830654144287},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.45184966921806335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36010944843292236},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.34091857075691223},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3146933317184448},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.2390952706336975},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3698587.3701420","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701420","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Zero hunger","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/2"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2604155846","https://openalex.org/W2994966085","https://openalex.org/W3044286215","https://openalex.org/W4402517148","https://openalex.org/W2621141937","https://openalex.org/W4312476285","https://openalex.org/W2793187602","https://openalex.org/W3016347906","https://openalex.org/W3044328089","https://openalex.org/W2333607221"],"abstract_inverted_index":{"Gut":[0],"microbiome":[1],"dysbiosis":[2],"is":[3],"considered":[4],"to":[5],"play":[6],"a":[7,63,159,209],"critical":[8],"role":[9],"in":[10,25,44,142,173,178,190],"the":[11,39,45,86,131,143,166,213],"development":[12],"of":[13,66,130,138,161,168,216],"colorectal":[14],"cancer.":[15],"While":[16],"numerous":[17],"studies":[18],"have":[19],"identified":[20,93,158],"specific":[21],"microbial":[22,68,87,187,201],"species":[23],"enriched":[24],"cancer":[26,196],"patients,":[27],"knowledge":[28],"about":[29],"their":[30],"genomic":[31,42,188],"variants":[32,73,77],"remains":[33],"limited.":[34],"Here,":[35],"we":[36,92,157],"systematically":[37],"investigated":[38],"compositional":[40,193],"and":[41,74,81,89,111,125,140,146,176,198],"alterations":[43,124],"gut":[46],"metagenomic":[47,117],"sequencing":[48],"data":[49],"using":[50],"1723":[51],"samples":[52],"collected":[53],"from":[54],"10":[55],"different":[56],"CRC":[57,80,100],"datasets.":[58,180],"Our":[59],"combined":[60],"analysis":[61,184],"revealed":[62],"core":[64],"set":[65],"250":[67],"genomes,":[69],"4365":[70],"single":[71],"nucleotide":[72],"21":[75],"structural":[76],"differed":[78],"between":[79],"healthy":[82],"control":[83],"groups.":[84],"Utilizing":[85],"SNV":[88],"SV":[90],"profiles,":[91],"strain":[94],"level":[95],"phylogenetic":[96],"diversity":[97],"among":[98],"27":[99],"related":[101],"species,":[102,163],"such":[103],"as":[104],"Faecalibacterium":[105],"prausnitzii,":[106],"Coprococcus_B":[107],"comes,":[108],"Fusicatenibacter":[109],"saccharivorans,":[110],"Ruminococcus_D":[112],"bicirculans.":[113],"We":[114],"also":[115],"constructed":[116],"classification":[118],"models":[119],"based":[120],"on":[121],"these":[122],"multi-dimensional":[123,132],"observed":[126],"superior":[127],"diagnostic":[128],"capability":[129],"model,":[133],"achieving":[134],"an":[135],"average":[136],"AUC":[137,167],"0.82":[139],"0.80":[141],"discovery":[144,174],"stage":[145],"validation":[147,179],"stage,":[148],"respectively.":[149],"Compared":[150],"with":[151,192,203],"fecal":[152],"occult":[153],"blood":[154],"test":[155],"(FOBT),":[156],"combination":[160],"4":[162],"could":[164],"increase":[165],"FOBT":[169,205],"testing":[170,206],"by":[171],"13%":[172],"datasets":[175],"3.5%":[177],"Collectively,":[181],"our":[182],"integrated":[183],"uncovers":[185],"how":[186],"variations,":[189],"conjunction":[191],"changes,":[194],"influence":[195],"progression":[197],"suggests":[199],"combining":[200],"features":[202],"cost-effective":[204],"may":[207],"be":[208],"promising":[210],"approach":[211],"for":[212],"mass":[214],"screening":[215],"CRC.":[217]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}