{"id":"https://openalex.org/W4387636939","doi":"https://doi.org/10.1093/bib/bbad362","title":"MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection","display_name":"MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection","publication_year":2023,"publication_date":"2023-09-22","ids":{"openalex":"https://openalex.org/W4387636939","doi":"https://doi.org/10.1093/bib/bbad362","pmid":"https://pubmed.ncbi.nlm.nih.gov/37833839"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad362","pdf_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad362/52085101/bbad362.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad362/52085101/bbad362.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100641607","display_name":"Yang Cao","orcid":"https://orcid.org/0000-0001-7787-8506"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang Cao","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117387366","display_name":"Dan Wang","orcid":"https://orcid.org/0000-0001-7281-4853"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dan Wang","raw_affiliation_strings":["Department of Bioinformatics, Yicon (Beijing) Biomedical Technology Inc"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Yicon (Beijing) Biomedical Technology Inc","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112610096","display_name":"Jin Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jin Wu","raw_affiliation_strings":["Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104056757","display_name":"Zhanxin Yao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhanxin Yao","raw_affiliation_strings":["Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114020204","display_name":"Si Shen","orcid":null},"institutions":[{"id":"https://openalex.org/I5740404","display_name":"Tianjin Medical University","ror":"https://ror.org/02mh8wx89","country_code":"CN","type":"education","lineage":["https://openalex.org/I5740404"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Si Shen","raw_affiliation_strings":["School and Hospital of Stomatology, Tianjin Medical University , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"School and Hospital of Stomatology, Tianjin Medical University , Tianjin 300050 , China","institution_ids":["https://openalex.org/I5740404"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100612851","display_name":"Chao Niu","orcid":"https://orcid.org/0000-0002-0416-0613"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chao Niu","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100414438","display_name":"Ying Liu","orcid":"https://orcid.org/0000-0003-2805-7976"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100365982","display_name":"Pengcheng Zhang","orcid":"https://orcid.org/0000-0002-4546-0022"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pengcheng Zhang","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019212202","display_name":"Quannian Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I151893264","display_name":"Jiamusi University","ror":"https://ror.org/01vasff55","country_code":"CN","type":"education","lineage":["https://openalex.org/I151893264"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quannian Wang","raw_affiliation_strings":["School of Basic Medicine, Jiamusi University"],"affiliations":[{"raw_affiliation_string":"School of Basic Medicine, Jiamusi University","institution_ids":["https://openalex.org/I151893264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102752402","display_name":"Jinhao Wang","orcid":"https://orcid.org/0009-0008-7747-1851"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jinhao Wang","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100344257","display_name":"Hua Li","orcid":"https://orcid.org/0000-0003-1903-836X"},"institutions":[{"id":"https://openalex.org/I2802573037","display_name":"Tianjin Medical University Cancer Institute and Hospital","ror":"https://ror.org/0152hn881","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802573037"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Li","raw_affiliation_strings":["Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital , Tianjin 300060 , China"],"affiliations":[{"raw_affiliation_string":"Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital , Tianjin 300060 , China","institution_ids":["https://openalex.org/I2802573037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033367677","display_name":"Xi Wei","orcid":"https://orcid.org/0000-0003-4734-3900"},"institutions":[{"id":"https://openalex.org/I2802573037","display_name":"Tianjin Medical University Cancer Institute and Hospital","ror":"https://ror.org/0152hn881","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802573037"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xi Wei","raw_affiliation_strings":["Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital , Tianjin 300060 , China"],"affiliations":[{"raw_affiliation_string":"Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital , Tianjin 300060 , China","institution_ids":["https://openalex.org/I2802573037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100740800","display_name":"Xinxing Wang","orcid":"https://orcid.org/0000-0003-2894-783X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Xinxing Wang","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101911013","display_name":"Qingyang Dong","orcid":"https://orcid.org/0000-0001-5664-9093"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Qingyang Dong","raw_affiliation_strings":["Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine , Tianjin 300050 , China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5033367677","https://openalex.org/A5100740800","https://openalex.org/A5101911013"],"corresponding_institution_ids":["https://openalex.org/I2802573037"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.9103,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.86131282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"24","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9986000061035156,"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/T11482","display_name":"RNA modifications and cancer","score":0.9986000061035156,"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9959999918937683,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/microsatellite-instability","display_name":"Microsatellite instability","score":0.825385332107544},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5398601293563843},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5380337834358215},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5314620733261108},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5200043320655823},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5109614133834839},{"id":"https://openalex.org/keywords/microsatellite","display_name":"Microsatellite","score":0.38291722536087036},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.290728896856308},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26542186737060547},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1811099350452423},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10035929083824158},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.07460957765579224},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.05538323521614075}],"concepts":[{"id":"https://openalex.org/C2779767149","wikidata":"https://www.wikidata.org/wiki/Q488212","display_name":"Microsatellite instability","level":5,"score":0.825385332107544},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5398601293563843},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5380337834358215},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5314620733261108},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5200043320655823},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5109614133834839},{"id":"https://openalex.org/C61320498","wikidata":"https://www.wikidata.org/wiki/Q265193","display_name":"Microsatellite","level":4,"score":0.38291722536087036},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.290728896856308},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26542186737060547},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1811099350452423},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10035929083824158},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.07460957765579224},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.05538323521614075},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad362","pdf_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad362/52085101/bbad362.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37833839","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37833839","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad362","pdf_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad362/52085101/bbad362.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.7799999713897705,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5745379083","display_name":null,"funder_award_id":"21JCYBJC01110","funder_id":"https://openalex.org/F4320323993","funder_display_name":"Natural Science Foundation of Tianjin City"}],"funders":[{"id":"https://openalex.org/F4320323993","display_name":"Natural Science Foundation of Tianjin City","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4387636939.pdf"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W1924830843","https://openalex.org/W1940241680","https://openalex.org/W1945650577","https://openalex.org/W1965997942","https://openalex.org/W1985987855","https://openalex.org/W2026035097","https://openalex.org/W2034066784","https://openalex.org/W2035618305","https://openalex.org/W2042126900","https://openalex.org/W2042797183","https://openalex.org/W2049397238","https://openalex.org/W2050658928","https://openalex.org/W2107972234","https://openalex.org/W2117564738","https://openalex.org/W2128502368","https://openalex.org/W2130430382","https://openalex.org/W2139015332","https://openalex.org/W2148667972","https://openalex.org/W2152344392","https://openalex.org/W2154941270","https://openalex.org/W2156021518","https://openalex.org/W2172251832","https://openalex.org/W2287918349","https://openalex.org/W2318233342","https://openalex.org/W2409025966","https://openalex.org/W2529308344","https://openalex.org/W2567051070","https://openalex.org/W2574604975","https://openalex.org/W2606495925","https://openalex.org/W2735687500","https://openalex.org/W2739031619","https://openalex.org/W2747719411","https://openalex.org/W2795441313","https://openalex.org/W2796207838","https://openalex.org/W2796408191","https://openalex.org/W2800289222","https://openalex.org/W2908503672","https://openalex.org/W2940627982","https://openalex.org/W2945608646","https://openalex.org/W2953390364","https://openalex.org/W2964015378","https://openalex.org/W2972317931","https://openalex.org/W2972751531","https://openalex.org/W2982559021","https://openalex.org/W2984359187","https://openalex.org/W3006211741","https://openalex.org/W3009218715","https://openalex.org/W3010653800","https://openalex.org/W3012375969","https://openalex.org/W3013189440","https://openalex.org/W3033520100","https://openalex.org/W3038063066","https://openalex.org/W3110528877","https://openalex.org/W3128706472","https://openalex.org/W3129517686","https://openalex.org/W3162215872","https://openalex.org/W3213780772","https://openalex.org/W4200158487","https://openalex.org/W4200501196","https://openalex.org/W4224985744","https://openalex.org/W4225655924","https://openalex.org/W4226477522","https://openalex.org/W4281732693","https://openalex.org/W4291020489","https://openalex.org/W4291903684","https://openalex.org/W4297733535","https://openalex.org/W4300861989","https://openalex.org/W4319072029","https://openalex.org/W4322384924","https://openalex.org/W4323806397","https://openalex.org/W4376121436","https://openalex.org/W4386045964","https://openalex.org/W6640120484","https://openalex.org/W6640695300","https://openalex.org/W6682087902","https://openalex.org/W6767288045","https://openalex.org/W6855315815"],"related_works":["https://openalex.org/W2067665082","https://openalex.org/W2473005840","https://openalex.org/W2969016060","https://openalex.org/W1982747239","https://openalex.org/W4389733843","https://openalex.org/W2902329290","https://openalex.org/W2139872319","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877"],"abstract_inverted_index":{"Microsatellite":[0],"instability":[1],"(MSI)":[2],"is":[3,28,98],"a":[4,29,82,106,121,227],"hypermutator":[5],"phenotype":[6],"caused":[7],"by":[8],"DNA":[9,62,94],"mismatch":[10],"repair":[11],"deficiency.":[12],"MSI":[13,27,47,88,126,168,236,240,249],"has":[14],"been":[15,44],"reported":[16],"in":[17,71],"various":[18],"human":[19],"cancers,":[20],"particularly":[21],"colorectal,":[22],"gastric":[23],"and":[24,35,67,74,93,147,149,178,180,184,210,219,229,238],"endometrial":[25],"cancers.":[26],"promising":[30],"biomarker":[31],"for":[32,46,86,202,234,247],"cancer":[33],"prognosis":[34],"immune":[36,211],"checkpoint":[37,212],"blockade":[38],"immunotherapy.":[39],"Several":[40],"computational":[41,84],"methods":[42,139],"have":[43],"developed":[45,80],"detection":[48],"using":[49,90],"DNA-":[50],"or":[51],"RNA-based":[52],"approaches":[53],"based":[54],"on":[55,161],"next-generation":[56],"sequencing.":[57],"Epigenetic":[58],"mechanisms,":[59],"such":[60,204,214],"as":[61,205,215],"methylation,":[63],"regulate":[64],"gene":[65],"expression":[66],"play":[68],"critical":[69],"roles":[70],"the":[72,116,187],"development":[73],"progression":[75],"of":[76,171],"cancer.":[77],"We":[78],"here":[79],"MSI-XGNN,":[81,128],"new":[83],"framework":[85],"predicting":[87,235],"status":[89,237],"bulk":[91],"RNA-sequencing":[92],"methylation":[95,173],"data.":[96],"MSI-XGNN":[97,156,165],"an":[99],"explainable":[100,230],"deep":[101,231],"learning":[102,232],"model":[103,111,123,233],"that":[104,140,242],"combines":[105],"graph":[107],"neural":[108],"network":[109,119],"(GNN)":[110],"to":[112,124],"extract":[113],"features":[114],"from":[115],"gene-methylation":[117],"probe":[118],"with":[120,136,197],"CatBoost":[122],"classify":[125],"status.":[127],"which":[129],"requires":[130],"tumor-only":[131],"samples,":[132],"exhibited":[133],"comparable":[134],"performance":[135,151],"two":[137,181],"well-known":[138],"require":[141],"tumor-normal":[142],"paired":[143],"sequencing":[144],"data,":[145],"MSIsensor":[146],"MANTIS":[148],"better":[150],"than":[152],"several":[153],"other":[154],"tools.":[155],"also":[157],"showed":[158],"good":[159],"generalizability":[160],"independent":[162],"validation":[163],"datasets.":[164],"identified":[166],"six":[167,192],"markers":[169,193,241],"consisting":[170],"four":[172],"probes":[174],"(EPM2AIP1|MLH1:cg14598950,":[175],"EPM2AIP1|MLH1:cg27331401,":[176],"LNP1:cg05428436":[177],"TSC22D2:cg15048832)":[179],"genes":[182],"(RPL22L1":[183],"MSH4)":[185],"constituting":[186],"optimal":[188],"feature":[189],"subset.":[190],"All":[191],"were":[194],"significantly":[195],"associated":[196],"beneficial":[198],"tumor":[199,206],"microenvironment":[200],"characteristics":[201],"immunotherapy,":[203],"mutation":[207],"burden,":[208],"neoantigens":[209],"molecules":[213],"programmed":[216],"cell":[217],"death-1":[218],"cytotoxic":[220],"T-lymphocyte":[221],"antigen-4.":[222],"Overall,":[223],"our":[224],"study":[225],"provides":[226],"powerful":[228],"identifying":[239],"can":[243],"potentially":[244],"be":[245],"used":[246],"clinical":[248],"evaluation.":[250]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7}],"updated_date":"2026-03-03T08:47:05.690250","created_date":"2025-10-10T00:00:00"}
