{"id":"https://openalex.org/W4414064820","doi":"https://doi.org/10.1093/bib/bbaf455","title":"TMBquant: an explainable AI-powered caller advancing tumor mutation burden quantification across heterogeneous samples","display_name":"TMBquant: an explainable AI-powered caller advancing tumor mutation burden quantification across heterogeneous samples","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414064820","doi":"https://doi.org/10.1093/bib/bbaf455","pmid":"https://pubmed.ncbi.nlm.nih.gov/40919911"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf455","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf455/64220278/bbaf455.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf455/64220278/bbaf455.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5115694725","display_name":"Shenjie Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]},{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shenjie Wang","raw_affiliation_strings":["Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100410946","display_name":"Xiaonan Wang","orcid":"https://orcid.org/0000-0002-7749-2811"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]},{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]},{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaonan Wang","raw_affiliation_strings":["Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China","School of Computer Science and Technology, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","institution_ids":["https://openalex.org/I36399199"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China","institution_ids":["https://openalex.org/I36399199"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100452974","display_name":"Xiaoyan Zhu","orcid":"https://orcid.org/0000-0002-7173-7793"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyan Zhu","raw_affiliation_strings":["School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054657033","display_name":"Xuwen Wang","orcid":"https://orcid.org/0000-0003-3022-6513"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]},{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]},{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuwen Wang","raw_affiliation_strings":["Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","institution_ids":["https://openalex.org/I36399199"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067706647","display_name":"Yuqian Liu","orcid":"https://orcid.org/0000-0001-6210-1147"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuqian Liu","raw_affiliation_strings":["School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101338835","display_name":"Minchao Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minchao Zhao","raw_affiliation_strings":["Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","institution_ids":["https://openalex.org/I36399199"]},{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081685345","display_name":"Zhili Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhili Chang","raw_affiliation_strings":["Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","institution_ids":["https://openalex.org/I36399199"]},{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003742311","display_name":"Yang Shao","orcid":"https://orcid.org/0000-0003-4585-1792"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Shao","raw_affiliation_strings":["Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China"],"raw_orcid":"https://orcid.org/0000-0003-4585-1792","affiliations":[{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc. , 128 Huakang Road, Pukou, Nanjing 211800 ,","institution_ids":["https://openalex.org/I36399199"]},{"raw_affiliation_string":"Nanjing Geneseeq Technology Inc., 128 Huakang Road, Pukou, Nanjing 211800, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100454605","display_name":"Haitao Zhang","orcid":"https://orcid.org/0009-0006-7538-4696"},"institutions":[{"id":"https://openalex.org/I4210154136","display_name":"Tang Du Hospital","ror":"https://ror.org/04yvdan45","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210154136"]},{"id":"https://openalex.org/I9916479","display_name":"Air Force Medical University","ror":"https://ror.org/00ms48f15","country_code":"CN","type":"education","lineage":["https://openalex.org/I9916479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haitao Zhang","raw_affiliation_strings":["Department of Respiratory Medicine , Tangdu Hospital, , 569 Xinsi Road, Baqiao District, Xi'an, Shaanxi 710038 ,","The Fourth Military Medical University , Tangdu Hospital, , 569 Xinsi Road, Baqiao District, Xi'an, Shaanxi 710038 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine , Tangdu Hospital, , 569 Xinsi Road, Baqiao District, Xi'an, Shaanxi 710038 ,","institution_ids":["https://openalex.org/I4210154136"]},{"raw_affiliation_string":"The Fourth Military Medical University , Tangdu Hospital, , 569 Xinsi Road, Baqiao District, Xi'an, Shaanxi 710038 ,","institution_ids":["https://openalex.org/I9916479","https://openalex.org/I4210154136"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115592818","display_name":"Shuanying Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuanying Yang","raw_affiliation_strings":["Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027360778","display_name":"Jiayin Wang","orcid":"https://orcid.org/0000-0002-3862-6557"},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]},{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayin Wang","raw_affiliation_strings":["Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China"],"raw_orcid":"https://orcid.org/0000-0002-3862-6557","affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Xincheng District, Xi'an 710004 ,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , 28 Xianning West Road, Beilin, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, 28 Xianning West Road, Beilin, Xi'an 710049, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China","institution_ids":["https://openalex.org/I4210131893"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26800891,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9965999722480774,"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/T10417","display_name":"Lung Cancer Treatments and Mutations","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"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/generalizability-theory","display_name":"Generalizability theory","score":0.6248000264167786},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"Lung cancer","score":0.48669999837875366},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.40400001406669617},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.3937999904155731},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.3531999886035919},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.3499000072479248},{"id":"https://openalex.org/keywords/adenocarcinoma","display_name":"Adenocarcinoma","score":0.3116999864578247}],"concepts":[{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.6248000264167786},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5842000246047974},{"id":"https://openalex.org/C2776256026","wikidata":"https://www.wikidata.org/wiki/Q47912","display_name":"Lung cancer","level":2,"score":0.48669999837875366},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4749000072479248},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.40400001406669617},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.3937999904155731},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3531999886035919},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3529999852180481},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3499000072479248},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3325999975204468},{"id":"https://openalex.org/C2781182431","wikidata":"https://www.wikidata.org/wiki/Q356033","display_name":"Adenocarcinoma","level":3,"score":0.3116999864578247},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3102000057697296},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3025999963283539},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.3018999993801117},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30169999599456787},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.2992999851703644},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29319998621940613},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.29170000553131104},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.28790000081062317},{"id":"https://openalex.org/C2779767149","wikidata":"https://www.wikidata.org/wiki/Q488212","display_name":"Microsatellite instability","level":5,"score":0.28790000081062317},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2653000056743622},{"id":"https://openalex.org/C3018028425","wikidata":"https://www.wikidata.org/wiki/Q15917291","display_name":"Tumor heterogeneity","level":3,"score":0.26409998536109924},{"id":"https://openalex.org/C3020404979","wikidata":"https://www.wikidata.org/wiki/Q1058438","display_name":"Risk stratification","level":2,"score":0.2524000108242035}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002289","descriptor_name":"Carcinoma, Non-Small-Cell Lung","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf455","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf455/64220278/bbaf455.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40919911","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40919911","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12415849","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12415849/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf455","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf455/64220278/bbaf455.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2715084110","display_name":null,"funder_award_id":"62402376","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3180425335","display_name":null,"funder_award_id":"72293581","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G516663181","display_name":null,"funder_award_id":"72274152","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414064820.pdf","grobid_xml":"https://content.openalex.org/works/W4414064820.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1940241680","https://openalex.org/W2049553585","https://openalex.org/W2104885590","https://openalex.org/W2155943701","https://openalex.org/W2180481128","https://openalex.org/W2198093519","https://openalex.org/W2299181842","https://openalex.org/W2323851578","https://openalex.org/W2527905628","https://openalex.org/W2560367415","https://openalex.org/W2572174216","https://openalex.org/W2606495925","https://openalex.org/W2747774814","https://openalex.org/W2783897381","https://openalex.org/W2784868445","https://openalex.org/W2798160602","https://openalex.org/W2800160190","https://openalex.org/W2867868648","https://openalex.org/W2900082702","https://openalex.org/W2909679049","https://openalex.org/W2925446385","https://openalex.org/W2943688939","https://openalex.org/W2962862931","https://openalex.org/W3093528466","https://openalex.org/W3136109706","https://openalex.org/W3174077356","https://openalex.org/W4321350922","https://openalex.org/W4391033579","https://openalex.org/W4394917946","https://openalex.org/W4403925918"],"related_works":["https://openalex.org/W2118717649","https://openalex.org/W2413243053","https://openalex.org/W410723623","https://openalex.org/W2015341305","https://openalex.org/W2035068594","https://openalex.org/W4225593417","https://openalex.org/W2573498121","https://openalex.org/W3022298670","https://openalex.org/W3160494304","https://openalex.org/W2388888344"],"abstract_inverted_index":{"Accurate":[0],"tumor":[1,20],"mutation":[2],"burden":[3],"(TMB)":[4],"quantification":[5],"is":[6,194],"critical":[7],"for":[8,189,214],"immunotherapy":[9],"stratification,":[10],"yet":[11],"remains":[12],"challenging":[13],"due":[14],"to":[15,35,149],"variability":[16],"across":[17,68,110,159,170],"sequencing":[18,96],"platforms,":[19],"heterogeneity,":[21],"and":[22,45,62,66,87,122,129,163,185,197,210],"variant":[23,57,78],"calling":[24],"pipelines.":[25],"Here,":[26],"we":[27,103,205],"introduce":[28],"TMBquant,":[29],"an":[30],"explainable":[31],"AI-powered":[32],"caller":[33],"designed":[34],"optimize":[36],"TMB":[37],"estimation":[38],"through":[39,107],"dynamic":[40],"feature":[41],"selection,":[42],"ensemble":[43],"learning,":[44],"automated":[46],"strategy":[47],"adaptation.":[48],"Built":[49],"upon":[50],"the":[51,123,140,217],"H2O":[52],"AutoML":[53],"framework,":[54],"TMBquant":[55,73,106,137,154,180,215],"integrates":[56],"features,":[58],"minimizes":[59],"classification":[60],"errors,":[61],"enhances":[63],"both":[64,160],"accuracy":[65],"stability":[67],"diverse":[69],"datasets.":[70],"We":[71],"benchmarked":[72],"against":[74],"nine":[75],"widely":[76],"used":[77],"callers,":[79],"including":[80],"traditional":[81],"tools":[82],"(e.g.":[83],"Mutect2,":[84],"VarScan2,":[85],"Strelka2)":[86],"recent":[88],"AI-based":[89],"methods":[90],"(DeepSomatic,":[91],"Octopus),":[92],"using":[93],"706":[94],"whole-exome":[95],"tumor-control":[97],"pairs.":[98],"To":[99,202],"evaluate":[100],"clinical":[101],"relevance,":[102],"further":[104],"assessed":[105],"survival":[108],"analyses":[109],"immunotherapy-treated":[111],"cohorts":[112],"of":[113],"non-small":[114],"cell":[115,132],"lung":[116,127,130],"cancer":[117,171],"(NSCLC),":[118],"nasopharyngeal":[119],"carcinoma":[120],"(NPC),":[121],"two":[124],"NSCLC":[125],"subtypes:":[126],"adenocarcinoma":[128],"squamous":[131],"carcinoma.":[133],"In":[134],"each":[135],"cohort,":[136],"consistently":[138],"achieved":[139],"highest":[141],"hazard":[142],"ratios,":[143],"demonstrating":[144],"superior":[145],"patient":[146],"stratification":[147],"compared":[148],"all":[150],"other":[151],"methods.":[152],"Importantly,":[153],"maintained":[155],"robust":[156],"predictive":[157],"performance":[158],"high-TMB":[161],"(NSCLC)":[162],"low-TMB":[164],"(NPC)":[165],"settings,":[166],"highlighting":[167],"its":[168],"generalizability":[169],"types":[172],"with":[173],"distinct":[174],"biological":[175],"characteristics.":[176],"These":[177],"findings":[178],"establish":[179],"as":[181],"a":[182],"reliable,":[183],"reproducible,":[184],"clinically":[186],"actionable":[187],"tool":[188],"precision":[190],"oncology.":[191],"The":[192],"software":[193],"open":[195],"source":[196],"freely":[198],"available":[199],"at":[200],"https://github.com/SomaticCaller/SomaticCaller.":[201],"enhance":[203],"reproducibility,":[204],"provide":[206],"detailed":[207],"usage":[208],"instructions":[209],"representative":[211],"code":[212],"snippets":[213],"in":[216],"Methods":[218],"section":[219],"(see":[220],"Code":[221],"Availability).":[222]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
