{"id":"https://openalex.org/W4413885430","doi":"https://doi.org/10.1093/bioinformatics/btaf485","title":"MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples","display_name":"MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples","publication_year":2025,"publication_date":"2025-09-01","ids":{"openalex":"https://openalex.org/W4413885430","doi":"https://doi.org/10.1093/bioinformatics/btaf485","pmid":"https://pubmed.ncbi.nlm.nih.gov/40889285"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf485","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf485/64176731/btaf485.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf485/64176731/btaf485.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Tianci Wang","orcid":"https://orcid.org/0000-0002-4875-3488"},"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":"Tianci Wang","raw_affiliation_strings":["School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China"],"raw_orcid":"https://orcid.org/0000-0002-4875-3488","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066454748","display_name":"Xin Lai","orcid":"https://orcid.org/0000-0002-2565-1833"},"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":"Xin Lai","raw_affiliation_strings":["School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":null,"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, Shaanxi, 710003,","School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,"],"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, Shaanxi, 710003,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101861916","display_name":"Yuqian Liu","orcid":"https://orcid.org/0000-0003-1436-3489"},"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 , Xi\u2019an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101603854","display_name":"Xiaoyan Zhu","orcid":null},"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 , Xi\u2019an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113900404","display_name":"Jiayin Wang","orcid":null},"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":"Jiayin Wang","raw_affiliation_strings":["School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,"],"raw_orcid":"https://orcid.org/0000-0002-3862-6557","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data , Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University Shaanxi Engineering Research Center of Medical and Health Big Data, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Xi\u2019an Jiaotong University School of Computer Science and Technology, , Xi\u2019an,","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25863204,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"9","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":0.9325000047683716,"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":0.9325000047683716,"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/T10862","display_name":"AI in cancer detection","score":0.010999999940395355,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.009999999776482582,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/computer-science","display_name":"Computer science","score":0.7388980388641357},{"id":"https://openalex.org/keywords/residual","display_name":"Residual","score":0.5850168466567993},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5364201068878174},{"id":"https://openalex.org/keywords/circulating-tumor-dna","display_name":"Circulating tumor DNA","score":0.4862445890903473},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.43638911843299866},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.41978150606155396},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37729305028915405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34498652815818787},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3425348401069641},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.25807613134384155},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.14979243278503418},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10234516859054565}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7388980388641357},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.5850168466567993},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5364201068878174},{"id":"https://openalex.org/C2781335228","wikidata":"https://www.wikidata.org/wiki/Q19596321","display_name":"Circulating tumor DNA","level":3,"score":0.4862445890903473},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.43638911843299866},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.41978150606155396},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37729305028915405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34498652815818787},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3425348401069641},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25807613134384155},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.14979243278503418},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10234516859054565},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000074141","descriptor_name":"Circulating Tumor DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000074141","descriptor_name":"Circulating Tumor DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000074141","descriptor_name":"Circulating Tumor DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000074141","descriptor_name":"Circulating Tumor DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018365","descriptor_name":"Neoplasm, Residual","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf485","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf485/64176731/btaf485.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40889285","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40889285","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11270890","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12462387","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12462387","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12462387/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf485","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf485/64176731/btaf485.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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"},{"id":"https://openalex.org/G6671363317","display_name":null,"funder_award_id":"62572389","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/W4413885430.pdf","grobid_xml":"https://content.openalex.org/works/W4413885430.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1565378970","https://openalex.org/W1579111454","https://openalex.org/W1964807436","https://openalex.org/W1982324510","https://openalex.org/W2024092628","https://openalex.org/W2060965924","https://openalex.org/W2110390205","https://openalex.org/W2155943701","https://openalex.org/W2517179206","https://openalex.org/W2929354011","https://openalex.org/W2949522823","https://openalex.org/W2951331911","https://openalex.org/W2963186762","https://openalex.org/W2972314425","https://openalex.org/W2974398825","https://openalex.org/W2998732476","https://openalex.org/W3093528466","https://openalex.org/W3100789280","https://openalex.org/W3131055609","https://openalex.org/W3164222795","https://openalex.org/W3196007724","https://openalex.org/W3206476260","https://openalex.org/W3214897392","https://openalex.org/W4285043533","https://openalex.org/W4292363360","https://openalex.org/W4379534149","https://openalex.org/W4385647408","https://openalex.org/W4389763605","https://openalex.org/W4391164176","https://openalex.org/W4394927283","https://openalex.org/W4404816318","https://openalex.org/W4405044382","https://openalex.org/W4405050525","https://openalex.org/W4409952587"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W188202134","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"MOTIVATION:":[0],"Minimal":[1],"residual":[2],"disease":[3],"(MRD)":[4],"as":[5],"critical":[6],"biomarker":[7],"for":[8,73,122,195],"cancer":[9],"prognosis":[10],"and":[11,42,45,98,129,140,174,181,187,200,216],"management":[12],"plays":[13],"a":[14,115,155],"crucial":[15],"role":[16],"in":[17,198],"improving":[18],"patient":[19],"outcomes.":[20],"However,":[21],"detecting":[22],"MRD":[23,61,123,196],"via":[24],"next-generation":[25],"sequencing-based":[26],"circulating":[27],"tumor":[28],"DNA":[29],"variant":[30,39,95,117],"calling":[31],"remains":[32,63],"unstable":[33],"due":[34,65],"to":[35,66,164],"the":[36,54,71,86,100,152],"extremely":[37],"low":[38],"allele":[40],"frequency":[41],"significant":[43],"inter-":[44],"intra-sample":[46],"heterogeneity.":[47],"Although":[48],"parameter":[49,75,89,105,167],"optimization":[50,106,131],"can":[51],"theoretically":[52],"enhance":[53],"detection":[55,62,96,118,197],"performance":[56],"of":[57,94,102,134,149,154],"variants,":[58],"achieving":[59],"stable":[60,188],"challenging":[64],"three":[67],"key":[68,147],"factors:":[69],"(i)":[70],"necessity":[72],"individualized":[74],"tuning":[76],"across":[77,91,144],"numerous":[78],"heterogeneous":[79],"genomic":[80],"intervals":[81],"within":[82],"each":[83],"sample,":[84],"(ii)":[85],"tightly":[87],"interdependent":[88],"requirements":[90],"different":[92],"stages":[93],"workflows,":[97],"(iii)":[99],"limitations":[101],"current":[103],"automated":[104],"methods.":[107],"RESULTS:":[108],"In":[109],"this":[110],"study,":[111],"we":[112],"propose":[113],"MRDagent,":[114],"novel":[116],"tool":[119],"designed":[120],"specifically":[121],"detection.":[124],"MRDagent":[125,150,207],"incorporates":[126],"an":[127,191],"iterative":[128],"self-adaptive":[130],"framework":[132],"capable":[133],"handling":[135],"unknown":[136],"objectives,":[137],"varying":[138],"constraints,":[139],"highly":[141],"coupled":[142],"parameters":[143],"stages.":[145],"A":[146],"innovation":[148],"is":[151,208],"integration":[153],"convolutional":[156],"neural":[157],"network-based":[158],"meta-model,":[159],"trained":[160],"on":[161,179],"historical":[162],"data":[163],"enable":[165],"rapid":[166],"prediction.":[168],"This":[169],"significantly":[170],"enhances":[171],"computational":[172],"efficiency":[173],"generalization":[175],"performance.":[176],"Extensive":[177],"evaluations":[178],"simulated":[180],"real-world":[182],"datasets":[183],"demonstrate":[184],"MRDagent's":[185],"superior":[186],"performance,":[189],"providing":[190],"efficient,":[192],"reliable":[193],"solution":[194],"clinical":[199],"high-throughput":[201],"research":[202],"applications.":[203],"AVAILABILITY":[204],"AND":[205],"IMPLEMENTATION:":[206],"freely":[209],"available":[210,220],"at":[211,221],"https://github.com/aAT0047/MRDagent.git.":[212],"The":[213],"corresponding":[214],"dataset":[215],"software":[217],"archive":[218],"are":[219],"Zenodo:":[222],"https://doi.org/10.5281/zenodo.15458496.":[223]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-09-01T00:00:00"}
