{"doi":"10.1093/bioinformatics/btab661","title":"AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data","abstract":"SUMMARY: T cells participate directly in the body's immune response to cancer, allowing immunotherapy treatments to effectively recognize and target cancer cells. We previously developed DeepCAT to demonstrate that T cells serve as a biomarker of immune response in cancer patients and can be utilized as a diagnostic tool to differentiate healthy and cancer patient samples. However, DeepCAT's reliance on tumor bulk RNA-seq samples as training data limited its further performance improvement. Here, we benchmarked a new approach, AutoCAT, to predict tumor-associated TCRs from targeted TCR-seq data as a new form of input for DeepCAT, and observed the same level of predictive accuracy. AVAILABILITY AND IMPLEMENTATION: Source code is freely available at https://github.com/cew88/AutoCAT, and data is available at 10.5281/zenodo.5176884. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2021,"id":194195,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9358,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":670,"name":"Bo Li","orcid":"0000-0002-8617-900X","position":1,"is_corresponding":false},{"id":599946,"name":"Christina S.F. Wong","orcid":"0000-0002-1650-5383","position":0,"is_corresponding":true}],"reference_count":17,"raw_metadata":null,"created_at":"2026-07-18T23:49:55.282992Z","pmid":"34529039","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}