{"id":"https://openalex.org/W3200585592","doi":"https://doi.org/10.1093/bioinformatics/btab661","title":"AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data","display_name":"AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data","publication_year":2021,"publication_date":"2021-09-13","ids":{"openalex":"https://openalex.org/W3200585592","doi":"https://doi.org/10.1093/bioinformatics/btab661","mag":"3200585592","pmid":"https://pubmed.ncbi.nlm.nih.gov/34529039"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab661","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab661","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10060699/pdf/btab661.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021283020","display_name":"Christina S.F. Wong","orcid":null},"institutions":[{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina Wong","raw_affiliation_strings":["Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center , Dallas, TX 75390, USA"],"affiliations":[{"raw_affiliation_string":"Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center , Dallas, TX 75390, USA","institution_ids":["https://openalex.org/I867280407","https://openalex.org/I4210096815","https://openalex.org/I4388891891"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100374468","display_name":"Bo Li","orcid":"https://orcid.org/0000-0002-8617-900X"},"institutions":[{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bo Li","raw_affiliation_strings":["Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center , Dallas, TX 75390, USA"],"affiliations":[{"raw_affiliation_string":"Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center , Dallas, TX 75390, USA","institution_ids":["https://openalex.org/I867280407","https://openalex.org/I4210096815","https://openalex.org/I4388891891"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100374468"],"corresponding_institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I4388891891","https://openalex.org/I867280407"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4067,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.5972649,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"38","issue":"2","first_page":"589","last_page":"591"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9980999827384949,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.7728686928749084},{"id":"https://openalex.org/keywords/cancer-immunotherapy","display_name":"Cancer immunotherapy","score":0.6236217617988586},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.5866130590438843},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5837111473083496},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5596336722373962},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.524539053440094},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48291799426078796},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48163357377052307},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.4179912209510803},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.360613077878952},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3297697901725769},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2856702208518982},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.21139469742774963},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20061534643173218},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09736242890357971},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.09535011649131775}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.7728686928749084},{"id":"https://openalex.org/C2780674031","wikidata":"https://www.wikidata.org/wiki/Q2012719","display_name":"Cancer immunotherapy","level":4,"score":0.6236217617988586},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.5866130590438843},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5837111473083496},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5596336722373962},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.524539053440094},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48291799426078796},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48163357377052307},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.4179912209510803},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.360613077878952},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3297697901725769},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2856702208518982},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.21139469742774963},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20061534643173218},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09736242890357971},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.09535011649131775},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D007167","descriptor_name":"Immunotherapy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007167","descriptor_name":"Immunotherapy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007167","descriptor_name":"Immunotherapy","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":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab661","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab661","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34529039","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34529039","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:pubmedcentral.nih.gov:10060699","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10060699","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10060699/pdf/btab661.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10060699","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10060699","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10060699/pdf/btab661.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7699999809265137,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2582829953","display_name":null,"funder_award_id":"1R01CA245318","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3565367895","display_name":null,"funder_award_id":"CA245318","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4791203545","display_name":null,"funder_award_id":"1R01CA245318-01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G513672869","display_name":null,"funder_award_id":"1R01CA245318-01A1","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3200585592.pdf","grobid_xml":"https://content.openalex.org/works/W3200585592.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2131682431","https://openalex.org/W2336513938","https://openalex.org/W2411861063","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2744653597","https://openalex.org/W2808717540","https://openalex.org/W2912273667","https://openalex.org/W2952324549","https://openalex.org/W2995682549","https://openalex.org/W3020331344","https://openalex.org/W3063526921","https://openalex.org/W3083146163","https://openalex.org/W3132841322","https://openalex.org/W3167871643","https://openalex.org/W3187834303","https://openalex.org/W6752975422"],"related_works":["https://openalex.org/W3111580887","https://openalex.org/W3185708072","https://openalex.org/W2893846263","https://openalex.org/W3049036915","https://openalex.org/W3158104901","https://openalex.org/W4313343001","https://openalex.org/W4223914026","https://openalex.org/W2400599632","https://openalex.org/W2999675030","https://openalex.org/W2806333505"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
