{"id":"https://openalex.org/W4414026914","doi":"https://doi.org/10.3389/fbinf.2025.1641491","title":"TCRscape: a single-cell multi-omic TCR profiling toolkit","display_name":"TCRscape: a single-cell multi-omic TCR profiling toolkit","publication_year":2025,"publication_date":"2025-09-05","ids":{"openalex":"https://openalex.org/W4414026914","doi":"https://doi.org/10.3389/fbinf.2025.1641491","pmid":"https://pubmed.ncbi.nlm.nih.gov/40980694"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1641491","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1641491","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1641491/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1641491/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006412523","display_name":"Roman Perik-Zavodskii","orcid":"https://orcid.org/0000-0002-5055-4859"},"institutions":[{"id":"https://openalex.org/I4210102846","display_name":"Research Institute of Fundamental and Clinical Immunology","ror":"https://ror.org/01b3qhp76","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210102846","https://openalex.org/I4210110862"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Roman Perik-Zavodskii","raw_affiliation_strings":["Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia","institution_ids":["https://openalex.org/I4210102846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057161720","display_name":"Olga Perik-Zavodskaia","orcid":"https://orcid.org/0000-0003-4911-1994"},"institutions":[{"id":"https://openalex.org/I4210102846","display_name":"Research Institute of Fundamental and Clinical Immunology","ror":"https://ror.org/01b3qhp76","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210102846","https://openalex.org/I4210110862"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Olga Perik-Zavodskaia","raw_affiliation_strings":["Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia","institution_ids":["https://openalex.org/I4210102846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075126715","display_name":"Marina Volynets","orcid":"https://orcid.org/0000-0003-1683-8951"},"institutions":[{"id":"https://openalex.org/I4210102846","display_name":"Research Institute of Fundamental and Clinical Immunology","ror":"https://ror.org/01b3qhp76","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210102846","https://openalex.org/I4210110862"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Marina Volynets","raw_affiliation_strings":["Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia","institution_ids":["https://openalex.org/I4210102846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018497405","display_name":"Saleh Alrhmoun","orcid":"https://orcid.org/0000-0003-0788-5385"},"institutions":[{"id":"https://openalex.org/I4210102846","display_name":"Research Institute of Fundamental and Clinical Immunology","ror":"https://ror.org/01b3qhp76","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210102846","https://openalex.org/I4210110862"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Saleh Alrhmoun","raw_affiliation_strings":["Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia","institution_ids":["https://openalex.org/I4210102846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069358824","display_name":"\u0421. \u0412. \u0421\u0435\u043d\u043d\u0438\u043a\u043e\u0432","orcid":"https://orcid.org/0000-0002-7366-7768"},"institutions":[{"id":"https://openalex.org/I4210102846","display_name":"Research Institute of Fundamental and Clinical Immunology","ror":"https://ror.org/01b3qhp76","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210102846","https://openalex.org/I4210110862"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Sergey Sennikov","raw_affiliation_strings":["Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia","institution_ids":["https://openalex.org/I4210102846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5006412523"],"corresponding_institution_ids":["https://openalex.org/I4210102846"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.7244,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.7420968,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"5","issue":null,"first_page":"1641491","last_page":"1641491"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11491","display_name":"CAR-T cell therapy research","score":0.9922999739646912,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.7609091997146606},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6476650238037109},{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.6256047487258911},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4801206588745117},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3127913177013397},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.178156316280365},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10614296793937683},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07987344264984131}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7609091997146606},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6476650238037109},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.6256047487258911},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4801206588745117},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3127913177013397},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.178156316280365},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10614296793937683},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07987344264984131},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2025.1641491","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1641491","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1641491/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40980694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40980694","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c81dc55601784993b61bb7e39b0f9c33","is_oa":true,"landing_page_url":"https://doaj.org/article/c81dc55601784993b61bb7e39b0f9c33","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11255918","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12446293","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:12446293","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12446293/","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":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1641491","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1641491","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1641491/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G666597642","display_name":null,"funder_award_id":"124112200103-3","funder_id":"https://openalex.org/F4320327494","funder_display_name":"Ministry of Science and Higher Education of the Russian Federation"}],"funders":[{"id":"https://openalex.org/F4320327494","display_name":"Ministry of Science and Higher Education of the Russian Federation","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414026914.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1969956705","https://openalex.org/W2076948707","https://openalex.org/W2077264333","https://openalex.org/W2078989706","https://openalex.org/W2105195133","https://openalex.org/W2185265351","https://openalex.org/W2601243251","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2728919089","https://openalex.org/W2800392236","https://openalex.org/W2889326414","https://openalex.org/W2898824002","https://openalex.org/W2950477675","https://openalex.org/W2971477701","https://openalex.org/W3035965352","https://openalex.org/W3037322279","https://openalex.org/W3044112499","https://openalex.org/W3099878876","https://openalex.org/W3134236823","https://openalex.org/W3161420752","https://openalex.org/W3185560091","https://openalex.org/W4285212248","https://openalex.org/W4311666516","https://openalex.org/W4378212544","https://openalex.org/W4385685674","https://openalex.org/W4387706823","https://openalex.org/W4401503524","https://openalex.org/W4403312817","https://openalex.org/W4404971446","https://openalex.org/W6931115787"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189"],"abstract_inverted_index":{"By":[0],"bridging":[1],"clonotype":[2],"detection":[3],"with":[4],"immune":[5,30],"cell":[6],"transcriptome,":[7],"proteome,":[8],"and":[9,21,32],"antigen":[10],"specificity":[11],"profiling,":[12],"TCRscape":[13,36],"supports":[14],"rapid":[15],"identification":[16],"of":[17],"dominant":[18],"T-cell":[19],"clones":[20],"their":[22],"functional":[23],"phenotypes,":[24],"offering":[25],"a":[26],"powerful":[27],"resource":[28],"for":[29],"monitoring":[31],"TCR-engineered":[33],"therapeutic":[34],"development.":[35],"can":[37],"be":[38],"found":[39],"at":[40],"https://github.com/Perik-Zavodskii/TCRscape/.":[41]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
