{"id":"https://openalex.org/W2185265351","doi":"https://doi.org/10.1371/journal.pcbi.1004503","title":"VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires","display_name":"VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires","publication_year":2015,"publication_date":"2015-11-25","ids":{"openalex":"https://openalex.org/W2185265351","doi":"https://doi.org/10.1371/journal.pcbi.1004503","mag":"2185265351","pmid":"https://pubmed.ncbi.nlm.nih.gov/26606115"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004503","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004503","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004503&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004503&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079193050","display_name":"Mikhail Shugay","orcid":"https://orcid.org/0000-0001-7826-7942"},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Mikhail Shugay","raw_affiliation_strings":["Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089140534","display_name":"Dmitriy V. Bagaev","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitriy V. Bagaev","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060662301","display_name":"Maria A. Turchaninova","orcid":"https://orcid.org/0000-0002-8874-0286"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Maria A. Turchaninova","raw_affiliation_strings":["Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060953538","display_name":"Dmitriy A. Bolotin","orcid":"https://orcid.org/0000-0002-8484-6067"},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitriy A. Bolotin","raw_affiliation_strings":["Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018375058","display_name":"Olga V. Britanova","orcid":"https://orcid.org/0000-0002-6295-1392"},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]}],"countries":["CZ","RU"],"is_corresponding":false,"raw_author_name":"Olga V. Britanova","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech Republic","Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012241793","display_name":"Ekaterina V. Putintseva","orcid":"https://orcid.org/0000-0003-4421-3844"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]}],"countries":["CZ","RU"],"is_corresponding":false,"raw_author_name":"Ekaterina V. Putintseva","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech Republic","Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074563161","display_name":"Mikhail V. Pogorelyy","orcid":"https://orcid.org/0000-0003-0773-1204"},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Mikhail V. Pogorelyy","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084245406","display_name":"Vadim I. Nazarov","orcid":"https://orcid.org/0000-0003-3659-2709"},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vadim I. Nazarov","raw_affiliation_strings":["National Research University Higher School of Economics, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057434715","display_name":"Ivan V. Zvyagin","orcid":"https://orcid.org/0000-0002-1769-9116"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ","RU"],"is_corresponding":false,"raw_author_name":"Ivan V. Zvyagin","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech Republic","Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032359738","display_name":"Vitalina Kirgizova","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vitalina I. Kirgizova","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077754985","display_name":"\u041a. \u0418. \u041a\u0438\u0440\u0433\u0438\u0437\u043e\u0432","orcid":"https://orcid.org/0000-0002-2945-284X"},"institutions":[{"id":"https://openalex.org/I4210110829","display_name":"Russian Children's Clinical Hospital","ror":"https://ror.org/01wvtht83","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I4210110829"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Kirill I. Kirgizov","raw_affiliation_strings":["Russian Children's Hospital, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Russian Children's Hospital, Moscow, Russia","institution_ids":["https://openalex.org/I4210110829"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041371660","display_name":"\u0415. \u0412. \u0421\u043a\u043e\u0440\u043e\u0431\u043e\u0433\u0430\u0442\u043e\u0432\u0430","orcid":"https://orcid.org/0000-0003-4431-1444"},"institutions":[{"id":"https://openalex.org/I4210110829","display_name":"Russian Children's Clinical Hospital","ror":"https://ror.org/01wvtht83","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I4210110829"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Elena V. Skorobogatova","raw_affiliation_strings":["Russian Children's Hospital, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Russian Children's Hospital, Moscow, Russia","institution_ids":["https://openalex.org/I4210110829"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060028352","display_name":"Dmitriy M. Chudakov","orcid":"https://orcid.org/0000-0003-0430-790X"},"institutions":[{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]}],"countries":["CZ","RU"],"is_corresponding":true,"raw_author_name":"Dmitriy M. Chudakov","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech Republic","Pirogov Russian National Research Medical University, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5060028352"],"corresponding_institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I337778094","https://openalex.org/I4210090417","https://openalex.org/I4210105571"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":11.6653,"has_fulltext":true,"cited_by_count":647,"citation_normalized_percentile":{"value":0.98998133,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"11","issue":"11","first_page":"e1004503","last_page":"e1004503"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.9995999932289124,"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"}},{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9821000099182129,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.7032052278518677},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.6373310685157776},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5997834801673889},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5792825818061829},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5416910648345947},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5084394812583923},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.48783472180366516},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.4275839328765869},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3619268536567688},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31584271788597107},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.2843495011329651},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.22632893919944763},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14972177147865295},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.14379802346229553},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.09579956531524658},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.08926236629486084}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.7032052278518677},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.6373310685157776},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5997834801673889},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5792825818061829},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5416910648345947},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5084394812583923},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.48783472180366516},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.4275839328765869},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3619268536567688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31584271788597107},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.2843495011329651},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.22632893919944763},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14972177147865295},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.14379802346229553},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.09579956531524658},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.08926236629486084},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000293","descriptor_name":"Adolescent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000293","descriptor_name":"Adolescent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000293","descriptor_name":"Adolescent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000328","descriptor_name":"Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000328","descriptor_name":"Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000328","descriptor_name":"Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","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":"D009103","descriptor_name":"Multiple Sclerosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009103","descriptor_name":"Multiple Sclerosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009103","descriptor_name":"Multiple Sclerosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D014427","descriptor_name":"Twins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014427","descriptor_name":"Twins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014427","descriptor_name":"Twins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018380","descriptor_name":"Hematopoietic Stem Cell Transplantation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018380","descriptor_name":"Hematopoietic Stem Cell Transplantation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018380","descriptor_name":"Hematopoietic Stem Cell Transplantation","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D055815","descriptor_name":"Young Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055815","descriptor_name":"Young Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055815","descriptor_name":"Young Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1004503","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004503","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004503&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26606115","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26606115","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1004503","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004503","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:450c0b60a1b045c1b9cda00e1a45601a","is_oa":true,"landing_page_url":"https://doaj.org/article/450c0b60a1b045c1b9cda00e1a45601a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 11, p e1004503 (2015)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3642654","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4659587","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:figshare.com:article/1612661","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_VDJtools_Unifying_Post_analysis_of_T_Cell_Receptor_Repertoires_/1612661","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004503","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004503","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004503&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4697993837","display_name":null,"funder_award_id":"14-14-00533","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2185265351.pdf","grobid_xml":"https://content.openalex.org/works/W2185265351.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W135571511","https://openalex.org/W1528875746","https://openalex.org/W1639799914","https://openalex.org/W1643112662","https://openalex.org/W1966354650","https://openalex.org/W1969192442","https://openalex.org/W1970688528","https://openalex.org/W1973639800","https://openalex.org/W1979781154","https://openalex.org/W1985012922","https://openalex.org/W1985833884","https://openalex.org/W1989223689","https://openalex.org/W1989465798","https://openalex.org/W1990386528","https://openalex.org/W1992683442","https://openalex.org/W1993928780","https://openalex.org/W1995875735","https://openalex.org/W1998927848","https://openalex.org/W2019359431","https://openalex.org/W2023897896","https://openalex.org/W2027941603","https://openalex.org/W2029525307","https://openalex.org/W2031435453","https://openalex.org/W2034860726","https://openalex.org/W2041677964","https://openalex.org/W2042786738","https://openalex.org/W2043071551","https://openalex.org/W2045740840","https://openalex.org/W2046794038","https://openalex.org/W2051241958","https://openalex.org/W2058178349","https://openalex.org/W2059785103","https://openalex.org/W2066930665","https://openalex.org/W2083190337","https://openalex.org/W2084781910","https://openalex.org/W2086595383","https://openalex.org/W2087189381","https://openalex.org/W2089041106","https://openalex.org/W2107243418","https://openalex.org/W2107794977","https://openalex.org/W2107974372","https://openalex.org/W2111480581","https://openalex.org/W2116601594","https://openalex.org/W2119736800","https://openalex.org/W2123402141","https://openalex.org/W2124989514","https://openalex.org/W2127500306","https://openalex.org/W2130142616","https://openalex.org/W2131159440","https://openalex.org/W2132457769","https://openalex.org/W2137890831","https://openalex.org/W2138968719","https://openalex.org/W2142081242","https://openalex.org/W2145044321","https://openalex.org/W2150743590","https://openalex.org/W2151537948","https://openalex.org/W2152241467","https://openalex.org/W2161976732","https://openalex.org/W2168109746","https://openalex.org/W2174247606","https://openalex.org/W2338760001","https://openalex.org/W2410413428","https://openalex.org/W4240607226","https://openalex.org/W4242749002","https://openalex.org/W4297944090","https://openalex.org/W4365410999"],"related_works":["https://openalex.org/W4255048859","https://openalex.org/W3120300186","https://openalex.org/W2084831119","https://openalex.org/W4389385869","https://openalex.org/W4378635687","https://openalex.org/W2060496539","https://openalex.org/W4280506224","https://openalex.org/W2018330851","https://openalex.org/W2143290387","https://openalex.org/W3201606428"],"abstract_inverted_index":{"Despite":[0],"the":[1,9,82],"growing":[2],"number":[3],"of":[4,18,35,56,67],"immune":[5],"repertoire":[6],"sequencing":[7],"studies,":[8],"field":[10],"still":[11],"lacks":[12],"software":[13,28,91],"for":[14,63],"analysis":[15,83],"and":[16,48,51,72,84,92],"comprehension":[17],"this":[19],"high-dimensional":[20],"data.":[21],"Here":[22],"we":[23,76],"report":[24],"VDJtools,":[25],"a":[26,32,44,57,64],"complementary":[27],"suite":[29],"that":[30,78],"solves":[31],"wide":[33],"range":[34],"T":[36],"cell":[37],"receptor":[38],"(TCR)":[39],"repertoires":[40],"post-analysis":[41],"tasks,":[42],"provides":[43],"detailed":[45],"tabular":[46],"output":[47],"publication-ready":[49],"graphics,":[50],"is":[52],"built":[53],"on":[54],"top":[55],"flexible":[58],"API.":[59],"Using":[60],"TCR":[61],"datasets":[62],"large":[65],"cohort":[66],"unrelated":[68],"healthy":[69],"donors,":[70],"twins,":[71],"multiple":[73],"sclerosis":[74],"patients":[75],"demonstrate":[77],"VDJtools":[79,90],"greatly":[80],"facilitates":[81],"leads":[85],"to":[86],"sound":[87],"biological":[88],"conclusions.":[89],"documentation":[93],"are":[94],"available":[95],"at":[96],"https://github.com/mikessh/vdjtools.":[97]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":59},{"year":2024,"cited_by_count":93},{"year":2023,"cited_by_count":89},{"year":2022,"cited_by_count":73},{"year":2021,"cited_by_count":89},{"year":2020,"cited_by_count":76},{"year":2019,"cited_by_count":69},{"year":2018,"cited_by_count":42},{"year":2017,"cited_by_count":28},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
