{"id":"https://openalex.org/W2132983397","doi":"https://doi.org/10.1093/bioinformatics/btu523","title":"Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence","display_name":"Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence","publication_year":2014,"publication_date":"2014-08-05","ids":{"openalex":"https://openalex.org/W2132983397","doi":"https://doi.org/10.1093/bioinformatics/btu523","mag":"2132983397","pmid":"https://pubmed.ncbi.nlm.nih.gov/25095879"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu523","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu523","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":"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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btu523","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039325097","display_name":"Niclas Thomas","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Niclas Thomas","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062299077","display_name":"Katharine Best","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Katharine Best","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010777346","display_name":"Mattia Cinelli","orcid":"https://orcid.org/0000-0001-9306-8079"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Mattia Cinelli","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073973652","display_name":"Shlomit Reich-Zeliger","orcid":"https://orcid.org/0000-0002-7029-8151"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Shlomit Reich-Zeliger","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044928987","display_name":"Hilah Gal","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Hilah Gal","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060786300","display_name":"Eric Shifrut","orcid":"https://orcid.org/0000-0001-6827-0128"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Eric Shifrut","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086398539","display_name":"Asaf Madi","orcid":"https://orcid.org/0000-0003-3441-3228"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Asaf Madi","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101925767","display_name":"Nir Friedman","orcid":"https://orcid.org/0000-0002-1078-3921"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Nir Friedman","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047980012","display_name":"John Shawe\u2010Taylor","orcid":"https://orcid.org/0000-0002-2030-0073"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"John Shawe-Taylor","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038209629","display_name":"Benny Chain","orcid":"https://orcid.org/0000-0002-7417-3970"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Benny Chain","raw_affiliation_strings":["1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UCL CoMPLEX, 2 UCL Division of Infection and Immunity, London WC1 6BT, UK, 3 Weizmann Institute of Science, Rehovot 76000, Israel and 4 UCL Computer Science, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I53964585","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":2623,"currency":"EUR","value_usd":2828},"fwci":3.7038,"has_fulltext":false,"cited_by_count":121,"citation_normalized_percentile":{"value":0.94051434,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"30","issue":"22","first_page":"3181","last_page":"3188"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9620000123977661,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9620000123977661,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.012000000104308128,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.008299999870359898,"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/repertoire","display_name":"Repertoire","score":0.8560298681259155},{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.8388549089431763},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7515007257461548},{"id":"https://openalex.org/keywords/complementarity-determining-region","display_name":"Complementarity determining region","score":0.7171241044998169},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.6480562090873718},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.46755707263946533},{"id":"https://openalex.org/keywords/antibody-repertoire","display_name":"Antibody Repertoire","score":0.4484376013278961},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3912287652492523},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38467082381248474},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.3622821569442749},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.31754177808761597},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.31563711166381836},{"id":"https://openalex.org/keywords/immunoglobulin-light-chain","display_name":"Immunoglobulin light chain","score":0.20719200372695923}],"concepts":[{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.8560298681259155},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.8388549089431763},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7515007257461548},{"id":"https://openalex.org/C85630698","wikidata":"https://www.wikidata.org/wiki/Q3826179","display_name":"Complementarity determining region","level":4,"score":0.7171241044998169},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.6480562090873718},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.46755707263946533},{"id":"https://openalex.org/C2910693471","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody Repertoire","level":3,"score":0.4484376013278961},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3912287652492523},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38467082381248474},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3622821569442749},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.31754177808761597},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.31563711166381836},{"id":"https://openalex.org/C36394416","wikidata":"https://www.wikidata.org/wiki/Q949267","display_name":"Immunoglobulin light chain","level":3,"score":0.20719200372695923},{"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007114","descriptor_name":"Immunization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007114","descriptor_name":"Immunization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007114","descriptor_name":"Immunization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007114","descriptor_name":"Immunization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","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":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btu523","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu523","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":"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:25095879","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25095879","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:eprints.ucl.ac.uk.OAI2:1443235","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1443235/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   Bioinformatics , 30  (22)   3181 - 3188.   (2014)      ","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:3195239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4221123","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu523","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu523","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":"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":[{"display_name":"Partnerships for the goals","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2107972360","display_name":null,"funder_award_id":"MR/K006584/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320308943","display_name":"Microsoft Research","ror":"https://ror.org/00d0nc645"},{"id":"https://openalex.org/F4320315026","display_name":"Weizmann UK","ror":null},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W29164706","https://openalex.org/W1489575091","https://openalex.org/W1563088657","https://openalex.org/W1625255723","https://openalex.org/W1967195968","https://openalex.org/W1976445111","https://openalex.org/W1978391087","https://openalex.org/W2000483236","https://openalex.org/W2014040859","https://openalex.org/W2014161666","https://openalex.org/W2021158172","https://openalex.org/W2021945571","https://openalex.org/W2022824615","https://openalex.org/W2023038954","https://openalex.org/W2035521005","https://openalex.org/W2035866208","https://openalex.org/W2043071551","https://openalex.org/W2051947926","https://openalex.org/W2061720803","https://openalex.org/W2068983684","https://openalex.org/W2073078847","https://openalex.org/W2073355552","https://openalex.org/W2091142825","https://openalex.org/W2099367604","https://openalex.org/W2105195133","https://openalex.org/W2107425660","https://openalex.org/W2107535503","https://openalex.org/W2108147510","https://openalex.org/W2109839728","https://openalex.org/W2118852930","https://openalex.org/W2123151433","https://openalex.org/W2124386111","https://openalex.org/W2132742682","https://openalex.org/W2143513209","https://openalex.org/W2146074801","https://openalex.org/W2149684865","https://openalex.org/W2164989695","https://openalex.org/W4211183651","https://openalex.org/W4285719527","https://openalex.org/W6636494156","https://openalex.org/W6676236601"],"related_works":["https://openalex.org/W2060496539","https://openalex.org/W4280506224","https://openalex.org/W2018330851","https://openalex.org/W3201606428","https://openalex.org/W3087255036","https://openalex.org/W2581256546","https://openalex.org/W2143290387","https://openalex.org/W2074913234","https://openalex.org/W2055138174","https://openalex.org/W2089637072"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,173,280],"clonal":[2],"theory":[3],"of":[4,18,30,41,56,84,94,121,124,131,144,157,161,178,190,203,225,257],"adaptive":[5],"immunity":[6],"proposes":[7],"that":[8,63,80,189],"immunological":[9],"responses":[10],"are":[11,303],"encoded":[12],"by":[13,106,117,254],"increases":[14],"in":[15,35,230,241,284,294],"the":[16,28,57,92,103,112,119,135,201,215,222,226,237,247,261],"frequency":[17,29,120],"lymphocytes":[19],"carrying":[20],"antigen-specific":[21],"receptors.":[22],"In":[23],"this":[24,109],"study,":[25],"we":[26],"measure":[27],"different":[31,122,145,159,187],"T-cell":[32,97,238],"receptors":[33],"(TcR)":[34],"CD4":[36,95,174],"+":[37,96,175],"T":[38],"cell":[39],"populations":[40],"mice":[42,169,179,192,204,213,244],"immunized":[43,166],"with":[44,170],"a":[45,270],"complex":[46],"antigen,":[47],"killed":[48],"Mycobacterium":[49],"tuberculosis,":[50],"using":[51],"high":[52],"throughput":[53],"parallel":[54],"sequencing":[55],"TcR\u03b2":[58],"chain.":[59],"Our":[60,219],"initial":[61],"hypothesis":[62],"immunization":[64,107],"would":[65],"induce":[66],"repertoire":[67,143],"convergence":[68],"proved":[69],"to":[70,236,246,273],"be":[71,292],"incorrect,":[72],"and":[73,87,151,167,181,214,268,286,288],"therefore":[74],"an":[75],"alternative":[76],"approach":[77,272],"was":[78,282],"developed":[79],"allows":[81],"accurate":[82],"stratification":[83],"TcR":[85,176,227,266,274],"repertoires":[86,177,202],"provides":[88],"novel":[89],"insights":[90],"into":[91],"nature":[93],"receptor":[98],"recognition.":[99],"RESULTS:":[100],"To":[101],"track":[102],"changes":[104],"induced":[105],"within":[108,134,260],"heterogeneous":[110],"repertoire,":[111,228],"sequence":[113,162,275],"data":[114,302],"were":[115,185,194,208],"classified":[116],"counting":[118],"clusters":[123,163],"short":[125,255],"(3":[126],"or":[127],"4)":[128],"continuous":[129],"stretches":[130,256],"amino":[132,258],"acids":[133,259],"antigen":[136],"binding":[137],"complementarity":[138],"determining":[139],"region":[140,263],"3":[141],"(CDR3)":[142],"mice.":[146],"Both":[147],"unsupervised":[148],"(hierarchical":[149],"clustering)":[150],"supervised":[152],"(support":[153],"vector":[154],"machine)":[155],"analyses":[156],"these":[158],"distributions":[160],"differentiated":[164],"between":[165],"unimmunized":[168,191],"100%":[171],"efficiency.":[172],"5":[180],"14":[182],"days":[183,206],"postimmunization":[184,207],"clearly":[186],"from":[188,197,211],"but":[193],"not":[195],"distinguishable":[196],"each":[198],"other.":[199],"However,":[200,250],"60":[205],"distinct":[209],"both":[210],"naive":[212],"day":[216],"5/14":[217],"animals.":[218],"results":[220],"reinforce":[221],"remarkable":[223],"diversity":[224],"resulting":[229],"many":[231],"diverse":[232],"private":[233],"TcRs":[234],"contributing":[235],"response":[239],"even":[240],"genetically":[242],"identical":[243],"responding":[245],"same":[248],"antigen.":[249],"specific":[251],"motifs":[252],"defined":[253],"CDR3":[262],"may":[264],"determine":[265],"specificity":[267],"define":[269],"new":[271],"classification.":[276],"AVAILABILITY":[277],"AND":[278],"IMPLEMENTATION:":[279],"analysis":[281],"implemented":[283],"R":[285],"Python,":[287],"source":[289],"code":[290],"can":[291],"found":[293],"Supplementary":[295,301],"Data.":[296],"CONTACT:":[297],"b.chain@ucl.ac.uk":[298],"SUPPLEMENTARY":[299],"INFORMATION:":[300],"available":[304],"at":[305],"Bioinformatics":[306],"online.":[307]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":18},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":10}],"updated_date":"2026-07-11T18:08:03.149640","created_date":"2025-10-10T00:00:00"}