{"id":"https://openalex.org/W4396981066","doi":"https://doi.org/10.1093/bib/bbae221","title":"Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data","display_name":"Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data","publication_year":2024,"publication_date":"2024-03-27","ids":{"openalex":"https://openalex.org/W4396981066","doi":"https://doi.org/10.1093/bib/bbae221","pmid":"https://pubmed.ncbi.nlm.nih.gov/38752856"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae221","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae221/57678713/bbae221.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae221/57678713/bbae221.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053964003","display_name":"Ayelet Peres","orcid":"https://orcid.org/0000-0002-0188-7315"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ayelet Peres","raw_affiliation_strings":["Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]},{"raw_affiliation_string":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109717181","display_name":"Vered Klein","orcid":"https://orcid.org/0009-0002-4289-4017"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Vered Klein","raw_affiliation_strings":["Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]},{"raw_affiliation_string":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008093768","display_name":"Boaz Frankel","orcid":null},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Boaz Frankel","raw_affiliation_strings":["Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]},{"raw_affiliation_string":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001972889","display_name":"William Lees","orcid":"https://orcid.org/0000-0001-9834-6840"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I4210166615","display_name":"INESC TEC","ror":"https://ror.org/05fa8ka61","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590","https://openalex.org/I4210166615"]},{"id":"https://openalex.org/I98259816","display_name":"Birkbeck, University of London","ror":"https://ror.org/02mb95055","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}],"countries":["GB","PT"],"is_corresponding":false,"raw_author_name":"William Lees","raw_affiliation_strings":["INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal","Institute of Structural and Molecular Biology, Birkbeck College , University of London, London , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal","institution_ids":["https://openalex.org/I4210166615"]},{"raw_affiliation_string":"Institute of Structural and Molecular Biology, Birkbeck College , University of London, London , United Kingdom","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I98259816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046033939","display_name":"Pazit Polak","orcid":"https://orcid.org/0000-0001-8363-0734"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Pazit Polak","raw_affiliation_strings":["Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]},{"raw_affiliation_string":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098670374","display_name":"Mark Meehan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210166615","display_name":"INESC TEC","ror":"https://ror.org/05fa8ka61","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590","https://openalex.org/I4210166615"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Mark Meehan","raw_affiliation_strings":["INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal","institution_ids":["https://openalex.org/I4210166615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089030744","display_name":"Artur Rocha","orcid":"https://orcid.org/0000-0002-5637-1041"},"institutions":[{"id":"https://openalex.org/I4210166615","display_name":"INESC TEC","ror":"https://ror.org/05fa8ka61","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590","https://openalex.org/I4210166615"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Artur Rocha","raw_affiliation_strings":["INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal","institution_ids":["https://openalex.org/I4210166615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059381700","display_name":"Jo\u00e3o Correia Lopes","orcid":"https://orcid.org/0000-0002-9040-0889"},"institutions":[{"id":"https://openalex.org/I4210166615","display_name":"INESC TEC","ror":"https://ror.org/05fa8ka61","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590","https://openalex.org/I4210166615"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o Correia Lopes","raw_affiliation_strings":["INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC TEC \u2013 Institute for Systems and Computer Engineering, Technology and Science Porto , Portugal","institution_ids":["https://openalex.org/I4210166615"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084475280","display_name":"Gur Yaari","orcid":"https://orcid.org/0000-0001-9311-9884"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Gur Yaari","raw_affiliation_strings":["Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]},{"raw_affiliation_string":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan , Israel","institution_ids":["https://openalex.org/I13955877"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.1524,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.76353026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"25","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"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":0.9990000128746033,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9815999865531921,"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/repertoire","display_name":"Repertoire","score":0.7577621936798096},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5943402051925659},{"id":"https://openalex.org/keywords/acquired-immune-system","display_name":"Acquired immune system","score":0.4541170597076416},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.44810572266578674},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4386039078235626},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.410377562046051},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32896190881729126},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.15742847323417664},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1567876636981964},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11529278755187988}],"concepts":[{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.7577621936798096},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5943402051925659},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.4541170597076416},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.44810572266578674},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4386039078235626},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.410377562046051},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32896190881729126},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.15742847323417664},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1567876636981964},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11529278755187988},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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}],"mesh":[{"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056704","descriptor_name":"Adaptive Immunity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae221","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae221/57678713/bbae221.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38752856","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38752856","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11097599","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11097599","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11097599/pdf/bbae221.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae221","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae221/57678713/bbae221.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G11755292","display_name":null,"funder_award_id":"U24AI177622","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G233522572","display_name":null,"funder_award_id":"2940/21","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"},{"id":"https://openalex.org/G3049837784","display_name":null,"funder_award_id":"U24 AI177622","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4439859712","display_name":null,"funder_award_id":"2940/21","funder_id":"https://openalex.org/F4320313643","funder_display_name":"Iowa Science Foundation"},{"id":"https://openalex.org/G5493932354","display_name":"ARCHITECTURE AND TOOLS FOR THE QUERY OF ANTIBODY AND T-CELL RECEPTOR SEQUENCING DATA REPOSITORIES FOR ENABLING IMPROVED PERSONALIZED MEDICINE AND IMMUNOTHERAPY","funder_award_id":"825821","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320313643","display_name":"Iowa Science Foundation","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396981066.pdf"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1802312377","https://openalex.org/W2008985174","https://openalex.org/W2013903972","https://openalex.org/W2022406334","https://openalex.org/W2029525307","https://openalex.org/W2036318837","https://openalex.org/W2089041106","https://openalex.org/W2096525273","https://openalex.org/W2097816699","https://openalex.org/W2110417468","https://openalex.org/W2113392525","https://openalex.org/W2120358246","https://openalex.org/W2125604001","https://openalex.org/W2151558930","https://openalex.org/W2170654913","https://openalex.org/W2175702062","https://openalex.org/W2296335794","https://openalex.org/W2302501749","https://openalex.org/W2565989705","https://openalex.org/W2605897695","https://openalex.org/W2607211817","https://openalex.org/W2613409207","https://openalex.org/W2766414528","https://openalex.org/W2768618120","https://openalex.org/W2808144819","https://openalex.org/W2810419619","https://openalex.org/W2811364409","https://openalex.org/W2893410333","https://openalex.org/W2905884391","https://openalex.org/W2912715963","https://openalex.org/W2917207851","https://openalex.org/W2977872441","https://openalex.org/W2979982423","https://openalex.org/W3016669560","https://openalex.org/W3111287171","https://openalex.org/W3115714399","https://openalex.org/W3132826558","https://openalex.org/W3200776886","https://openalex.org/W3206187363","https://openalex.org/W3211434666","https://openalex.org/W4214827908","https://openalex.org/W4245543257","https://openalex.org/W4249802798","https://openalex.org/W4311825851","https://openalex.org/W4321376551","https://openalex.org/W4366427880","https://openalex.org/W4385620513","https://openalex.org/W4386391214","https://openalex.org/W4391689453","https://openalex.org/W6677946334","https://openalex.org/W6697144307"],"related_works":["https://openalex.org/W2486559672","https://openalex.org/W2496337048","https://openalex.org/W2949171194","https://openalex.org/W4386773231","https://openalex.org/W2981095100","https://openalex.org/W4211175172","https://openalex.org/W4293119383","https://openalex.org/W3196885069","https://openalex.org/W4213165391","https://openalex.org/W2177192300"],"abstract_inverted_index":{"Enhancing":[0],"the":[1,72,97,101],"reproducibility":[2],"and":[3,28,53,62,71,94,115,127],"comprehension":[4],"of":[5,31,67],"adaptive":[6],"immune":[7],"receptor":[8],"repertoire":[9],"sequencing":[10],"(AIRR-seq)":[11],"data":[12,26,86,119],"analysis":[13,69,87],"is":[14,56,88,108],"critical":[15],"for":[16,23,50,125],"scientific":[17],"progress.":[18],"This":[19,55,110],"study":[20],"presents":[21],"guidelines":[22,98],"reproducible":[24],"AIRR-seq":[25,85,118],"analysis,":[27,120],"a":[29,47,123],"collection":[30],"ready-to-use":[32],"pipelines":[33,42,130],"with":[34],"comprehensive":[35],"documentation.":[36],"To":[37],"this":[38],"end,":[39],"ten":[40],"common":[41],"were":[43],"implemented":[44],"using":[45,96],"ViaFoundry,":[46],"user-friendly":[48],"interface":[49],"pipeline":[51,76],"management":[52],"automation.":[54],"accompanied":[57],"by":[58],"versioned":[59],"containers,":[60],"documentation":[61],"archiving":[63],"capabilities.":[64],"The":[65],"automation":[66],"pre-processing":[68],"steps":[70],"ability":[73,102],"to":[74,79,91,103],"modify":[75],"parameters":[77,93],"according":[78],"specific":[80],"research":[81,133],"needs":[82],"are":[83],"emphasized.":[84],"highly":[89],"sensitive":[90],"varying":[92],"setups;":[95],"presented":[99],"here,":[100],"reproduce":[104],"previously":[105],"published":[106],"results":[107],"demonstrated.":[109],"work":[111],"promotes":[112],"transparency,":[113],"reproducibility,":[114],"collaboration":[116],"in":[117,131],"serving":[121],"as":[122],"model":[124],"handling":[126],"documenting":[128],"bioinformatics":[129],"other":[132],"domains.":[134]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
