{"id":"https://openalex.org/W2109911015","doi":"https://doi.org/10.1093/bioinformatics/btv238","title":"IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis","display_name":"IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis","publication_year":2015,"publication_date":"2015-06-10","ids":{"openalex":"https://openalex.org/W2109911015","doi":"https://doi.org/10.1093/bioinformatics/btv238","mag":"2109911015","pmid":"https://pubmed.ncbi.nlm.nih.gov/26072509"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv238","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i53/49014157/bioinformatics_31_12_i53.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bioinformatics/article-pdf/31/12/i53/49014157/bioinformatics_31_12_i53.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005373810","display_name":"Yana Safonova","orcid":"https://orcid.org/0000-0002-9634-4216"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Yana Safonova","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076759120","display_name":"Stefano Bonissone","orcid":"https://orcid.org/0000-0003-2633-3500"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Stefano Bonissone","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043212346","display_name":"Eugene Kurpilyansky","orcid":null},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Eugene Kurpilyansky","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014082336","display_name":"Ekaterina V. Starostina","orcid":"https://orcid.org/0000-0002-1733-9524"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Ekaterina Starostina","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025927694","display_name":"Alla Lapidus","orcid":"https://orcid.org/0000-0003-0427-8731"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Alla Lapidus","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112051548","display_name":"Jeremy Stinson","orcid":null},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Jeremy Stinson","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011423053","display_name":"Laura DePalatis","orcid":null},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Laura DePalatis","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006272129","display_name":"Wendy Sandoval","orcid":"https://orcid.org/0000-0002-4672-0762"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Wendy Sandoval","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069238387","display_name":"Jennie R. Lill","orcid":"https://orcid.org/0000-0002-7142-253X"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Jennie Lill","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027480961","display_name":"Pavel A. Pevzner","orcid":"https://orcid.org/0000-0002-0418-165X"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Pavel A. Pevzner","raw_affiliation_strings":["1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, 2Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, 3Bioinformatics Program, University of California, San Diego, CA, USA, 4Genentech, South San Francisco, CA, USA and 5Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027480961"],"corresponding_institution_ids":["https://openalex.org/I172901346","https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.3824,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.96066275,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"31","issue":"12","first_page":"i53","last_page":"i61"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.8219000101089478,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.8219000101089478,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.07020000368356705,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.045499999076128006,"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/computer-science","display_name":"Computer science","score":0.6551873683929443},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6121174097061157},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6038990020751953},{"id":"https://openalex.org/keywords/antibody-repertoire","display_name":"Antibody Repertoire","score":0.5841993689537048},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5550800561904907},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5402123928070068},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.4436929523944855},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.43760427832603455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33120930194854736},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23937660455703735},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19335538148880005}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6551873683929443},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6121174097061157},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6038990020751953},{"id":"https://openalex.org/C2910693471","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody Repertoire","level":3,"score":0.5841993689537048},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5550800561904907},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5402123928070068},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.4436929523944855},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.43760427832603455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33120930194854736},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23937660455703735},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19335538148880005},{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv238","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i53/49014157/bioinformatics_31_12_i53.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26072509","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26072509","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:europepmc.org:3519937","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4542777","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/12/i53","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/12/i53","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv238","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i53/49014157/bioinformatics_31_12_i53.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2393961018","display_name":null,"funder_award_id":"5P41GM103484","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G440499006","display_name":null,"funder_award_id":"14\u201050\u201000069","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"},{"id":"https://openalex.org/G6853156662","display_name":null,"funder_award_id":"P41GM103484","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7131804313","display_name":null,"funder_award_id":"14-50-","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320309432","display_name":"F. Hoffmann-La Roche","ror":"https://ror.org/00by1q217"},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109911015.pdf","grobid_xml":"https://content.openalex.org/works/W2109911015.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W321911115","https://openalex.org/W1546874952","https://openalex.org/W1565321014","https://openalex.org/W1968091806","https://openalex.org/W1978391087","https://openalex.org/W1989223689","https://openalex.org/W1993928780","https://openalex.org/W1996995255","https://openalex.org/W2006759360","https://openalex.org/W2009518556","https://openalex.org/W2011039300","https://openalex.org/W2013903972","https://openalex.org/W2022824615","https://openalex.org/W2026433130","https://openalex.org/W2027566319","https://openalex.org/W2028673251","https://openalex.org/W2029525307","https://openalex.org/W2040135401","https://openalex.org/W2043071551","https://openalex.org/W2043828494","https://openalex.org/W2049886753","https://openalex.org/W2050139272","https://openalex.org/W2051241958","https://openalex.org/W2051541780","https://openalex.org/W2070232376","https://openalex.org/W2075013491","https://openalex.org/W2079405439","https://openalex.org/W2086119402","https://openalex.org/W2090647436","https://openalex.org/W2097816699","https://openalex.org/W2099314206","https://openalex.org/W2099391799","https://openalex.org/W2101637028","https://openalex.org/W2105273832","https://openalex.org/W2111098506","https://openalex.org/W2117713095","https://openalex.org/W2118290743","https://openalex.org/W2120902911","https://openalex.org/W2127143454","https://openalex.org/W2129718327","https://openalex.org/W2133956160","https://openalex.org/W2136651963","https://openalex.org/W2138067488","https://openalex.org/W2148495628","https://openalex.org/W2160265768","https://openalex.org/W2160578795","https://openalex.org/W2160770624","https://openalex.org/W2161248563","https://openalex.org/W2165567657","https://openalex.org/W2346974685","https://openalex.org/W2611831635","https://openalex.org/W6632844827","https://openalex.org/W6668370225","https://openalex.org/W6672082448"],"related_works":["https://openalex.org/W2581256546","https://openalex.org/W2074913234","https://openalex.org/W2729870279","https://openalex.org/W2055138174","https://openalex.org/W2053091829","https://openalex.org/W124590862","https://openalex.org/W2616207459","https://openalex.org/W4323236833","https://openalex.org/W2558727788","https://openalex.org/W2780245662"],"abstract_inverted_index":{"UNLABELLED:":[0],"The":[1,21,154],"analysis":[2,27],"of":[3,5,28,69,103,120],"concentrations":[4],"circulating":[6,72],"antibodies":[7,44,73],"in":[8,19,49],"serum":[9],"(antibody":[10],"repertoire)":[11],"is":[12,74,137,157],"a":[13,81,97,104,144],"fundamental,":[14],"yet":[15],"poorly":[16],"studied,":[17],"problem":[18],"immunoinformatics.":[20],"two":[22],"current":[23],"approaches":[24],"to":[25,127],"the":[26,50,62,67,88,107,114,129],"antibody":[29,131],"repertoires":[30],"[next":[31],"generation":[32],"sequencing":[33],"(NGS)":[34],"and":[35,59,95,123,140,146],"mass":[36,125],"spectrometry":[37],"(MS)]":[38],"present":[39,113],"difficult":[40],"computational":[41],"challenges":[42],"since":[43],"are":[45,53,93,167],"not":[46],"directly":[47],"encoded":[48],"germline":[51],"but":[52],"extensively":[54],"diversified":[55],"by":[56,91,106],"somatic":[57],"recombination":[58],"hypermutations.":[60],"Therefore,":[61],"protein":[63],"database":[64,82],"required":[65],"for":[66,76],"interpretation":[68],"spectra":[70,126],"from":[71,159],"custom":[75],"each":[77],"individual.":[78],"Although":[79],"such":[80],"can":[83],"be":[84],"constructed":[85,130],"via":[86],"NGS,":[87],"reads":[89,122],"generated":[90],"NGS":[92],"error-prone":[94],"even":[96],"single":[98],"nucleotide":[99],"error":[100],"precludes":[101],"identification":[102],"peptide":[105],"standard":[108],"proteomics":[109],"tools.":[110],"Here,":[111],"we":[112],"IgRepertoireConstructor":[115,136],"algorithm":[116],"that":[117],"performs":[118],"error-correction":[119],"immunosequencing":[121],"uses":[124],"validate":[128],"repertoires.":[132],"AVAILABILITY":[133],"AND":[134],"IMPLEMENTATION:":[135],"open":[138],"source":[139,155],"freely":[141],"available":[142,158,168],"as":[143],"C++":[145],"Python":[147],"program":[148],"running":[149],"on":[150],"all":[151],"Unix-compatible":[152],"platforms.":[153],"code":[156],"http://bioinf.spbau.ru/igtools.":[160],"CONTACT:":[161],"ppevzner@ucsd.edu":[162],"SUPPLEMENTARY":[163],"INFORMATION:":[164],"Supplementary":[165],"data":[166],"at":[169],"Bioinformatics":[170],"online.":[171]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":8}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
