{"id":"https://openalex.org/W3011885318","doi":"https://doi.org/10.1093/bioinformatics/btaa158","title":"immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking","display_name":"immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking","publication_year":2020,"publication_date":"2020-03-06","ids":{"openalex":"https://openalex.org/W3011885318","doi":"https://doi.org/10.1093/bioinformatics/btaa158","mag":"3011885318","pmid":"https://pubmed.ncbi.nlm.nih.gov/32154832"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa158","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa158","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3594/33463940/btaa158.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","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://academic.oup.com/bioinformatics/article-pdf/36/11/3594/33463940/btaa158.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053602616","display_name":"C\u00e9dric R. Weber","orcid":"https://orcid.org/0000-0003-4802-8996"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"C\u00e9dric R Weber","raw_affiliation_strings":["Department of Biosystems Science and Engineering , ETH Z\u00fcrich, 4058 Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-4802-8996","affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering , ETH Z\u00fcrich, 4058 Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017929614","display_name":"Rahmad Akbar","orcid":"https://orcid.org/0000-0002-6692-0876"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Rahmad Akbar","raw_affiliation_strings":["Department of Immunology , University of Oslo, 0372 Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology , University of Oslo, 0372 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067719585","display_name":"Alexander Yermanos","orcid":"https://orcid.org/0000-0001-6238-0588"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Alexander Yermanos","raw_affiliation_strings":["Department of Biosystems Science and Engineering , ETH Z\u00fcrich, 4058 Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering , ETH Z\u00fcrich, 4058 Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037853098","display_name":"Milena Pavlovi\u0107","orcid":"https://orcid.org/0000-0002-2484-3868"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Milena Pavlovi\u0107","raw_affiliation_strings":["Department of Informatics , University of Oslo, 0373 Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics , University of Oslo, 0373 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031331381","display_name":"Igor Snapkov","orcid":"https://orcid.org/0000-0001-5341-685X"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Igor Snapkov","raw_affiliation_strings":["Department of Immunology , University of Oslo, 0372 Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology , University of Oslo, 0372 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054500587","display_name":"Geir Kjetil Sandve","orcid":"https://orcid.org/0000-0002-4959-1409"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Geir K Sandve","raw_affiliation_strings":["Department of Informatics , University of Oslo, 0373 Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics , University of Oslo, 0373 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072818273","display_name":"Sai T. Reddy","orcid":"https://orcid.org/0000-0002-9177-0857"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Sai T Reddy","raw_affiliation_strings":["Department of Biosystems Science and Engineering , ETH Z\u00fcrich, 4058 Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering , ETH Z\u00fcrich, 4058 Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089158926","display_name":"Victor Greiff","orcid":"https://orcid.org/0000-0003-2622-5032"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Victor Greiff","raw_affiliation_strings":["Department of Immunology , University of Oslo, 0372 Oslo, Norway"],"raw_orcid":"https://orcid.org/0000-0003-2622-5032","affiliations":[{"raw_affiliation_string":"Department of Immunology , University of Oslo, 0372 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5072818273","https://openalex.org/A5089158926"],"corresponding_institution_ids":["https://openalex.org/I184942183","https://openalex.org/I35440088"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.918,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.94753784,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"36","issue":"11","first_page":"3594","last_page":"3596"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.8863999843597412,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.8863999843597412,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.09440000355243683,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.0035000001080334187,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.9187805652618408},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.7211065292358398},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5908225178718567},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5059463381767273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26576822996139526},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.12098437547683716}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9187805652618408},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.7211065292358398},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5908225178718567},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5059463381767273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26576822996139526},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.12098437547683716},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa158","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa158","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3594/33463940/btaa158.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","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:32154832","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32154832","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:pubmedcentral.nih.gov:7334888","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7334888","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.duo.uio.no:10852/81574","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/81574","pdf_url":null,"source":{"id":"https://openalex.org/S4306401717","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa158","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa158","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3594/33463940/btaa158.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","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":[],"awards":[{"id":"https://openalex.org/G8048330624","display_name":null,"funder_award_id":"31003A_170110","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3011885318.pdf","grobid_xml":"https://content.openalex.org/works/W3011885318.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1952757896","https://openalex.org/W2040660380","https://openalex.org/W2175702062","https://openalex.org/W2605177850","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2752678066","https://openalex.org/W2766414528","https://openalex.org/W2926687552","https://openalex.org/W2951124440","https://openalex.org/W3101138461","https://openalex.org/W3102596196","https://openalex.org/W6660685664"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699"],"abstract_inverted_index":{"SUMMARY:":[0],"B-":[1],"and":[2,18,44,78,96,102,112,120,161,170,186],"T-cell":[3],"receptor":[4,59,85,92,153],"repertoires":[5,60],"of":[6,28,36,76,110,133,147],"the":[7,74,89,130,145],"adaptive":[8],"immune":[9,32,58,84,91,152],"system":[10],"have":[11],"become":[12],"a":[13,24],"key":[14,148],"target":[15],"for":[16,31,41,61,151,174],"diagnostics":[17],"therapeutics":[19],"research.":[20],"Consequently,":[21],"there":[22],"is":[23,39,127,182,193],"rapidly":[25],"growing":[26],"number":[27],"bioinformatics":[29],"tools":[30,38,150],"repertoire":[33],"analysis.":[34],"Benchmarking":[35],"such":[37,155],"crucial":[40],"ensuring":[42],"reproducible":[43],"generalizable":[45],"computational":[46,149],"analyses.":[47],"Currently,":[48],"however,":[49],"it":[50],"remains":[51],"challenging":[52],"to":[53,138],"create":[54],"standardized":[55],"ground":[56],"truth":[57],"immunoinformatics":[62],"tool":[63],"benchmarking.":[64],"Therefore,":[65],"we":[66],"developed":[67],"immuneSIM,":[68],"an":[69],"R":[70],"package":[71,181],"that":[72,136],"allows":[73],"simulation":[75,134],"native-like":[77],"aberrant":[79],"synthetic":[80],"full-length":[81],"variable":[82],"region":[83],"sequences":[86],"by":[87,129],"tuning":[88],"following":[90],"features:":[93],"(i)":[94],"species":[95],"chain":[97],"type":[98],"(BCR,":[99],"TCR,":[100],"single":[101],"paired),":[103],"(ii)":[104],"germline":[105,157],"gene":[106,158],"usage,":[107],"(iii)":[108],"occurrence":[109],"insertions":[111],"deletions,":[113],"(iv)":[114],"clonal":[115],"abundance,":[116],"(v)":[117],"somatic":[118],"hypermutation":[119],"(vi)":[121],"sequence":[122,126,164],"motifs.":[123],"Each":[124],"simulated":[125],"annotated":[128],"complete":[131],"set":[132],"events":[135],"contributed":[137],"its":[139],"in":[140],"silico":[141],"generation.":[142],"immuneSIM":[143],"permits":[144],"benchmarking":[146],"analysis,":[154],"as":[156],"annotation,":[159],"diversity":[160],"overlap":[162],"estimation,":[163],"similarity,":[165],"network":[166],"architecture,":[167],"clustering":[168],"analysis":[169],"machine":[171],"learning":[172],"methods":[173],"motif":[175],"detection.":[176],"AVAILABILITY":[177],"AND":[178],"IMPLEMENTATION:":[179],"The":[180,191],"available":[183,206],"via":[184],"https://github.com/GreiffLab/immuneSIM":[185],"on":[187],"CRAN":[188],"at":[189,195,207],"https://cran.r-project.org/web/packages/immuneSIM.":[190],"documentation":[192],"hosted":[194],"https://immuneSIM.readthedocs.io.":[196],"CONTACT:":[197],"sai.reddy@ethz.ch":[198],"or":[199],"victor.greiff@medisin.uio.no.":[200],"SUPPLEMENTARY":[201],"INFORMATION:":[202],"Supplementary":[203],"data":[204],"are":[205],"Bioinformatics":[208],"online.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":7}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
