{"id":"https://openalex.org/W4415502752","doi":"https://doi.org/10.1093/bioinformatics/btaf576","title":"Detection of PCR chimeras in adaptive immune receptor repertoire sequences","display_name":"Detection of PCR chimeras in adaptive immune receptor repertoire sequences","publication_year":2025,"publication_date":"2025-10-15","ids":{"openalex":"https://openalex.org/W4415502752","doi":"https://doi.org/10.1093/bioinformatics/btaf576","pmid":"https://pubmed.ncbi.nlm.nih.gov/41124049"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf576","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf576","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf576/64857513/btaf576.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/41/11/btaf576/64857513/btaf576.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038166269","display_name":"Mark Chernyshev","orcid":"https://orcid.org/0000-0003-1622-9240"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Mark Chernyshev","raw_affiliation_strings":["Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082810573","display_name":"Aron St\u00e5lmarck","orcid":"https://orcid.org/0000-0002-2632-6266"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Aron St\u00e5lmarck","raw_affiliation_strings":["Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024322805","display_name":"Martin Corcoran","orcid":"https://orcid.org/0000-0002-2774-0936"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Martin Corcoran","raw_affiliation_strings":["Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083386185","display_name":"Gunilla B. Karlsson Hedestam","orcid":"https://orcid.org/0000-0001-7255-9047"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Gunilla B Karlsson Hedestam","raw_affiliation_strings":["Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033401033","display_name":"Ben Murrell","orcid":"https://orcid.org/0000-0002-0393-4445"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Ben Murrell","raw_affiliation_strings":["Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm 171 77,","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Karolinska Institutet Department of Microbiology, Tumor and Cell Biology, , Stockholm, 171 77,","institution_ids":["https://openalex.org/I28166907"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038166269"],"corresponding_institution_ids":["https://openalex.org/I28166907"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7542,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76775196,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"41","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9904999732971191,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9898999929428101,"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/repertoire","display_name":"Repertoire","score":0.7050999999046326},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.567300021648407},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.48730000853538513},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.43709999322891235},{"id":"https://openalex.org/keywords/acquired-immune-system","display_name":"Acquired immune system","score":0.3337000012397766},{"id":"https://openalex.org/keywords/hemocyte","display_name":"Hemocyte","score":0.3163999915122986}],"concepts":[{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.7050999999046326},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6965000033378601},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6338000297546387},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.567300021648407},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.48730000853538513},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.43709999322891235},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3790000081062317},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34200000762939453},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.3337000012397766},{"id":"https://openalex.org/C2779625713","wikidata":"https://www.wikidata.org/wiki/Q211709","display_name":"Hemocyte","level":3,"score":0.3163999915122986},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.3077000081539154},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.29910001158714294},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.29789999127388},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.29440000653266907},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.2865999937057495},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2549000084400177}],"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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":true},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf576","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf576","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf576/64857513/btaf576.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41124049","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41124049","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:11427669","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12619642","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf576","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf576","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf576/64857513/btaf576.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1305528480","display_name":null,"funder_award_id":"NIH/NIAID","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3053346827","display_name":null,"funder_award_id":"2022-05034","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G5903061775","display_name":null,"funder_award_id":"NIAID","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6802567210","display_name":null,"funder_award_id":"R01 AI157854","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"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/W4415502752.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1973667633","https://openalex.org/W1980835154","https://openalex.org/W1993476635","https://openalex.org/W2001751895","https://openalex.org/W2010295342","https://openalex.org/W2086699924","https://openalex.org/W2097376441","https://openalex.org/W2101120467","https://openalex.org/W2106944866","https://openalex.org/W2113392525","https://openalex.org/W2122421045","https://openalex.org/W2125838338","https://openalex.org/W2148495628","https://openalex.org/W2157539385","https://openalex.org/W2174584480","https://openalex.org/W2310172832","https://openalex.org/W2520140228","https://openalex.org/W2565989705","https://openalex.org/W2762377150","https://openalex.org/W2768215828","https://openalex.org/W2894112953","https://openalex.org/W2928755087","https://openalex.org/W2939422961","https://openalex.org/W2977872441","https://openalex.org/W2984387027","https://openalex.org/W3088674399","https://openalex.org/W3111125496","https://openalex.org/W3135361699","https://openalex.org/W4321167256","https://openalex.org/W4366446600","https://openalex.org/W4401045931"],"related_works":[],"abstract_inverted_index":{"CHMMAIRRa":[0],"is":[1,9,19],"published":[2],"on":[3],"the":[4,26,31],"Julia":[5],"package":[6],"registry":[7],"and":[8,25],"available":[10,20],"at":[11,21,36],"https://github.com/MurrellGroup/CHMMAIRRa.jl":[12],"(DOI:":[13,23,38],"10.5281/zenodo.17279881).":[14],"The":[15],"core":[16],"HMM":[17],"implementation":[18],"https://github.com/MurrellGroup/CHMMera.jl":[22],"10.5281/zenodo.17279998),":[24],"scripts":[27],"used":[28],"to":[29],"generate":[30],"results":[32],"in":[33],"this":[34],"paper":[35],"https://github.com/MurrellGroup/CHMMAIRRaAnalyses":[37],"10.5281/zenodo.17281446).":[39]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-24T00:00:00"}
