{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:41:41Z","timestamp":1753875701256,"version":"3.41.2"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T00:00:00Z","timestamp":1697068800000},"content-version":"vor","delay-in-days":20,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transcriptome sequencing has become common in cancer research, resulting in the generation of a substantial volume of RNA sequencing (RNA-Seq) data. The ability to extract immune repertoires from these data is crucial for obtaining information on infiltrating T- and B-lymphocyte clones when dedicated amplicon T-cell\/B-cell receptors sequencing (TCR-Seq\/BCR-Seq) methods are unavailable. In response to this demand, several dedicated computational methods have been developed, including MiXCR, TRUST and ImRep. In the recent publication in Briefings in Bioinformatics, Peng et\u00a0al. have conducted an intensive, systematic comparison of the three previously mentioned tools. Although their effort is commendable, we do have a few constructive critiques regarding technical elements of their analysis.<\/jats:p>","DOI":"10.1093\/bib\/bbad354","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T18:41:16Z","timestamp":1697136076000},"source":"Crossref","is-referenced-by-count":0,"title":["Comment on \u2018rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing\u2019"],"prefix":"10.1093","volume":"24","author":[{"given":"Alexey N","family":"Davydov","sequence":"first","affiliation":[{"name":"MiLaboratories Inc , San Francisco, CA , USA"},{"name":"Central European Institute of Technology , Brno , Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry A","family":"Bolotin","sequence":"additional","affiliation":[{"name":"MiLaboratories Inc , San Francisco, CA , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stanislav V","family":"Poslavsky","sequence":"additional","affiliation":[{"name":"MiLaboratories Inc , San Francisco, CA , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry M","family":"Chudakov","sequence":"additional","affiliation":[{"name":"MiLaboratories Inc , San Francisco, CA , USA"},{"name":"Central European Institute of Technology , Brno , Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,10,11]]},"reference":[{"key":"2023101218410052600_ref1","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbad220","article-title":"Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing","volume":"24","author":"Peng","year":"2023","journal-title":"Brief Bioinform"},{"key":"2023101218410052600_ref2","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/ng.3581","article-title":"Landscape of tumor-infiltrating T cell repertoire of human cancers","volume":"48","author":"Li","year":"2016","journal-title":"Nat Genet"},{"key":"2023101218410052600_ref3","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1038\/s41588-018-0339-x","article-title":"Landscape of B cell immunity and related immune evasion in human cancers","volume":"51","author":"Hu","year":"2019","journal-title":"Nat Genet"},{"key":"2023101218410052600_ref4","doi-asserted-by":"crossref","first-page":"3126","DOI":"10.1038\/s41467-020-16857-7","article-title":"Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing","volume":"11","author":"Mandric","year":"2020","journal-title":"Nat Commun"},{"key":"2023101218410052600_ref5","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat Methods"},{"key":"2023101218410052600_ref6","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1038\/nbt.4296","article-title":"Reply to \"evaluation of immune repertoire inference methods from RNA-seq data\"","volume":"36","author":"Bolotin","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2023101218410052600_ref7","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/nbt.3979","article-title":"Antigen receptor repertoire profiling from RNA-seq data","volume":"35","author":"Bolotin","year":"2017","journal-title":"Nat Biotechnol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/6\/bbad354\/52011658\/bbad354.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/6\/bbad354\/52011658\/bbad354.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T18:41:21Z","timestamp":1697136081000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad354\/7306821"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,22]]},"references-count":7,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,9,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad354","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2023,11,1]]},"published":{"date-parts":[[2023,9,22]]},"article-number":"bbad354"}}