{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T21:07:01Z","timestamp":1776373621551,"version":"3.51.2"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T00:00:00Z","timestamp":1720224000000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["2238125"],"award-info":[{"award-number":["2238125"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["NIH R01 HG 009299-6A1"],"award-info":[{"award-number":["NIH R01 HG 009299-6A1"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["NIH R01 EY 030546-01A1"],"award-info":[{"award-number":["NIH R01 EY 030546-01A1"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DARPA W911NF-23-2-0023"],"award-info":[{"award-number":["DARPA W911NF-23-2-0023"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Computational cell-type deconvolution is an important analytic technique for modeling the compositional heterogeneity of bulk gene expression data. A conceptually new Bayesian approach to this problem, BayesPrism, has recently been proposed and has subsequently been shown to be superior in accuracy and robustness against model misspecifications by independent studies; however, given that BayesPrism relies on Gibbs sampling, it is orders of magnitude more computationally expensive than standard approaches. Here, we introduce the InstaPrism package which re-implements BayesPrism in a derandomized framework by replacing the time-consuming Gibbs sampling step with a fixed-point algorithm. We demonstrate that the new algorithm is effectively equivalent to BayesPrism while providing a considerable speed and memory advantage. Furthermore, the InstaPrism package is equipped with a precompiled, curated set of references tailored for a variety of cancer types, streamlining the deconvolution process.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The package InstaPrism is freely available at: https:\/\/github.com\/humengying0907\/InstaPrism. The source code and evaluation pipeline used in this paper can be found at: https:\/\/github.com\/humengying0907\/InstaPrismSourceCode.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae440","type":"journal-article","created":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T08:03:55Z","timestamp":1720253035000},"source":"Crossref","is-referenced-by-count":18,"title":["InstaPrism: an R package for fast implementation of BayesPrism"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4827-3051","authenticated-orcid":false,"given":"Mengying","family":"Hu","sequence":"first","affiliation":[{"name":"Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, 15260, United States"},{"name":"Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh , Pittsburgh, 15260, United States"}]},{"given":"Maria","family":"Chikina","sequence":"additional","affiliation":[{"name":"Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, 15260, United States"},{"name":"Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh , Pittsburgh, 15260, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,7,5]]},"reference":[{"key":"2024071222004931400_btae440-B1","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s43018-022-00356-3","article-title":"Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology","volume":"3","author":"Chu","year":"2022","journal-title":"Nat Cancer"},{"key":"2024071222004931400_btae440-B2","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/s41592-023-02166-6","article-title":"Challenges and perspectives in computational deconvolution of genomics data","volume":"21","author":"Garmire","year":"2024","journal-title":"Nat Methods"},{"key":"2024071222004931400_btae440-B3","doi-asserted-by":"crossref","first-page":"625783","DOI":"10.3389\/fimmu.2021.625783","article-title":"The impact of Tregs on the anticancer immunity and the efficacy of immune checkpoint inhibitor therapies","volume":"12","author":"Gonz\u00e1lez-Navajas","year":"2021","journal-title":"Front Immunol"},{"key":"2024071222004931400_btae440-B4","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-023-03077-7","article-title":"Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors","volume":"24","author":"Hippen","year":"2023","journal-title":"Genome Biol"},{"key":"2024071222004931400_btae440-B5","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1186\/s13059-024-03292-w","article-title":"Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods","volume":"25","author":"Hu","year":"2024","journal-title":"Genome Biol"},{"key":"2024071222004931400_btae440-B6","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1016\/j.ccell.2022.11.001","article-title":"Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer","volume":"40","author":"Li","year":"2022","journal-title":"Cancer Cell"},{"key":"2024071222004931400_btae440-B7","doi-asserted-by":"crossref","first-page":"4734","DOI":"10.1016\/j.cell.2021.08.003","article-title":"Spatially organized multicellular immune hubs in human colorectal cancer","volume":"184","author":"Pelka","year":"2021","journal-title":"Cell"},{"key":"2024071222004931400_btae440-B8","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/s41416-020-01048-4","article-title":"Cytotoxic CD8+ t cells in cancer and cancer immunotherapy","volume":"124","author":"Raskov","year":"2021","journal-title":"Br J Cancer"},{"key":"2024071222004931400_btae440-B9","author":"Ruiz-Moreno","year":"2022"},{"key":"2024071222004931400_btae440-B10","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"Tirosh","year":"2016","journal-title":"Science (New York, NY)"},{"key":"2024071222004931400_btae440-B11","doi-asserted-by":"crossref","first-page":"5758","DOI":"10.1038\/s41467-023-41385-5","article-title":"Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures","volume":"14","author":"Tran","year":"2023","journal-title":"Nat Commun"},{"key":"2024071222004931400_btae440-B12","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1038\/s41586-022-05496-1","article-title":"Ovarian cancer mutational processes drive site-specific immune evasion","volume":"612","author":"V\u00e1zquez-Garc\u00eda","year":"2022","journal-title":"Nature"},{"key":"2024071222004931400_btae440-B13","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1038\/s41588-021-00911-1","article-title":"A single-cell and spatially resolved atlas of human breast cancers","volume":"53","author":"Wu","year":"2021","journal-title":"Nat Genet"},{"key":"2024071222004931400_btae440-B14","doi-asserted-by":"crossref","first-page":"eabd9738","DOI":"10.1126\/sciadv.abd9738","article-title":"Decoding the multicellular ecosystem of lung adenocarcinoma manifested as pulmonary subsolid nodules by single-cell RNA sequencing","volume":"7","author":"Xing","year":"2021","journal-title":"Sci Adv"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae440\/58459030\/btae440.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/7\/btae440\/58531203\/btae440.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/7\/btae440\/58531203\/btae440.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T22:15:45Z","timestamp":1720822545000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae440\/7708397"}},"subtitle":[],"editor":[{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,7,1]]},"references-count":14,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae440","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7]]},"published":{"date-parts":[[2024,7,1]]},"article-number":"btae440"}}