{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T00:59:19Z","timestamp":1774054759547,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,1,20]],"date-time":"2021-01-20T00:00:00Z","timestamp":1611100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Genome Canada\/Genome BC","award":["264PRO"],"award-info":[{"award-number":["264PRO"]}]},{"name":"WestGrid and Compute Canada"},{"name":"Advanced Research Computing at the University of British Columbia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present PrInCE, an R\/Bioconductor package that employs a machine-learning approach to infer protein\u2013protein interaction networks from co-fractionation mass spectrometry (CF-MS) data. Previously distributed as a collection of Matlab scripts, our ground-up rewrite of this software package in an open-source language dramatically improves runtime and memory requirements. We describe several new features in the R implementation, including a test for the detection of co-eluting protein complexes and a method for differential network analysis. PrInCE is extensively documented and fully compatible with Bioconductor classes, ensuring it can fit seamlessly into existing proteomics workflows.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PrInCE is available from Bioconductor (https:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/PrInCE.html). Source code is freely available from GitHub under the MIT license (https:\/\/github.com\/fosterlab\/PrInCE). Support is provided via the GitHub issues tracker (https:\/\/github.com\/fosterlab\/PrInCE\/issues).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab022","type":"journal-article","created":{"date-parts":[[2021,1,9]],"date-time":"2021-01-09T20:56:00Z","timestamp":1610225760000},"page":"2775-2777","source":"Crossref","is-referenced-by-count":19,"title":["PrInCE: an R\/Bioconductor package for protein\u2013protein interaction network inference from co-fractionation mass spectrometry data"],"prefix":"10.1093","volume":"37","author":[{"given":"Michael A.","family":"Skinnider","sequence":"first","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}]},{"given":"Charley","family":"Cai","sequence":"additional","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4496-8131","authenticated-orcid":false,"given":"R. Greg","family":"Stacey","sequence":"additional","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8551-4817","authenticated-orcid":false,"given":"Leonard J.","family":"Foster","sequence":"additional","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"},{"name":"Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada"}]}],"member":"286","published-online":{"date-parts":[[2021,1,20]]},"reference":[{"key":"2023051609165610400_btab022-B1","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkq1069","article-title":"RBPDB: a database of RNA-binding specificities","volume":"39","author":"Cook","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023051609165610400_btab022-B2","doi-asserted-by":"crossref","first-page":"D559","DOI":"10.1093\/nar\/gky973","article-title":"CORUM: the comprehensive resource of mammalian protein complexes\u20142019","volume":"47","author":"Giurgiu","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023051609165610400_btab022-B3","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41592-019-0461-4","article-title":"EPIC: software toolkit for elution profile-based inference of protein complexes","volume":"16","author":"Hu","year":"2019","journal-title":"Nat. Methods"},{"key":"2023051609165610400_btab022-B4","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s13059-020-02050-y","article-title":"Dynamic rewiring of the human interactome by interferon signaling","volume":"21","author":"Kerr","year":"2020","journal-title":"Genome Biol"},{"key":"2023051609165610400_btab022-B5","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/nmeth.2131","article-title":"A high-throughput approach for measuring temporal changes in the interactome","volume":"9","author":"Kristensen","year":"2012","journal-title":"Nat. Methods"},{"key":"2023051609165610400_btab022-B6","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1016\/j.celrep.2019.09.060","article-title":"Systematic discovery of endogenous human ribonucleoprotein complexes","volume":"29","author":"Mallam","year":"2019","journal-title":"Cell. Rep"},{"key":"2023051609165610400_btab022-B7","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.jprot.2014.10.024","article-title":"Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments","volume":"118","author":"Scott","year":"2015","journal-title":"J. Proteomics"},{"key":"2023051609165610400_btab022-B8","doi-asserted-by":"crossref","first-page":"906","DOI":"10.15252\/msb.20167067","article-title":"Interactome disassembly during apoptosis occurs independent of caspase cleavage","volume":"13","author":"Scott","year":"2017","journal-title":"Mol. Syst. Biol"},{"key":"2023051609165610400_btab022-B9","doi-asserted-by":"crossref","first-page":"e1006474","DOI":"10.1371\/journal.pcbi.1006474","article-title":"Genomic data integration systematically biases interactome mapping","volume":"14","author":"Skinnider","year":"2018","journal-title":"PLoS Comput. Biol"},{"key":"2023051609165610400_btab022-B10","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1186\/s12859-017-1865-8","article-title":"A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)","volume":"18","author":"Stacey","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023051609165610400_btab022-B11","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1126\/science.aan0346","article-title":"Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells","volume":"359","author":"Tan","year":"2018","journal-title":"Science"},{"key":"2023051609165610400_btab022-B12","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nature14877","article-title":"Panorama of ancient metazoan macromolecular complexes","volume":"525","author":"Wan","year":"2015","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab022\/36171273\/btab022.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/17\/2775\/50339173\/btab022.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/17\/2775\/50339173\/btab022.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T09:20:11Z","timestamp":1684228811000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/17\/2775\/6104839"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,1,20]]},"references-count":12,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2021,9,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab022","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,9,1]]},"published":{"date-parts":[[2021,1,20]]}}}