{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T12:00:01Z","timestamp":1722686401312},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2706,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question \u2018is this probe\/region altered?\u2019 RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found.<\/jats:p>\n               <jats:p>Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http:\/\/cran.r-project.org\/web\/packages).<\/jats:p>\n               <jats:p>Contact: \u00a0rueda.om@gmail.com; rueda.om@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp307","type":"journal-article","created":{"date-parts":[[2009,5,7]],"date-time":"2009-05-07T00:44:24Z","timestamp":1241657064000},"page":"1959-1960","source":"Crossref","is-referenced-by-count":9,"title":["RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions"],"prefix":"10.1093","volume":"25","author":[{"given":"Oscar M.","family":"Rueda","sequence":"first","affiliation":[{"name":"Structural Biology and Biocomputing Programme, Spanish National Cancer Center (CNIO), Melchor Fern\u00e1ndez Almagro 3, Madrid, 28029, Spain"}]},{"given":"Ramon","family":"Diaz-Uriarte","sequence":"additional","affiliation":[{"name":"Structural Biology and Biocomputing Programme, Spanish National Cancer Center (CNIO), Melchor Fern\u00e1ndez Almagro 3, Madrid, 28029, Spain"}]}],"member":"286","published-online":{"date-parts":[[2009,5,6]]},"reference":[{"key":"2023013112051686000_B1","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1093\/bioinformatics\/btl035","article-title":"Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model","volume":"22","author":"Bro\u00ebt","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112051686000_B2","doi-asserted-by":"crossref","DOI":"10.1007\/0-387-28982-8","volume-title":"Inference in Hidden Markov Models (Springer Series in Statistics)","author":"Capp\u00e9","year":"2005"},{"key":"2023013112051686000_B3","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1101\/gr.5076506","article-title":"Stac: a method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments","volume":"16","author":"Diskin","year":"2006","journal-title":"Genome Res."},{"key":"2023013112051686000_B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v023.i03","article-title":"bcp: an R package for performing a Bayesian analysis of change point problems","volume":"23","author":"Erdman","year":"2007","journal-title":"J. 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