{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T19:52:10Z","timestamp":1772135530984,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2017,2,4]],"date-time":"2017-02-04T00:00:00Z","timestamp":1486166400000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["2012-AdG"],"award-info":[{"award-number":["2012-AdG"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["322986"],"award-info":[{"award-number":["322986"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cancer Center Amsterdam, VU University Medical Center","award":["CCA 2014-5-20"],"award-info":[{"award-number":["CCA 2014-5-20"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Our aim is to improve omics based prediction and feature selection using multiple sources of auxiliary information: co-data. Adaptive group regularized ridge regression (GRridge) was proposed to achieve this by estimating additional group-based penalty parameters through an empirical Bayes method at a low computational cost. We illustrate the GRridge method and software on RNA sequencing datasets. The method boosts the performance of an ordinary ridge regression and outperforms other classifiers. Post-hoc feature selection maintains the predictive ability of the classifier with far fewer markers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>GRridge is an R package that includes a vignette. It is freely available at (https:\/\/bioconductor.org\/packages\/GRridge\/). All information and R scripts used in this study, including those on retrieval and processing of the co-data, are available from http:\/\/github.com\/markvdwiel\/GRridgeCodata.<\/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\/btw837","type":"journal-article","created":{"date-parts":[[2017,1,9]],"date-time":"2017-01-09T09:34:36Z","timestamp":1483954476000},"page":"1572-1574","source":"Crossref","is-referenced-by-count":17,"title":["Better diagnostic signatures from RNAseq data through use of auxiliary co-data"],"prefix":"10.1093","volume":"33","author":[{"given":"Putri W","family":"Novianti","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands"},{"name":"Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands"}]},{"given":"Barbara C","family":"Snoek","sequence":"additional","affiliation":[{"name":"Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands"}]},{"given":"Saskia M","family":"Wilting","sequence":"additional","affiliation":[{"name":"Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands"}]},{"given":"Mark A","family":"van de Wiel","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands"},{"name":"Department of Mathematics, VU University, Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2017,1,20]]},"reference":[{"key":"2023020205110767500_btw837-B1","doi-asserted-by":"crossref","first-page":"e05005.","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"eLife"},{"key":"2023020205110767500_btw837-B2","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1055\/s-0037-1613622","article-title":"Messenger RNA profiling of human platelets by microarray hybridization","volume":"90","author":"Bugert","year":"2003","journal-title":"Thromb. Haemost"},{"key":"2023020205110767500_btw837-B3","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1182\/blood-2002-09-2797","article-title":"Transcript profiling of human platelets using microarray and serial analysis of gene expression","volume":"101","author":"Gnatenko","year":"2003","journal-title":"Blood"},{"key":"2023020205110767500_btw837-B4","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.immuni.2015.12.006","article-title":"Compendium of immune signatures identifies conserved and species-specific biology in response to inflammation","volume":"44","author":"Godec","year":"2016","journal-title":"Immunity"},{"key":"2023020205110767500_btw837-B5","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1080\/10618600.2012.681250","article-title":"A sparse-group lasso","volume":"22","author":"Simon","year":"2013","journal-title":"J. Comp. Graph. Stat"},{"key":"2023020205110767500_btw837-B6","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020205110767500_btw837-B7","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1002\/sim.6732","article-title":"Better prediction by use of co-data: adaptive group-regularized ridge regression","volume":"35","author":"van de Wiel","year":"2016","journal-title":"Stat. Med"},{"key":"2023020205110767500_btw837-B8","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.ccell.2015.09.018","article-title":"RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass, and molecular pathway cancer diagnostics","volume":"28","author":"Wurdinger","year":"2015","journal-title":"Cancer Cell"},{"key":"2023020205110767500_btw837-B10","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1111\/j.1467-9868.2005.00532.x","article-title":"Model selection and estimation in regression with grouped variables","volume":"68","author":"Yuan","year":"2007","journal-title":"J. R. Stat. Soc. Ser. B Stat. Methodol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/10\/1572\/49039028\/bioinformatics_33_10_1572.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/10\/1572\/49039028\/bioinformatics_33_10_1572.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:17:19Z","timestamp":1675315039000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/10\/1572\/2884246"}},"subtitle":[],"editor":[{"given":"Ivo","family":"Hofacker","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,1,20]]},"references-count":9,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2017,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw837","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,5,15]]},"published":{"date-parts":[[2017,1,20]]}}}