{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T12:27:42Z","timestamp":1761395262843,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,15]],"date-time":"2018-06-15T00:00:00Z","timestamp":1529020800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["295504","310507"],"award-info":[{"award-number":["295504","310507"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006383","name":"Cancer Society of Finland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006383","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sigrid Juselius Foundation"},{"DOI":"10.13039\/501100003125","name":"Finnish Cultural Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003125","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["16X064"],"award-info":[{"award-number":["16X064"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Prognostic models are widely used in clinical decision-making, such as risk stratification and tailoring treatment strategies, with the aim to improve patient outcomes while reducing overall healthcare costs. While prognostic models have been adopted into clinical use, benchmarking their performance has been difficult due to lack of open clinical datasets. The recent DREAM 9.5 Prostate Cancer Challenge carried out an extensive benchmarking of prognostic models for metastatic Castration-Resistant Prostate Cancer (mCRPC), based on multiple cohorts of open clinical trial data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We make available an open-source implementation of the top-performing model, ePCR, along with an extended toolbox for its further re-use and development, and demonstrate how to best apply the implemented model to real-world data cohorts of advanced prostate cancer patients.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The open-source R-package ePCR and its reference documentation are available at the Central R Archive Network (CRAN): https:\/\/CRAN.R-project.org\/package=ePCR. R-vignette provides step-by-step examples for the ePCR usage.<\/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\/bty477","type":"journal-article","created":{"date-parts":[[2018,6,12]],"date-time":"2018-06-12T19:10:33Z","timestamp":1528830633000},"page":"3957-3959","source":"Crossref","is-referenced-by-count":5,"title":["ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts"],"prefix":"10.1093","volume":"34","author":[{"given":"Teemu D","family":"Laajala","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, University of Turku, Turku, Finland"},{"name":"Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mika","family":"Murtoj\u00e4rvi","sequence":"additional","affiliation":[{"name":"Department of Future Technologies, University of Turku, Turku, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arho","family":"Virkki","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Turku, Turku, Finland"},{"name":"Centre for Clinical Informatics, Turku University Hospital, Turku, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tero","family":"Aittokallio","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Turku, Turku, Finland"},{"name":"Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,6,15]]},"reference":[{"key":"2023012712353506000_bty477-B1","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1056\/NEJMsb1702054","article-title":"Advantages of a truly open-access data-sharing model","volume":"376","author":"Bertagnolli","year":"2017","journal-title":"N. Engl. J. Med."},{"key":"2023012712353506000_bty477-B2","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/S1470-2045(16)30560-5","article-title":"Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data","volume":"18","author":"Guinney","year":"2017","journal-title":"Lancet. Oncol."},{"key":"2023012712353506000_bty477-B3","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1200\/JCO.2013.52.3696","article-title":"Updated prognostic model for predicting overall survival in first-line chemotherapy for patients with metastatic castration-resistant prostate cancer","volume":"32","author":"Halabi","year":"2014","journal-title":"J. Clin. Oncol."},{"key":"2023012712353506000_bty477-B4","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/nrd.2017.26","article-title":"From big data to smart data: FDA\u2019S INFORMED initiative","volume":"16","author":"Khozin","year":"2017","journal-title":"Nat. Rev. Drug Discov."},{"key":"2023012712353506000_bty477-B5","doi-asserted-by":"crossref","first-page":"81721","DOI":"10.18632\/oncotarget.20853","article-title":"Community mining of open clinical trial data","volume":"8","author":"Laajala","year":"2017","journal-title":"Oncotarget"},{"key":"2023012712353506000_bty477-B6","first-page":"838","article-title":"How reliable are trial-based prognostic models in real-world patients with metastatic castration-resistant prostate cancer? Eur","volume":"71","author":"Seyednasrollah","year":"2017","journal-title":"Urol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3957\/48920889\/bioinformatics_34_22_3957.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3957\/48920889\/bioinformatics_34_22_3957.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:25:28Z","timestamp":1674825928000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/22\/3957\/5038459"}},"subtitle":[],"editor":[{"given":"Wren","family":"Jonathan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,6,15]]},"references-count":6,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2018,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty477","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,11,15]]},"published":{"date-parts":[[2018,6,15]]}}}