{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T16:49:15Z","timestamp":1773247755115,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,11,24]],"date-time":"2017-11-24T00:00:00Z","timestamp":1511481600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Large pharmacogenomic screenings integrate heterogeneous cancer genomic datasets as well as anti-cancer drug responses on thousand human cancer cell lines. Mining this data to identify new therapies for cancer sub-populations would benefit from common data structures, modular computational biology tools and user-friendly interfaces.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed GDSCTools: a software aimed at the identification of clinically relevant genomic markers of drug response. The Genomics of Drug Sensitivity in Cancer (GDSC) database (www.cancerRxgene.org) integrates heterogeneous cancer genomic datasets as well as anti-cancer drug responses on a thousand cancer cell lines. Including statistical tools (analysis of variance) and predictive methods (Elastic Net), as well as common data structures, GDSCTools allows users to reproduce published results from GDSC and to implement new analytical methods. In addition, non-GDSC data resources can also be analysed since drug responses and genomic features can be encoded as CSV files.<\/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\/btx744","type":"journal-article","created":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T15:16:26Z","timestamp":1511450186000},"page":"1226-1228","source":"Crossref","is-referenced-by-count":62,"title":["GDSCTools for mining pharmacogenomic interactions in cancer"],"prefix":"10.1093","volume":"34","author":[{"given":"Thomas","family":"Cokelaer","sequence":"first","affiliation":[{"name":"Institut Pasteur\u2014Bioinformatics and Biostatistics Hub\u2014C3BI, USR IP CNRS, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elisabeth","family":"Chen","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Iorio","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael P","family":"Menden","sequence":"additional","affiliation":[{"name":"Oncology Innovative Medicines and Early Development, AstraZeneca, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Howard","family":"Lightfoot","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julio","family":"Saez-Rodriguez","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"},{"name":"RWTH Aachen University, Joint Research Centre for Computational Biomedicine, Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathew J","family":"Garnett","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,11,24]]},"reference":[{"key":"2023012712562602800_btx744-B1","doi-asserted-by":"crossref","first-page":"290.","DOI":"10.1038\/nature11735","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"492","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2023012712562602800_btx744-B2","doi-asserted-by":"crossref","first-page":"3241","DOI":"10.1093\/bioinformatics\/btt547","article-title":"BioServices: a common Python package to access biological Web Services programmatically","volume":"29","author":"Cokelaer","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712562602800_btx744-B3","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1038\/nature11005","article-title":"Systematic identification of genomic markers of drug sensitivity in cancer cells","volume":"483","author":"Garnett","year":"2012","journal-title":"Nature"},{"key":"2023012712562602800_btx744-B4","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1016\/j.cell.2016.06.017","article-title":"A landscape of pharmacogenomic interactions in cancer","volume":"166","author":"Iorio","year":"2016","journal-title":"Cell"},{"key":"2023012712562602800_btx744-B5","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2013a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012712562602800_btx744-B6","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1093\/bioinformatics\/btv723","article-title":"PharmacoGx: an R package for analysis of large pharmacogenomic datasets","volume":"32","author":"Smirnov","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012712562602800_btx744-B7","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.4077","article-title":"OmniPath: guidelines and gateway for literature-curated signaling pathway resources","volume":"13","author":"Turei","year":"2016","journal-title":"Nat. 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