{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T02:55:24Z","timestamp":1777431324702,"version":"3.51.4"},"reference-count":33,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2015,9,29]],"date-time":"2015-09-29T00:00:00Z","timestamp":1443484800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004498","type":"journal-article","created":{"date-parts":[[2015,9,29]],"date-time":"2015-09-29T18:03:33Z","timestamp":1443549813000},"page":"e1004498","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":176,"title":["Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model"],"prefix":"10.1371","volume":"11","author":[{"given":"Naiqian","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiyun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Fang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqi","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"X. Shirley","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,9,29]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.ccr.2012.03.030","article-title":"Personalized medicine: patient-predictive panel power","volume":"21","author":"P Workman","year":"2012","journal-title":"Cancer cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1056\/NEJMp1114866","article-title":"Preparing for precision medicine","volume":"366","author":"R Mirnezami","year":"2012","journal-title":"N Engl J Med"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1002\/wsbm.1198","article-title":"Promise of personalized omics to precision medicine","volume":"5","author":"R Chen","year":"2013","journal-title":"Wiley interdisciplinary reviews Systems biology and medicine"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1093\/nar\/gkq960","article-title":"An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer","volume":"39","author":"J Cui","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"5705","DOI":"10.1158\/1078-0432.CCR-11-0196","article-title":"Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients","volume":"17","author":"Y Xie","year":"2011","journal-title":"Clin Cancer Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1158\/1078-0432.CCR-13-2127","article-title":"Adaptive prediction model in prospective molecular signature-based clinical studies","volume":"20","author":"G Xiao","year":"2014","journal-title":"Clin Cancer Res"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"19936","DOI":"10.1073\/pnas.0707498104","article-title":"Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling","volume":"104","author":"U McDermott","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1126\/science.275.5298.343","article-title":"An information-intensive approach to the molecular pharmacology of cancer","volume":"275","author":"JN Weinstein","year":"1997","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nrc1951","article-title":"The NCI60 human tumour cell line anticancer drug screen","volume":"6","author":"RH Shoemaker","year":"2006","journal-title":"Nature reviews Cancer"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"13086","DOI":"10.1073\/pnas.0610292104","article-title":"A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery","volume":"104","author":"JK Lee","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1093\/bioinformatics\/btq628","article-title":"Predicting in vitro drug sensitivity using Random Forests","volume":"27","author":"G Riddick","year":"2011","journal-title":"Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.jconrel.2008.09.074","article-title":"Drug targeting and tumor heterogeneity. Journal of controlled release: official journal of the","volume":"133","author":"YH Bae","year":"2009","journal-title":"Controlled Release Society"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"J Barretina","year":"2012","journal-title":"Nature"},{"key":"ref14","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":"MJ Garnett","year":"2012","journal-title":"Nature"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"R47","DOI":"10.1186\/gb-2014-15-3-r47","article-title":"Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines","volume":"15","author":"P Geeleher","year":"2014","journal-title":"Genome Biol"},{"key":"ref16","first-page":"125","article-title":"Drug Intervention Response Predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance","author":"D Brubaker","year":"2014","journal-title":"Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e61318","DOI":"10.1371\/journal.pone.0061318","article-title":"Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties","volume":"8","author":"MP Menden","year":"2013","journal-title":"PLoS One"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1021\/ci500152b","article-title":"Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization","volume":"54","author":"M Ammad-ud-din","year":"2014","journal-title":"J Chem Inf Model"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1093\/bioinformatics\/bts360","article-title":"Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization","volume":"28","author":"M Gonen","year":"2012","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/msb.2008.27","article-title":"Network-based global inference of human disease genes","volume":"4","author":"X Wu","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1002694","DOI":"10.1371\/journal.pcbi.1002694","article-title":"Tissue-specific functional networks for prioritizing phenotype and disease genes","volume":"8","author":"Y Guan","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"W623","DOI":"10.1093\/nar\/gkp456","article-title":"PubChem: a public information system for analyzing bioactivities of small molecules","volume":"37","author":"Y Wang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1002\/jcc.21707","article-title":"PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints","volume":"32","author":"CW Yap","year":"2011","journal-title":"Journal of computational chemistry"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/nature12831","article-title":"Inconsistency in large pharmacogenomic studies","volume":"504","author":"B Haibe-Kains","year":"2013","journal-title":"Nature"},{"key":"ref25","unstructured":"Hastie T <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.russpoldrack.org\/2012\/12\/the-perils-of-leave-one-out.html\" xlink:type=\"simple\">http:\/\/www.russpoldrack.org\/2012\/12\/the-perils-of-leave-one-out.html<\/ext-link>."},{"key":"ref26","doi-asserted-by":"crossref","first-page":"11335","DOI":"10.1158\/0008-5472.CAN-07-1502","article-title":"Drug sensitivity prediction by CpG island methylation profile in the NCI-60 cancer cell line panel","volume":"67","author":"L Shen","year":"2007","journal-title":"Cancer Res"},{"key":"ref27","article-title":"A community effort to assess and improve drug sensitivity prediction algorithms","author":"JC Costello","year":"2014","journal-title":"Nat Biotechnol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3325","DOI":"10.1093\/bioinformatics\/btu542","article-title":"Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation","volume":"30","author":"F Zhu","year":"2014","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2772","DOI":"10.1093\/bioinformatics\/btu382","article-title":"Predicting dynamic signaling network response under unseen perturbations","volume":"30","author":"F Zhu","year":"2014","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/msb.2011.71","article-title":"Systematic exploration of synergistic drug pairs","volume":"7","author":"M Cokol","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref31","first-page":"394","article-title":"Kappa shape indices for similarity analysis","volume":"7","author":"LB Kier","year":"1997","journal-title":"Med Chem Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/0169-7439(91)80051-Q","article-title":"Novel graph theoretical approach to heteroatoms in quantitative structure\u2014activity relationships","volume":"10","author":"M Randic","year":"1991","journal-title":"Chemom Intell Lab Sys"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1021\/ci000104t","article-title":"The overall Wiener index\u2014a new tool for characterization of molecular topology","volume":"41","author":"D Bonchev","year":"2001","journal-title":"Journal of chemical information and computer sciences"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004498","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,31]],"date-time":"2019-08-31T03:00:20Z","timestamp":1567220420000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004498"}},"subtitle":[],"editor":[{"given":"Christina S.","family":"Leslie","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,9,29]]},"references-count":33,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2015,9,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004498","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9,29]]}}}