{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T17:53:22Z","timestamp":1770832402759,"version":"3.50.1"},"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T00:00:00Z","timestamp":1572825600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871070"],"award-info":[{"award-number":["11871070"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61503419"],"award-info":[{"award-number":["61503419"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003453","name":"Guangdong Nature Science Foundation","doi-asserted-by":"crossref","award":["2016A030313234"],"award-info":[{"award-number":["2016A030313234"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Opening Project of Guangdong Province Key Laboratory of Computational Science at Sun Yat-Sen University","award":["2018003"],"award-info":[{"award-number":["2018003"]}]},{"DOI":"10.13039\/501100012166","name":"National key research and development program","doi-asserted-by":"crossref","award":["2018YFC0910500"],"award-info":[{"award-number":["2018YFC0910500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007435","type":"journal-article","created":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T13:24:10Z","timestamp":1572873850000},"page":"e1007435","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data"],"prefix":"10.1371","volume":"15","author":[{"given":"Jiajun","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Wenbo","family":"Zhu","sequence":"additional","affiliation":[]},{"given":"Qianliang","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Jiayu","family":"Gu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0322-6078","authenticated-orcid":true,"given":"L. Frank","family":"Huang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3399-7260","authenticated-orcid":true,"given":"Xiaoqiang","family":"Sun","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,11,4]]},"reference":[{"issue":"2","key":"pcbi.1007435.ref001","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1016\/j.celrep.2016.12.037","article-title":"The Anti-Warburg Effect Elicited by the cAMP-PGC1\u03b1 Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes","volume":"18","author":"F Xing","year":"2017","journal-title":"Cell Reports"},{"issue":"33","key":"pcbi.1007435.ref002","doi-asserted-by":"crossref","first-page":"13438","DOI":"10.1073\/pnas.0701990104","article-title":"Cholera Toxin Induces Malignant Glioma Cell Differentiation via the PKA\/CREB Pathway","volume":"104","author":"Y Li","year":"2007","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"14","key":"pcbi.1007435.ref003","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1093\/bioinformatics\/btu164","article-title":"Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles","volume":"30","author":"BA Aksoy","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1007435.ref004","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1158\/1078-0432.CCR-1025-3","article-title":"Identification of Genes with Differential Expression in Acquired Drug-Resistant Gastric Cancer Cells Using High-Density Oligonucleotide Microarrays","volume":"10","author":"HC Kang","year":"2004","journal-title":"Clinical Cancer Research"},{"issue":"4","key":"pcbi.1007435.ref005","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.semcancer.2013.06.002","article-title":"Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks","volume":"23","author":"E Wang","year":"2013","journal-title":"Seminars in Cancer Biology"},{"issue":"4","key":"pcbi.1007435.ref006","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.semcancer.2013.06.001","article-title":"Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance","volume":"23","author":"E Wang","year":"2013","journal-title":"Seminars in Cancer Biology"},{"issue":"9","key":"pcbi.1007435.ref007","doi-asserted-by":"crossref","first-page":"e1004498","DOI":"10.1371\/journal.pcbi.1004498","article-title":"Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model","volume":"11","author":"N Zhang","year":"2015","journal-title":"PLOS Computational Biology"},{"issue":"8","key":"pcbi.1007435.ref008","doi-asserted-by":"crossref","first-page":"e8202","DOI":"10.15252\/msb.20188202","article-title":"Identification of an oncogenic network with prognostic and therapeutic value in prostate cancer","volume":"14","author":"F Magani","year":"2018","journal-title":"Molecular Systems Biology"},{"issue":"1","key":"pcbi.1007435.ref009","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"P Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1007435.ref010","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1186\/1471-2105-11-497","article-title":"Jansen RCJBB. DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules","volume":"11","author":"BM Tesson","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"pcbi.1007435.ref011","doi-asserted-by":"crossref","first-page":"e1002955","DOI":"10.1371\/journal.pcbi.1002955","article-title":"Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression","volume":"9","author":"D Amar","year":"2013","journal-title":"PLOS Computational Biology"},{"issue":"21","key":"pcbi.1007435.ref012","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1093\/bioinformatics\/btp502","article-title":"Statistical methods for gene set co-expression analysis","volume":"25","author":"Y Choi","year":"2009","journal-title":"Bioinformatics"},{"issue":"3","key":"pcbi.1007435.ref013","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1093\/bioinformatics\/btt687","article-title":"Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets","volume":"30","author":"Y Rahmatallah","year":"2013","journal-title":"Bioinformatics"},{"issue":"8","key":"pcbi.1007435.ref014","doi-asserted-by":"crossref","first-page":"e0135831","DOI":"10.1371\/journal.pone.0135831","article-title":"CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra","volume":"10","author":"SdS Santos","year":"2015","journal-title":"PLOS ONE"},{"issue":"5","key":"pcbi.1007435.ref015","first-page":"2605","article-title":"Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis","volume":"9","author":"C Mu-Shui","year":"2015","journal-title":"American journal of cancer research"},{"issue":"9","key":"pcbi.1007435.ref016","first-page":"4241293","article-title":"Differential Regulatory Analysis Based on Coexpression Network in Cancer Research","author":"J Li","year":"2016","journal-title":"BioMed Research International"},{"issue":"9","key":"pcbi.1007435.ref017","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"pcbi.1007435.ref018","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"International Human Genome Sequencing Consortium","year":"2001","journal-title":"Nature"},{"issue":"2","key":"pcbi.1007435.ref019","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"S Anders","year":"2015","journal-title":"Bioinformatics"},{"issue":"10","key":"pcbi.1007435.ref020","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"S Anders","year":"2010","journal-title":"Genome Biology"},{"issue":"1","key":"pcbi.1007435.ref021","first-page":"31","article-title":"Chi3l3: a potential key orchestrator of eosinophil recruitment in meningitis induced by Angiostrongylus cantonensis","volume":"15","author":"S Wan","year":"2018"},{"issue":"186","key":"pcbi.1007435.ref022","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1090\/S0025-5718-1989-0962209-1","article-title":"Nonnegativity-, monotonicity-, or convexity-preserving cubic and quintic Hermite interpolation","volume":"52","author":"RL Dougherty","year":"1989","journal-title":"Mathematics of Computation"},{"issue":"1","key":"pcbi.1007435.ref023","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression Shrinkage and Selection via the Lasso","volume":"58","author":"R Tibshirani","year":"1996","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"issue":"1","key":"pcbi.1007435.ref024","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization Paths for Generalized Linear Models via Coordinate Descent","volume":"33","author":"J Friedman","year":"2010","journal-title":"Journal of statistical software"},{"key":"pcbi.1007435.ref025","author":"MB Priestley","year":"1981"},{"issue":"17","key":"pcbi.1007435.ref026","first-page":"2713","article-title":"DyNet: visualization and analysis of dynamic molecular interaction networks","volume":"32","author":"IH Goenawan","year":"2016"},{"issue":"1","key":"pcbi.1007435.ref027","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"M Ashburner","year":"2000","journal-title":"The Gene Ontology Consortium. Nature Genetics"},{"issue":"1","key":"pcbi.1007435.ref028","first-page":"baq020","article-title":"GeneCards Version 3: the human gene integrator","volume":"2010","author":"M Safran","year":"2010","journal-title":"Database (Oxford)"},{"issue":"1","key":"pcbi.1007435.ref029","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/1752-0509-4-104","article-title":"Increased entropy of signal transduction in the cancer metastasis phenotype","volume":"4","author":"AE Teschendorff","year":"2010","journal-title":"BMC Systems Biology"},{"issue":"2","key":"pcbi.1007435.ref030","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/j.2517-6161.1972.tb00899.x","article-title":"Regression Models and Life-Tables","volume":"34","author":"DR Cox","year":"1972","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"key":"pcbi.1007435.ref031","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/978-1-4939-7717-8_9","volume-title":"Computational Systems Biology: Methods and Protocols","author":"B-H Liu","year":"2018"},{"issue":"9","key":"pcbi.1007435.ref032","doi-asserted-by":"crossref","first-page":"e12776","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring Regulatory Networks from Expression Data Using Tree-Based Methods","volume":"5","author":"VA Huynh-Thu","year":"2010","journal-title":"PLOS ONE"},{"key":"pcbi.1007435.ref033","article-title":"GRENITS: Gene Regulatory Network Inference Using Time Series","author":"E Morrissey","year":"2018","journal-title":"R package version 1.34.0"},{"issue":"8","key":"pcbi.1007435.ref034","doi-asserted-by":"crossref","first-page":"e6799","DOI":"10.1371\/journal.pone.0006799","article-title":"Incorporating Existing Network Information into Gene Network Inference","volume":"4","author":"S Christley","year":"2009","journal-title":"PLOS ONE"},{"issue":"1","key":"pcbi.1007435.ref035","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1752-0509-8-3","article-title":"Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns","volume":"8","author":"Z Zheng","year":"2014","journal-title":"BMC Systems Biology"},{"issue":"12","key":"pcbi.1007435.ref036","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Anders SJGB. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biology"},{"key":"pcbi.1007435.ref037","first-page":"359","article-title":"Using dynamic time warping to find patterns in time series","volume-title":"KDD Workshop","author":"DJ Berndt","year":"1994"},{"key":"pcbi.1007435.ref038","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1214\/aos\/1176344722","article-title":"Multivariate generalizations of the Wald-Wolfowitz and Smirnov two sample tests","volume":"7","author":"J, C. Friedman","year":"1979","journal-title":"Ann Stat"},{"issue":"9","key":"pcbi.1007435.ref039","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev-pathol-011110-130324","article-title":"Glioblastoma: from molecular pathology to targeted treatment","volume":"9","author":"TF Cloughesy","year":"2014","journal-title":"Annual Review of Pathology"},{"issue":"10","key":"pcbi.1007435.ref040","first-page":"421","article-title":"Radiotherapy Plus Concomitant and Adjuvant Temozolomide for Glioblastoma\u2014A Critical Review","volume":"2","author":"RJ Komotar","year":"2005","journal-title":"Clinical Medicine Oncology"},{"issue":"8","key":"pcbi.1007435.ref041","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1056\/NEJMoa1308345","article-title":"Bevacizumab plus Radiotherapy\u2013Temozolomide for Newly Diagnosed Glioblastoma","volume":"370","author":"OL Chinot","year":"2014","journal-title":"N Engl J Med"},{"issue":"2\u20133","key":"pcbi.1007435.ref042","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/S0163-7258(01)00132-2","article-title":"Differentiation therapy of human cancer: basic science and clinical applications","volume":"90","author":"M Leszczyniecka","year":"2001","journal-title":"Pharmacology & Therapeutics"},{"issue":"3","key":"pcbi.1007435.ref043","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1158\/2159-8290.CD-12-0012","article-title":"Circumventing cancer drug resistance in the era of personalized medicine","volume":"2","author":"LA Garraway","year":"2012","journal-title":"Cancer Discovery"},{"issue":"10","key":"pcbi.1007435.ref044","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1038\/nrc3599","article-title":"Cancer Drug Resistance: An Evolving Paradigm","volume":"13","author":"C Holohan","year":"2013","journal-title":"Nature Reviews Cancer"},{"issue":"6","key":"pcbi.1007435.ref045","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1093\/bib\/bbx065","article-title":"Mathematical modeling and computational prediction of cancer drug resistance","volume":"19","author":"X Sun","year":"2018","journal-title":"Briefings in Bioinformatics"},{"issue":"12","key":"pcbi.1007435.ref046","first-page":"3364","article-title":"Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type\u2013Specific Dynamic Logic Models","volume":"77","author":"F Eduati","year":"2017"},{"issue":"8","key":"pcbi.1007435.ref047","first-page":"2168","article-title":"Cell cycle-mediated drug resistance: an emerging concept in cancer therapy","volume":"7","author":"M A Shah","year":"2001","journal-title":"Clinical Cancer Research An Official Journal of the American Association for Cancer Research"},{"issue":"3","key":"pcbi.1007435.ref048","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.cels.2017.07.005","article-title":"Cell-Cycle Position of Single MYC-Driven Cancer Cells Dictates Their Susceptibility to a Chemotherapeutic Drug","volume":"5","author":"T Ryl","year":"2017","journal-title":"Cell Systems"},{"key":"pcbi.1007435.ref049","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1186\/1471-2407-10-684","article-title":"Induction of cell cycle arrest at G1 and S phase and cAMP-dependent differentiation in C6 glioma by low concentration of cycloheximide","volume":"10","author":"X Liu","year":"2010","journal-title":"BMC Cancer"},{"issue":"12","key":"pcbi.1007435.ref050","doi-asserted-by":"crossref","first-page":"e1003358","DOI":"10.1371\/journal.pcbi.1003358","article-title":"Systems modeling of anti-apoptotic pathways in prostate cancer: psychological stress triggers a synergism pattern switch in drug combination therapy","volume":"9","author":"X Sun","year":"2013","journal-title":"Plos Computational Biology"},{"issue":"18","key":"pcbi.1007435.ref051","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1016\/j.febslet.2015.07.014","article-title":"Mathematical modeling reveals a critical role for cyclin D1 dynamics in phenotype switching during glioma differentiation","volume":"589","author":"X Sun","year":"2015","journal-title":"Febs Letters"},{"key":"pcbi.1007435.ref052","doi-asserted-by":"crossref","first-page":"22498","DOI":"10.1038\/srep22498","article-title":"Mathematical Modeling of Therapy-induced Cancer Drug Resistance: Connecting Cancer Mechanisms to Population Survival Rates","volume":"6","author":"X Sun","year":"2016","journal-title":"Scientific Reports"},{"issue":"39","key":"pcbi.1007435.ref053","first-page":"763995","article-title":"Modeling of signaling crosstalk-mediated drug resistance and its implications on drug combination","author":"X Sun","year":"2016","journal-title":"Oncotarget"},{"key":"pcbi.1007435.ref054","doi-asserted-by":"crossref","first-page":"bbz040","DOI":"10.1093\/bib\/bbz040","article-title":"Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas","author":"J Zhang","year":"2019","journal-title":"Briefings in Bioinformatics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007435","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T20:12:19Z","timestamp":1588968739000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007435"}},"subtitle":[],"editor":[{"given":"Qing","family":"Nie","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,11,4]]},"references-count":54,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2019,11,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007435","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,4]]}}}