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Bollag","year":"2010","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1995","DOI":"10.1056\/NEJMoa1014618","article-title":"Abiraterone and increased survival in metastatic prostate cancer","volume":"364","author":"JS de Bono","year":"2011","journal-title":"N Engl J Med"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1126\/science.1168175","article-title":"Development of a second-generation antiandrogen for treatment of advanced prostate cancer","volume":"324","author":"C Tran","year":"2009","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1056\/NEJM200104053441401","article-title":"Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia","volume":"344","author":"BJ Druker","year":"2001","journal-title":"N Engl J 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In Proc 24th Conference on Uncertainty in Articial Intelligence (UAI)."},{"key":"ref33","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/msb.2008.53","article-title":"Models from experiments: combinatorial drug perturbations of cancer cells","volume":"4","author":"S Nelander","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1103\/PhysRevLett.59.2229","article-title":"Generalization of back-propagation to recurrent neural networks","volume":"59","author":"FJ Pineda","year":"1987","journal-title":"Phys Rev Lett"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"mr7","DOI":"10.1126\/scisignal.2002212","article-title":"Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge","volume":"4","author":"RJ Prill","year":"2011","journal-title":"Science signaling"},{"key":"ref36","unstructured":"Yedida JS, Freeman WT, Weiss Y (2003) Understanding Belief Propagation and its generalizations. 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Application to gene regulatory networks. International Conference on Artificial Intelligence and Statistics: 757\u2013764."},{"key":"ref49","unstructured":"Zhana D, Yong W, Shigeru S, Katsuhisa H (2012) Inferring gene regulatory network for cell reprogramming. Control Conference (CCC), 2012 31st Chinese: 7437\u20137442."},{"key":"ref50","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1089\/cmb.2007.0185","article-title":"On the Sparse Reconstruction of Gene Networks","volume":"15","author":"M Andrecut","year":"2008","journal-title":"Journal of Computational Biology"},{"key":"ref51","first-page":"2755","article-title":"Identification of stable genetic networks using convex programming","volume":"2008","author":"MM Zavlanos","year":"2008","journal-title":"American Control Conference"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/msb.2008.52","article-title":"Survival of the sparsest: robust gene networks are parsimonious","volume":"4","author":"RD Leclerc","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1093\/bioinformatics\/btm151","article-title":"Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method","volume":"23","author":"A Fujita","year":"2007","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"e14147","DOI":"10.1371\/journal.pone.0014147","article-title":"Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge","volume":"5","author":"P Menendez","year":"2010","journal-title":"PLoS One"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"2413","DOI":"10.1093\/bioinformatics\/btl396","article-title":"Inferring gene regulatory networks from multiple microarray datasets","volume":"22","author":"Y Wang","year":"2006","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1023\/A:1022221005097","article-title":"The cavity method at zero temperature","volume":"111","author":"M Mezard","year":"2003","journal-title":"Journal of Statistical Physics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1209\/0295-5075\/1\/2\/006","article-title":"SK Model: the replica solution without replicas","volume":"1","author":"M M\u00e9zard","year":"1986","journal-title":"Europhys Lett"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1103\/PhysRevLett.35.1792","article-title":"Solvable Model of a Spin-Glass","volume":"35","author":"D Sherrington","year":"1975","journal-title":"Phys Rev Lett"},{"key":"ref59","first-page":"133","article-title":"Reverend Bayes on inference engines: A distributed hierarchical approach","volume":"AAAI-82","author":"J Pearl","year":"1982","journal-title":"Proceedings of the Second National Conference on Artificial Intelligence"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1109\/18.910572","article-title":"Factor Graphs and the Sum-Product Algorithm","volume":"47","author":"FR Kschischang","year":"2001","journal-title":"IEEE TRANSACTIONS ON INFORMATION THEORY"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1002\/rsa.20057","article-title":"Survey propagation: An algorithm for satisfiability","volume":"27","author":"A Braunstein","year":"2005","journal-title":"Random Structures & Algorithms"},{"key":"ref62","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevLett.96.030201","article-title":"Learning by message passing in networks of discrete synapses","volume":"96","author":"A Braunstein","year":"2006","journal-title":"Physical Review Letters"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1126\/science.1136800","article-title":"Clustering by passing messages between data points","volume":"315","author":"BJ Frey","year":"2007","journal-title":"Science"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"2708","DOI":"10.1093\/bioinformatics\/btm414","article-title":"Clustering by soft-constraint affinity propagation: applications to gene-expression data","volume":"23","author":"M Leone","year":"2007","journal-title":"Bioinformatics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1143\/JPSJ.74.2233","article-title":"Statistical mechanical development of a sparse Bayesian classifier","volume":"74","author":"S Uda","year":"2005","journal-title":"Journal of the Physical Society of Japan"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"P12001","DOI":"10.1088\/1742-5468\/2008\/12\/P12001","article-title":"Inference algorithms for gene networks: a statistical mechanics analysis","volume":"2008","author":"A Braunstein","year":"2008","journal-title":"Journal of Statistical Mechanics: Theory and Experiment"},{"key":"ref67","doi-asserted-by":"crossref","unstructured":"Ando S, Iba H (2001) Inference of gene regulatory model by genetic algorithms. IEEE Congress on Evolutionary Computation. 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Hache","year":"2009","journal-title":"Bioinformatics"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1214\/09-SS057","article-title":"Causal inference in statistics: An overview","volume":"3","author":"J Pearl","year":"2009","journal-title":"Statistics Surveys"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"2747","DOI":"10.1093\/bioinformatics\/btm397","article-title":"An error model for protein quantification","volume":"23","author":"C Kreutz","year":"2007","journal-title":"Bioinformatics"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1038\/nature09627","article-title":"COT drives resistance to RAF inhibition through MAP kinase pathway reactivation","volume":"468","author":"CM Johannessen","year":"2010","journal-title":"Nature"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nature09626","article-title":"Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS 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Solit","year":"2006","journal-title":"Nature"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"2512","DOI":"10.1158\/1535-7163.MCT-06-0334","article-title":"Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells","volume":"5","author":"R Tibes","year":"2006","journal-title":"Mol Cancer Ther"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1126\/science.296.5573.1655","article-title":"The phosphoinositide 3-kinase pathway","volume":"296","author":"LC Cantley","year":"2002","journal-title":"Science"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1016\/j.ccr.2010.10.031","article-title":"AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression and activity","volume":"19","author":"S Chandarlapaty","year":"2011","journal-title":"Cancer 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Ther"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"9527","DOI":"10.1128\/MCB.24.21.9527-9541.2004","article-title":"Disruption of the Rb\u2013Raf-1 interaction inhibits tumor growth and angiogenesis","volume":"24","author":"P Dasgupta","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"10406","DOI":"10.1128\/MCB.24.23.10406-10415.2004","article-title":"Genetic interaction between Rb and K-ras in the control of differentiation and tumor suppression","volume":"24","author":"C Takahashi","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"5256","DOI":"10.1128\/MCB.23.15.5256-5268.2003","article-title":"Rb and N-ras function together to control differentiation in the mouse","volume":"23","author":"C Takahashi","year":"2003","journal-title":"Mol Cell Biol"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/ng1703","article-title":"Nras loss induces metastatic conversion of Rb1-deficient neuroendocrine thyroid tumor","volume":"38","author":"C Takahashi","year":"2006","journal-title":"Nat Genet"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/S0092-8674(03)00194-6","article-title":"Structural basis for the autoinhibition of c-Abl tyrosine kinase","volume":"112","author":"B Nagar","year":"2003","journal-title":"Cell"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1139\/o03-077","article-title":"SRC gene expression in human cancer: the role of transcriptional activation","volume":"82","author":"SM Dehm","year":"2004","journal-title":"Biochem Cell Biol"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"4495","DOI":"10.1038\/sj.onc.1209473","article-title":"Histone deacetylase 3 localizes to the plasma membrane and is a substrate of Src","volume":"25","author":"MS Longworth","year":"2006","journal-title":"Oncogene"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/nrd3184","article-title":"Multifaceted polo-like kinases: drug targets and antitargets for cancer therapy","volume":"9","author":"K Strebhardt","year":"2010","journal-title":"Nat Rev Drug Discov"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/msb.2008.53","article-title":"Models from experiments: combinatorial drug perturbations of cancer cells","volume":"4","author":"S Nelander","year":"2008","journal-title":"Molecular systems biology"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1126\/science.1105809","article-title":"Causal protein-signaling networks derived from multiparameter single-cell data","volume":"308","author":"K Sachs","year":"2005","journal-title":"Science"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.cell.2010.02.011","article-title":"Protein dynamics in drug combinations: a linear superposition of individual-drug responses","volume":"140","author":"N Geva-Zatorsky","year":"2010","journal-title":"Cell"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"e1000654","DOI":"10.1371\/journal.pcbi.1000654","article-title":"Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells","volume":"6","author":"S Gupta","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref101","unstructured":"Hindmarsh AC (1993) ODEPACK, a systematized collection of ODE solvers. In: Stepleman RS, Carver M, Peskin R, Ames WF, Vichnevetsky R, editors. Scientific Computing. Amsterdam: North-Holland Publishing Company. pp. 55\u201364."}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003290","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T20:44:04Z","timestamp":1588970644000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003290"}},"subtitle":[],"editor":[{"given":"Florian","family":"Markowetz","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2013,12,19]]},"references-count":101,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2013,12,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003290","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12,19]]}}}