Classifying tumors by supervised network propagation
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Wei Zhang | Trey Ideker | Jianzhu Ma | T. Ideker | Wei Zhang | Jianzhu Ma
[1] Dan Wang,et al. Integrating genomic, epigenomic, and transcriptomic features reveals modular signatures underlying poor prognosis in ovarian cancer. , 2013, Cell reports.
[2] Seth Blackshaw,et al. PIKE A Nuclear GTPase that Enhances PI3Kinase Activity and Is Regulated by Protein 4.1N , 2000, Cell.
[3] Scott H. Harrison,et al. Pattern Discovery in Breast Cancer Specific Protein Interaction Network , 2009, Summit on translational bioinformatics.
[4] Steven J. M. Jones,et al. Comprehensive molecular portraits of human breast tumours , 2013 .
[5] T. Hubbard,et al. A census of human cancer genes , 2004, Nature Reviews Cancer.
[6] Chad J. Miller,et al. Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling , 2015, Cell.
[7] Jing Chen,et al. NDEx, the Network Data Exchange. , 2015, Cell systems.
[8] Boleslaw K. Szymanski,et al. Supplemental Methods For: Identifying Robust Communities and Multi-community Nodes by Combining Top-down and Bottom-up Approaches to Clustering , 2022 .
[9] Gavin MacBeath,et al. A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks , 2014, Nature Genetics.
[10] Alan M. Frieze,et al. Random graphs , 2006, SODA '06.
[11] Kern Rei Chng,et al. Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles , 2015, Nucleic acids research.
[12] F. Supek,et al. MUFFINN: cancer gene discovery via network analysis of somatic mutation data , 2016, Genome Biology.
[13] Rayleigh. The Problem of the Random Walk , 1905, Nature.
[14] Andrew M. Gross,et al. Network-based stratification of tumor mutations , 2013, Nature Methods.
[15] C. Sander,et al. Mutual exclusivity analysis identifies oncogenic network modules. , 2012, Genome research.
[16] Jure Leskovec,et al. Supervised random walks: predicting and recommending links in social networks , 2010, WSDM '11.
[17] Martin L. Smith,et al. Regulation of the c-met Proto-oncogene Promoter by p53* , 1999, The Journal of Biological Chemistry.
[18] C. C. Santini,et al. Unmasking Determinants of Specificity in the Human Kinome , 2015, Cell.
[19] O. Pereira-smith,et al. Primary and Compensatory Roles for RB Family Members at Cell Cycle Gene Promoters That Are Deacetylated and Downregulated in Doxorubicin-Induced Senescence of Breast Cancer Cells , 2006, Molecular and Cellular Biology.
[20] D. Bikle,et al. The Recruitment of Phosphatidylinositol 3-Kinase to the E-cadherin-Catenin Complex at the Plasma Membrane Is Required for Calcium-induced Phospholipase C-γ1 Activation and Human Keratinocyte Differentiation* , 2007, Journal of Biological Chemistry.
[21] Gary D Bader,et al. International network of cancer genome projects , 2010, Nature.
[22] Christian A. Rees,et al. Molecular portraits of human breast tumours , 2000, Nature.
[23] Benjamin J. Raphael,et al. Network propagation: a universal amplifier of genetic associations , 2017, Nature Reviews Genetics.
[24] Gary D Bader,et al. Pathway and network analysis of cancer genomes , 2015, Nature Methods.
[25] Jun Wang,et al. C/EBPδ targets cyclin D1 for proteasome-mediated degradation via induction of CDC27/APC3 expression , 2010, Proceedings of the National Academy of Sciences.
[26] S. Gabriel,et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.
[27] D. Haussler,et al. The Somatic Genomic Landscape of Glioblastoma , 2013, Cell.
[28] Albert-László Barabási,et al. Statistical mechanics of complex networks , 2001, ArXiv.
[29] Joshua D. Campbell,et al. NetSig: network-based discovery from cancer genomes , 2017, Nature Methods.
[30] Christopher A. Miller,et al. Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors , 2011, BMC Medical Genomics.
[31] A. Nobel,et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[32] Steven J. M. Jones,et al. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer , 2015, Cell.
[33] A. Sarin,et al. The Anti-apoptotic Effect of Notch-1 Requires p56lck-dependent, Akt/PKB-mediated Signaling in T Cells* , 2004, Journal of Biological Chemistry.
[34] Dexter Pratt,et al. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. , 2017, Cancer research.
[35] Dexter Pratt,et al. NDEx: A Community Resource for Sharing and Publishing of Biological Networks. , 2017, Methods in molecular biology.
[36] Gary D. Bader,et al. Pathway Commons, a web resource for biological pathway data , 2010, Nucleic Acids Res..
[37] S. Deb,et al. Transcriptional activation of the human epidermal growth factor receptor promoter by human p53 , 1996, Molecular and cellular biology.
[38] Charles M. Perou,et al. Deconstructing the molecular portraits of breast cancer , 2010, Molecular oncology.
[39] Xia Li,et al. Network-based survival-associated module biomarker and its crosstalk with cell death genes in ovarian cancer , 2015, Scientific Reports.
[40] Joshua M. Stuart,et al. The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.
[41] Benjamin J. Raphael,et al. Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.
[42] Lee A. D. Cooper,et al. The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies , 2017, Nature Communications.
[43] K. Fujiki,et al. Detrimental effects of Notch1 signaling activated by cadmium in renal proximal tubular epithelial cells , 2014, Cell Death and Disease.
[44] David Z. Chen,et al. Architecture of the human regulatory network derived from ENCODE data , 2012, Nature.
[45] Emanuel J. V. Gonçalves,et al. A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.
[46] Roded Sharan,et al. Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer , 2015, PLoS Comput. Biol..
[47] Leslie M Shaw,et al. Activation of Phosphoinositide 3-OH Kinase by the α6β4 Integrin Promotes Carcinoma Invasion , 1997, Cell.
[48] K. Kinzler,et al. Cancer Genome Landscapes , 2013, Science.
[49] D Jamieson,et al. Influence of pharmacogenetics on response and toxicity in breast cancer patients treated with doxorubicin and cyclophosphamide , 2010, British Journal of Cancer.
[50] Teresa M. Przytycka,et al. Understanding Genotype-Phenotype Effects in Cancer via Network Approaches , 2016, PLoS Comput. Biol..
[51] Benjamin J. Raphael,et al. Pan-Cancer Network Analysis Identifies Combinations of Rare Somatic Mutations across Pathways and Protein Complexes , 2014, Nature Genetics.
[52] David Owen,et al. Molecular structure, function, and dynamics of clathrin-mediated membrane traffic. , 2014, Cold Spring Harbor perspectives in biology.
[53] A. Toker,et al. Protein Kinase C–Dependent Mobilization of the α6β4 Integrin from Hemidesmosomes and Its Association with Actin-Rich Cell Protrusions Drive the Chemotactic Migration of Carcinoma Cells , 1999, The Journal of cell biology.
[54] Nan Qiao,et al. Gene expression-based classification and regulatory networks of pediatric acute lymphoblastic leukemia. , 2009, Blood.
[55] P. Kleihues,et al. Epidemiology and etiology of gliomas , 2005, Acta Neuropathologica.
[56] Michael C. Mozer,et al. Optimizing Classifier Performance via an Approximation to the Wilcoxon-Mann-Whitney Statistic , 2003, ICML.
[57] Jimmy Ba,et al. Adam: A Method for Stochastic Optimization , 2014, ICLR.