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Oncogenic pathway signatures in human cancers as a guide to targeted therapies

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Cited by:

  1. David Lindgren & Gottfrid Sjödahl & Martin Lauss & Johan Staaf & Gunilla Chebil & Kristina Lövgren & Sigurdur Gudjonsson & Fredrik Liedberg & Oliver Patschan & Wiking Månsson & Mårten Fernö & Mattias , 2012. "Integrated Genomic and Gene Expression Profiling Identifies Two Major Genomic Circuits in Urothelial Carcinoma," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-11, June.
  2. Xuan Bich Trinh & Wiebren A A Tjalma & Luc Y Dirix & Peter B Vermeulen & Dieter J Peeters & Dimcho Bachvarov & Marie Plante & Els M Berns & Jozien Helleman & Steven J Van Laere & Peter A van Dam, 2011. "Microarray-Based Oncogenic Pathway Profiling in Advanced Serous Papillary Ovarian Carcinoma," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-9, July.
  3. Matthias Weber & Martin Schumacher & Harald Binder, 2014. "Regularized Regression Incorporating Network Information: Simultaneous Estimation of Covariate Coefficients and Connection Signs," Tinbergen Institute Discussion Papers 14-089/I, Tinbergen Institute.
  4. Junjie Su & Byung-Jun Yoon & Edward R Dougherty, 2009. "Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-10, December.
  5. Carey K Anders & Chaitanya R Acharya & David S Hsu & Gloria Broadwater & Katherine Garman & John A Foekens & Yi Zhang & Yixin Wang & Kelly Marcom & Jeffrey R Marks & Sayan Mukherjee & Joseph R Nevins , 2008. "Age-Specific Differences in Oncogenic Pathway Deregulation Seen in Human Breast Tumors," PLOS ONE, Public Library of Science, vol. 3(1), pages 1-8, January.
  6. Raul Aguirre-Gamboa & Hugo Gomez-Rueda & Emmanuel Martínez-Ledesma & Antonio Martínez-Torteya & Rafael Chacolla-Huaringa & Alberto Rodriguez-Barrientos & José G Tamez-Peña & Victor Treviño, 2013. "SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-9, September.
  7. Andrew E Teschendorff & Michel Journée & Pierre A Absil & Rodolphe Sepulchre & Carlos Caldas, 2007. "Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis," PLOS Computational Biology, Public Library of Science, vol. 3(8), pages 1-16, August.
  8. Dario Zimmerli & Chiara S. Brambillasca & Francien Talens & Jinhyuk Bhin & Renske Linstra & Lou Romanens & Arkajyoti Bhattacharya & Stacey E. P. Joosten & Ana Moises Silva & Nuno Padrao & Max D. Welle, 2022. "MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  9. Lucas Joseph & Carvalho Carlos & West Mike, 2009. "A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-28, February.
  10. Balázs Győrffy & Pawel Surowiak & Jan Budczies & András Lánczky, 2013. "Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-8, December.
  11. Brian D Bennett & Qing Xiong & Sayan Mukherjee & Terrence S Furey, 2012. "A Predictive Framework for Integrating Disparate Genomic Data Types Using Sample-Specific Gene Set Enrichment Analysis and Multi-Task Learning," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-13, September.
  12. Tae J Lee & Guang Yao & Dorothy C Bennett & Joseph R Nevins & Lingchong You, 2010. "Stochastic E2F Activation and Reconciliation of Phenomenological Cell-Cycle Models," PLOS Biology, Public Library of Science, vol. 8(9), pages 1-11, September.
  13. Verena Jabs & Karolina Edlund & Helena König & Marianna Grinberg & Katrin Madjar & Jörg Rahnenführer & Simon Ekman & Michael Bergkvist & Lars Holmberg & Katja Ickstadt & Johan Botling & Jan G Hengstle, 2017. "Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-23, November.
  14. Haleh Yasrebi & Peter Sperisen & Viviane Praz & Philipp Bucher, 2009. "Can Survival Prediction Be Improved By Merging Gene Expression Data Sets?," PLOS ONE, Public Library of Science, vol. 4(10), pages 1-14, October.
  15. Mariëlle I Gallegos Ruiz & Karijn Floor & Paul Roepman & José A Rodriguez & Gerrit A Meijer & Wolter J Mooi & Ewa Jassem & Jacek Niklinski & Thomas Muley & Nico van Zandwijk & Egbert F Smit & Kristin , 2008. "Integration of Gene Dosage and Gene Expression in Non-Small Cell Lung Cancer, Identification of HSP90 as Potential Target," PLOS ONE, Public Library of Science, vol. 3(3), pages 1-8, March.
  16. Eun Sung Park & Ju-Seog Lee & Hyun Goo Woo & Fenghuang Zhan & Joanna H Shih & John D Shaughnessy Jr. & J Frederic Mushinski, 2007. "Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis," PLOS ONE, Public Library of Science, vol. 2(1), pages 1-16, January.
  17. Hu, Jianwei & Chai, Hao, 2013. "Adjusted regularized estimation in the accelerated failure time model with high dimensional covariates," Journal of Multivariate Analysis, Elsevier, vol. 122(C), pages 96-114.
  18. Hung-Chia Chen & Wen Zou & Tzu-Pin Lu & James J Chen, 2014. "A Composite Model for Subgroup Identification and Prediction via Bicluster Analysis," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-14, October.
  19. Ju Han Kim, 2012. "Chapter 8: Biological Knowledge Assembly and Interpretation," PLOS Computational Biology, Public Library of Science, vol. 8(12), pages 1-12, December.
  20. Dennis Kostka & Rainer Spang, 2008. "Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures," PLOS Computational Biology, Public Library of Science, vol. 4(2), pages 1-6, February.
  21. Ilya Kupershmidt & Qiaojuan Jane Su & Anoop Grewal & Suman Sundaresh & Inbal Halperin & James Flynn & Mamatha Shekar & Helen Wang & Jenny Park & Wenwu Cui & Gregory D Wall & Robert Wisotzkey & Satnam , 2010. "Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-13, September.
  22. Xinan Yang & Kelly Regan & Yong Huang & Qingbei Zhang & Jianrong Li & Tanguy Y Seiwert & Ezra E W Cohen & H Rosie Xing & Yves A Lussier, 2012. "Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-18, January.
  23. Kuang Du & Shiyou Wei & Zhi Wei & Dennie T. Frederick & Benchun Miao & Tabea Moll & Tian Tian & Eric Sugarman & Dmitry I. Gabrilovich & Ryan J. Sullivan & Lunxu Liu & Keith T. Flaherty & Genevieve M. , 2021. "Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
  24. Peter Langfelder & Paul S Mischel & Steve Horvath, 2013. "When Is Hub Gene Selection Better than Standard Meta-Analysis?," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-16, April.
  25. David P A Cohen & Loredana Martignetti & Sylvie Robine & Emmanuel Barillot & Andrei Zinovyev & Laurence Calzone, 2015. "Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration," PLOS Computational Biology, Public Library of Science, vol. 11(11), pages 1-29, November.
  26. Daphne R Friedman & Joseph E Lucas & J Brice Weinberg, 2013. "Clinical and Biological Relevance of Genomic Heterogeneity in Chronic Lymphocytic Leukemia," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-11, February.
  27. Ruoqi Peng & Sriram Sridhar & Gaurav Tyagi & Jonathan E Phillips & Rosario Garrido & Paul Harris & Lisa Burns & Lorena Renteria & John Woods & Leena Chen & John Allard & Palanikumar Ravindran & Hans B, 2013. "Bleomycin Induces Molecular Changes Directly Relevant to Idiopathic Pulmonary Fibrosis: A Model for “Active” Disease," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-15, April.
  28. Yun-Yong Park & Eun Sung Park & Sang Bae Kim & Sang Cheol Kim & Bo Hwa Sohn & In-Sun Chu & Woojin Jeong & Gordon B Mills & Lauren Averett Byers & Ju-Seog Lee, 2012. "Development and Validation of a Prognostic Gene-Expression Signature for Lung Adenocarcinoma," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-10, September.
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