Gene Network Inference using Machine Learning and Graph Algorithms on Big Biomedical Data
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[1] Adrian E. Raftery,et al. Bayesian Model Averaging: A Tutorial , 2016 .
[2] Ka Yee Yeung,et al. Model-Based Clustering With Data Correction For Removing Artifacts In Gene Expression Data. , 2016, The annals of applied statistics.
[3] Leroy Hood,et al. Systems Biology and P4 Medicine: Past, Present, and Future , 2013, Rambam Maimonides medical journal.
[4] G. Schwarz. Estimating the Dimension of a Model , 1978 .
[5] Md. Islam,et al. Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks , 2013, Journal of Clinical Bioinformatics.
[6] Kai Wang,et al. Characterizing Dynamic Changes in the Human Blood Transcriptional Network , 2010, PLoS Comput. Biol..
[7] Avi Ma'ayan,et al. ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome , 2013, CD-ARES.
[8] S. Horvath,et al. Statistical Applications in Genetics and Molecular Biology , 2011 .
[9] Michal Linial,et al. Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..
[10] D. Madigan,et al. Model Selection and Accounting for Model Uncertainty in Graphical Models Using Occam's Window , 1994 .
[11] T. Ideker,et al. A decade of systems biology. , 2010, Annual review of cell and developmental biology.
[12] Ziv Bar-Joseph,et al. Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu , 2014, PLoS Comput. Biol..
[13] T. Golub,et al. A method for high-throughput gene expression signature analysis , 2006, Genome Biology.
[14] A. Califano,et al. Dialogue on Reverse‐Engineering Assessment and Methods , 2007, Annals of the New York Academy of Sciences.
[15] Korbinian Strimmer,et al. Identifying periodically expressed transcripts in microarray time series data , 2008, Bioinform..
[16] Adrian E. Raftery,et al. Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data , 2005, Bioinform..
[17] Roger E Bumgarner. Overview of DNA microarrays: types, applications, and their future. , 2013, Current protocols in molecular biology.
[18] A. Raftery. Bayesian Model Selection in Social Research , 1995 .
[19] Luis Ramirez,et al. Big Data Analysis Using Modern Statistical and Machine Learning Methods in Medicine , 2014, International neurourology journal.
[20] Matthias Dehmer,et al. Comparing large graphs efficiently by margins of feature vectors , 2007, Appl. Math. Comput..
[21] Vladimir Filkov,et al. Identifying Gene Regulatory Networks from Gene Expression Data , 2005 .
[22] S. Klamt,et al. Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation , 2013, BMC Systems Biology.
[23] Nir Friedman,et al. Inferring subnetworks from perturbed expression profiles , 2001, ISMB.
[24] H. Sebastian Seung,et al. Learning the parts of objects by non-negative matrix factorization , 1999, Nature.
[25] Andrew D. Rouillard,et al. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures , 2014, Nucleic Acids Res..
[26] Kevin Murphy,et al. Modelling Gene Expression Data using Dynamic Bayesian Networks , 2006 .
[27] Adrian E. Raftery,et al. Bayesian Model Averaging methods and R package for gene network construction , 2016 .
[28] B. Palsson,et al. The model organism as a system: integrating 'omics' data sets , 2006, Nature Reviews Molecular Cell Biology.
[29] Roger E Bumgarner,et al. Construction of regulatory networks using expression time-series data of a genotyped population , 2011, Proceedings of the National Academy of Sciences.
[30] A. G. de la Fuente,et al. From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis , 2010, PloS one.
[31] R. Tibshirani. Regression Shrinkage and Selection via the Lasso , 1996 .
[32] E. Schadt. Molecular networks as sensors and drivers of common human diseases , 2009, Nature.
[33] H. Zou,et al. Regularization and variable selection via the elastic net , 2005 .
[34] Elena Pereira,et al. Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers , 2015, PloS one.
[35] Diego di Bernardo,et al. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles , 2006, Bioinform..
[36] Andrey Alexeyenko,et al. Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis , 2014, BMC Bioinformatics.
[37] Pooja Jain,et al. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae , 2005, Nucleic Acids Res..
[38] Xin Chen,et al. TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..
[39] Stephan C. Schürer,et al. Kinome-wide activity models from diverse high-quality datasets , 2013 .
[40] Dario Floreano,et al. Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods , 2009, J. Comput. Biol..
[41] N. D. Clarke,et al. Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges , 2010, PloS one.
[42] Swarup Roy,et al. Big Data Analytics in Bioinformatics: A Machine Learning Perspective , 2015, ArXiv.
[43] D. Madigan,et al. Bayesian Model Averaging for Linear Regression Models , 1997 .
[44] Adrian E. Raftery,et al. CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks , 2015, Source Code for Biology and Medicine.
[45] Avi Ma'ayan,et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.
[46] B. Haibe-Kains,et al. Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks , 2014, Front. Cell Dev. Biol..
[47] Ronald W. Davis,et al. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.
[48] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[49] Adrian E. Raftery,et al. Fast Bayesian inference for gene regulatory networks using ScanBMA , 2014, BMC Systems Biology.
[50] John R Yates,et al. Mass spectrometry in high-throughput proteomics: ready for the big time , 2010, Nature Methods.
[51] M. Schroeder,et al. Drug target prioritization by perturbed gene expression and network information , 2015, Scientific Reports.
[52] T. Ideker,et al. Differential network biology , 2012, Molecular systems biology.
[53] S. Friend,et al. A network view of disease and compound screening , 2009, Nature Reviews Drug Discovery.
[54] Willem P. A. Ligtenberg,et al. Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors , 2012, BMC Bioinformatics.
[55] Patrik D'haeseleer,et al. Linear Modeling of mRNA Expression Levels During CNS Development and Injury , 1998, Pacific Symposium on Biocomputing.
[56] Julio Saez-Rodriguez,et al. Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge , 2011, Science Signaling.
[57] Jinwen Ma,et al. Compound signature detection on LINCS L1000 big data. , 2015, Molecular bioSystems.
[58] Adrian E. Raftery,et al. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data , 2012, BMC Systems Biology.
[59] S. Gabriel,et al. Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.
[60] Ziv Bar-Joseph,et al. STEM: a tool for the analysis of short time series gene expression data , 2006, BMC Bioinformatics.
[61] D. Floreano,et al. Revealing strengths and weaknesses of methods for gene network inference , 2010, Proceedings of the National Academy of Sciences.
[62] P. Brown,et al. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.