Providing an accessible overview of both Bayesian methods and gene expression, Bayesian Analysis of Gene Expression Data features numerous problems and solutions that emphasize methodology and application. Offering a clear introduction to the computational methods required for Bayesian statistics, the book provides an extensive review of Bayesian analysis and advanced topics for bioinformatics. A supplementary website including relevant software and further datasets round out the coverage in this text destined to become a vital resource for graduate students, medical consultants, and employees…mehr
Providing an accessible overview of both Bayesian methods and gene expression, Bayesian Analysis of Gene Expression Data features numerous problems and solutions that emphasize methodology and application. Offering a clear introduction to the computational methods required for Bayesian statistics, the book provides an extensive review of Bayesian analysis and advanced topics for bioinformatics. A supplementary website including relevant software and further datasets round out the coverage in this text destined to become a vital resource for graduate students, medical consultants, and employees of private firms working with gene expression data. This book provides an introduction to both Bayesian methods and gene expression, accessible to people with backgrounds in either. The text is enhanced by the inclusion of numerous problems and solutions, designed with an emphasis on methodology and application. There is also a supplementary website including the relevant software and further datasets. The book provides an extensive review of Bayesian analysis and advanced topics for bioinformatics, including an advanced section that extensively details the necessary applications and offers an introduction to the computational methods required for Bayesian statistics.
The book is split into four parts, Part I introducing the fundamentals of Bayesian statistics, both modeling and computation. Part II builds on this, providing a more detailed introduction to the computational methods necessary for Bayesian statistics. Part III presents an introduction to the basic biology needed to work with microarrays, written specifically to enable those readers with no experience in the laboratory to understand. Part IV elaborates extensively on applications, including advanced topics for Bioinformatics research.
Bani Mallick, Department of Statistics, Texas A&M University, USA. Veera Balandandayuthapani, Department of Biostatistics, Anderson Cancer Center, Texas, USA. David L. Gold, Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, The State University of New York, USA.
Inhaltsangabe
Table of Notation. 1 Bioinformatics and Gene Expression Experiments. 1.1 Introduction. 1.2 About This Book. 2 Basic Biology. 2.1 Background. 2.1.1 DNA Structures and Transcription. 2.2 Gene Expression Microarray Experiments. 3 Bayesian Linear Models for Gene Expression. 3.1 Introduction. 3.2 Bayesian Analysis of a Linear Model. 3.3 Bayesian Linear Models for Differential Expression. 3.4 Bayesian ANOVA for Gene Selection. 3.5 Robust ANOVA model with Mixtures of Singular Distributions. 3.6 Case Study. 3.7 Accounting for Nuisance Effects. 3.8 Summary and Further Reading. 4 Bayesian Multiple Testing and False Discovery Rate Analysis. 4.1 Introduction to Multiple Testing. 4.2 False Discovery Rate Analysis. 4.3 Bayesian False Discovery Rate Analysis. 4.4 Bayesian Estimation of FDR. 4.5 FDR and Decision Theory. 4.6 FDR and bFDR Summary. 5 Bayesian Classification for Microarray Data. 5.1 Introduction. 5.2 Classification and Discriminant Rules. 5.3 Bayesian Discriminant Analysis. 5.4 Bayesian Regression Based Approaches to Classification. 5.5 Bayesian Nonlinear Classification. 5.6 Prediction and Model Choice. 5.7 Examples. 5.8 Discussion. 6 Bayesian Hypothesis Inference for Gene Classes. 6.1 Interpreting Microarray Results. 6.2 Gene Classes. 6.3 Bayesian Enrichment Analysis. 6.4 Multivariate Gene Class Detection. 6.5 Summary. 7 Unsupervised Classification and Bayesian Clustering. 7.1 Introduction to Bayesian Clustering for Gene Expression Data. 7.2 Hierarchical Clustering. 7.3 K-Means Clustering. 7.4 Model-Based Clustering. 7.5 Model-Based Agglomerative Hierarchical Clustering. 7.6 Bayesian Clustering. 7.7 Principal Components. 7.8 Mixture Modeling. 7.8.1 Label Switching. 7.9 Clustering Using Dirichlet Process Prior. 7.9.1 Infinite Mixture of Gaussian Distributions. 8 Bayesian Graphical Models. 8.1 Introduction. 8.2 Probabilistic Graphical Models. 8.3 Bayesian Networks. 8.4 Inference for Network Models. 9 Advanced Topics. 9.1 Introduction. 9.2 Analysis of Time Course Gene Expression Data. 9.3 Survival Prediction Using Gene Expression Data. Appendix A: Basics of Bayesian Modeling. A.1 Basics. A.1.1 The General Representation Theorem. A.1.2 Bayes' Theorem. A.1.3 Models Based on Partial Exchangeability. A.1.4 Modeling with Predictors. A.1.5 Prior Distributions. A.1.6 Decision Theory and Posterior and Predictive Inferences. A.1.7 Predictive Distributions. A.1.8 Examples. A.2 Bayesian Model Choice. A.3 Hierarchical Modeling. A.4 Bayesian Mixture Modeling. A.5 Bayesian Model Averaging. Appendix B: Bayesian Computation Tools. B.1 Overview. B.2 Large-Sample Posterior Approximations. B.2.1 The Bayesian Central Limit Theorem. B.2.2 Laplace's Method. B.3 Monte Carlo Integration. B.4 Importance Sampling. B.5 Rejection Sampling. B.6 Gibbs Sampling. B.7 The Metropolis Algorithm and Metropolis-Hastings. B.8 Advanced Computational Methods. B.8.1 Block MCMC. B.8.2 Truncated Posterior Spaces. B.8.3 Latent Variables and the Auto-Probit Model. B.8.4 Bayesian Simultaneous Credible Envelopes. B.8.5 Proposal Updating. B.9 Posterior Convergence Diagnostics. B.10 MCMC Convergence and the Proposal. B.10.1 Graphical Checks for MCMC Methods. B.10.2 Convergence Statistics. B.10.3 MCMC in High-Throughput Analysis. B.11 Summary. References. Index.
Table of Notation. 1 Bioinformatics and Gene Expression Experiments. 1.1 Introduction. 1.2 About This Book. 2 Basic Biology. 2.1 Background. 2.1.1 DNA Structures and Transcription. 2.2 Gene Expression Microarray Experiments. 3 Bayesian Linear Models for Gene Expression. 3.1 Introduction. 3.2 Bayesian Analysis of a Linear Model. 3.3 Bayesian Linear Models for Differential Expression. 3.4 Bayesian ANOVA for Gene Selection. 3.5 Robust ANOVA model with Mixtures of Singular Distributions. 3.6 Case Study. 3.7 Accounting for Nuisance Effects. 3.8 Summary and Further Reading. 4 Bayesian Multiple Testing and False Discovery Rate Analysis. 4.1 Introduction to Multiple Testing. 4.2 False Discovery Rate Analysis. 4.3 Bayesian False Discovery Rate Analysis. 4.4 Bayesian Estimation of FDR. 4.5 FDR and Decision Theory. 4.6 FDR and bFDR Summary. 5 Bayesian Classification for Microarray Data. 5.1 Introduction. 5.2 Classification and Discriminant Rules. 5.3 Bayesian Discriminant Analysis. 5.4 Bayesian Regression Based Approaches to Classification. 5.5 Bayesian Nonlinear Classification. 5.6 Prediction and Model Choice. 5.7 Examples. 5.8 Discussion. 6 Bayesian Hypothesis Inference for Gene Classes. 6.1 Interpreting Microarray Results. 6.2 Gene Classes. 6.3 Bayesian Enrichment Analysis. 6.4 Multivariate Gene Class Detection. 6.5 Summary. 7 Unsupervised Classification and Bayesian Clustering. 7.1 Introduction to Bayesian Clustering for Gene Expression Data. 7.2 Hierarchical Clustering. 7.3 K-Means Clustering. 7.4 Model-Based Clustering. 7.5 Model-Based Agglomerative Hierarchical Clustering. 7.6 Bayesian Clustering. 7.7 Principal Components. 7.8 Mixture Modeling. 7.8.1 Label Switching. 7.9 Clustering Using Dirichlet Process Prior. 7.9.1 Infinite Mixture of Gaussian Distributions. 8 Bayesian Graphical Models. 8.1 Introduction. 8.2 Probabilistic Graphical Models. 8.3 Bayesian Networks. 8.4 Inference for Network Models. 9 Advanced Topics. 9.1 Introduction. 9.2 Analysis of Time Course Gene Expression Data. 9.3 Survival Prediction Using Gene Expression Data. Appendix A: Basics of Bayesian Modeling. A.1 Basics. A.1.1 The General Representation Theorem. A.1.2 Bayes' Theorem. A.1.3 Models Based on Partial Exchangeability. A.1.4 Modeling with Predictors. A.1.5 Prior Distributions. A.1.6 Decision Theory and Posterior and Predictive Inferences. A.1.7 Predictive Distributions. A.1.8 Examples. A.2 Bayesian Model Choice. A.3 Hierarchical Modeling. A.4 Bayesian Mixture Modeling. A.5 Bayesian Model Averaging. Appendix B: Bayesian Computation Tools. B.1 Overview. B.2 Large-Sample Posterior Approximations. B.2.1 The Bayesian Central Limit Theorem. B.2.2 Laplace's Method. B.3 Monte Carlo Integration. B.4 Importance Sampling. B.5 Rejection Sampling. B.6 Gibbs Sampling. B.7 The Metropolis Algorithm and Metropolis-Hastings. B.8 Advanced Computational Methods. B.8.1 Block MCMC. B.8.2 Truncated Posterior Spaces. B.8.3 Latent Variables and the Auto-Probit Model. B.8.4 Bayesian Simultaneous Credible Envelopes. B.8.5 Proposal Updating. B.9 Posterior Convergence Diagnostics. B.10 MCMC Convergence and the Proposal. B.10.1 Graphical Checks for MCMC Methods. B.10.2 Convergence Statistics. B.10.3 MCMC in High-Throughput Analysis. B.11 Summary. References. Index.
Rezensionen
"The target audience for this book is clearly statisticians rather than biologists ... It does provide a very useful overview of statistical genomics for anyone working in the field." (The Quarterly Review of Biology, 1 March 2012)
"Bioinformatics researchers from many fields will find much value in this book." (Mathematical Reviews, 2011)
"Experienced readers will find the review of advanced methods for bioinformatics challenging and attainable. This book will interest graduate students in statistics and bioinformatics researchers from many fields." (Book News, December 2009)
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