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Bayesian inference for gene expression and proteomics
Authors: --- ---
ISBN: 052186092X 9780521860925 9781107636989 9780511584589 Year: 2006 Publisher: Cambridge Cambridge University Press

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Abstract

The interdisciplinary nature of bioinformatics presents a challenge in integrating concepts, methods, software, and multi-platform data. Although there have been rapid developments in new technology and an inundation of statistical methodology and software for the analysis of microarray gene expression arrays, there exist few rigorous statistical methods for addressing other types of high-throughput data, such as proteomic profiles that arise from mass spectrometry experiments. This book discusses the development and application of Bayesian methods in the analysis of high-throughput bioinformatics data from medical research and molecular and structural biology. The Bayesian approach has the advantage that evidence can be easily and flexibly incorporated into statistical models. A basic overview of the biological and technical principles behind multi-platform high-throughput experimentation is followed by expert reviews of Bayesian methodology, tools, and software for single group inference, group comparisons, classification and clustering, motif discovery and regulatory networks, and Bayesian networks and gene interactions.


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Advances in statistical bioinformatics : models and integrative inference for high-throughput data
Authors: --- ---
ISBN: 9781107027527 9781139226448 9781107250246 1107250242 1139226444 9781299707511 1299707513 9781107247758 1107247756 1107027527 1139891189 1107249414 1107248582 1107251079 Year: 2013 Publisher: Cambridge : Cambridge University Press,

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"Chapter 1 An introduction to next-generation biological platforms Virginia Mohlere, Wenting Wang, and Ganiraju Manyam The University of Texas. MD Anderson Cancer Center 1.1 Introduction When Sanger and Coulson first described a reliable, efficient method for DNA sequencing in 1975 (Sanger and Coulson, 1975), they made possible the full sequencing of both genes and entire genomes. Although the method was resource-intensive, many institutions invested in the necessary equipment, and Sanger sequencing remained the standard for the next 30 years. Refinement of the process increased read lengths from around 25 to 2 Mohlere, Wang, and Manyam almost 750 base pairs (Schadt et al., 2010, fig. 1). While this greatly increased efficiency and reliability, the Sanger method still required not only large equipment but significant human investment, as the process requires the work of several people. This prompted researchers and companies such as Applied Biosystems to seek improved sequencing techniques and instruments. Starting in the late 2000s, new instruments came on the market that, although they actually decreased read length, lessened run time and could be operated more easily with fewer human resources (Schadt et al., 2010). Despite discoveries that have illuminated new therapeutic targets, clarified the role of specific mutations in clinical response, and yielded new methods for diagnosis and predicting prognosis (Chin et al., 2011), the initial promise of genomic data has largely remained so far unfulfilled. The difficulties are numerous"--


Book
Bayesian inference for gene expression and proteomics
Authors: --- ---
ISBN: 051158458X Year: 2006 Publisher: Cambridge : Cambridge University Press,

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Abstract

The interdisciplinary nature of bioinformatics presents a research challenge in integrating concepts, methods, software and multiplatform data. Although there have been rapid developments in new technology and an inundation of statistical methods for addressing other types of high-throughput data, such as proteomic profiles that arise from mass spectrometry experiments. This book discusses the development and application of Bayesian methods in the analysis of high-throughput bioinformatics data that arise from medical, in particular, cancer research, as well as molecular and structural biology. The Bayesian approach has the advantage that evidence can be easily and flexibly incorporated into statistical methods. A basic overview of the biological and technical principles behind multi-platform high-throughput experimentation is followed by expert reviews of Bayesian methodology, tools and software for single group inference, group comparisons, classification and clustering, motif discovery and regulatory networks, and Bayesian networks and gene interactions.

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