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Bayesian Mixtures And Gene Expression Profiling With Missing Data
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Book Synopsis Bayesian Mixtures and Gene Expression Profiling with Missing Data by : Xiaoqing Chang
Download or read book Bayesian Mixtures and Gene Expression Profiling with Missing Data written by Xiaoqing Chang and published by . This book was released on 2008 with total page 58 pages. Available in PDF, EPUB and Kindle. Book excerpt: Missing values are one of the problems encountered in microarray data analysis. For many of the clustering algorithms applied in microarray data analysis, a complete data matrix is required. The traditional approach to solving the missing value problem is to fill in with estimates by imputation. Once the missing value estimates are imputed, they remain fixed during the following clustering process. Poorly estimated missing data points will impair reliability of the cluster analysis. In this particular study, we tested the ability of a novel clustering method based on a Bayesian infinite mixtures model (IMM) to accommodate missing data. In a simulation study and a prostate cancer dataset, by examining the specificity and sensitivity of clusters we demonstrated that the IMM method has increased precision of the cluster analysis without requirement of a prior imputation. IMM is more robust in clustering an incomplete dataset than traditional clustering methods, which require prior imputation.
Book Synopsis Mixture Models for Microarray Data Analysis by : Zhenyu Jia
Download or read book Mixture Models for Microarray Data Analysis written by Zhenyu Jia and published by . This book was released on 2006 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Nonlinear Mixture Models: A Bayesian Approach by : Tatiana V Tatarinova
Download or read book Nonlinear Mixture Models: A Bayesian Approach written by Tatiana V Tatarinova and published by World Scientific. This book was released on 2014-12-30 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, written by two mathematicians from the University of Southern California, provides a broad introduction to the important subject of nonlinear mixture models from a Bayesian perspective. It contains background material, a brief description of Markov chain theory, as well as novel algorithms and their applications. It is self-contained and unified in presentation, which makes it ideal for use as an advanced textbook by graduate students and as a reference for independent researchers. The explanations in the book are detailed enough to capture the interest of the curious reader, and complete enough to provide the necessary background material needed to go further into the subject and explore the research literature.In this book the authors present Bayesian methods of analysis for nonlinear, hierarchical mixture models, with a finite, but possibly unknown, number of components. These methods are then applied to various problems including population pharmacokinetics and gene expression analysis. In population pharmacokinetics, the nonlinear mixture model, based on previous clinical data, becomes the prior distribution for individual therapy. For gene expression data, one application included in the book is to determine which genes should be associated with the same component of the mixture (also known as a clustering problem). The book also contains examples of computer programs written in BUGS. This is the first book of its kind to cover many of the topics in this field.
Book Synopsis Bayesian Analysis of Gene Expression Data by : Bani K. Mallick
Download or read book Bayesian Analysis of Gene Expression Data written by Bani K. Mallick and published by John Wiley & Sons. This book was released on 2009-07-20 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of high-throughput genetic experimentation is evolving rapidly, with the advent of new technologies and new venues for data mining. Bayesian methods play a role central to the future of data and knowledge integration in the field of Bioinformatics. This book is devoted exclusively to Bayesian methods of analysis for applications to high-throughput gene expression data, exploring the relevant methods that are changing Bioinformatics. Case studies, illustrating Bayesian analyses of public gene expression data, provide the backdrop for students to develop analytical skills, while the more experienced readers will find the review of advanced methods challenging and attainable. This book: Introduces the fundamentals in Bayesian methods of analysis for applications to high-throughput gene expression data. Provides an extensive review of Bayesian analysis and advanced topics for Bioinformatics, including examples that extensively detail the necessary applications. Accompanied by website featuring datasets, exercises and solutions. Bayesian Analysis of Gene Expression Data offers a unique introduction to both Bayesian analysis and gene expression, aimed at graduate students in Statistics, Biomedical Engineers, Computer Scientists, Biostatisticians, Statistical Geneticists, Computational Biologists, applied Mathematicians and Medical consultants working in genomics. Bioinformatics researchers from many fields will find much value in this book.
Book Synopsis Bayesian Inference for Gene Expression and Proteomics by : Kim-Anh Do
Download or read book Bayesian Inference for Gene Expression and Proteomics written by Kim-Anh Do and published by Cambridge University Press. This book was released on 2006-07-24 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Expert overviews of Bayesian methodology, tools and software for multi-platform high-throughput experimentation.
Book Synopsis Bayesian Modeling in Bioinformatics by : Dipak K. Dey
Download or read book Bayesian Modeling in Bioinformatics written by Dipak K. Dey and published by CRC Press. This book was released on 2010-09-03 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. It presents a broad overview of statistical inference, clustering, and c
Book Synopsis Case Studies in Bayesian Statistical Modelling and Analysis by : Clair L. Alston
Download or read book Case Studies in Bayesian Statistical Modelling and Analysis written by Clair L. Alston and published by John Wiley & Sons. This book was released on 2012-10-10 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides an accessible foundation to Bayesian analysis using real world models This book aims to present an introduction to Bayesian modelling and computation, by considering real case studies drawn from diverse fields spanning ecology, health, genetics and finance. Each chapter comprises a description of the problem, the corresponding model, the computational method, results and inferences as well as the issues that arise in the implementation of these approaches. Case Studies in Bayesian Statistical Modelling and Analysis: Illustrates how to do Bayesian analysis in a clear and concise manner using real-world problems. Each chapter focuses on a real-world problem and describes the way in which the problem may be analysed using Bayesian methods. Features approaches that can be used in a wide area of application, such as, health, the environment, genetics, information science, medicine, biology, industry and remote sensing. Case Studies in Bayesian Statistical Modelling and Analysis is aimed at statisticians, researchers and practitioners who have some expertise in statistical modelling and analysis, and some understanding of the basics of Bayesian statistics, but little experience in its application. Graduate students of statistics and biostatistics will also find this book beneficial.
Book Synopsis Current Topics in Human Genetics by : Hong-wen Deng
Download or read book Current Topics in Human Genetics written by Hong-wen Deng and published by World Scientific. This book was released on 2007 with total page 963 pages. Available in PDF, EPUB and Kindle. Book excerpt: The sequencing of the human genome has brought human genetics into a new era of study resulting in the generation of an explosive amount of information. Application of genomic, proteomic, and bioinformatics technologies to the study of human genetics has made it possible for human genetic diseases to be studied on an unprecedented scale, both in silico and in the wet lab. This volume provides up-to-date coverage of the broad range of research topics in this fascinating area. In the first part of the book, a whole spectrum of approaches to human genetics research is reviewed for both background and the latest progress. In the second, important topics related to genetic research of various complex human diseases are discussed. The robust content and diverse array of subjects allow the book to serve as both a concise ?encyclopedia? that introduces basic and essential concepts of human genetics and an in-depth review of the current understanding of genetic research in human diseases.
Book Synopsis Bayesian Inference of Robust Growth Mixture Models with Non-ignorable Missing Data by : Laura Lu
Download or read book Bayesian Inference of Robust Growth Mixture Models with Non-ignorable Missing Data written by Laura Lu and published by . This book was released on 2011 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modern Inference Based on Health-Related Markers by : Albert Vexler
Download or read book Modern Inference Based on Health-Related Markers written by Albert Vexler and published by Academic Press. This book was released on 2024-03-18 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern Inference Based on Health Related Markers: Biomarkers and Statistical Decision Making provides a compendium of biomarkers based methodologies for respective health related fields and health related marker-specific biostatistical techniques. These methodologies may be applied to various problems encountered in medical and epidemiological studies. This book introduces correct and efficient testing mechanisms including procedures based on bootstrap and permutation methods with the aim of making these techniques assessable to practical researchers. In the biostatistical aspect, it describes how to correctly state testing problems, but it also includes novel results, which have appeared in current statistical publications. The book discusses also modern applied statistical developments that consider data-driven techniques, including empirical likelihood methods and other simple and efficient methods to derive statistical tools for use in health related studies. The title is a valuable source for biostaticians, practitioners, theoretical and applied investigators, and several members of the biomedical field who are interested in learning more about efficient evidence-based inference incorporating several forms of markers measurements. Combines modern epidemiological and public health discoveries with cutting-edge biostatistical tools, including relevant software codes, offering one full package to meet the demand of practical investigators Includes the emerging topics from real health fields in order to display recent advances and trends in Biomarkers and associated Decision Making areas Written by researchers who are leaders of Epidemiological and Biostatistical fields, presenting up-to-date investigations related to the measuring health issues, emerging fields of biomarkers, designing health studies and their implementations, clinical trials and their practices and applications, different aspects of genetic markers
Book Synopsis Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics by : Christine Sinoquet
Download or read book Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics written by Christine Sinoquet and published by Oxford University Press, USA. This book was released on 2014 with total page 483 pages. Available in PDF, EPUB and Kindle. Book excerpt: At the crossroads between statistics and machine learning, probabilistic graphical models (PGMs) provide a powerful formal framework to model complex data. An expanding volume of biological data of various types, the so-called 'omics', is in need of accurate and efficient methods for modelling and PGMs are expected to have a prominent role to play.
Book Synopsis Bayesian Infinite Mixture Models for Gene Clustering and Simultaneous Context Selection Using High-throughput Gene Expression Data by : Johannes M. Freudenberg
Download or read book Bayesian Infinite Mixture Models for Gene Clustering and Simultaneous Context Selection Using High-throughput Gene Expression Data written by Johannes M. Freudenberg and published by . This book was released on 2009 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applying clustering algorithms to identify groups of co-expressed genes is an important step in the analysis of high-throughput genomics data in order to elucidate affected biological pathways and transcriptional regulatory mechanisms. As these data are becoming ever more abundant the integration with both, existing biological knowledge and other experimental data becomes as crucial as the ability to perform such analysis in a meaningful but virtually unsupervised fashion. Clustering analysis often relies on ad-hoc methods such as k-means or hierarchical clustering with Euclidean distance but model-based methods such as the Bayesian Infinite Mixtures approach have been shown to produce better, more reproducible results. Further improvements have been accomplished by context-specific gene clustering algorithms designed to determine groups of co-expressed genes within a given subset of biological samples termed context. The complementary problem of finding differentially co-expressed genes given two or more contexts has been addressed but relies on the a priori definition of contexts and has not been used to facilitate the clustering of biological samples. Here we describe a new computational method using Bayesian infinite mixture models to cluster genes simultaneously utilizing the concept of differential co-expression as a unique similarity measure to find groups of similar samples. We compute a novel per-gene differential co-expression score that is reproducible and biologically meaningful. To evaluate, annotate, and display clustering results we present the integrated software package CLEAN which contains functionality for performing Clustering Enrichment Analysis, a method to functionally annotate clustering results and to assign a novel gene-specific functional coherence score. We apply our method to a number of simulated datasets comparing it to other commonly used clustering algorithms, and we re-analyze several breast cancer studies. We find that our unsupervised method determines patient groupings highly predictive of clinically relevant factors such as estrogen receptor status, tumor grade, and disease specific survival. Integrating these data with computationally and literature-derived information by applying CLEAN to the corresponding clusterings as well as the DCS signature substantiates these findings. Our results demonstrate the range of applications our methodology provides, offering a comprehensive analysis tool to study gene co-expression and differential co-expression patterns specific to the biological conditions of interest while simultaneously determining subsets of such biological conditions using a unique similarity measure that is complementary to the currently existing methods. It allows us to further our understanding of highly complex diseases such as breast cancer, and it has the potential to greatly facilitate research in many other, not yet as intensively studied areas.
Book Synopsis Handbook of Big Data Analytics by : Wolfgang Karl Härdle
Download or read book Handbook of Big Data Analytics written by Wolfgang Karl Härdle and published by Springer. This book was released on 2018-07-20 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: Addressing a broad range of big data analytics in cross-disciplinary applications, this essential handbook focuses on the statistical prospects offered by recent developments in this field. To do so, it covers statistical methods for high-dimensional problems, algorithmic designs, computation tools, analysis flows and the software-hardware co-designs that are needed to support insightful discoveries from big data. The book is primarily intended for statisticians, computer experts, engineers and application developers interested in using big data analytics with statistics. Readers should have a solid background in statistics and computer science.
Book Synopsis Computational Science - ICCS 2006 by :
Download or read book Computational Science - ICCS 2006 written by and published by Springer Science & Business Media. This book was released on 2006 with total page 1157 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Functional Plant Genomics by : J F Morot-Gaudry
Download or read book Functional Plant Genomics written by J F Morot-Gaudry and published by CRC Press. This book was released on 2013-11-13 with total page 714 pages. Available in PDF, EPUB and Kindle. Book excerpt: The openings offered by functional genomics reconciles organism biology and molecular biology, in order to define an integrative biology that should allow new insights about how a phenotype is built up from a genotype in interaction with its environment. This book covers a wide area of concepts and methods in genomics. This range from international
Book Synopsis Machine Learning and Computational Intelligence Techniques for Data Engineering by : Pradeep Singh
Download or read book Machine Learning and Computational Intelligence Techniques for Data Engineering written by Pradeep Singh and published by Springer Nature. This book was released on 2023-05-15 with total page 885 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprises the proceedings of the 4th International Conference on Machine Intelligence and Signal Processing (MISP2022). The contents of this book focus on research advancements in machine intelligence, signal processing, and applications. The book covers the real-time challenges involved while processing big data analytics and stream processing with the integration of smart data computing services and interconnectivity. It also includes the progress in signal processing to process the normal and abnormal categories of real-world signals such as signals generated from IoT devices, smart systems, speech, videos and involves biomedical signal processing: electrocardiogram (ECG), electroencephalogram (EEG), magnetoencephalography (MEG), electromyogram (EMG), etc. This book proves to be a valuable resource for those in academia and industry.
Book Synopsis Bioinformatics Algorithms by : Ion Mandoiu
Download or read book Bioinformatics Algorithms written by Ion Mandoiu and published by John Wiley & Sons. This book was released on 2008-02-25 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.
