Exploration and Analysis of DNA Microarray and Protein Array Data

Exploration and Analysis of DNA Microarray and Protein Array Data

Author: Dhammika Amaratunga

Publisher: John Wiley & Sons

Published: 2009-09-25

Total Pages: 270

ISBN-13: 0470317965

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A cutting-edge guide to the analysis of DNA microarray data Genomics is one of the major scientific revolutions of this century, and the use of microarrays to rapidly analyze numerous DNA samples has enabled scientists to make sense of mountains of genomic data through statistical analysis. Today, microarrays are being used in biomedical research to study such vital areas as a drug’s therapeutic value–or toxicity–and cancer-spreading patterns of gene activity. Exploration and Analysis of DNA Microarray and Protein Array Data answers the need for a comprehensive, cutting-edge overview of this important and emerging field. The authors, seasoned researchers with extensive experience in both industry and academia, effectively outline all phases of this revolutionary analytical technique, from the preprocessing to the analysis stage. Highlights of the text include: A review of basic molecular biology, followed by an introduction to microarrays and their preparation Chapters on processing scanned images and preprocessing microarray data Methods for identifying differentially expressed genes in comparative microarray experiments Discussions of gene and sample clustering and class prediction Extension of analysis methods to protein array data Numerous exercises for self-study as well as data sets and a useful collection of computational tools on the authors’ Web site make this important text a valuable resource for both students and professionals in the field.


Exploration and Analysis of DNA Microarray and Other High-Dimensional Data

Exploration and Analysis of DNA Microarray and Other High-Dimensional Data

Author: Dhammika Amaratunga

Publisher: John Wiley & Sons

Published: 2014-01-27

Total Pages: 320

ISBN-13: 111836452X

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Praise for the First Edition “...extremely well written...a comprehensive and up-to-date overview of this important field.” – Journal of Environmental Quality Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, Second Edition provides comprehensive coverage of recent advancements in microarray data analysis. A cutting-edge guide, the Second Edition demonstrates various methodologies for analyzing data in biomedical research and offers an overview of the modern techniques used in microarray technology to study patterns of gene activity. The new edition answers the need for an efficient outline of all phases of this revolutionary analytical technique, from preprocessing to the analysis stage. Utilizing research and experience from highly-qualified authors in fields of data analysis, Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, Second Edition features: A new chapter on the interpretation of findings that includes a discussion of signatures and material on gene set analysis, including network analysis New topics of coverage including ABC clustering, biclustering, partial least squares, penalized methods, ensemble methods, and enriched ensemble methods Updated exercises to deepen knowledge of the presented material and provide readers with resources for further study The book is an ideal reference for scientists in biomedical and genomics research fields who analyze DNA microarrays and protein array data, as well as statisticians and bioinformatics practitioners. Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, Second Edition is also a useful text for graduate-level courses on statistics, computational biology, and bioinformatics.


Design and Analysis of DNA Microarray Investigations

Design and Analysis of DNA Microarray Investigations

Author: Richard M. Simon

Publisher: Springer Science & Business Media

Published: 2006-05-09

Total Pages: 205

ISBN-13: 0387218661

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The analysis of gene expression profile data from DNA micorarray studies are discussed in this book. It provides a review of available methods and presents it in a manner that is intelligible to biologists. It offers an understanding of the design and analysis of experiments utilizing microarrays to benefit scientists. It includes an Appendix tutorial on the use of BRB-ArrayTools and step by step analyses of several major datasets using this software which is available from the National Cancer Institute.


Analyzing Microarray Gene Expression Data

Analyzing Microarray Gene Expression Data

Author: Geoffrey J. McLachlan

Publisher: John Wiley & Sons

Published: 2005-02-18

Total Pages: 366

ISBN-13: 0471726125

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A multi-discipline, hands-on guide to microarray analysis of biological processes Analyzing Microarray Gene Expression Data provides a comprehensive review of available methodologies for the analysis of data derived from the latest DNA microarray technologies. Designed for biostatisticians entering the field of microarray analysis as well as biologists seeking to more effectively analyze their own experimental data, the text features a unique interdisciplinary approach and a combined academic and practical perspective that offers readers the most complete and applied coverage of the subject matter to date. Following a basic overview of the biological and technical principles behind microarray experimentation, the text provides a look at some of the most effective tools and procedures for achieving optimum reliability and reproducibility of research results, including: An in-depth account of the detection of genes that are differentially expressed across a number of classes of tissues Extensive coverage of both cluster analysis and discriminant analysis of microarray data and the growing applications of both methodologies A model-based approach to cluster analysis, with emphasis on the use of the EMMIX-GENE procedure for the clustering of tissue samples The latest data cleaning and normalization procedures The uses of microarray expression data for providing important prognostic information on the outcome of disease


DNA Microarrays and Gene Expression

DNA Microarrays and Gene Expression

Author: Pierre Baldi

Publisher:

Published: 2002

Total Pages: 213

ISBN-13: 9780511071676

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DNA microarrays are revolutionizing biology and medicine. They can provide a snapshot of the level of gene expression in a cell and are therefore a powerful tool with which to study biological phenomena at the molecular level. This inter-disciplinary introduction will be essential reading for researchers of all disciplines.


Proteomic and Metabolomic Approaches to Biomarker Discovery

Proteomic and Metabolomic Approaches to Biomarker Discovery

Author: Haleem J. Issaq

Publisher: Academic Press

Published: 2013-05-20

Total Pages: 489

ISBN-13: 0123947952

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Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution


Functional Genomics

Functional Genomics

Author: Chris Town

Publisher: Springer Science & Business Media

Published: 2002-04-30

Total Pages: 222

ISBN-13: 9781402004568

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This volume provides an overview of the current state of plant genomics using a number of different approaches at a time when we celebrate the completion of the Arabidopsis genome sequence and begin the transition from structural to functional studies of this and other plant genomes. Topics covered include comparative genomics, computational approaches to gene identification and annotation and data management, high throughput methodologies for functional analysis at the levels of transcript, protein and metabolite, and methods for genome modification by both homologous and site-specific recombination. The book will provide a good introduction to some of the many aspects of genomics both for established plant biologists who wish to understand this rapidly developing area and for scientists early in their careers. It is also very suitable for a one-semester course in Plant Genomics at the upper-level undergraduate/graduate student level, where the individual chapters provide a framework that can be readily expanded by use of some of the many articles in the bibliographies.


Data Mining for Genomics and Proteomics

Data Mining for Genomics and Proteomics

Author: Darius M. Dziuda

Publisher: John Wiley & Sons

Published: 2010-07-16

Total Pages: 348

ISBN-13: 0470593407

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Data Mining for Genomics and Proteomics uses pragmatic examples and a complete case study to demonstrate step-by-step how biomedical studies can be used to maximize the chance of extracting new and useful biomedical knowledge from data. It is an excellent resource for students and professionals involved with gene or protein expression data in a variety of settings.


Multivariate Density Estimation

Multivariate Density Estimation

Author: David W. Scott

Publisher: John Wiley & Sons

Published: 2015-03-12

Total Pages: 384

ISBN-13: 1118575539

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Clarifies modern data analysis through nonparametric density estimation for a complete working knowledge of the theory and methods Featuring a thoroughly revised presentation, Multivariate Density Estimation: Theory, Practice, and Visualization, Second Edition maintains an intuitive approach to the underlying methodology and supporting theory of density estimation. Including new material and updated research in each chapter, the Second Edition presents additional clarification of theoretical opportunities, new algorithms, and up-to-date coverage of the unique challenges presented in the field of data analysis. The new edition focuses on the various density estimation techniques and methods that can be used in the field of big data. Defining optimal nonparametric estimators, the Second Edition demonstrates the density estimation tools to use when dealing with various multivariate structures in univariate, bivariate, trivariate, and quadrivariate data analysis. Continuing to illustrate the major concepts in the context of the classical histogram, Multivariate Density Estimation: Theory, Practice, and Visualization, Second Edition also features: Over 150 updated figures to clarify theoretical results and to show analyses of real data sets An updated presentation of graphic visualization using computer software such as R A clear discussion of selections of important research during the past decade, including mixture estimation, robust parametric modeling algorithms, and clustering More than 130 problems to help readers reinforce the main concepts and ideas presented Boxed theorems and results allowing easy identification of crucial ideas Figures in color in the digital versions of the book A website with related data sets Multivariate Density Estimation: Theory, Practice, and Visualization, Second Edition is an ideal reference for theoretical and applied statisticians, practicing engineers, as well as readers interested in the theoretical aspects of nonparametric estimation and the application of these methods to multivariate data. The Second Edition is also useful as a textbook for introductory courses in kernel statistics, smoothing, advanced computational statistics, and general forms of statistical distributions.


Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions

Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions

Author: Gisa Gerold

Publisher: Elsevier

Published: 2021-05-05

Total Pages: 268

ISBN-13: 0128230428

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Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions, Volume 109 in the Advances in Virus Research series, highlights state-of-the art mass spectrometry techniques to elucidate the tight interplay of vertebrate viruses and their host cells. The volume includes chapters on Spatio-temporal resolution of host protein complexes during virus entry, Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis, Applications of Mass Spectrometry Imaging in Virus Research, Mapping surfaceome dynamics during viral infection, Characterization of proteolytic events in virus-host interactions, Dynamic protein network modulation upon viral infection, and much more. Discusses the latest methodological breakthroughs in mass spectrometry-based proteomics Reviews how technology has advanced our knowledge on virus-host interactions Provides future perspectives on proteomics research in virology