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Microarray Image Analysis

Author: Karl Fraser
Publisher: CRC Press
ISBN: 9781420091540
Size: 16.71 MB
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To harness the high-throughput potential of DNA microarray technology, it is crucial that the analysis stages of the process are decoupled from the requirements of operator assistance. Microarray Image Analysis: An Algorithmic Approach presents an automatic system for microarray image processing to make this decoupling a reality. The proposed system integrates and extends traditional analytical-based methods and custom-designed novel algorithms. The book first explores a new technique that takes advantage of a multiview approach to image analysis and addresses the challenges of applying powerful traditional techniques, such as clustering, to full-scale microarray experiments. It then presents an effective feature identification approach, an innovative technique that renders highly detailed surface models, a new approach to subgrid detection, a novel technique for the background removal process, and a useful technique for removing "noise." The authors also develop an expectation–maximization (EM) algorithm for modeling gene regulatory networks from gene expression time series data. The final chapter describes the overall benefits of these techniques in the biological and computer sciences and reviews future research topics. This book systematically brings together the fields of image processing, data analysis, and molecular biology to advance the state of the art in this important area. Although the text focuses on improving the processes involved in the analysis of microarray image data, the methods discussed can be applied to a broad range of medical and computer vision analysis areas.

Foundations Of Statistical Algorithms

Author: Claus Weihs
Publisher: CRC Press
ISBN: 1439878870
Size: 32.69 MB
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A new and refreshingly different approach to presenting the foundations of statistical algorithms, Foundations of Statistical Algorithms: With References to R Packages reviews the historical development of basic algorithms to illuminate the evolution of today’s more powerful statistical algorithms. It emphasizes recurring themes in all statistical algorithms, including computation, assessment and verification, iteration, intuition, randomness, repetition and parallelization, and scalability. Unique in scope, the book reviews the upcoming challenge of scaling many of the established techniques to very large data sets and delves into systematic verification by demonstrating how to derive general classes of worst case inputs and emphasizing the importance of testing over a large number of different inputs. Broadly accessible, the book offers examples, exercises, and selected solutions in each chapter as well as access to a supplementary website. After working through the material covered in the book, readers should not only understand current algorithms but also gain a deeper understanding of how algorithms are constructed, how to evaluate new algorithms, which recurring principles are used to tackle some of the tough problems statistical programmers face, and how to take an idea for a new method and turn it into something practically useful.

Statistical Learning And Data Science

Author: Mireille Gettler Summa
Publisher: CRC Press
ISBN: 143986764X
Size: 15.32 MB
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Data analysis is changing fast. Driven by a vast range of application domains and affordable tools, machine learning has become mainstream. Unsupervised data analysis, including cluster analysis, factor analysis, and low dimensionality mapping methods continually being updated, have reached new heights of achievement in the incredibly rich data world that we inhabit. Statistical Learning and Data Science is a work of reference in the rapidly evolving context of converging methodologies. It gathers contributions from some of the foundational thinkers in the different fields of data analysis to the major theoretical results in the domain. On the methodological front, the volume includes conformal prediction and frameworks for assessing confidence in outputs, together with attendant risk. It illustrates a wide range of applications, including semantics, credit risk, energy production, genomics, and ecology. The book also addresses issues of origin and evolutions in the unsupervised data analysis arena, and presents some approaches for time series, symbolic data, and functional data. Over the history of multidimensional data analysis, more and more complex data have become available for processing. Supervised machine learning, semi-supervised analysis approaches, and unsupervised data analysis, provide great capability for addressing the digital data deluge. Exploring the foundations and recent breakthroughs in the field, Statistical Learning and Data Science demonstrates how data analysis can improve personal and collective health and the well-being of our social, business, and physical environments.

Exploratory Data Analysis With Matlab Second Edition

Author: Wendy L. Martinez
Publisher: CRC Press
ISBN: 1439812217
Size: 44.37 MB
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Since the publication of the bestselling first edition, many advances have been made in exploratory data analysis (EDA). Covering innovative approaches for dimensionality reduction, clustering, and visualization, Exploratory Data Analysis with MATLAB®, Second Edition uses numerous examples and applications to show how the methods are used in practice. New to the Second Edition Discussions of nonnegative matrix factorization, linear discriminant analysis, curvilinear component analysis, independent component analysis, and smoothing splines An expanded set of methods for estimating the intrinsic dimensionality of a data set Several clustering methods, including probabilistic latent semantic analysis and spectral-based clustering Additional visualization methods, such as a rangefinder boxplot, scatterplots with marginal histograms, biplots, and a new method called Andrews’ images Instructions on a free MATLAB GUI toolbox for EDA Like its predecessor, this edition continues to focus on using EDA methods, rather than theoretical aspects. The MATLAB codes for the examples, EDA toolboxes, data sets, and color versions of all figures are available for download at http://pi-sigma.info

Statistical Analysis Of Gene Expression Microarray Data

Author: Terry Speed
Publisher: CRC Press
ISBN: 9780203011232
Size: 63.77 MB
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Although less than a decade old, the field of microarray data analysis is now thriving and growing at a remarkable pace. Biologists, geneticists, and computer scientists as well as statisticians all need an accessible, systematic treatment of the techniques used for analyzing the vast amounts of data generated by large-scale gene expression studies. And there is arguably no group better qualified to do so than the authors of this book. Statistical Analysis of Gene Expression Microarray Data promises to become the definitive basic reference in the field. Under the editorship of Terry Speed, some of the world's most pre-eminent authorities have joined forces to present the tools, features, and problems associated with the analysis of genetic microarray data. These include:: Model-based analysis of oligonucleotide arrays, including expression index computation, outlier detection, and standard error applications Design and analysis of comparative experiments involving microarrays, with focus on \ two-color cDNA or long oligonucleotide arrays on glass slides Classification issues, including the statistical foundations of classification and an overview of different classifiers Clustering, partitioning, and hierarchical methods of analysis, including techniques related to principal components and singular value decomposition Although the technologies used in large-scale, high throughput assays will continue to evolve, statistical analysis will remain a cornerstone of their success and future development. Statistical Analysis of Gene Expression Microarray Data will help you meet the challenges of large, complex datasets and contribute to new methodological and computational advances.

Statistics And Data Analysis For Microarrays Using R And Bioconductor Second Edition

Author: Sorin Drăghici
Publisher: CRC Press
ISBN: 1439809763
Size: 14.25 MB
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Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems. New to the Second Edition Completely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying CD-ROM. With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data.

Structural Bioinformatics

Author: Forbes J. Burkowski
Publisher: CRC Press
ISBN: 1420011790
Size: 47.50 MB
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The Beauty of Protein Structures and the Mathematics behind Structural Bioinformatics Providing the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure. Helps Students Go Further in Their Study of Structural Biology Following some introductory material in the first few chapters, the text solves the longest common subsequence problem using dynamic programming and explains the science models for the Nussinov and MFOLD algorithms. It then reviews sequence alignment, along with the basic mathematical calculations needed for measuring the geometric properties of macromolecules. After looking at how coordinate transformations facilitate the translation and rotation of molecules in a 3D space, the author introduces structural comparison techniques, superposition algorithms, and algorithms that compare relationships within a protein. The final chapter explores how regression and classification are becoming more useful in protein analysis and drug design. At the Crossroads of Biology, Mathematics, and Computer Science Connecting biology, mathematics, and computer science, this practical text presents various bioinformatics topics and problems within a scientific methodology that emphasizes nature (the source of empirical observations), science (the mathematical modeling of the natural process), and computation (the science of calculating predictions and mathematical objects based on mathematical models).

Rough Fuzzy Image Analysis

Author: Sankar K. Pal
Publisher: CRC Press
ISBN: 9781439803301
Size: 38.29 MB
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Fuzzy sets, near sets, and rough sets are useful and important stepping stones in a variety of approaches to image analysis. These three types of sets and their various hybridizations provide powerful frameworks for image analysis. Emphasizing the utility of fuzzy, near, and rough sets in image analysis, Rough Fuzzy Image Analysis: Foundations and Methodologies introduces the fundamentals and applications in the state of the art of rough fuzzy image analysis. In the first chapter, the distinguished editors explain how fuzzy, near, and rough sets provide the basis for the stages of pictorial pattern recognition: image transformation, feature extraction, and classification. The text then discusses hybrid approaches that combine fuzzy sets and rough sets in image analysis, illustrates how to perform image analysis using only rough sets, and describes tolerance spaces and a perceptual systems approach to image analysis. It also presents a free, downloadable implementation of near sets using the Near Set Evaluation and Recognition (NEAR) system, which visualizes concepts from near set theory. In addition, the book covers an array of applications, particularly in medical imaging involving breast cancer diagnosis, laryngeal pathology diagnosis, and brain MR segmentation. Edited by two leading researchers and with contributions from some of the best in the field, this volume fully reflects the diversity and richness of rough fuzzy image analysis. It deftly examines the underlying set theories as well as the diverse methods and applications.

Primer To Analysis Of Genomic Data Using R

Author: Cedric Gondro
Publisher: Springer
ISBN: 3319144758
Size: 72.76 MB
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Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website./p

Introduction To Computational Biology

Author: Michael S. Waterman
Publisher: CRC Press
ISBN: 9780412993916
Size: 58.97 MB
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Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.