Data Mining for Genomics and Proteomics. Analysis of Gene and Protein Expression Data

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.

Praise for the First Edition “…a well-written book on data analysis and data mining that provides an excellent foundation…” —CHOICE “This is a must-read book for learning practical statistics and data analysis…” —Computing Reviews.com A proven go-to guide for data analysis, Making Sense of Data I: A Practical Guide to Exploratory Data Analysis and Data Mining, Second Edition focuses on basic data analysis approaches that are necessary to make timely and accurate decisions in a diverse range of projects. Based on the authors’ practical experience in implementing data analysis and data mining, the new edition provides clear explanations that guide readers from almost every field of study. In order to facilitate the needed steps when handling a data analysis or data mining project, a step-by-step approach aids professionals in carefully analyzing data and implementing results, leading to the development of smarter business decisions. The tools to summarize and interpret data in order to master data analysis are integrated throughout, and the Second Edition also features: Updated exercises for both manual and computer-aided implementation with accompanying worked examples New appendices with coverage on the freely available Traceis™ software, including tutorials using data from a variety of disciplines such as the social sciences, engineering, and finance New topical coverage on multiple linear regression and logistic regression to provide a range of widely used and transparent approaches Additional real-world examples of data preparation to establish a practical background for making decisions from data Making Sense of Data I: A Practical Guide to Exploratory Data Analysis and Data Mining, Second Edition is an excellent reference for researchers and professionals who need to achieve effective decision making from data. The Second Edition is also an ideal textbook for undergraduate and graduate-level courses in data analysis and data mining and is appropriate for cross-disciplinary courses found within computer science and engineering departments.

Written for practitioners of data mining, data cleaning and database management. Presents a technical treatment of data quality including process, metrics, tools and algorithms. Focuses on developing an evolving modeling strategy through an iterative data exploration loop and incorporation of domain knowledge. Addresses methods of detecting, quantifying and correcting data quality issues that can have a significant impact on findings and decisions, using commercially available tools as well as new algorithmic approaches. Uses case studies to illustrate applications in real life scenarios. Highlights new approaches and methodologies, such as the DataSphere space partitioning and summary based analysis techniques. Exploratory Data Mining and Data Cleaning will serve as an important reference for serious data analysts who need to analyze large amounts of unfamiliar data, managers of operations databases, and students in undergraduate or graduate level courses dealing with large scale data analys is and data mining.

Plant research has stood at the forefront of the genomics revolution. One of the first genome projects, the sequencing of the commonly used model organism Arabidopsis, has already yielded important results for the study of a broad array of crops such as corn and soybeans. With crop and food bioengineering only in its infancy, the need to understand the fundamental genetic mechanisms of plants will only become more pressing. A comprehensive guide to this fascinating area of genomics, Plant Genomics and Proteomics presents an integrated, broadly accessible treatment of the complex relationship between the genome, transcriptome, and proteome of plants. This clearly written text introduces the reader to the range of molecular techniques applicable to investigating the unique facets of plant growth, development, and response to the environment. Coverage includes: Functional and structural genomics addressed within the context of current techniques and challenges to come How to utilize DNA and protein sequence data Practical considerations for choosing and employing the most commonly available computer applications A review of applications for biotechnology, including genetic modification and defense against pathogens Bioinformatics tools and Web resources Numerous examples from the latest research throughout Assuming no specialized knowledge of plant biology on the part of its reader, Plant Genomics and Proteomics provides an invaluable resource for students and researchers in biotechnology, plant biology, genomics, and bioinformatics.

Data mining is the process of automatically searching large volumes of data for models and patterns using computational techniques from statistics, machine learning and information theory; it is the ideal tool for such an extraction of knowledge. Data mining is usually associated with a business or an organization's need to identify trends and profiles, allowing, for example, retailers to discover patterns on which to base marketing objectives. This book looks at both classical and recent techniques of data mining, such as clustering, discriminant analysis, logistic regression, generalized linear models, regularized regression, PLS regression, decision trees, neural networks, support vector machines, Vapnik theory, naive Bayesian classifier, ensemble learning and detection of association rules. They are discussed along with illustrative examples throughout the book to explain the theory of these methods, as well as their strengths and limitations. Key Features: Presents a comprehensive introduction to all techniques used in data mining and statistical learning, from classical to latest techniques. Starts from basic principles up to advanced concepts. Includes many step-by-step examples with the main software (R, SAS, IBM SPSS) as well as a thorough discussion and comparison of those software. Gives practical tips for data mining implementation to solve real world problems. Looks at a range of tools and applications, such as association rules, web mining and text mining, with a special focus on credit scoring. Supported by an accompanying website hosting datasets and user analysis. Statisticians and business intelligence analysts, students as well as computer science, biology, marketing and financial risk professionals in both commercial and government organizations across all business and industry sectors will benefit from this book.

In the last decade DNA sequencing costs have decreased over a magnitude, largely because of increasing throughput by incremental advances in tools, technologies and process improvements. Further cost reductions in this and in related proteomics technologies are expected as a result of the development of new high-throughput techniques and the computational machinery needed to analyze data generated. Automation in Proteomics & Genomics: An Engineering Case-Based Approach describes the automation technology currently in the areas of analysis, design, and integration, as well as providing basic biology concepts behind proteomics and genomics. The book also discusses the current technological limitations that can be viewed as an emerging market rather than a research bottleneck. Topics covered include: molecular biology fundamentals: from ‘blueprint’ (DNA) to ‘task list’ (RNA) to ‘molecular machine’ (protein); proteomics methods and technologies; modelling protein networks and interactions analysis via automation: DNA sequencing; microarrays and other parallelization technologies; protein characterization and identification; protein interaction and gene regulatory networks design via automation: DNA synthesis; RNA by design; building protein libraries; synthetic networks integration: multiple modalities; computational and experimental methods; trends in automation for genomics and proteomics new enabling technologies and future applications Automation in Proteomics & Genomics: An Engineering Case-Based Approach is an essential guide to the current capabilities and challenges of high-throughput analysis of genes and proteins for bioinformaticians, engineers, chemists, and biologists interested in developing a cross-discipline problem-solving based approach to systems biology.

Modeling and Analysis of Compositional Data presents a practical and comprehensive introduction to the analysis of compositional data along with numerous examples to illustrate both theory and application of each method. Based upon short courses delivered by the authors, it provides a complete and current compendium of fundamental to advanced methodologies along with exercises at the end of each chapter to improve understanding, as well as data and a solutions manual which is available on an accompanying website. Complementing Pawlowsky-Glahn’s earlier collective text that provides an overview of the state-of-the-art in this field, Modeling and Analysis of Compositional Data fills a gap in the literature for a much-needed manual for teaching, self learning or consulting.

Learn methods of data analysis and their application to real-world data sets This updated second edition serves as an introduction to data mining methods and models, including association rules, clustering, neural networks, logistic regression, and multivariate analysis. The authors apply a unified “white box” approach to data mining methods and models. This approach is designed to walk readers through the operations and nuances of the various methods, using small data sets, so readers can gain an insight into the inner workings of the method under review. Chapters provide readers with hands-on analysis problems, representing an opportunity for readers to apply their newly-acquired data mining expertise to solving real problems using large, real-world data sets. Data Mining and Predictive Analytics, Second Edition: Offers comprehensive coverage of association rules, clustering, neural networks, logistic regression, multivariate analysis, and R statistical programming language Features over 750 chapter exercises, allowing readers to assess their understanding of the new material Provides a detailed case study that brings together the lessons learned in the book Includes access to the companion website, www.dataminingconsultant.com, with exclusive password-protected instructor content Data Mining and Predictive Analytics, Second Edition will appeal to computer science and statistic students, as well as students in MBA programs, and chief executives.

The increasing integration between gene manipulation and genomics is embraced in this new book, Principles of Gene Manipulation and Genomics, which brings together for the first time the subjects covered by the best-selling books Principles of Gene Manipulation and Principles of Genome Analysis & Genomics. Comprehensively revised, updated and rewritten to encompass within one volume, basic and advanced gene manipulation techniques, genome analysis, genomics, transcriptomics, proteomics and metabolomics Includes two new chapters on the applications of genomics An accompanying website – www.blackwellpublishing.com/primrose – provides instructional materials for both student and lecturer use, including multiple choice questions, related websites, and all the artwork in a downloadable format. An essential reference for upper level undergraduate and graduate students of genetics, genomics, molecular biology and recombinant DNA technology.

Addresses the impacts of data mining on education and reviews applications in educational research teaching, and learning This book discusses the insights, challenges, issues, expectations, and practical implementation of data mining (DM) within educational mandates. Initial series of chapters offer a general overview of DM, Learning Analytics (LA), and data collection models in the context of educational research, while also defining and discussing data mining’s four guiding principles— prediction, clustering, rule association, and outlier detection. The next series of chapters showcase the pedagogical applications of Educational Data Mining (EDM) and feature case studies drawn from Business, Humanities, Health Sciences, Linguistics, and Physical Sciences education that serve to highlight the successes and some of the limitations of data mining research applications in educational settings. The remaining chapters focus exclusively on EDM’s emerging role in helping to advance educational research—from identifying at-risk students and closing socioeconomic gaps in achievement to aiding in teacher evaluation and facilitating peer conferencing. This book features contributions from international experts in a variety of fields. Includes case studies where data mining techniques have been effectively applied to advance teaching and learning Addresses applications of data mining in educational research, including: social networking and education; policy and legislation in the classroom; and identification of at-risk students Explores Massive Open Online Courses (MOOCs) to study the effectiveness of online networks in promoting learning and understanding the communication patterns among users and students Features supplementary resources including a primer on foundational aspects of educational mining and learning analytics Data Mining and Learning Analytics: Applications in Educational Research is written for both scientists in EDM and educators interested in using and integrating DM and LA to improve education and advance educational research.