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Author : Jean W. MacCluer
Publisher :
ISBN 13 :
Total Pages : 110 pages
Book Rating : 4.:/5 (17 download)
Download or read book Approaches to Analysis of Genome Wide Data written by Jean W. MacCluer and published by . This book was released on 2009 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Altuna Akalin
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 462 pages
Book Rating : 4.4/5 (987 download)
Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Author : Gad Abraham
Publisher :
ISBN 13 :
Total Pages : 282 pages
Book Rating : 4.:/5 (816 download)
Download or read book Scalable Approaches for Analysis of Human Genome-wide Expression and Genetic Variation Data written by Gad Abraham and published by . This book was released on 2012 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Daniel O. Stram
Publisher : Springer Science & Business Media
ISBN 13 : 1461494435
Total Pages : 344 pages
Book Rating : 4.4/5 (614 download)
Download or read book Design, Analysis, and Interpretation of Genome-Wide Association Scans written by Daniel O. Stram and published by Springer Science & Business Media. This book was released on 2013-11-23 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the statistical aspects of designing, analyzing and interpreting the results of genome-wide association scans (GWAS studies) for genetic causes of disease using unrelated subjects. Particular detail is given to the practical aspects of employing the bioinformatics and data handling methods necessary to prepare data for statistical analysis. The goal in writing this book is to give statisticians, epidemiologists, and students in these fields the tools to design a powerful genome-wide study based on current technology. The other part of this is showing readers how to conduct analysis of the created study. Design and Analysis of Genome-Wide Association Studies provides a compendium of well-established statistical methods based upon single SNP associations. It also provides an introduction to more advanced statistical methods and issues. Knowing that technology, for instance large scale SNP arrays, is quickly changing, this text has significant lessons for future use with sequencing data. Emphasis on statistical concepts that apply to the problem of finding disease associations irrespective of the technology ensures its future applications. The author includes current bioinformatics tools while outlining the tools that will be required for use with extensive databases from future large scale sequencing projects. The author includes current bioinformatics tools while outlining additional issues and needs arising from the extensive databases from future large scale sequencing projects.
Author : Robert C. Elston
Publisher : John Wiley & Sons
ISBN 13 : 9780471486312
Total Pages : 860 pages
Book Rating : 4.4/5 (863 download)
Download or read book Biostatistical Genetics and Genetic Epidemiology written by Robert C. Elston and published by John Wiley & Sons. This book was released on 2002-04-22 with total page 860 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Human Genetics and Genetic Epidemiology" ist der 3. Band aus der sehr erfolgreichen Reihe 'Wiley Biostatistics Reference Series', die auf Artikeln der "Encyclopedia of Biostatistics" basiert. Dieser Band gibt einen topaktuellen und umfassenden Überblick über ein Forschungsgebiet, das insbesondere im Zuge des Human-Genomprojekts eine regelrechte Explosion an Forschungsaktivitäten erlebt hat. Enthalten sind komplett aktualisierte Artikel aus der "Encyclopedia of Biostatistics" sowie über 25% neue Artikel. Mit einem komplexen System an Querverweisen, die das Auffinden der gewünschten Information erheblich erleichtern. Eine interessante Lektüre für Genetiker, Epidemiologen, Biostatistiker und Forscher in diesen Bereichen.
Author : 陳偉銘
Publisher :
ISBN 13 :
Total Pages : 107 pages
Book Rating : 4.:/5 (87 download)
Download or read book Systems Biology Approaches for Analysis of High-Throughput Genome-Wide Data written by 陳偉銘 and published by . This book was released on 2013 with total page 107 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Xiangqing Sun
Publisher : Frontiers Media SA
ISBN 13 : 2889199320
Total Pages : 86 pages
Book Rating : 4.8/5 (891 download)
Download or read book Novel Approaches to the Analysis of Family Data in Genetic Epidemiology written by Xiangqing Sun and published by Frontiers Media SA. This book was released on 2016-08-17 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome-wide association studies (GWAS) for complex disorders with large case-control populations have been performed on hundreds of traits in more than 1200 published studies (http://www.genome.gov/gwastudies/) but the variants detected by GWAS account for little of the heritability of these traits, leading to an increasing interest in using family based designs. While GWAS studies are designed to find common variants with low to moderate attributable risks, family based studies are expected to find rare variants with high attributable risk. Because family-based designs can better control both genetic and environmental background, this study design is robust to heterogeneity and population stratification. Moreover, in family-based analysis, the background genetic variation can be modeled to control the residual variance which could increase the power to identify disease associated rare variants. Analysis of families can also help us gain knowledge about disease transmission and inheritance patterns. Although a family-based design has the advantage of being robust to false positives, novel and powerful methods to analyze families in genetic epidemiology continue to be needed, especially for the interaction between genetic and environmental factors associated with disease. Moreover, with the rapid development of sequencing technology, advances in approaches to the design and analysis of sequencing data in families are also greatly needed. The 11 articles in this book all introduce new methodology and, using family data, substantial new findings are presented in the areas of infectious diseases, diabetes, eye traits, autism spectrum disorder and prostate cancer.
Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309224187
Total Pages : 354 pages
Book Rating : 4.3/5 (92 download)
Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Author : Cedric Gondro
Publisher : Springer
ISBN 13 : 3319144758
Total Pages : 283 pages
Book Rating : 4.3/5 (191 download)
Download or read book Primer to Analysis of Genomic Data Using R written by Cedric Gondro and published by Springer. This book was released on 2015-05-18 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Krishnarao Appasani
Publisher : Cambridge University Press
ISBN 13 : 1107042763
Total Pages : 449 pages
Book Rating : 4.1/5 (7 download)
Download or read book Genome-Wide Association Studies written by Krishnarao Appasani and published by Cambridge University Press. This book was released on 2016-01-14 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experts from academia and industry highlight the potential of genome-wide association studies from basic science to clinical and biotechnological/pharmaceutical applications.
Author : Rudy Guerra
Publisher : Chapman and Hall/CRC
ISBN 13 : 9781584885221
Total Pages : 360 pages
Book Rating : 4.8/5 (852 download)
Download or read book Meta-analysis and Combining Information in Genetics and Genomics written by Rudy Guerra and published by Chapman and Hall/CRC. This book was released on 2009-07-07 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Novel Techniques for Analyzing and Combining Data from Modern Biological Studies Broadens the Traditional Definition of Meta-Analysis With the diversity of data and meta-data now available, there is increased interest in analyzing multiple studies beyond statistical approaches of formal meta-analysis. Covering an extensive range of quantitative information combination methods, Meta-analysis and Combining Information in Genetics and Genomics looks at how to analyze multiple studies from a broad perspective. After presenting the basic ideas and tools of meta-analysis, the book addresses the combination of similar data types: genotype data from genome-wide linkage scans and data derived from microarray gene expression experiments. The expert contributors show how some data combination problems can arise even within the same basic framework and offer solutions to these problems. They also discuss the combined analysis of different data types, giving readers an opportunity to see data combination approaches in action across a wide variety of genome-scale investigations. As heterogeneous data sets become more common, biological understanding will be significantly aided by jointly analyzing such data using fundamentally sound statistical methodology. This book provides many novel techniques for analyzing data from modern biological studies that involve multiple data sets, either of the same type or multiple data sources.
Author : Nan M. Laird
Publisher : Springer Science & Business Media
ISBN 13 : 1441973389
Total Pages : 226 pages
Book Rating : 4.4/5 (419 download)
Download or read book The Fundamentals of Modern Statistical Genetics written by Nan M. Laird and published by Springer Science & Business Media. This book was released on 2010-12-13 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the statistical models and methods that are used to understand human genetics, following the historical and recent developments of human genetics. Starting with Mendel’s first experiments to genome-wide association studies, the book describes how genetic information can be incorporated into statistical models to discover disease genes. All commonly used approaches in statistical genetics (e.g. aggregation analysis, segregation, linkage analysis, etc), are used, but the focus of the book is modern approaches to association analysis. Numerous examples illustrate key points throughout the text, both of Mendelian and complex genetic disorders. The intended audience is statisticians, biostatisticians, epidemiologists and quantitatively- oriented geneticists and health scientists wanting to learn about statistical methods for genetic analysis, whether to better analyze genetic data, or to pursue research in methodology. A background in intermediate level statistical methods is required. The authors include few mathematical derivations, and the exercises provide problems for students with a broad range of skill levels. No background in genetics is assumed.
Author : William K. Scott
Publisher : John Wiley & Sons
ISBN 13 : 1118123913
Total Pages : 340 pages
Book Rating : 4.1/5 (181 download)
Download or read book Genetic Analysis of Complex Disease written by William K. Scott and published by John Wiley & Sons. This book was released on 2021-12-06 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic Analysis of Complex Diseases An up-to-date and complete treatment of the strategies, designs and analysis methods for studying complex genetic disease in human beings In the newly revised Third Edition of Genetic Analysis of Complex Diseases, a team of distinguished geneticists delivers a comprehensive introduction to the most relevant strategies, designs and methods of analysis for the study of complex genetic disease in humans. The book focuses on concepts and designs, thereby offering readers a broad understanding of common problems and solutions in the field based on successful applications in the design and execution of genetic studies. This edited volume contains contributions from some of the leading voices in the area and presents new chapters on high-throughput genomic sequencing, copy-number variant analysis and epigenetic studies. Providing clear and easily referenced overviews of the considerations involved in genetic analysis of complex human genetic disease, including sampling, design, data collection, linkage and association studies and social, legal and ethical issues. Genetic Analysis of Complex Diseases also provides: A thorough introduction to study design for the identification of genes in complex traits Comprehensive explorations of basic concepts in genetics, disease phenotype definition and the determination of the genetic components of disease Practical discussions of modern bioinformatics tools for analysis of genetic data Reflecting on responsible conduct of research in genetic studies, as well as linkage analysis and data management New expanded chapter on complex genetic interactions This latest edition of Genetic Analysis of Complex Diseases is a must-read resource for molecular biologists, human geneticists, genetic epidemiologists and pharmaceutical researchers. It is also invaluable for graduate students taking courses in statistical genetics or genetic epidemiology.
Author : Andrea S. Foulkes
Publisher : Springer Science & Business Media
ISBN 13 : 038789554X
Total Pages : 264 pages
Book Rating : 4.3/5 (878 download)
Download or read book Applied Statistical Genetics with R written by Andrea S. Foulkes and published by Springer Science & Business Media. This book was released on 2009-04-28 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.
Author : Florian Frommlet
Publisher : Springer
ISBN 13 : 1447153103
Total Pages : 232 pages
Book Rating : 4.4/5 (471 download)
Download or read book Phenotypes and Genotypes written by Florian Frommlet and published by Springer. This book was released on 2016-02-12 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: This timely text presents a comprehensive guide to genetic association, a new and rapidly expanding field that aims to elucidate how our genetic code (genotypes) influences the traits we possess (phenotypes). The book provides a detailed review of methods of gene mapping used in association with experimental crosses, as well as genome-wide association studies. Emphasis is placed on model selection procedures for analyzing data from large-scale genome scans based on specifically designed modifications of the Bayesian information criterion. Features: presents a thorough introduction to the theoretical background to studies of genetic association (both genetic and statistical); reviews the latest advances in the field; illustrates the properties of methods for mapping quantitative trait loci using computer simulations and the analysis of real data; discusses open challenges; includes an extensive statistical appendix as a reference for those who are not totally familiar with the fundamentals of statistics.
Author : Philip Chester Cooley
Publisher : RTI Press
ISBN 13 : 1934831166
Total Pages : 163 pages
Book Rating : 4.9/5 (348 download)
Download or read book Methods in Statistical Genomics written by Philip Chester Cooley and published by RTI Press. This book was released on 2016-08-29 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: The objective of this book is to describe procedures for analyzing genome-wide association studies (GWAS). Some of the material is unpublished and contains commentary and unpublished research; other chapters (Chapters 4 through 7) have been published in other journals. Each previously published chapter investigates a different genomics model, but all focus on identifying the strengths and limitations of various statistical procedures that have been applied to different GWAS scenarios.
Author : Michael J. Korenberg
Publisher : Springer Science & Business Media
ISBN 13 : 1597453900
Total Pages : 569 pages
Book Rating : 4.5/5 (974 download)
Download or read book Microarray Data Analysis written by Michael J. Korenberg and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 569 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this new volume, renowned authors contribute fascinating, cutting-edge insights into microarray data analysis. Information on an array of topics is included in this innovative book including in-depth insights into presentations of genomic signal processing. Also detailed is the use of tiling arrays for large genomes analysis. The protocols follow the successful Methods in Molecular BiologyTM series format, offering step-by-step instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls.
