Computational Exome And Genome Analysis

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Computational Exome And Genome Analysis

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Author : Peter N. Robinson
language : en
Publisher: CRC Press
Release Date : 2017-09-13

Computational Exome And Genome Analysis written by Peter N. Robinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-13 with Computers categories.

Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.

Computational Exome And Genome Analysis

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Author : Peter N. Robinson
language : en
Publisher: CRC Press
Release Date : 2017-09-13

Computational Exome And Genome Analysis written by Peter N. Robinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-13 with Computers categories.

Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.

Computational Exome And Genome Analysis

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Author : Peter Nicholas Robinson
language : en
Publisher: Chapman & Hall/CRC Mathematical and Computational Biology
Release Date : 2017

Computational Exome And Genome Analysis written by Peter Nicholas Robinson and has been published by Chapman & Hall/CRC Mathematical and Computational Biology this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with Computational biology categories.

Cover -- Half Title -- Series Editor -- Published Titles -- Title -- Copyright -- Dedication -- Contents -- Who is this book for? -- Preface -- Contributors -- Part I Introduction -- Chapter 1 Introduction: Whole Exome and Genome Sequencing -- Chapter 2 NGS Technology -- Chapter 3 Illumina Technology -- Chapter 4 Data -- Part II Raw Data Processing -- Chapter 5 FASTQ Format -- Chapter 6 Raw Data: Quality Control -- Chapter 7 Trimming -- Part III Alignment -- Chapter 8 Alignment: Mapping Reads to the Reference Genome -- Chapter 9 SAM/BAM Format -- Chapter 10 Postprocessing the Alignment -- Chapter 11 Alignment Data: Quality Control -- Part IV Variant Calling -- Chapter 12 Variant Calling and Quality- Based Filtering -- Chapter 13 Variant Call Format (VCF) -- Chapter 14 Jannovar -- Chapter 15 Variant Annotation -- Chapter 16 Variant Calling: Quality Control -- Chapter 17 Integrative Genomics Viewer (IGV): Visualizing Alignments and Variants -- Chapter 18 De Novo Variants -- Chapter 19 Structural Variation -- Part V Variant Filtering -- Chapter 20 Pedigree and Linkage Analysis -- Chapter 21 Intersection Analysis and Rare Variant Association Studies -- Chapter 22 Variant Frequency Analysis -- Chapter 23 Variant Pathogenicity Prediction -- Part VI Prioritization -- Chapter 24 Variant Prioritization -- Chapter 25 Prioritization by Random Walk Analysis -- Chapter 26 Phenotype Analysis -- Chapter 27 Exomiser and Genomiser -- Chapter 28 Medical Interpretation -- Part VII Cancer -- Chapter 29 A (Very) Short Introduction to Cancer -- Chapter 30 Somatic Variants in Cancer -- Chapter 31 Tumor Evolution and Sample Purity -- Chapter 32 Driver Mutations and Mutational Signatures -- Appendix A Hints and Answers -- References -- Index

Computational Immunology

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Author : Shyamasree Ghosh
language : en
Publisher: CRC Press
Release Date : 2020-01-31

Computational Immunology written by Shyamasree Ghosh and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-01-31 with Medical categories.

Computational Immunology: Applications focuses on different mathematical models, statistical tools, techniques, and computational modelling that helps in understanding complex phenomena of the immune system and its biological functions. The book also focuses on the latest developments in computational biology in designing of drugs, targets, biomarkers for early detection and prognosis of a disease. It highlights the applications of computational methods in deciphering the complex processes of the immune system and its role in health and disease. This book discusses the most essential topics, including Next generation sequencing (NGS) and computational immunology Computational modelling and biology of diseases Drug designing Computation and identification of biomarkers Application in organ transplantation Application in disease detection and therapy Computational methods and applications in understanding of the invertebrate immune system S Ghosh is MSc, PhD, PGDHE, PGDBI, is PhD from IICB, CSIR, Kolkata, awarded the prestigious National Scholarship from the Government of India. She has worked and published extensively in glycobiology, sialic acids, immunology, stem cells and nanotechnology. She has authored several publications that include books and encyclopedia chapters in reputed journals and books.

Analyzing High Dimensional Gene Expression And Dna Methylation Data With R

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Author : Hongmei Zhang
language : en
Publisher: CRC Press
Release Date : 2020-05-14

Analyzing High Dimensional Gene Expression And Dna Methylation Data With R written by Hongmei Zhang and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-05-14 with Computers categories.

Analyzing high-dimensional gene expression and DNA methylation data with R is the first practical book that shows a ``pipeline" of analytical methods with concrete examples starting from raw gene expression and DNA methylation data at the genome scale. Methods on quality control, data pre-processing, data mining, and further assessments are presented in the book, and R programs based on simulated data and real data are included. Codes with example data are all reproducible. Features: • Provides a sequence of analytical tools for genome-scale gene expression data and DNA methylation data, starting from quality control and pre-processing of raw genome-scale data. • Organized by a parallel presentation with explanation on statistical methods and corresponding R packages/functions in quality control, pre-processing, and data analyses (e.g., clustering and networks). • Includes source codes with simulated and real data to reproduce the results. Readers are expected to gain the ability to independently analyze genome-scaled expression and methylation data and detect potential biomarkers. This book is ideal for students majoring in statistics, biostatistics, and bioinformatics and researchers with an interest in high dimensional genetic and epigenetic studies.

Computational Biology And Bioinformatics

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Author : Ka-Chun Wong
language : en
Publisher: CRC Press
Release Date : 2016-04-27

Computational Biology And Bioinformatics written by Ka-Chun Wong and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-27 with Science categories.

The advances in biotechnology such as the next generation sequencing technologies are occurring at breathtaking speed. Advances and breakthroughs give competitive advantages to those who are prepared. However, the driving force behind the positive competition is not only limited to the technological advancement, but also to the companion data analy

Big Data In Omics And Imaging

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Author : Momiao Xiong
language : en
Publisher: CRC Press
Release Date : 2017-12-01

Big Data In Omics And Imaging written by Momiao Xiong and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-12-01 with Mathematics categories.

Big Data in Omics and Imaging: Association Analysis addresses the recent development of association analysis and machine learning for both population and family genomic data in sequencing era. It is unique in that it presents both hypothesis testing and a data mining approach to holistically dissecting the genetic structure of complex traits and to designing efficient strategies for precision medicine. The general frameworks for association analysis and machine learning, developed in the text, can be applied to genomic, epigenomic and imaging data. FEATURES Bridges the gap between the traditional statistical methods and computational tools for small genetic and epigenetic data analysis and the modern advanced statistical methods for big data Provides tools for high dimensional data reduction Discusses searching algorithms for model and variable selection including randomization algorithms, Proximal methods and matrix subset selection Provides real-world examples and case studies Will have an accompanying website with R code The book is designed for graduate students and researchers in genomics, bioinformatics, and data science. It represents the paradigm shift of genetic studies of complex diseases– from shallow to deep genomic analysis, from low-dimensional to high dimensional, multivariate to functional data analysis with next-generation sequencing (NGS) data, and from homogeneous populations to heterogeneous population and pedigree data analysis. Topics covered are: advanced matrix theory, convex optimization algorithms, generalized low rank models, functional data analysis techniques, deep learning principle and machine learning methods for modern association, interaction, pathway and network analysis of rare and common variants, biomarker identification, disease risk and drug response prediction.

Encyclopedia Of Bioinformatics And Computational Biology

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Author :
language : en
Publisher: Elsevier
Release Date : 2018-08-21

Encyclopedia Of Bioinformatics And Computational Biology written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-21 with Medical categories.

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Stochastic Modelling For Systems Biology Third Edition

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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2018-12-07

Stochastic Modelling For Systems Biology Third Edition written by Darren J. Wilkinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-07 with Mathematics categories.

Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Metabolomics

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Author : Ron Wehrens
language : en
Publisher: CRC Press
Release Date : 2019-08-19

Metabolomics written by Ron Wehrens and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-08-19 with Mathematics categories.

Metabolomics is the scientific study of the chemical processes in a living system, environment and nutrition. It is a relatively new omics science, but the potential applications are wide, including medicine, personalized medicine and intervention studies, food and nutrition, plants, agriculture and environmental science. The topics presented and discussed in this book are based on the European Molecular Biology Organization (EMBO) practical courses in metabolomics bioinformatics taught to those working in the field, from masters to postgraduate students, PhDs, postdoctoral and early PIs. The book covers the basics and fundamentals of data acquisition and analytical technologies, but the primary focus is data handling and data analysis. The mentioning and usage of a particular data analysis tool has been avoided; rather, the focus is on the concepts and principles of data processing and analysis. The material has been class-tested and includes lots of examples, computing and exercises. Key Features: Provides an overview of qualitative /quantitative methods in metabolomics Offers an introduction to the key concepts of metabolomics, including experimental design and technology Covers data handling, processing, analysis, data standards and sharing Contains lots of examples to illustrate the topics Includes contributions from some of the leading researchers in the field of metabolomics with extensive teaching experiences