GENOME ANNOTATION CHAPMAN HALL CRC MATHEMATICAL AND COMPUTATIONAL BIOLOGY

Download Genome Annotation Chapman Hall Crc Mathematical And Computational Biology ebook PDF or Read Online books in PDF, EPUB, and Mobi Format. Click Download or Read Online button to GENOME ANNOTATION CHAPMAN HALL CRC MATHEMATICAL AND COMPUTATIONAL BIOLOGY book pdf for free now.

Genome Annotation

Author : Jung Soh
ISBN : 9781439841181
Genre : Science
File Size : 31.31 MB
Format : PDF, ePub, Mobi
Download : 601
Read : 490

The success of individualized medicine, advanced crops, and new and sustainable energy sources requires thoroughly annotated genomic information and the integration of this information into a coherent model. A thorough overview of this field, Genome Annotation explores automated genome analysis and annotation from its origins to the challenges of next-generation sequencing data analysis. The book initially takes you through the last 16 years since the sequencing of the first complete microbial genome. It explains how current analysis strategies were developed, including sequencing strategies, statistical models, and early annotation systems. The authors then present visualization techniques for displaying integrated results as well as state-of-the-art annotation tools, including MAGPIE, Ensembl, Bluejay, and Galaxy. They also discuss the pipelines for the analysis and annotation of complex, next-generation DNA sequencing data. Each chapter includes references and pointers to relevant tools. As very few existing genome annotation pipelines are capable of dealing with the staggering amount of DNA sequence information, new strategies must be developed to accommodate the needs of today’s genome researchers. Covering this topic in detail, Genome Annotation provides you with the foundation and tools to tackle this challenging and evolving area. Suitable for both students new to the field and professionals who deal with genomic information in their work, the book offers two genome annotation systems on an accompanying CD-ROM.
Category: Science

Computational Exome And Genome Analysis

Author : Peter N. Robinson
ISBN : 9781351650816
Genre : Mathematics
File Size : 79.59 MB
Format : PDF, Kindle
Download : 916
Read : 256

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.
Category: Mathematics

Rna Seq Data Analysis

Author : Eija Korpelainen
ISBN : 9781466595019
Genre : Mathematics
File Size : 38.18 MB
Format : PDF, ePub, Docs
Download : 745
Read : 1261

The State of the Art in Transcriptome Analysis RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes. Balanced Coverage of Theory and Practice Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools and practical examples. Accessible to both bioinformaticians and nonprogramming wet lab scientists, the examples illustrate the use of command-line tools, R, and other open source tools, such as the graphical Chipster software. The Tools and Methods to Get Started in Your Lab Taking readers through the whole data analysis workflow, this self-contained guide provides a detailed overview of the main RNA-seq data analysis methods and explains how to use them in practice. It is suitable for researchers from a wide variety of backgrounds, including biology, medicine, genetics, and computer science. The book can also be used in a graduate or advanced undergraduate course.
Category: Mathematics

Computational Systems Biology Of Cancer

Author : Emmanuel Barillot
ISBN : 9781439831441
Genre : Science
File Size : 20.72 MB
Format : PDF, Docs
Download : 811
Read : 735

The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models—integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencing. Offering promising insights on how to defeat cancer, the emerging field of systems biology captures the complexity of biological phenomena using mathematical and computational tools. Novel Approaches to Fighting Cancer Drawn from the authors’ decade-long work in the cancer computational systems biology laboratory at Institut Curie (Paris, France), Computational Systems Biology of Cancer explains how to apply computational systems biology approaches to cancer research. The authors provide proven techniques and tools for cancer bioinformatics and systems biology research. Effectively Use Algorithmic Methods and Bioinformatics Tools in Real Biological Applications Suitable for readers in both the computational and life sciences, this self-contained guide assumes very limited background in biology, mathematics, and computer science. It explores how computational systems biology can help fight cancer in three essential aspects: Categorising tumours Finding new targets Designing improved and tailored therapeutic strategies Each chapter introduces a problem, presents applicable concepts and state-of-the-art methods, describes existing tools, illustrates applications using real cases, lists publically available data and software, and includes references to further reading. Some chapters also contain exercises. Figures from the text and scripts/data for reproducing a breast cancer data analysis are available at www.cancer-systems-biology.net.
Category: Science

Meta Analysis And Combining Information In Genetics And Genomics

Author : Rudy Guerra
ISBN : 142001062X
Genre : Mathematics
File Size : 53.21 MB
Format : PDF, ePub
Download : 543
Read : 563

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.
Category: Mathematics

Bioinformatics

Author : Shui Qing Ye
ISBN : 1584888113
Genre : Science
File Size : 63.35 MB
Format : PDF
Download : 640
Read : 1058

An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer specialists must possess a fundamental understanding of biological problems. Bridging the gap between biology and computer science, Bioinformatics: A Practical Approach assimilates current bioinformatics knowledge and tools relevant to the omics age into one cohesive, concise, and self-contained volume. Written by expert contributors from around the world, this practical book presents the most state-of-the-art bioinformatics applications. The first part focuses on genome analysis, common DNA analysis tools, phylogenetics analysis, and SNP and haplotype analysis. After chapters on microarray, SAGE, regulation of gene expression, miRNA, and siRNA, the book presents widely applied programs and tools in proteome analysis, protein sequences, protein functions, and functional annotation of proteins in murine models. The last part introduces the programming languages used in biology, website and database design, and the interchange of data between Microsoft Excel and Access. Keeping complex mathematical deductions and jargon to a minimum, this accessible book offers both the theoretical underpinnings and practical applications of bioinformatics.
Category: Science

Python For Bioinformatics Second Edition

Author : Sebastian Bassi
ISBN : 9781351976954
Genre : Mathematics
File Size : 43.78 MB
Format : PDF, Mobi
Download : 642
Read : 393

In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.
Category: Mathematics

Introduction To Bioinformatics

Author : Anna Tramontano
ISBN : 1584885696
Genre : Science
File Size : 28.32 MB
Format : PDF, ePub
Download : 133
Read : 590

Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. Requiring only a limited mathematical and statistical background, the book shows how to efficiently apply these approaches to biological data and evaluate the resulting information. The author, an expert bioinformatics researcher, first addresses the ways of storing and retrieving the enormous amount of biological data produced every day and the methods of decrypting the information encoded by a genome. She then covers the tools that can detect and exploit the evolutionary and functional relationships among biological elements. Subsequent chapters illustrate how to predict the three-dimensional structure of a protein. The book concludes with a discussion of the future of bioinformatics. Even though the future will undoubtedly offer new tools for tackling problems, most of the fundamental aspects of bioinformatics will not change. This resource provides the essential information to understand bioinformatics methods, ultimately facilitating in the solution of biological problems.
Category: Science

Bioinformatics

Author : Andrzej Polanski
ISBN : 9783540241669
Genre : Computers
File Size : 40.6 MB
Format : PDF, ePub, Mobi
Download : 595
Read : 1170

This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.
Category: Computers

Introduction To Bio Ontologies

Author : Peter N. Robinson
ISBN : 9781439836668
Genre : Computers
File Size : 66.17 MB
Format : PDF, Docs
Download : 950
Read : 232

Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications. The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL. The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology. The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications. With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies. Web Resource Software and data designed to complement material in the text are available on the book’s website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a compressed archive of data and ontology files used in some of the exercises. It also offers teaching/presentation slides and links to other relevant websites. This book provides readers with the foundation to use ontologies as a starting point for new bioinformatics research projects or to support current molecular genetics research projects. By supplying a self-contained introduction to OBO ontologies and the Semantic Web, it bridges the gap between both fields and helps readers see what each can contribute to the analysis and understanding of biomedical data.
Category: Computers