Introduction to Bio Ontologies

Author: Peter N. Robinson
Publisher: CRC Press
ISBN: 1439836663
Format: PDF
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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.

Computational Systems Biology of Cancer

Author: Emmanuel Barillot
Publisher: CRC Press
ISBN: 1439831440
Format: PDF, Kindle
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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.

Phenomics

Author: John M. Hancock
Publisher: CRC Press
ISBN: 1466590963
Format: PDF, Docs
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As our ability to acquire massive amounts of information about genome variation accelerates it is becoming increasingly clear that to make maximum use of this information we also need well-structured, systematic data on the phenotypic consequences of genomic changes. Phenomics is the new discipline of using standardized measurement techniques to characterize the phenotypic effects of random or systematic genome modifications (for example randomly generated mutations or systematic gene knockouts). This approach is now being used in an increasing range of species and systems. In this book, experts working in phenomics in most of the major species and systems that are currently being studied present overviews of the field from their different, but overlapping perspectives.

Methods in Medical Informatics

Author: Jules J. Berman
Publisher: CRC Press
ISBN: 9781439841846
Format: PDF
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Too often, healthcare workers are led to believe that medical informatics is a complex field that can only be mastered by teams of professional programmers. This is simply not the case. With just a few dozen simple algorithms, easily implemented with open source programming languages, you can fully utilize the medical information contained in clinical and research datasets. The common computational tasks of medical informatics are accessible to anyone willing to learn the basics. Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby demonstrates that biomedical professionals with fundamental programming knowledge can master any kind of data collection. Providing you with access to data, nomenclatures, and programming scripts and languages that are all free and publicly available, this book — Describes the structure of data sources used, with instructions for downloading Includes a clearly written explanation of each algorithm Offers equivalent scripts in Perl, Python, and Ruby, for each algorithm Shows how to write short, quickly learned scripts, using a minimal selection of commands Teaches basic informatics methods for retrieving, organizing, merging, and analyzing data sources Provides case studies that detail the kinds of questions that biomedical scientists can ask and answer with public data and an open source programming language Requiring no more than a working knowledge of Perl, Python, or Ruby, Methods in Medical Informatics will have you writing powerful programs in just a few minutes. Within its chapters, you will find descriptions of the basic methods and implementations needed to complete many of the projects you will encounter in your biomedical career.

Computational Exome and Genome Analysis

Author: Peter N. Robinson
Publisher: CRC Press
ISBN: 1351650815
Format: PDF, ePub
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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.

Meta analysis and Combining Information in Genetics and Genomics

Author: Rudy Guerra
Publisher: CRC Press
ISBN: 9781420010626
Format: PDF, ePub
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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.

An Introduction to Systems Biology

Author: Uri Alon
Publisher: CRC Press
ISBN: 1584886420
Format: PDF, Kindle
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Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.

Statistics and Data Analysis for Microarrays Using R and Bioconductor Second Edition

Author: Sorin Drăghici
Publisher: CRC Press
ISBN: 1439809763
Format: PDF, ePub, Mobi
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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.

Systems Biology

Author: Edda Klipp
Publisher: John Wiley & Sons
ISBN: 3527336362
Format: PDF, ePub, Mobi
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This advanced textbook is tailored for an introductory course in Systems Biology and is well-suited for biologists as well as engineers and computer scientists. It comes with student-friendly reading lists and a companion website featuring a short exam prep version of the book and educational modeling programs. The text is written in an easily accessible style and includes numerous worked examples and study questions in each chapter. For this edition, a section on medical systems biology has been included.

Mathematics as a Tool

Author: Johannes Lenhard
Publisher: Springer
ISBN: 3319544691
Format: PDF
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This book puts forward a new role for mathematics in the natural sciences. In the traditional understanding, a strong viewpoint is advocated, on the one hand, according to which mathematics is used for truthfully expressing laws of nature and thus for rendering the rational structure of the world. In a weaker understanding, many deny that these fundamental laws are of an essentially mathematical character, and suggest that mathematics is merely a convenient tool for systematizing observational knowledge. The position developed in this volume combines features of both the strong and the weak viewpoint. In accordance with the former, mathematics is assigned an active and even shaping role in the sciences, but at the same time, employing mathematics as a tool is taken to be independent from the possible mathematical structure of the objects under consideration. Hence the tool perspective is contextual rather than ontological. Furthermore, tool-use has to respect conditions like suitability, efficacy, optimality, and others. There is a spectrum of means that will normally differ in how well they serve particular purposes. The tool perspective underlines the inevitably provisional validity of mathematics: any tool can be adjusted, improved, or lose its adequacy upon changing practical conditions.