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Systems Biology is now entering a mature phase in which the key issues are characterising uncertainty and stochastic effects in mathematical models of biological systems. The area is moving towards a full statistical analysis and probabilistic reasoning over the inferences that can be made from mathematical models. This handbook presents a comprehensive guide to the discipline for practitioners and educators, in providing a full and detailed treatment of these important and emerging subjects. Leading experts in systems biology and statistics have come together to provide insight in to the major ideas in the field, and in particular methods of specifying and fitting models, and estimating the unknown parameters. This book: Provides a comprehensive account of inference techniques in systems biology. Introduces classical and Bayesian statistical methods for complex systems. Explores networks and graphical modeling as well as a wide range of statistical models for dynamical systems. Discusses various applications for statistical systems biology, such as gene regulation and signal transduction. Features statistical data analysis on numerous technologies, including metabolic and transcriptomic technologies. Presents an in-depth presentation of reverse engineering approaches. Provides colour illustrations to explain key concepts. This handbook will be a key resource for researchers practising systems biology, and those requiring a comprehensive overview of this important field.
Now in its second edition, this handbook collects authoritative contributions on modern methods and tools in statistical bioinformatics with a focus on the interface between computational statistics and cutting-edge developments in computational biology. The three parts of the book cover statistical methods for single-cell analysis, network analysis, and systems biology, with contributions by leading experts addressing key topics in probabilistic and statistical modeling and the analysis of massive data sets generated by modern biotechnology. This handbook will serve as a useful reference source for students, researchers and practitioners in statistics, computer science and biological and biomedical research, who are interested in the latest developments in computational statistics as applied to computational biology.
Handbook of Statistical Analysis and Data Mining Applications, Second Edition, is a comprehensive professional reference book that guides business analysts, scientists, engineers and researchers, both academic and industrial, through all stages of data analysis, model building and implementation. The handbook helps users discern technical and business problems, understand the strengths and weaknesses of modern data mining algorithms and employ the right statistical methods for practical application. This book is an ideal reference for users who want to address massive and complex datasets with novel statistical approaches and be able to objectively evaluate analyses and solutions. It has clear, intuitive explanations of the principles and tools for solving problems using modern analytic techniques and discusses their application to real problems in ways accessible and beneficial to practitioners across several areas—from science and engineering, to medicine, academia and commerce. - Includes input by practitioners for practitioners - Includes tutorials in numerous fields of study that provide step-by-step instruction on how to use supplied tools to build models - Contains practical advice from successful real-world implementations - Brings together, in a single resource, all the information a beginner needs to understand the tools and issues in data mining to build successful data mining solutions - Features clear, intuitive explanations of novel analytical tools and techniques, and their practical applications
The Handbook for Statistical Genetics is widely regarded as the reference work in the field. However, the field has developed considerably over the past three years. In particular the modeling of genetic networks has advanced considerably via the evolution of microarray analysis. As a consequence the 3rd edition of the handbook contains a much expanded section on Network Modeling, including 5 new chapters covering metabolic networks, graphical modeling and inference and simulation of pedigrees and genealogies. Other chapters new to the 3rd edition include Human Population Genetics, Genome-wide Association Studies, Family-based Association Studies, Pharmacogenetics, Epigenetics, Ethic and Insurance. As with the second Edition, the Handbook includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between the chapters, tying the different areas together. With heavy use of up-to-date examples, real-life case studies and references to web-based resources, this continues to be must-have reference in a vital area of research. Edited by the leading international authorities in the field. David Balding - Department of Epidemiology & Public Health, Imperial College An advisor for our Probability & Statistics series, Professor Balding is also a previous Wiley author, having written Weight-of-Evidence for Forensic DNA Profiles, as well as having edited the two previous editions of HSG. With over 20 years teaching experience, he’s also had dozens of articles published in numerous international journals. Martin Bishop – Head of the Bioinformatics Division at the HGMP Resource Centre As well as the first two editions of HSG, Dr Bishop has edited a number of introductory books on the application of informatics to molecular biology and genetics. He is the Associate Editor of the journal Bioinformatics and Managing Editor of Briefings in Bioinformatics. Chris Cannings – Division of Genomic Medicine, University of Sheffield With over 40 years teaching in the area, Professor Cannings has published over 100 papers and is on the editorial board of many related journals. Co-editor of the two previous editions of HSG, he also authored a book on this topic.
A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
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.
This book provides simultaneously a design blueprint, user guide, research agenda, and communication platform for current and future developments in artificial intelligence (AI) approaches to systems biology. It places an emphasis on the molecular dimension of life phenomena and in one chapter on anatomical and functional modeling of the brain. As design blueprint, the book is intended for scientists and other professionals tasked with developing and using AI technologies in the context of life sciences research. As a user guide, this volume addresses the requirements of researchers to gain a basic understanding of key AI methodologies for life sciences research. Its emphasis is not on an intricate mathematical treatment of the presented AI methodologies. Instead, it aims at providing the users with a clear understanding and practical know-how of the methods. As a research agenda, the book is intended for computer and life science students, teachers, researchers, and managers who want to understand the state of the art of the presented methodologies and the areas in which gaps in our knowledge demand further research and development. Our aim was to maintain the readability and accessibility of a textbook throughout the chapters, rather than compiling a mere reference manual. The book is also intended as a communication platform seeking to bride the cultural and technological gap among key systems biology disciplines. To support this function, contributors have adopted a terminology and approach that appeal to audiences from different backgrounds.
Many new challenges have arisen in the area of oncology clinical trials. New cancer therapies are often based on cytostatic or targeted agents, which pose new challenges in the design and analysis of all phases of trials. The literature on adaptive trial designs and early stopping has been exploding. Inclusion of high-dimensional data and imaging techniques have become common practice, and statistical methods on how to analyse such data have been refined in this area. A compilation of statistical topics relevant to these new advances in cancer research, this third edition of Handbook of Statistics in Clinical Oncology focuses on the design and analysis of oncology clinical trials and translational research. Addressing the many challenges that have arisen since the publication of its predecessor, this third edition covers the newest developments involved in the design and analysis of cancer clinical trials, incorporating updates to all four parts: Phase I trials: Updated recommendations regarding the standard 3 + 3 and continual reassessment approaches, along with new chapters on phase 0 trials and phase I trial design for targeted agents. Phase II trials: Updates to current experience in single-arm and randomized phase II trial designs. New chapters include phase II designs with multiple strata and phase II/III designs. Phase III trials: Many new chapters include interim analyses and early stopping considerations, phase III trial designs for targeted agents and for testing the ability of markers, adaptive trial designs, cure rate survival models, statistical methods of imaging, as well as a thorough review of software for the design and analysis of clinical trials. Exploratory and high-dimensional data analyses: All chapters in this part have been thoroughly updated since the last edition. New chapters address methods for analyzing SNP data and for developing a score based on gene expression data. In addition, chapters on risk calculators and forensic bioinformatics have been added. Accessible to statisticians and oncologists interested in clinical trial methodology, the book is a single-source collection of up-to-date statistical approaches to research in clinical oncology.
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
Mathematical models can be used to meet many of the challenges and opportunities offered by modern biology. The description of biological phenomena requires a range of mathematical theories. This is the case particularly for the emerging field of systems biology. Mathematical Methods in Biology and Neurobiology introduces and develops these mathematical structures and methods in a systematic manner. It studies: • discrete structures and graph theory • stochastic processes • dynamical systems and partial differential equations • optimization and the calculus of variations. The biological applications range from molecular to evolutionary and ecological levels, for example: • cellular reaction kinetics and gene regulation • biological pattern formation and chemotaxis • the biophysics and dynamics of neurons • the coding of information in neuronal systems • phylogenetic tree reconstruction • branching processes and population genetics • optimal resource allocation • sexual recombination • the interaction of species. Written by one of the most experienced and successful authors of advanced mathematical textbooks, this book stands apart for the wide range of mathematical tools that are featured. It will be useful for graduate students and researchers in mathematics and physics that want a comprehensive overview and a working knowledge of the mathematical tools that can be applied in biology. It will also be useful for biologists with some mathematical background that want to learn more about the mathematical methods available to deal with biological structures and data.