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Methods In Systems Biology
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Book Synopsis Methods in Computational Biology by : Ross Carlson
Download or read book Methods in Computational Biology written by Ross Carlson and published by MDPI. This book was released on 2019-07-03 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections: • Reviews of Computational Methods • Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels • The Interface of Biotic and Abiotic Processes • Processing of Large Data Sets for Enhanced Analysis • Parameter Optimization and Measurement
Book Synopsis Modeling Methods for Medical Systems Biology by : María Elena Álvarez-Buylla Roces
Download or read book Modeling Methods for Medical Systems Biology written by María Elena Álvarez-Buylla Roces and published by . This book was released on 2018 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contributes to better understand how lifestyle modulations can effectively halt the emergence and progression of human diseases. The book will allow the reader to gain a better understanding of the mechanisms by which the environment interferes with the bio-molecular regulatory processes underlying the emergence and progression of complex diseases, such as cancer. Focusing on key and early cellular bio-molecular events giving rise to the emergence of degenerative chronic disease, it builds on previous experience on the development of multi-cellular organisms, to propose a mathematical and computer based framework that allows the reader to analyze the complex interplay between bio-molecular processes and the (micro)-environment from an integrative, mechanistic, quantitative and dynamical perspective. Taking the wealth of empirical evidence that exists it will show how to build and analyze models of core regulatory networks involved in the emergence and progression of chronic degenerative diseases, using a bottom-up approach.
Book Synopsis Kernel Methods in Computational Biology by : Bernhard Schölkopf
Download or read book Kernel Methods in Computational Biology written by Bernhard Schölkopf and published by MIT Press. This book was released on 2004 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: A detailed overview of current research in kernel methods and their application to computational biology.
Book Synopsis Microbial Systems Biology by : Ali Navid
Download or read book Microbial Systems Biology written by Ali Navid and published by Humana Press. This book was released on 2012-05-27 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being directed toward examining systems biology in complex multi-cellular organisms, the bulk of system-level analyses conducted to date have focused on the biology of microbes. In, Microbial Systems Biology: Methods and Protocols expert researchers in the field describe the utility and attributes of different tools (both experimental and computational) that are used for studying microbial systems. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Systems Biology: Methods and Protocols introduces and aids scientists in using the various tools that are currently available for analysis, modification and utilization of microbial organisms.
Book Synopsis A Guide to Numerical Modelling in Systems Biology by : Peter Deuflhard
Download or read book A Guide to Numerical Modelling in Systems Biology written by Peter Deuflhard and published by Springer. This book was released on 2015-07-06 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks and identification of model parameters by means of comparisons with real data. Throughout the text, the strengths and weaknesses of numerical algorithms with respect to various systems biological issues are discussed. Web addresses for downloading the corresponding software are also included.
Book Synopsis Mathematical Modeling in Systems Biology by : Brian P. Ingalls
Download or read book Mathematical Modeling in Systems Biology written by Brian P. Ingalls and published by MIT Press. This book was released on 2022-06-07 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.
Book Synopsis Methods in Systems Biology by : Daniel Jameson
Download or read book Methods in Systems Biology written by Daniel Jameson and published by Academic Press. This book was released on 2011-09-26 with total page 775 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is a term used to describe a number of trends in bioscience research and a movement that draws on those trends. This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology. With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research. This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research
Download or read book Systems Biology written by A.K. Konopka and published by CRC Press. This book was released on 2006-11-20 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: With extraordinary clarity,the Systems Biology: Principles, Methods, and Concepts focuses on the technical practical aspects of modeling complex or organic general systems. It also provides in-depth coverage of modeling biochemical, thermodynamic, engineering, and ecological systems. Among other methods and concepts based in logic, computer
Book Synopsis Computational Systems Biology by : Andres Kriete
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
Book Synopsis Computational Methods in Synthetic Biology by : Mario Andrea Marchisio
Download or read book Computational Methods in Synthetic Biology written by Mario Andrea Marchisio and published by Humana. This book was released on 2021-11-27 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition book provides complete coverage of the computational approaches currently used in Synthetic Biology. New chapters detail computational methods and algorithms for the design of bio-components, insight on CAD programs, analysis techniques, and distributed systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Computational Methods in Synthetic Biology, Second Edition aims to feature a broad overview of the research areas that can be met in the area of in silico Synthetic Biology.
Book Synopsis Computational Systems Biology of Cancer by : Emmanuel Barillot
Download or read book Computational Systems Biology of Cancer written by Emmanuel Barillot and published by CRC Press. This book was released on 2012-08-25 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Translational Bioinformatics and Systems Biology Methods for Personalized Medicine by : Qing Yan
Download or read book Translational Bioinformatics and Systems Biology Methods for Personalized Medicine written by Qing Yan and published by Academic Press. This book was released on 2017-04-18 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: Translational Bioinformatics and Systems Biology Methods for Personalized Medicine introduces integrative approaches in translational bioinformatics and systems biology to support the practice of personalized, precision, predictive, preventive, and participatory medicine. Through the description of important cutting-edge technologies in bioinformatics and systems biology, readers may gain an essential understanding of state-of-the-art methodologies. The book discusses topics such as the challenges and tasks in translational bioinformatics; pharmacogenomics, systems biology, and personalized medicine; and the applicability of translational bioinformatics for biomarker discovery, epigenomics, and molecular dynamics. It also discusses data integration and mining, immunoinformatics, and neuroinformatics. With broad coverage of both basic scientific and clinical applications, this book is suitable for a wide range of readers who may not be scientists but who are also interested in the practice of personalized medicine. Introduces integrative approaches in translational bioinformatics and systems biology to support the practice of personalized, precision, predictive, preventive, and participatory medicine Presents a problem-solving oriented methodology to deal with practical problems in various applications Covers both basic scientific and clinical applications in order to enhance the collaboration between researchers and clinicians Brings integrative and multidisciplinary approaches to bridge the gaps among various knowledge domains in the field
Book Synopsis Data Mining for Systems Biology by : Hiroshi Mamitsuka
Download or read book Data Mining for Systems Biology written by Hiroshi Mamitsuka and published by Humana. This book was released on 2019-08-04 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: This fully updated book collects numerous data mining techniques, reflecting the acceleration and diversity of the development of data-driven approaches to the life sciences. The first half of the volume examines genomics, particularly metagenomics and epigenomics, which promise to deepen our knowledge of genes and genomes, while the second half of the book emphasizes metabolism and the metabolome as well as relevant medicine-oriented subjects. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that is useful for getting optimal results. Authoritative and practical, Data Mining for Systems Biology: Methods and Protocols, Second Edition serves as an ideal resource for researchers of biology and relevant fields, such as medical, pharmaceutical, and agricultural sciences, as well as for the scientists and engineers who are working on developing data-driven techniques, such as databases, data sciences, data mining, visualization systems, and machine learning or artificial intelligence that now are central to the paradigm-altering discoveries being made with a higher frequency.
Book Synopsis Networks in Systems Biology by : Fabricio Alves Barbosa da Silva
Download or read book Networks in Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer Nature. This book was released on 2020-10-03 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.
Book Synopsis A First Course in Systems Biology by : Eberhard O. Voit
Download or read book A First Course in Systems Biology written by Eberhard O. Voit and published by Garland Science. This book was released on 2012-03-28 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: A First Course in Systems Biology is a textbook designed for advanced undergraduate and graduate students. Its main focus is the development of computational models and their applications to diverse biological systems. Because the biological sciences have become so complex that no individual can acquire complete knowledge in any given area of specialization, the education of future systems biologists must instead develop a student's ability to retrieve, reformat, merge, and interpret complex biological information. This book provides the reader with the background and mastery of methods to execute standard systems biology tasks, understand the modern literature, and launch into specialized courses or projects that address biological questions using theoretical and computational means. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and larger-scale, often open-ended questions for further reflection.
Book Synopsis Systems Biology by : Andreas Kremling
Download or read book Systems Biology written by Andreas Kremling and published by CRC Press. This book was released on 2013-11-12 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.
Book Synopsis Handbook of Statistical Systems Biology by : Michael Stumpf
Download or read book Handbook of Statistical Systems Biology written by Michael Stumpf and published by John Wiley & Sons. This book was released on 2011-09-09 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
