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Case Studies in Systems Biology by Pavel Kraikivski Pdf
This book provides case studies that can be used in Systems Biology related classes. Each case study has the same structure which answers the following questions: What is the biological problem and why is it interesting? What are the relevant details with regard to cell physiology and molecular mechanisms? How are the details put together into a mathematical model? How is the model analyzed and simulated? What are the results of the model? How do they compare to the known facts of the cell physiology? Does the model make predictions? What can be done to extend the model? The book presents a summary of results and references to more relevant sources. The volume contains the classic collection of topics and studies that are well established yet novel in the systems biology field.
Case Studies in Cell Biology by Merri Lynn Casem Pdf
Case Studies in Cell Biology presents real world scenarios to help readers use science process and reasoning skills. The case studies require application and analyzation of concepts beyond rote memory of biological concepts. The book is based on the student learning outcomes from the American Society for Cell Biology, offering practical application for both the classroom and research laboratory. Guides the reader in applying knowledge directly to real world scenarios Includes case studies to bridge foundational cell biological concepts to translational science Aids students in synthesizing information and applying science processes
Concepts and Case Studies in Chemical Biology by Herbert Waldmann,Petra Janning Pdf
Retaining the proven didactic concept of the successful "Chemical Biology - Learning through Case Studies", this sequel features 27 new case studies, reflecting the rapid growth in this interdisciplinary topic over the past few years. Edited by two of the world's leading researchers in the field, this textbook introduces students and researchers to the modern approaches in chemical biology, as well as important results, and the techniques and methods applied. Each chapter presents a different biological problem taken from everyday lab work, elucidated by an international team of renowned scientists. With its broad coverage, this is a valuable source of information for students, graduate students, and researchers working on the borderline between chemistry, biology, and biochemistry.
Case Studies for Understanding the Human Body by Stanton Braude,Deena Goran,Alexander Miceli Pdf
Completely revised and expanded, the second edition of Case Studies for Understanding the Human Body is the ideal resource for students enrolled in any Anatomy and Physiology or Human Biology Course. The case studies work well in a cooperative learning setting where students work together to review and solve open-ended questions associated with each case. The exercises are also perfect for individual homework assignments. The discussions cover common disease of all major organ systems and present related topics that are often part of course discussion. New topics for the second edition include:
A First Course in Systems Biology by Eberhard Voit Pdf
A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. 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 large-scale, often open-ended questions for further reflection.
Plant Systems Biology by Sacha Baginsky,Alisdair R. Fernie Pdf
This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.
Understanding the Dynamics of Biological Systems by Werner Dubitzky,Jennifer Southgate,Hendrik Fuß Pdf
This book is intended as a communication platform to bridge the cultural, conceptual, and technological gap among the key systems biology disciplines of biology, mathematics, and information technology. To support this goal, contributors were asked to adopts an approach that appeals to audiences from different backgrounds.
Parallel Computing for Bioinformatics and Computational Biology by Albert Y. Zomaya Pdf
Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.
Modeling in Systems Biology by Ina Koch,Wolfgang Reisig,Falk Schreiber Pdf
The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.
Modeling Methods for Medical Systems Biology by María Elena Álvarez-Buylla Roces,Juan Carlos Martínez-García,José Dávila-Velderrain,Elisa Domínguez-Hüttinger,Mariana Esther Martínez-Sánchez Pdf
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.
The unprecedented amount of data produced with high-throughput experimentation forces biologists to employ mathematical representation and computation methods to glean meaningful information in systems-level biology. Applying this approach to the underlying molecular mechanisms of tumorigenesis, cancer researchers can uncover a series of new discov
Contextualizing Systems Biology by Martin Döring,Imme Petersen,Anne Brüninghaus,Regine Kollek Pdf
This collective monograph aims at contributing to an improved understanding of the epistemic presumptions, sociocultural implications and historically backgrounds of the newly emerging and currently expanding approach of systems biology. In doing so, it offers empirically grounded, valuable and reflexive information about a paradigmatic shift in the biosciences for a wide range of scientists working in the interdisciplinary areas of systems biology, synthetic biology, molecular biology, biology, the philosophy of science, the sociology of science and scientific knowledge, science and technology studies, technology assessment and the like. The authors of this monograph share the theoretical methodological premise that science is a culturally and socially embedded practice which characterizes our culture as a scientific one and at the same time draws its innovative potential from its socio-cultural context. This dialectic relationship lies at the heart of the current development of systems biology which is conceived as a so-called successor of ‘-omics’ research and triggered by high-throughput information technologies. At the same time a need for a holistic conceptualization of complex biological processes emerges. The title Contextualizing Systems Biology suggests that this book analyzes the development and advent of systems biology from different theoretical and methodological perspectives. We investigate a variety of contexts ranging from the analysis of cognitive contexts (such as basic theoretical concepts) to regulative contexts (policies) to the concrete application of a systems biology in the socio-scientific context of a European research project. In empirically analyzing these different and interrelated layers and dimensions of systems biology, the scope of the book goes beyond present attempts to investigate the advent of new approaches in the biological sciences as it frames and assesses systems biology from an interdisciplinary and integrated perspective.
Applications of Calculus to Biology and Medicine by Nathan C Ryan,Dorothy Wallace Pdf
Biology majors and pre-health students at many colleges and universities are required to take a semester of calculus but rarely do such students see authentic applications of its techniques and concepts. Applications of Calculus to Biology and Medicine: Case Studies from Lake Victoria is designed to address this issue: it prepares students to engage with the research literature in the mathematical modeling of biological systems, assuming they have had only one semester of calculus. The text includes projects, problems and exercises: the projects ask the students to engage with the research literature, problems ask the students to extend their understanding of the materials and exercises ask the students to check their understanding as they read the text. Students who successfully work their way through the text will be able to engage in a meaningful way with the research literature to the point that they would be able to make genuine contributions to the literature. Request Inspection Copy Contents: Background:Lake VictoriaWhat is Calculus?Population Modeling:Introduction to Population ModelingLogistic GrowthHarvesting a Population with Logistic GrowthEuler's MethodModeling Interlude: The Modeling ProcessResearch Interlude: Reading a Research PaperBrief Introduction to SageProjects for Population ModelingDrug Modeling:Introduction to PharmacokineticsTwo Models for Lead in the BodyMethods of Drug AdministrationEuler's Method for Systems of Differential EquationsModeling Interlude: Sensitivity AnalysisResearch Interlude: Writing a Research PaperProjects for Pharmacokinetic ModelingPredator Prey Modeling:Undamped Lotka-Volterra EquationsDamped Lotka-Volterra EquationsPredator SatiationIsoclinesSpecies FormationTop PredatorsModeling Interlude: Potential Problems with ModelsResearch Interlude: Making FiguresProjects for Predatory-Prey ModelsInfectious Disease Modeling:SIR Model for Infectious DiseasesMalariaHIV/AIDSProjects for Infectious Disease ModelsClassroom Tested Projects Readership: Undergraduates in biomathematics, mathematical biology, mathematical modeling, applied mathematics, and dynamical systems.
Systems Biology by Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald Pdf
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.