An introduction to the mathematical, computational, and analytical techniques used for modeling biological rhythms, presenting tools from many disciplines and example applications. All areas of biology and medicine contain rhythms, and these behaviors are best understood through mathematical tools and techniques. This book offers a survey of mathematical, computational, and analytical techniques used for modeling biological rhythms, gathering these methods for the first time in one volume. Drawing on material from such disciplines as mathematical biology, nonlinear dynamics, physics, statistics, and engineering, it presents practical advice and techniques for studying biological rhythms, with a common language. The chapters proceed with increasing mathematical abstraction. Part I, on models, highlights the implicit assumptions and common pitfalls of modeling, and is accessible to readers with basic knowledge of differential equations and linear algebra. Part II, on behaviors, focuses on simpler models, describing common properties of biological rhythms that range from the firing properties of squid giant axon to human circadian rhythms. Part III, on mathematical techniques, guides readers who have specific models or goals in mind. Sections on “frontiers” present the latest research; “theory” sections present interesting mathematical results using more accessible approaches than can be found elsewhere. Each chapter offers exercises. Commented MATLAB code is provided to help readers get practical experience. The book, by an expert in the field, can be used as a textbook for undergraduate courses in mathematical biology or graduate courses in modeling biological rhythms and as a reference for researchers.

Two new volumes of Methods in Enzymology continue the legacy of this premier serial with quality chapters authored by leaders in the field. Circadian Rhythms and Biological Clocks Part A and Part B is an exceptional resource for anybody interested in the general area of circadian rhythms. As key elements of timekeeping are conserved in organisms across the phylogenetic tree, and our understanding of circadian biology has benefited tremendously from work done in many species, the volume provides a wide range of assays for different biological systems. Protocols are provided to assess clock function, entrainment of the clock to stimuli such as light and food, and output rhythms of behavior and physiology. This volume also delves into the impact of circadian disruption on human health. Contributions are from leaders in the field who have made major discoveries using the methods presented here. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in biomineralization science - Keeping with the interdisciplinary nature of the circadian rhythm field, the volume includes diverse approaches towards the study of rhythms, from assays of biochemical reactions in unicellular organisms to monitoring of behavior in humans.

This volume addresses the latest state-of-the-art systems biology-oriented approaches that--driven by big data and bioinformatics--are utilized by Computational Systems Biology, an interdisciplinary field that bridges experimental tools with computational tools to tackle complex questions at the frontiers of knowledge in medicine and biotechnology. The chapters in this book are organized into six parts: systems biology of the genome, epigenome, and redox proteome; metabolic networks; aging and longevity; systems biology of diseases; spatiotemporal patterns of rhythms, morphogenesis, and complex dynamics; and genome scale metabolic modeling in biotechnology. In every chapter, readers will find varied methodological approaches applied at different levels, from molecular, cellular, organ to organisms, genome to phenome, and health and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; criteria utilized for applying specific methodologies; lists of the necessary materials, reagents, software, databases, algorithms, mathematical models, and dedicated analytical procedures; step-by-step, readily reproducible laboratory, bioinformatics, and computational protocols all delivered in didactic and clear style and abundantly illustrated with express case studies and tutorials; and tips on troubleshooting and advice for achieving reproducibility while avoiding mistakes and misinterpretations. The overarching goal driving this volume is to excite the expert and stimulate the newcomer to the field of Computational Systems Biology. Cutting-edge and authoritative, Computational Systems Biology in Medicine and Biotechnology: Methods and Protocols is a valuable resource for pre- and post-graduate students in medicine and biotechnology, and in diverse areas ranging from microbiology to cellular and organismal biology, as well as computational and experimental biologists, and researchers interested in utilizing comprehensive systems biology oriented methods.

Praise for the first edition: ... superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. – Nature [This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology ... It assumes no prior knowledge of or even interest in biology ... One final aspect that must be mentioned is the wonderful set of exercises that accompany each chapter. ... Alon’s book should become a standard part of the training of graduate students. – Physics Today Written for students and researchers, the second edition of this best-selling textbook continues to offer a clear presentation of design principles that govern the structure and behavior of biological systems. It highlights simple, recurring circuit elements that make up the regulation of cells and tissues. Rigorously classroom-tested, this edition includes new chapters on exciting advances made in the last decade. Features: Includes seven new chapters The new edition has 189 exercises, the previous edition had 66 Offers new examples relevant to human physiology and disease The book website including course videos can be found here: https://www.weizmann.ac.il/mcb/UriAlon/introduction-systems-biology-design-principles-biological-circuits.

An intriguing class of biological periodicity consists of rhythms with about 24-hour periods occurring at every level of eukaryotic organization. Progress is being made in understanding these rhythms. The six chapters of this work include a brief introduction to circadian (24-hour) rhythms, a survey of circadian organization at the cellular level, and a description of the important microorganisms that have served as experimental models for biochemical analysis. Also considered are relations between cell division cycles and circadian oscillators, as well as some general and theoretical aspects. Where appropriate, parallels are drawn to neuronal oscillators. This volume will introduce and critically appraise modern chronobiology; its extensive illustrations and comprehensive up-to-date bibliography will make it an authoritative reference.

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.

This book constitutes the refereed proceedings of the 18th International Conference on Computational Methods in Systems Biology, CMSB 2020, held in Konstanz, Germany, in September 2020.* The 17 full papers and 5 tool papers were carefully reviewed and selected from 30 submissions. In addition 3 abstracts of invited talks and 2 tutorials have been included in this volume. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; computational approaches for synthetic biology; and case studies in systems and synthetic biology. * The conference was held virtually due to the COVID-19 pandemic.

This book is a concise, comprehensive and up-to-date account of fundamental concepts and potential applications of biological timekeeping mechanisms in animals and humans. It also discusses significant aspects of the organization and importance of timekeeping mechanisms in both groups. Divided into seven sections, it addresses important aspects including fundamental concepts; animal and human clocks; clock interactions; clocks and metabolism and immune functions; pineal, melatonin and timekeeping; and clocks, photoperiodism and seasonal behaviours. The book also focuses on biological clock applications in a 24x7 human society, particularly in connection with life-style associated disorders like obesity and diabetes. It is a valuable resource for advanced undergraduates, researchers and professionals engaged in the study of the science of biological timekeeping.

(Chapters 11 to 14) summarise important features of the biological clock at the level of whole animal covering all vertebrate classes (fish to mammal). Chapters 15 and 16 are on long term (seasonal) rhythms in plants and higher vertebrates. Short term rhythms (ultradian rhythms), the significance of having a clock system in animals living in extreme (arctic) environments, and the diversity of circadian responses to melatonin, the key endocrine element involved in regulation of biological rhythms, have been discussed in Chapters 17 to 19. Finally, a chapter on sensitivity to light of the photoperiodic clock is added which, using vertebrate examples, illustrates the importance of wavelength and intensity of light on circadian and non-circadian functions. A well-known expert writes each chapter. When presenting information, the text provides consistent thematic coverage and feeling for the methods of investigation. Reference citation within the body of the text adequately reflects the literature as subject is developed. A chapter begins with an abstract that enables a reader to know at the first glance the important points covered in that chapter. The chapter concludes with a full citation of references included in the text, which could be useful for further reading. The book ends with a comprehensive subject index that may be useful for quick searches.

With this volume of three essays, the authors want to create an opportunity for dialogue between different disciplines by taking a closer look at three cardio-physiological examples. In the essays presented, we will look at the exploration of different cardiological topics from the 20th century, all of which have contributed to a better understanding of certain aspects of cardiac activity. Not only do these insights provide a more complete picture of these cardiac phenomena, but it is also within this context that we can look for and into the patterns of regularities which govern this living organism. Our goal is to stimulate a dialogue on the philosophy of science in the spirit of Hans Reichenbach.