computational modeling of gene regulatory networks a primer

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Computational Modeling Of Gene Regulatory Networks

Author : Hamid Bolouri
ISBN : 9781848162204
Genre : Medical
File Size : 37. 96 MB
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This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.

Computational Modeling Of Genetic And Biochemical Networks

Author : James M. Bower
ISBN : 0262524236
Genre : Science
File Size : 73. 37 MB
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How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.

Handbook Of Research On Computational Methodologies In Gene Regulatory Networks

Author : Das, Sanjoy
ISBN : 9781605666860
Genre : Computers
File Size : 43. 16 MB
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"This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.

Personal Genomics And Personalized Medicine

Author : Hamid Bolouri
ISBN : 1848165641
Genre : Medical
File Size : 32. 68 MB
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Current research in genomics and pharmacogenomics is increasingly highlighting the need to move towards stratified disease descriptions and individualized treatment plans. This book explains how a confluence of recent biological, technological and methodological developments is making it possible to provide personalized diagnoses and treatments. By virtue of treating each person's condition as unique, personal genomics and personalized medicine require health professionals to understand the nature of the data, its health implications, and its limitations. This book provides a detailed scientific treatment of the emerging disciplines of personal genomics and personalized medicine. It also includes a comprehensive treatment of both the promises and challenges of personal genomics and medicine from technological, societal and medical perspectives. It offers a wide-ranging review of the state of the art across all aspects of a highly multi-disciplinary subject. This book will be immensely useful for practicing health professionals and researchers, as well as senior undergraduates and graduate students in biomedical sciences.

Epigenetic Technological Applications

Author : Yujun George Zheng
ISBN : 9780128013274
Genre : Science
File Size : 42. 67 MB
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Epigenetic Technological Applications is a compilation of state-of-the-art technologies involved in epigenetic research. Epigenetics is an exciting new field of biology research, and many technologies are invented and developed specifically for epigenetics study. With chapters covering the latest developments in crystallography, computational modeling, the uses of histones, and more, Epigenetic Technological Applications addresses the question of how these new ideas, procedures, and innovations can be applied to current epigenetics research, and how they can keep pushing discovery forward and beyond the epigenetic realm. Discusses technologies that are critical for epigenetic research and application Includes epigenetic applications for state-of-the-art technologies Contains a global perspective on the future of epigenetics

Bioinformatics For Biologists

Author : Pavel Pevzner
ISBN : 9781139501613
Genre : Science
File Size : 47. 37 MB
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The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. Rather than just presenting tools, the authors - each a leading scientist - engage the students' problem-solving skills, preparing them to meet the computational challenges of their life science careers.

Towards A Theory Of Development

Author : Alessandro Minelli
ISBN : 9780191651182
Genre : Science
File Size : 30. 18 MB
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Is it possible to explain and predict the development of living things? What is development? Articulate answers to these seemingly innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This novel work offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories. The two editors (one a biologist with long interest in the theoretical aspects of his discipline, the other a philosopher of science who has mainly worked on biological systems) have assembled a team of leading contributors who are representative of the scientific and philosophical community within which a diversity of thoughts are growing, and out of which a theory of development may eventually emerge. They analyse a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a 'programme' of development and its critiques, and the long-standing opposition between preformationist and epigenetic conceptions of development. Towards a Theory of Development is primarily aimed at students and researchers in the fields of 'evo-devo', developmental biology, theoretical biology, systems biology, biophysics, and the philosophy of science.

Mathematical Modeling In Systems Biology

Author : Brian P. Ingalls
ISBN : 9780262018883
Genre : Science
File Size : 54. 22 MB
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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.

Gene Activity In Early Development

Author : Eric H. Davidson
ISBN : 9781483261478
Genre : Science
File Size : 70. 71 MB
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Gene Activity in Early Development reviews the state of knowledge regarding genomic function in the programming and operation of what Bonnet, in 1762, described as "the miracle of epigenesis." The book is divided into four sections. Section I is concerned with gene activity in early embryogenesis, with the time of onset and the nature of embryo genome control, and with recent attempts to analyze the shifting patterns of gene expression as development proceeds. Section II reviews various classic and recent studies relevant to the phenomenon of cytoplasmic localization of morphogenetic potential and discusses the significance, from a contemporary vantage point, of this often neglected area of developmental biology. Section III deals with genomic function in oogenesis, beginning with a general survey of what could be described loosely as the natural history of the oocyte nucleus, and proceeding to current attempts to understand the character and the ultimate function of the oocyte gene products. Section IV discusses various aspects of the general problem of gene regulation in animal cells.

Systems Biology

Author : Andreas Kremling
ISBN : 9781466567894
Genre : Mathematics
File Size : 86. 48 MB
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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.

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