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 : 63. 84 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 : 32. 4 MB
Format : PDF
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How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.

Probabilistic Boolean Networks

Author : Ilya Shmulevich
ISBN : 9780898716924
Genre : Mathematics
File Size : 88. 92 MB
Format : PDF
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The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.

Handbook Of Research On Computational Methodologies In Gene Regulatory Networks

Author : Das, Sanjoy
ISBN : 9781605666860
Genre : Computers
File Size : 21. 13 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 : 70. 92 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.

Towards A Theory Of Development

Author : Alessandro Minelli
ISBN : 9780191651182
Genre : Science
File Size : 81. 29 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 : 90. 14 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.

Theoretical And Applied Aspects Of Systems Biology

Author : Fabricio Alves Barbosa da Silva
ISBN : 9783319749747
Genre : Computers
File Size : 88. 90 MB
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This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

Biomolecular Networks

Author : Luonan Chen
ISBN : 0470488050
Genre : Computers
File Size : 43. 91 MB
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Alternative techniques and tools for analyzing biomolecular networks With the recent rapid advances in molecular biology, high-throughput experimental methods have resulted in enormous amounts of data that can be used to study biomolecular networks in living organisms. With this development has come recognition of the fact that a complicated living organism cannot be fully understood by merely analyzing individual components. Rather, it is the interactions of components or biomolecular networks that are ultimately responsible for an organism's form and function. This book addresses the important need for a new set of computational tools to reveal essential biological mechanisms from a systems biology approach. Readers will get comprehensive coverage of analyzing biomolecular networks in cellular systems based on available experimental data with an emphasis on the aspects of network, system, integration, and engineering. Each topic is treated in depth with specific biological problems and novel computational methods: GENE NETWORKS—Transcriptional regulation; reconstruction of gene regulatory networks; and inference of transcriptional regulatory networks PROTEIN INTERACTION NETWORKS—Prediction of protein-protein interactions; topological structure of biomolecular networks; alignment of biomolecular networks; and network-based prediction of protein function METABOLIC NETWORKS AND SIGNALING NETWORKS—Analysis, reconstruction, and applications of metabolic networks; modeling and inference of signaling networks; and other topics and new trends In addition to theoretical results and methods, many computational software tools are referenced and available from the authors' Web sites. Biomolecular Networks is an indispensable reference for researchers and graduate students in bioinformatics, computational biology, systems biology, computer science, and applied mathematics.

Systems Biology For Signaling Networks

Author : Sangdun Choi
ISBN : 1441957979
Genre : Science
File Size : 53. 32 MB
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System Biology encompasses the knowledge from diverse fields such as Molecular Biology, Immunology, Genetics, Computational Biology, Mathematical Biology, etc. not only to address key questions that are not answerable by individual fields alone, but also to help in our understanding of the complexities of biological systems. Whole genome expression studies have provided us the means of studying the expression of thousands of genes under a particular condition and this technique had been widely used to find out the role of key macromolecules that are involved in biological signaling pathways. However, making sense of the underlying complexity is only possible if we interconnect various signaling pathways into human and computer readable network maps. These maps can then be used to classify and study individual components involved in a particular phenomenon. Apart from transcriptomics, several individual gene studies have resulted in adding to our knowledge of key components that are involved in a signaling pathway. It therefore becomes imperative to take into account of these studies also, while constructing our network maps to highlight the interconnectedness of the entire signaling pathways and the role of that particular individual protein in the pathway. This collection of articles will contain a collection of pioneering work done by scientists working in regulatory signaling networks and the use of large scale gene expression and omics data. The distinctive features of this book would be: Act a single source of information to understand the various components of different signaling network (roadmap of biochemical pathways, the nature of a molecule of interest in a particular pathway, etc.), Serve as a platform to highlight the key findings in this highly volatile and evolving field, and Provide answers to various techniques both related to microarray and cell signaling to the readers.

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