Computational Modeling Of Gene Regulatory Networks - A Primer
Computational Modeling Of Gene Regulatory Networks - A Primer

Author: Hamid Bolouri

Publisher: World Scientific Publishing Company

Published: 2008-08-13

Total Pages: 341

ISBN-13: 1848168187

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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./a

Computational Modeling of Gene Regulatory Networks
Computational Modeling of Gene Regulatory Networks

Author: Hamid Bolouri

Publisher: Imperial College Press

Published: 2008

Total Pages: 341

ISBN-13: 1848162200

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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.

Information Processing And Living Systems
Information Processing And Living Systems

Author: Vladimir B Bajic

Publisher: World Scientific

Published: 2005-06-01

Total Pages: 799

ISBN-13: 1783260270

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Information processing and information flow occur in the course of an organism's development and throughout its lifespan. Organisms do not exist in isolation, but interact with each other constantly within a complex ecosystem. The relationships between organisms, such as those between prey or predator, host and parasite, and between mating partners, are complex and multidimensional. In all cases, there is constant communication and information flow at many levels.This book focuses on information processing by life forms and the use of information technology in understanding them. Readers are first given a comprehensive overview of biocomputing before navigating the complex terrain of natural processing of biological information using physiological and analogous computing models. The remainder of the book deals with “artificial” processing of biological information as a human endeavor in order to derive new knowledge and gain insight into life forms and their functioning. Specific innovative applications and tools for biological discovery are provided as the link and complement to biocomputing.Since “artificial” processing of biological information is complementary to natural processing, a better understanding of the former helps us improve the latter. Consequently, readers are exposed to both domains and, when dealing with biological problems of their interest, will be better equipped to grasp relevant ideas.

Modeling Transcriptional Regulation
Modeling Transcriptional Regulation

Author: SHAHID MUKHTAR

Publisher: Humana

Published: 2022-07-27

Total Pages: 307

ISBN-13: 9781071615362

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This book provides methods and techniques used in construction of global transcriptional regulatory networks in diverse systems, various layers of gene regulation and mathematical as well as computational modeling of transcriptional gene regulation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Modeling Transcriptional Regulation: Methods and Protocols aims to provide an in depth understanding of new techniques in transcriptional gene regulation for specialized audience.

Gene Regulatory Networks
Gene Regulatory Networks

Author: Guido Sanguinetti

Publisher: Humana

Published: 2018-12-14

Total Pages: 0

ISBN-13: 9781493988815

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This volume explores recent techniques for the computational inference of gene regulatory networks (GRNs). The chapters in this book cover topics such as methods to infer GRNs from time-varying data; the extraction of causal information from biological data; GRN inference from multiple heterogeneous data sets; non-parametric and hybrid statistical methods; the joint inference of differential networks; and mechanistic models of gene regulation dynamics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, descriptions of recently developed methods for GRN inference, applications of these methods on real and/ or simulated biological data, and step-by-step tutorials on the usage of associated software tools. Cutting-edge and thorough, Gene Regulatory Networks: Methods and Protocols is an essential tool for evaluating the current research needed to further address the common challenges faced by specialists in this field.

Probabilistic Boolean Networks
Probabilistic Boolean Networks

Author: Ilya Shmulevich

Publisher: SIAM

Published: 2010-01-21

Total Pages: 276

ISBN-13: 0898716926

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The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.

Proceedings of the International Conference on Artificial Intelligence and Computer Vision (AICV2020)
Proceedings of the International Conference on Artificial Intelligence and Computer Vision (AICV2020)

Author: Aboul-Ella Hassanien

Publisher: Springer Nature

Published: 2020-03-23

Total Pages: 880

ISBN-13: 3030442896

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This book presents the proceedings of the 1st International Conference on Artificial Intelligence and Computer Visions (AICV 2020), which took place in Cairo, Egypt, from April 8 to 10, 2020. This international conference, which highlighted essential research and developments in the fields of artificial intelligence and computer visions, was organized by the Scientific Research Group in Egypt (SRGE). The book is divided into sections, covering the following topics: swarm-based optimization mining and data analysis, deep learning and applications, machine learning and applications, image processing and computer vision, intelligent systems and applications, and intelligent networks.

Mathematical Modeling in Systems Biology
Mathematical Modeling in Systems Biology

Author: Brian P. Ingalls

Publisher: MIT Press

Published: 2013-07-05

Total Pages: 423

ISBN-13: 0262018888

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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.

Artificial Chemistries
Artificial Chemistries

Author: Wolfgang Banzhaf

Publisher: MIT Press

Published: 2015-07-03

Total Pages: 572

ISBN-13: 026202943X

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An introduction to the fundamental concepts of the emerging field of Artificial Chemistries, covering both theory and practical applications. The field of Artificial Life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding of the emergence of life on Earth. The new field of Artificial Chemistries draws from chemistry, biology, computer science, mathematics, and other disciplines to work toward that goal. For if, as it has been argued, life emerged from primitive, prebiotic forms of self-organization, then studying models of chemical reaction systems could bring ALife closer to understanding the origins of life. In Artificial Chemistries (ACs), the emphasis is on creating new interactions rather than new materials. The results can be found both in the virtual world, in certain multiagent systems, and in the physical world, in new (artificial) reaction systems. This book offers an introduction to the fundamental concepts of ACs, covering both theory and practical applications. After a general overview of the field and its methodology, the book reviews important aspects of biology, including basic mechanisms of evolution; discusses examples of ACs drawn from the literature; considers fundamental questions of how order can emerge, emphasizing the concept of chemical organization (a closed and self-maintaining set of chemicals); and surveys a range of applications, which include computing, systems modeling in biology, and synthetic life. An appendix provides a Python toolkit for implementing ACs.