Systems Biology For Signaling Networks

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Systems Biology for Signaling Networks

Sangdun Choi
Systems Biology for Signaling Networks Book PDF

Author : Sangdun Choi
Publisher : Springer Science & Business Media
Page : 900 pages
File Size : 41,8 Mb
Release : 2010-08-09
Category : Science
ISBN : 9781441957979

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Systems Biology for Signaling Networks by Sangdun Choi Pdf

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.

Systems Biology of Metabolic and Signaling Networks

Miguel A. Aon,Valdur Saks,Uwe Schlattner
Systems Biology of Metabolic and Signaling Networks Book PDF

Author : Miguel A. Aon,Valdur Saks,Uwe Schlattner
Publisher : Springer Science & Business Media
Page : 375 pages
File Size : 50,8 Mb
Release : 2013-10-22
Category : Science
ISBN : 9783642385056

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Systems Biology of Metabolic and Signaling Networks by Miguel A. Aon,Valdur Saks,Uwe Schlattner Pdf

Systems Biology represents a new paradigm aiming at a whole-organism-level understanding of biological phenomena, emphasizing interconnections and functional interrelationships rather than component parts. The study of network properties, and how they control and regulate behavior from the cellular to organism level, constitutes a main focus of Systems Biology. This book addresses from a novel perspective a major unsolved biological problem: understanding how a cell works and what goes wrong in pathology. The task undertaken by the authors is in equal parts conceptual and methodological, integrative and analytical, experimental and theoretical, qualitative and quantitative, didactic and comprehensive. Essentially, they unravel the spatio-temporal unfolding of interacting mass-energy and information networks at the cellular and organ levels, as well as its modulation through activation or repression by signaling networks to produce a certain phenotype or (patho)physiological response. Starting with the historical roots, in thirteen chapters this work explores the Systems Biology of signaling networks, cellular structures and fluxes, organ and microorganism functions. In doing so, it establishes the basis of a 21st century approach to biological complexity.

Computational Systems Biology

Christina Kiel,Luis Serrano
Computational Systems Biology Book PDF

Author : Christina Kiel,Luis Serrano
Publisher : Elsevier Inc. Chapters
Page : 548 pages
File Size : 43,6 Mb
Release : 2013-11-26
Category : Medical
ISBN : 9780128070062

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Computational Systems Biology by Christina Kiel,Luis Serrano Pdf

This chapter brings mammalian signal transduction to the center of quantitative and integrative sciences. Historically imbedded within human physiology, thanks to proteomics, interactomics, and molecular biology approaches, signaling is now far beyond the “black box” principle. However, despite the large amount of data available, we still have only limited insight into general design principles, and we lack knowledge on how cell type-specific signaling is achieved. Here, we summarize recent efforts in elucidating cell type-specific signaling, and in particular the role of protein abundances, signaling complexes and modules. We further discuss the potential of using synthetic biology approaches to decipher signaling networks. All of this is discussed in light of complementary quantitative mathematical modeling approaches. Signaling, more than any other discipline, needs computational biology to capture the dynamic systems behavior, and to reach its final goal: to be truly predictive for both the physiological and disease perturbed cellular conditions.

Biomolecular Networks

Luonan Chen,Rui-Sheng Wang,Xiang-Sun Zhang
Biomolecular Networks Book PDF

Author : Luonan Chen,Rui-Sheng Wang,Xiang-Sun Zhang
Publisher : John Wiley & Sons
Page : 416 pages
File Size : 48,9 Mb
Release : 2009-06-29
Category : Computers
ISBN : 0470488050

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Biomolecular Networks by Luonan Chen,Rui-Sheng Wang,Xiang-Sun Zhang Pdf

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.

Advances in Systems Biology

Igor I. Goryanin,Andrew B. Goryachev
Advances in Systems Biology Book PDF

Author : Igor I. Goryanin,Andrew B. Goryachev
Publisher : Springer Science & Business Media
Page : 679 pages
File Size : 53,6 Mb
Release : 2011-12-08
Category : Science
ISBN : 9781441972095

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Advances in Systems Biology by Igor I. Goryanin,Andrew B. Goryachev Pdf

The International Society for Systems Biology (ISSB) is a society aimed at advancing world-wide systems biology research by providing a forum for scientific discussions and various academic services. The ISSB helps coordinate researchers to form alliances for meeting the unique needs of multidisciplinary and international systems biology research. The annual International Conference on Systems Biology (ICSB) serves as the main meeting for the society and is one of the largest academic and commercial gatherings under the broad heading of ‘Systems Biology’.

Computational Modeling of Signaling Networks

Lan K. Nguyen
Computational Modeling of Signaling Networks Book PDF

Author : Lan K. Nguyen
Publisher : Springer Nature
Page : 387 pages
File Size : 48,8 Mb
Release : 2023-04-19
Category : Science
ISBN : 9781071630082

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Computational Modeling of Signaling Networks by Lan K. Nguyen Pdf

This volume focuses on the computational modeling of cell signaling networks and the application of these models and model-based analysis to systems and personalized medicine. Chapters guide readers through various modeling approaches for signaling networks, new methods and techniques that facilitate model development and analysis, and new applications of signaling network modeling towards systems and personalized treatment of cancer. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Modeling of Signaling Networks aims to benefit a wide spectrum of readers including researchers from the biological as well as computational systems biology communities.

Systems Biology

Lilia Alberghina,Hans V. Westerhoff
Systems Biology Book PDF

Author : Lilia Alberghina,Hans V. Westerhoff
Publisher : Springer Science & Business Media
Page : 432 pages
File Size : 50,8 Mb
Release : 2007-10-04
Category : Computers
ISBN : 3540742697

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Systems Biology by Lilia Alberghina,Hans V. Westerhoff Pdf

For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.

Systems Biology

Isidore Rigoutsos,Gregory Stephanopoulos
Systems Biology Book PDF

Author : Isidore Rigoutsos,Gregory Stephanopoulos
Publisher : Oxford University Press
Page : 360 pages
File Size : 53,8 Mb
Release : 2006-09-14
Category : Science
ISBN : 9780195300802

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Systems Biology by Isidore Rigoutsos,Gregory Stephanopoulos Pdf

The advent of genome sequencing and associated technologies has transformed biologists' ability to measure important classes of molecules and their interactions. This expanded cellular view has opened the field to thousands of interactions that previously were outside the researchers' reach. The processing and interpretation of these new vast quantities of interconnected data call for sophisticated mathematical models and computational methods. Systems biology meets this need by combining genomic knowledge with theoretical, experimental and computational approaches from a number of traditional scientific disciplines to create a mechanistic explanation of cellular systems and processes.Systems Biology I: Genomics and Systems Biology II: Networks, Models, and Applications offer a much-needed study of genomic principles and their associated networks and models. Written for a wide audience, each volume presents a timely compendium of essential information that is necessary for a comprehensive study of the subject. The chapters in the two volumes reflect the hierarchical nature of systems biology. Chapter authors-world-recognized experts in their fields-provide authoritative discussions on a wide range of topics along this hierarchy. Volume I explores issues pertaining to genomics that range from prebiotic chemistry to noncoding RNAs. Volume II covers an equally wide spectrum, from mass spectrometry to embryonic stem cells. The two volumes are meant to provide a reliable reference for students and researchers alike.

Systems Biology

Shigetada Nakanishi,Ryoichiro Kageyama,Dai Watanabe
Systems Biology Book PDF

Author : Shigetada Nakanishi,Ryoichiro Kageyama,Dai Watanabe
Publisher : Springer Science & Business Media
Page : 245 pages
File Size : 45,8 Mb
Release : 2009-03-18
Category : Science
ISBN : 9784431877042

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Systems Biology by Shigetada Nakanishi,Ryoichiro Kageyama,Dai Watanabe Pdf

Biological signaling pathways dynamically interact with one another to form complex information networks intracellularly, intercellularly, and eventually at the level of the organism. Biology and medicine have conventionally focused on identification and characterization of functional elements in biological signaling pathways. Recently, research in this field has pursued a new approach, systems biology, to understand the dynamics, complexity, and physiological functions of the biological signaling networks. Instead of reductionistic analyses or large-scale studies of biomolecules piece by piece, systems biology emphasizes the need for interdisciplinary methods and analysis of the regulation and operation of information networks at the systems level. The contributors to this book are leading researchers in the rising field of systems biology. Readers will find not only the most recent advances in research, but also the latest information about interdisciplinary methods and related topics.

Systems Biology of Cell Signaling

James Ferrell
Systems Biology of Cell Signaling Book PDF

Author : James Ferrell
Publisher : Garland Science
Page : 285 pages
File Size : 47,8 Mb
Release : 2021-09-28
Category : Science
ISBN : 9781000430738

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Systems Biology of Cell Signaling by James Ferrell Pdf

How can we understand the complexity of genes, RNAs, and proteins and the associated regulatory networks? One approach is to look for recurring types of dynamical behavior. Mathematical models prove to be useful, especially models coming from theories of biochemical reactions such as ordinary differential equation models. Clever, careful experiments test these models and their basis in specific theories. This textbook aims to provide advanced students with the tools and insights needed to carry out studies of signal transduction drawing on modeling, theory, and experimentation. Early chapters summarize the basic building blocks of signaling systems: binding/dissociation, synthesis/destruction, and activation/inactivation. Subsequent chapters introduce various basic circuit devices: amplifiers, stabilizers, pulse generators, switches, stochastic spike generators, and oscillators. All chapters consistently use approaches and concepts from chemical kinetics and nonlinear dynamics, including rate-balance analysis, phase plane analysis, nullclines, linear stability analysis, stable nodes, saddles, unstable nodes, stable and unstable spirals, and bifurcations. This textbook seeks to provide quantitatively inclined biologists and biologically inclined physicists with the tools and insights needed to apply modeling and theory to interesting biological processes. Key Features: Full-color illustration program with diagrams to help illuminate the concepts Enables the reader to apply modeling and theory to the biological processes Further Reading for each chapter High-quality figures available for instructors to download

Systems Biology of Cell Signaling

Zhike Zi,Jianhua Xing,Denis Tsygankov
Systems Biology of Cell Signaling Book PDF

Author : Zhike Zi,Jianhua Xing,Denis Tsygankov
Publisher : Frontiers Media SA
Page : 224 pages
File Size : 52,6 Mb
Release : 2022-02-17
Category : Science
ISBN : 9782889742813

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Systems Biology of Cell Signaling by Zhike Zi,Jianhua Xing,Denis Tsygankov Pdf

Topic Editor Prof. Xing is in collaboration with ATCC (https://www.atcc.org/) on testing some of their cell lines in research. All other Topic Editors declare no competing interests with regards to the Research Topic subject.

Computational Systems Biology

Andres Kriete,Roland Eils
Computational Systems Biology Book PDF

Author : Andres Kriete,Roland Eils
Publisher : Academic Press
Page : 548 pages
File Size : 48,7 Mb
Release : 2013-11-26
Category : Computers
ISBN : 9780124059382

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Computational Systems Biology by Andres Kriete,Roland Eils Pdf

This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

Systems Biology of Transcription Regulation

Ekaterina Shelest,Edgar Wingender,Joerg Linde
Systems Biology of Transcription Regulation Book PDF

Author : Ekaterina Shelest,Edgar Wingender,Joerg Linde
Publisher : Frontiers Media SA
Page : 191 pages
File Size : 44,7 Mb
Release : 2016-09-09
Category : Biotechnology
ISBN : 9782889199679

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Systems Biology of Transcription Regulation by Ekaterina Shelest,Edgar Wingender,Joerg Linde Pdf

Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches. Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic.

Introduction to Systems Biology

Sangdun Choi
Introduction to Systems Biology Book PDF

Author : Sangdun Choi
Publisher : Springer Science & Business Media
Page : 549 pages
File Size : 51,9 Mb
Release : 2008-05-17
Category : Science
ISBN : 9781597455312

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Introduction to Systems Biology by Sangdun Choi Pdf

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Progress in Pattern Recognition, Image Analysis and Applications

Luis Rueda,Domingo Mery,Josef Kittler
Progress in Pattern Recognition Image Analysis and Applications Book PDF

Author : Luis Rueda,Domingo Mery,Josef Kittler
Publisher : Springer
Page : 972 pages
File Size : 45,7 Mb
Release : 2007-11-13
Category : Computers
ISBN : 9783540767251

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Progress in Pattern Recognition, Image Analysis and Applications by Luis Rueda,Domingo Mery,Josef Kittler Pdf

This book constitutes the refereed proceedings of the 12th Iberoamerican Congress on Pattern Recognition, CIARP 2007, held in Valparaiso, Chile, November 13-16, 2007. The 97 revised full papers presented together with four keynote articles were carefully reviewed and selected from 200 submissions. The papers cover ongoing research and mathematical methods for pattern recognition, image analysis, and applications in areas such as computer vision, robotics, industry and health.