Computational Modeling Of Signaling Networks

Author : Lan K. Nguyen
Publisher : Springer Nature
Page : 387 pages
File Size : 55,7 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.

Author : Sangdun Choi
Publisher : Springer Science & Business Media
Page : 900 pages
File Size : 42,8 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.

Author : Hamid Bolouri
Publisher : Imperial College Press
Page : 341 pages
File Size : 46,6 Mb
Release : 2008
Category : Medical
ISBN : 9781848162204

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Computational Modeling of Gene Regulatory Networks by Hamid Bolouri Pdf

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.

Author : Christina Kiel,Luis Serrano
Publisher : Elsevier Inc. Chapters
Page : 548 pages
File Size : 45,5 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.

Author : James M. Bower,Hamid Bolouri
Publisher : MIT Press
Page : 386 pages
File Size : 50,8 Mb
Release : 2001
Category : Computers
ISBN : 0262524236

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Computational Modeling of Genetic and Biochemical Networks by James M. Bower,Hamid Bolouri Pdf

How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.

Author : Lewis C. Cantley,Tony Hunter,Richard Sever,Jeremy Thorner
Publisher : Unknown
Page : 452 pages
File Size : 55,6 Mb
Release : 2014-05-31
Category : Science
ISBN : 0879699019

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Signal Transduction by Lewis C. Cantley,Tony Hunter,Richard Sever,Jeremy Thorner Pdf

"This textbook provides a comprehensive view of signal transduction, covering both the fundamental mechanisms involved and their roles in key biological processes. It first lays out the basic principles of signal transduction, explaining how different receptors receive information and transmit it via signaling proteins, ions, and second messengers. It then surveys the major signaling pathways that operate in cells, before examining in detail how these function in processes such as cell growth and division, cell movement, metabolism, development, reproduction, the nervous system, and immune function"--

Author : Zhong Shao
Publisher : Springer
Page : 436 pages
File Size : 41,7 Mb
Release : 2007-11-07
Category : Computers
ISBN : 3540766367

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Programming Languages and Systems by Zhong Shao Pdf

This book constitutes the refereed proceedings of the 5th Asian Symposium on Programming Languages and Systems, APLAS 2007, held in Singapore, in November/December 2007. The 25 revised full papers presented together with three invited talks were carefully reviewed and selected from 84 submissions. The symposium addresses all issues in programming languages and systems - ranging from foundational to practical issues. The papers focus on a broad range of topics.

Author : David Sterratt,Bruce Graham,Andrew Gillies,Gaute Einevoll,David Willshaw
Publisher : Cambridge University Press
Page : 553 pages
File Size : 48,9 Mb
Release : 2023-10-05
Category : Science
ISBN : 9781108483148

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Principles of Computational Modelling in Neuroscience by David Sterratt,Bruce Graham,Andrew Gillies,Gaute Einevoll,David Willshaw Pdf

Learn to use computational modelling techniques to understand the nervous system at all levels, from ion channels to networks.

Author : Hannu Eskola,Outi Väisänen,Jari Viik,Jari Hyttinen
Publisher : Springer
Page : 1139 pages
File Size : 43,6 Mb
Release : 2017-06-12
Category : Technology & Engineering
ISBN : 9789811051227

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EMBEC & NBC 2017 by Hannu Eskola,Outi Väisänen,Jari Viik,Jari Hyttinen Pdf

This volume presents the proceedings of the joint conference of the European Medical and Biological Engineering Conference (EMBEC) and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics (NBC), held in Tampere, Finland, in June 2017. The proceedings present all traditional biomedical engineering areas, but also highlight new emerging fields, such as tissue engineering, bioinformatics, biosensing, neurotechnology, additive manufacturing technologies for medicine and biology, and bioimaging, to name a few. Moreover, it emphasizes the role of education, translational research, and commercialization.

Author : Malcolm Whitman,Amy Sater
Publisher : CRC Press
Page : 435 pages
File Size : 51,7 Mb
Release : 2006-08-15
Category : Science
ISBN : 1420004786

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Analysis of Growth Factor Signaling in Embryos by Malcolm Whitman,Amy Sater Pdf

Developmental biologists have been driven to investigate growth factor signaling in embryos in order to understand the regulatory mechanisms underlying a given developmental process. Thus, it is critical to explore the technical methods and experimental designs for growth factor signaling in embryos. Focusing on specific pathways or pathway components, Analysis of Growth Factor Signaling in Embryos provides the methods and guidelines for experimental design to study major aspects of cell signaling in vertebrate embryos. The book covers a broad range of topics in signaling and a variety of current model organisms. Section I explores specific signaling pathways or pathway components. In this section, some chapters highlight the biochemistry of signaling pathways during development, which is often distinctive from that observed in cell culture systems. Section II discusses ionic regulatory mechanisms and the two chapters in Section III examine ways of investigating gene regulation in response to extracellular signals. Finally, Section IV addresses emerging strategies that facilitate integrated analyses of cell signaling in vivo in embryonic systems. Featuring contributions from expert researchers, Analysis of Growth Factor Signaling in Embryos will provide a foundation for further explorations of the cellular regulatory mechanisms governing vertebrate embryonic development.

Author : Anonim
Publisher : Academic Press
Page : 427 pages
File Size : 52,5 Mb
Release : 2012-05-31
Category : Science
ISBN : 9780123884213

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Computational Methods in Cell Biology by Anonim Pdf

Computational methods are playing an ever increasing role in cell biology. This volume of Methods in Cell Biology focuses on Computational Methods in Cell Biology and consists of two parts: (1) data extraction and analysis to distill models and mechanisms, and (2) developing and simulating models to make predictions and testable hypotheses. Focuses on computational methods in cell biology Split into 2 parts--data extraction and analysis to distill models and mechanisms, and developing and simulating models to make predictions and testable hypotheses Emphasizes the intimate and necessary connection with interpreting experimental data and proposing the next hypothesis and experiment

Author : Ursula Klingmüller,Marcel Schilling,Sofia Depner,Lorenza A. D’Alessandro
Publisher : Elsevier Inc. Chapters
Page : 548 pages
File Size : 54,5 Mb
Release : 2013-11-26
Category : Medical
ISBN : 9780128070055

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Computational Systems Biology by Ursula Klingmüller,Marcel Schilling,Sofia Depner,Lorenza A. D’Alessandro Pdf

Cellular communication is mediated by extracellular stimuli that bind cellular receptors and activate intracellular signaling pathways. Principal biochemical reactions used for signal transduction are protein or lipid phosphorylation, proteolytic cleavage, protein degradation and complex formation mediated by protein-protein interactions. Within the nucleus, signaling pathways regulate transcription factor activity and gene expression. Cells differ in their competence to respond to extracellular stimuli. A deeper understanding of complex biological responses cannot be achieved by traditional approaches but requires the combination of experimental data with mathematical modeling. Following a systems biology approach, data-based mathematical models describing sub-modules of signaling pathways have been established. By combining computer simulations with experimental verification systems properties of signaling pathway including cycling behavior or threshold response could be identified. Yet, to analyze complex growth and maturation processes at a systems level and quantitatively predict the outcome of perturbations further advances in experimental and theoretical methodologies are required.

Author : Xuedong Liu,Meredith D. Betterton
Publisher : Humana Press
Page : 327 pages
File Size : 50,8 Mb
Release : 2013-01-31
Category : Science
ISBN : 1617798347

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Computational Modeling of Signaling Networks by Xuedong Liu,Meredith D. Betterton Pdf

Signaling networks are composed of numerous signaling pathways and each has its own intricate component parts. Signaling outputs are dynamic, extraordinarily complex and yet highly specific. In, Computational Modeling of Signaling Networks: Methods and Protocols, expert researchers in the field provide key techniques to study signaling networks. Focusing on Systems of ODEs, parameterization of signaling models, signaling pathways, mass-action kinetics and ODEs, and how to use modeling to plan experiments. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Computational Modeling of Signaling Networks: Methods and Protocols aids scientists in continuing study of how signaling networks behave in space and time to generate specific biological responses and how those responses impact biology and medicine.

Author : John D. Haley,William John Gullick
Publisher : Springer Science & Business Media
Page : 393 pages
File Size : 43,8 Mb
Release : 2009-03-01
Category : Medical
ISBN : 9781597453561

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EGFR Signaling Networks in Cancer Therapy by John D. Haley,William John Gullick Pdf

The epidermal gro wth factor (EGF ) receptor and its downstream signal transduction networks have been implicated in the ontology and maintenance of tumor tissues, which has motivated the discovery and development of molecularly targeted anti-EGF receptor therapies. Over decades of study, the EGF receptor structure, its ligand binding domains, the physical biochemistry underlying its intrinsic tyrosine kinase catalytic function and the modular interactions with SH2, PTB, and SH3 domain containing signaling adaptor p- teins required for signal transduction, have been extensively dissected. Not only is the EGF receptor the nexus of many streams of information, but it also forms one part of a calcul- ing device by forming dimers and oligomers with the other three receptors in its family in response to at least eleven ligands (some of which are expressed in multiple forms with overlapping or quite distinct functions). This phenomenon, while recruiting to the inner surface of the cell membrane and activating multiple second messenger proteins, also allows the possibility of cross talk between these systems, permitting a further layer of information to be exchanged. Less well described are the cross re gulation of the EGF receptor and other anti-apoptotic, mitogenic and metabolic signaling systems. The study of these systems has yielded new surprises. One hurdle in these efforts has been that signal transduction pathways have frequently been defined in the generic absence of their tissue-specific or cell-interaction specific context.

Author : Steven Dooley,Kai Breuhahn,Andreas Teufel
Publisher : Frontiers Media SA
Page : 291 pages
File Size : 48,9 Mb
Release : 2020-01-03
Category : Electronic
ISBN : 9782889633494

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Systems Biology and Bioinformatics in Gastroenterology and Hepatology by Steven Dooley,Kai Breuhahn,Andreas Teufel Pdf