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Systems Biology

Integrative Biology and Simulation Tools

  • Book
  • © 2013

Overview

Editors:
  1. Aleš Prokop

    1. Chemical and Biological Engineering, Vanderbilt University, Nashville, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Béla Csukás

    1. Research Group on Process Network Engineering, Kaposvár University, Kaposvár, Hungary

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    You can also search for this editor in PubMed   Google Scholar

  • This multi-authored volume presents a unique update in the field of pharmaceutical drugs
  • The book presents a unique coverage of computational problems and tools related to this field
  • The selected authors are all experts in their field

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Table of contents (19 chapters)

  1. Front Matter

    Pages i-xxxi
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  2. Foundation of Systems Biology, Integrative Biology and Issues of Biosystem Complexity, Redundancy and of Other Network Properties

    1. Front Matter

      Pages 1-1
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    2. Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology

      • Stéphane Ballereau, Enrico Glaab, Alexei Kolodkin, Amphun Chaiboonchoe, Maria Biryukov, Nikos Vlassis et al.
      Pages 3-41

    3. Comparing Biological Networks: A Survey on Graph Classifying Techniques

      • Laurin A. J. Mueller, Matthias Dehmer, Frank Emmert-Streib
      Pages 43-63

    4. Emergent Properties of Gene Regulatory Networks: Models and Data

      • Roberto Serra, Marco Villani
      Pages 65-93

    5. Regulatory Crosstalk Analysis of Biochemical Networks in the Hippocampus and Nucleus Accumbens

      • Shinichi Kikuchi, Eberhard O. Voit
      Pages 95-127

    6. Properties of Biological Networks

      • Vlado Dančík, Amrita Basu, Paul Clemons
      Pages 129-178

  3. Modeling of Ill-Defined, Lack of Knowledge (Experimental) Problems in the Field of Complex Biosystems Including Identification and Validation: A Review of Enabling Technologies

    1. Front Matter

      Pages 179-179
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    2. On Different Aspects of Network Analysis in Systems Biology

      • Amphun Chaiboonchoe, Wiktor Jurkowski, Johann Pellet, Enrico Glaab, Alexey Kolodkin, Antonio Raussel et al.
      Pages 181-207

    3. Computational Approaches for Reconstruction of Time-Varying Biological Networks from Omics Data

      • Vinay Jethava, Chiranjib Bhattacharyya, Devdatt Dubhashi
      Pages 209-239

    4. Probabilistic Graphical Modeling in Systems Biology: A Framework for Integrative Approaches

      • Christine Sinoquet
      Pages 241-272

    5. Innovations of the Rule-Based Modeling Approach

      • Lily A. Chylek, Edward C. Stites, Richard G. Posner, William S. Hlavacek
      Pages 273-300

    6. Reproducibility of Model-Based Results in Systems Biology

      • Dagmar Waltemath, Ron Henkel, Felix Winter, Olaf Wolkenhauer
      Pages 301-320

    7. Parameter Identifiability and Redundancy, with Applications to a General Class of Stochastic Carcinogenesis Models

      • Mark P. Little, Wolfgang F. Heidenreich, Guangquan Li
      Pages 321-354

    8. Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery

      • Michel Dumontier, Leonid L. Chepelev, Robert Hoehndorf
      Pages 355-373

  4. Critical Analysis of Multi-Scale Computational Methods and Tools, Computational Tools for Crossing Levels and Applications

    1. Front Matter

      Pages 375-375
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    2. Computational Infrastructures for Data and Knowledge Management in Systems Biology

      • Fotis Georgatos, Stéphane Ballereau, Johann Pellet, Moustafa Ghanem, Nathan Price, Leroy Hood et al.
      Pages 377-397

    3. Computational Tools and Resources for Integrative Modeling in Systems Biology

      • Christoph Wierling, Hendrik Hache
      Pages 399-428

    4. Agent-Based Modeling Approaches to Multi-Scale Systems Biology: An Example Agent-Based Model of Acute Pulmonary Inflammation

      • Gary An, Michael Wandling, Scott Christley
      Pages 429-461

    5. Reconstruction and Comparison of Cellular Signaling Pathway Resources for the Systems-Level Analysis of Cross-Talks

      • Máté Pálfy, László Földvári-Nagy, Dezső Módos, Katalin Lenti, Tamás Korcsmáros
      Pages 463-477
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Keywords

About this book

Growth in the pharmaceutical market has slowed down – almost to a standstill. One reason is that governments and other payers are cutting costs in a faltering world economy. But a more fundamental problem is the failure of major companies to discover, develop and market new drugs. Major drugs losing patent protection or being withdrawn from the market are simply not being replaced by new therapies – the pharmaceutical market model is no longer functioning effectively and most pharmaceutical companies are failing to produce the innovation needed for success. This multi-authored new book looks at a vital strategy which can bring innovation to a market in need of new ideas and new products: Systems Biology (SB). Modeling is a significant task of systems biology. SB aims to develop and use efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of biological systems, such as the networks of metabolites comprise signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes. SB involves a series of operational protocols used for performing research, namely a cycle composed of theoretical, analytic or computational modeling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.

Reviews

From the reviews:

“This volume is the first of three planned books exploring the various tools used by the scientific community to deal with complexity in subjects such as big data, nonlinearity, and hidden interactions in systems biology. … welcomed by readers … who are directly or indirectly involved in the dynamic field of systems biology. The book offers insightful connections, knowledge that is often overlooked, and well-thought-out reasoning.” (Adrian Pasculescu, Computing Reviews, January, 2014)

Editors and Affiliations

  • Chemical and Biological Engineering, Vanderbilt University, Nashville, USA

    Aleš Prokop

  • Research Group on Process Network Engineering, Kaposvár University, Kaposvár, Hungary

    Béla Csukás

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