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Networks in Systems Biology

Applications for Disease Modeling

  • Book
  • © 2020

Overview

Editors:
  1. Fabricio Alves Barbosa da Silva

    1. Scientific Computing Program (PROCC), Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

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  2. Nicolas Carels

    1. CDTS, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

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  3. Marcelo Trindade dos Santos

    1. Department of Computational Modeling, National Laboratory of Scientific Computing, Petrópolis, Brazil

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  4. Francisco José Pereira Lopes

    1. Graduate Program in Nanobiosystems, Federal University of Rio de Janeiro, Duque de Caxias, Brazil

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  • Provides a detailed analysis of the latest research into biological networks and disease modeling
  • Gathers contributions from renowned experts in the field
  • Covers topics including networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer

Part of the book series: Computational Biology (COBO, volume 32)

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Table of contents (13 chapters)

  1. Front Matter

    Pages i-x
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  2. Biological Networks and Methods in Systems Biology

    1. Front Matter

      Pages 1-1
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    2. Network Medicine: Methods and Applications

      • Italo F. do Valle, Helder I. Nakaya
      Pages 3-18

    3. Computational Tools for Comparing Gene Coexpression Networks

      • Vinícius Carvalho Jardim, Camila Castro Moreno, André Fujita
      Pages 19-30

    4. Functional Gene Networks and Their Applications

      • Hong-Dong Li, Yuanfang Guan
      Pages 31-43

    5. A Review of Artificial Neural Networks for the Prediction of Essential Proteins

      • Kele Belloze, Luciana Campos, Ribamar Matias, Ivair Luques, Eduardo Bezerra
      Pages 45-68

    6. Transcriptograms: A Genome-Wide Gene Expression Analysis Method

      • Rita M. C. de Almeida, Lars L. S. de Souza, Diego Morais, Rodrigo J. S. Dalmolin
      Pages 69-91

    7. A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models

      • Michel Tosin, Adriano M. A. Côrtes, Americo Cunha
      Pages 93-118

    8. Reaction Network Models as a Tool to Study Gene Regulation and Cell Signaling in Development and Diseases

      • Francisco José Pereira Lopes, Claudio Daniel Tenório de Barros, Josué Xavier de Carvalho, Fernando de Magalhães Coutinho Vieira, Cristiano N. Costa
      Pages 119-159

  3. Disease and Pathogen Modeling

    1. Front Matter

      Pages 161-161
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    2. Challenges for the Optimization of Drug Therapy in the Treatment of Cancer

      • Nicolas Carels, Alessandra Jordano Conforte, Carlyle Ribeiro Lima, Fabricio Alves Barbosa da Silva
      Pages 163-198

    3. Opportunities and Challenges Provided by Boolean Modelling of Cancer Signalling Pathways

      • Petronela Buiga, Jean-Marc Schwartz
      Pages 199-216

    4. Integrating Omics Data to Prioritize Target Genes in Pathogenic Bacteria

      • Marisa Fabiana Nicolás, Maiana de Oliveira Cerqueira e Costa, Pablo Ivan P. Ramos, Marcelo Trindade dos Santos, Ernesto Perez-Rueda, Marcelo A. Marti et al.
      Pages 217-276

    5. Modelling Oxidative Stress Pathways

      • Harry Beaven, Ioly Kotta-Loizou
      Pages 277-300

    6. Computational Modeling in Virus Infections and Virtual Screening, Docking, and Molecular Dynamics in Drug Design

      • Rachel Siqueira de Queiroz Simões, Mariana Simões Ferreira, Nathalia Dumas de Paula, Thamires Rocco Machado, Pedro Geraldo Pascutti
      Pages 301-337

    7. Cellular Regulatory Network Modeling Applied to Breast Cancer

      • Luiz Henrique Oliveira Ferreira, Maria Clicia Stelling de Castro, Alessandra Jordano Conforte, Nicolas Carels, Fabrício Alves Barbosa da Silva
      Pages 339-365

  4. Back Matter

    Pages 367-377
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Keywords

About this book

This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.


Editors and Affiliations

  • Scientific Computing Program (PROCC), Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

    Fabricio Alves Barbosa da Silva

  • CDTS, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

    Nicolas Carels

  • Department of Computational Modeling, National Laboratory of Scientific Computing, Petrópolis, Brazil

    Marcelo Trindade dos Santos

  • Graduate Program in Nanobiosystems, Federal University of Rio de Janeiro, Duque de Caxias, Brazil

    Francisco José Pereira Lopes

About the editors

Dr. Fabrício Alves Barbosa da Silva is a Public Health Researcher in the Scientific Computing Program (PROCC) at the Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil. His other publications include the Springer title Theoretical and Applied Aspects of Systems Biology (with Dr. Carels).

Dr. Nicolas Carels is a Titular Researcher in the Centre for Technological Development in Health (CDTS) at FIOCRUZ.

Dr. Marcelo Trindade dos Santos is a Full Technologist at the  Department of Computational Modeling, National Laboratory of Scientific Computing (LNCC), Petrópolis, Brazil.

Dr. Francisco José Pereira Lopes is an Associate Professor in the Graduate Program in Nanobiosystems at the Federal University of Rio de Janeiro (UFRJ), Duque de Caxias, Brazil.

Bibliographic Information

  • Book Title: Networks in Systems Biology

  • Book Subtitle: Applications for Disease Modeling

  • Editors: Fabricio Alves Barbosa da Silva, Nicolas Carels, Marcelo Trindade dos Santos, Francisco José Pereira Lopes

  • Series Title: Computational Biology

  • DOI: https://doi.org/10.1007/978-3-030-51862-2

  • Publisher: Springer Cham

  • eBook Packages: Computer Science, Computer Science (R0)

  • Copyright Information: Springer Nature Switzerland AG 2020

  • Hardcover ISBN: 978-3-030-51861-5Published: 04 October 2020

  • Softcover ISBN: 978-3-030-51864-6Published: 05 October 2021

  • eBook ISBN: 978-3-030-51862-2Published: 03 October 2020

  • Series ISSN: 1568-2684

  • Series E-ISSN: 2662-2432

  • Edition Number: 1

  • Number of Pages: X, 377

  • Number of Illustrations: 11 b/w illustrations, 71 illustrations in colour

  • Topics: Computational Biology/Bioinformatics, Systems Biology, Simulation and Modeling, Health Informatics, Cancer Research

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