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Theoretical and Applied Aspects of Systems Biology

  • Book
  • © 2018

Overview

Editors:
  1. Fabricio Alves Barbosa da Silva

    1. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

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  2. Nicolas Carels

    1. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

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  3. Floriano Paes Silva Junior

    1. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

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  • Presents theoretical foundations of Systems Biology
  • Lists applications in studies on human hosts, pathogens and associated diseases
  • Topics discussed include computational modeling of multi-resistant bacteria, systems biology of cancer, systems immunology and networks in systems biology

Part of the book series: Computational Biology (COBO, volume 27)

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Table of contents (13 chapters)

  1. Front Matter

    Pages i-xviii
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  2. Fundamentals

    1. Front Matter

      Pages 1-1
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    2. Bio-modeling Using Petri Nets: A Computational Approach

      • Rafael V. Carvalho, Fons J. Verbeek, Clarimar J. Coelho
      Pages 3-26

    3. Modeling Gene Transcriptional Regulation: A Primer

      • Marcelo Trindade dos Santos, Ana Paula Barbosa do Nascimento, Fernando Medeiros Filho, Fabricio Alves Barbosa da Silva
      Pages 27-39

    4. Cellular Reprogramming

      • Domenico Sgariglia, Alessandra Jordano Conforte, Luis Alfredo Vidal de Carvalho, Nicolas Carels, Fabricio Alves Barbosa da Silva
      Pages 41-55

    5. Metabolic Models: From DNA to Physiology (and Back)

      • Marcio Argollo de Menezes
      Pages 57-69

    6. Analysis Methods for Shotgun Metagenomics

      • Stephen Woloszynek, Zhengqiao Zhao, Gregory Ditzler, Jacob R. Price, Erin R. Reichenberger, Yemin Lan et al.
      Pages 71-112

    7. ANOCVA: A Nonparametric Statistical Test to Compare Clustering Structures

      • Alexandre Galvão Patriota, Maciel Calebe Vidal, Davi Augusto Caetano de Jesus, André Fujita
      Pages 113-125

  3. Applied Systems Biology

    1. Front Matter

      Pages 127-127
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    2. Modeling of Cellular Systems: Application in Stem Cell Research and Computational Disease Modeling

      • Muhammad Ali, Antonio del Sol
      Pages 129-138

    3. Using Thermodynamic Functions as an Organizing Principle in Cancer Biology

      • Edward Rietman, Jack A. Tuszynski
      Pages 139-157

    4. Systems Immunology

      • Melissa Lever, Thiago C. Hirata, Pedro S. T. Russo, Helder I. Nakaya
      Pages 159-173

    5. The Challenge of Translating System Biology into Targeted Therapy of Cancer

      • Alessandra Jordano Conforte, Milena Magalhães, Tatiana Martins Tilli, Fabricio Alves Barbosa da Silva, Nicolas Carels
      Pages 175-194

    6. Computational Modeling of Multidrug-Resistant Bacteria

      • Fabricio Alves Barbosa da Silva, Fernando Medeiros Filho, Thiago Castanheira Merigueti, Thiago Giannini, Rafaela Brum, Laura Machado de Faria et al.
      Pages 195-220

    7. System Biology to Access Target Relevance in the Research and Development of Molecular Inhibitors

      • Larissa Catharina, Marcio Argollo de Menezes, Nicolas Carels
      Pages 221-242

    8. Mathematical-Computational Modeling in Behavior’s Study of Repetitive Discharge Neuronal Circuits

      • Celia Martins Cortez, Maria Clicia Stelling de Castro, Vanessa de Freitas Rodrigues, Camila Andrade Kalil, Dilson Silva
      Pages 243-259
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Keywords

About this book

This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. 

This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.




Editors and Affiliations

  • Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

    Fabricio Alves Barbosa da Silva, Nicolas Carels, Floriano Paes Silva Junior

About the editors

Prof. Dr. Fabrício Alves Barbosa da Silva is the PI of the research group on computational modeling of multidrug-resistant bacteria at FIOCRUZ. The research group on computational modeling of multidrug-resistant bacteria proposes the creation of innovative models, techniques and computational methods to identify new potential therapeutic targets in multidrug-resistant bacteria using a systems biology approach. This multidisciplinary group is composed of researchers from six different institutions in Brazil.  Dr. Silva has expertise on computational biology, with focus on systems biology, mathematical modeling and the analysis and processing of large biological datasets. 

Prof. Dr. Nicolas Carels is the coordinator of the Laboratory of Biological System Modeling (LMSB) from the Center for Technological Development in Health (CDTS) of Oswaldo Cruz Foundation. Since the 1990s, he accumulated expertise in the genetics, biotechnology and bioinformatics of plant systems. Morerecently due to the availability of high throughput datasets in the context of the post-genomics era, he dedicated his activities to the bioinformatics of diseases’ molecular networks in the context of translational medicine. He is also investigating the metagenomics of microbial communities in interaction with human protozoan parasites in invertebrate hosts.

Prof. Dr. Floriano Paes Silva Junior is the head of the Laboratory of Computational and Experimental Biochemistry of Drugs (LaBECFar) at Oswaldo Cruz Institute, FIOCRUZ. Dr. Silva-Jr has expertise on Medicinal Chemistry and Chemical Biology working on the interface between computational and experimental approaches for drug discovery. His contributions include discovery and biochemical characterization of new drug targets and bioactive compounds with relevance to both infectious and non-communicable diseases. 


Bibliographic Information

  • Book Title: Theoretical and Applied Aspects of Systems Biology

  • Editors: Fabricio Alves Barbosa da Silva, Nicolas Carels, Floriano Paes Silva Junior

  • Series Title: Computational Biology

  • DOI: https://doi.org/10.1007/978-3-319-74974-7

  • Publisher: Springer Cham

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

  • Copyright Information: Springer International Publishing AG, part of Springer Nature 2018

  • Hardcover ISBN: 978-3-319-74973-0Published: 06 July 2018

  • Softcover ISBN: 978-3-030-09117-0Published: 14 December 2018

  • eBook ISBN: 978-3-319-74974-7Published: 21 June 2018

  • Series ISSN: 1568-2684

  • Series E-ISSN: 2662-2432

  • Edition Number: 1

  • Number of Pages: XVIII, 259

  • Number of Illustrations: 16 b/w illustrations, 26 illustrations in colour

  • Topics: Computational Biology/Bioinformatics, Bioinformatics, Health Informatics, Cancer Research, Cell Biology

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