Our understanding of biology has undergone a revolution in the past 20 years, driven by our ability to capture, store, interrogate and analyze the ever-increasing volumes of ‘omics’ data. Computational Biology, an integrated approach employing high performance computers, state-of-the art software and algorithms, mathematical modeling and statistical analyses have enabled us to unravel the seemingly impenetrable complexity of biological systems. This book draws together many of the latest cutting-edge developments in the field of Computational Biology. Each chapter draws on the expertise of leading researchers in the field to highlight the utility of specific technologies. The breadth of the text is impressive - from integrative biology in human diseases through the various branches of epigenomics, metabolomics and proteomics to biological sequencing and deep learning. Computational biology approaches for image-based analysis of multicellular spheroids, feature selection using entropy and cellular cryo-electron tomography structural pattern mining are covered. In addition, the key role of statistics in the analysis of high-dimensional multiset omics data and RNA sequencing are discussed in dedicated chapters. This book would have broad appeal to anyone with an interest in cutting edge computational biology.

Contents

• Foreword
• Preface
• List of Contributors
• 1. An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians
  Sabine C. Fischer.
  • INTRODUCTION
  • METHODS
  • FIRST WORKFLOW: CELL BIOLOGY
  • SECOND WORKFLOW: CANCER BIOLOGY
  • THIRD WORKFLOW: BIOPRINTING
  • OUTLOOK: EXPERIMENTS INSPIRED BY THE MATHEMATICAL MODELS
  • CONCLUSION
  • REFERENCES
• 2. Integrative Biology Approaches Applied to Human Diseases
  Alysson H. Urbanski, José D. Araujo, Rachel Creighton, and Helder I. Nakaya.
  • INTRODUCTION
  • APPLICATIONS OF SINGLE-LAYER HIGH-THROUGHPUT DATA
  • TOOLS FOR THE ANALYSIS OF SINGLE-LAYER HIGH-THROUGHPUT DATA
  • APPLICATIONS OF INTEGRATIVE BIOLOGY TO HUMAN DISEASES
  • TOOLS FOR INTEGRATIVE ANALYSIS
  • CHALLENGES
  • CONCLUSION
  • REFERENCES
• 3. Deep Learning in Omics Data Analysis and Precision Medicine
  Jordi Martorell-Marugán, Siham Tabik, Yassir Benhammou, Coral del Val, Igor Zwir, Francisco Herrera, and Pedro Carmona-Sáez.
  • INTRODUCTION
  • DEEP LEARNING METHODS
  • DEEP LEARNING APPLICATIONS IN OMICS DATA ANALYSIS
  • CLINICAL APPLICATIONS AND PRECISION MEDICINE
  • CONCLUSION
  • REFERENCES
• 4. Biological Sequence Analysis
  Usman Saeed and Zainab Usman.
  • INTRODUCTION
  • PAIRWISE ALIGNMENT AND DYNAMIC PROGRAMMING
  • HEURISTIC LOCAL ALIGNMENT
  • MACHINE LEARNING AND SEQUENCE ANALYSIS
  • NEXT-GENERATION SEQUENCING
  • APPLICATIONS OF NGS IN CLINICAL PRACTICE
  • CONCLUSION
  • REFERENCES
• 5. Multivariate Statistical Methods for High-Dimensional Multiset Omics Data Analysis
  Attila Csala and Aeilko H. Zwinderman.
  • INTRODUCTION
  • EARLY 2000s: THE UNIVARIATE APPROACH
  • LATE 2000s: MULTIVARIATE APPROACHES
  • EARLY 2010s: MULTISET MULTIVARIATE APPROACHES
  • LATE 2010s: HIERARCHICAL MULTISET MULTIVARIATE APPROACHES
  • CONCLUSION
  • References
• 6. Statistical Methods for RNA Sequencing Data Analysis
  Dongmei Li.
  • INTRODUCTION
  • STATISTICAL METHODS FOR BULK RNA SEQUENCING DIFFERENTIAL ANALYSIS
  • STATISTICAL METHODS COMPARISONS FOR BULK RNA SEQUENCING DIFFERENTIAL ANALYSIS
  • STATISTICAL METHODS FOR SINGLE-CELL RNA SEQUENCING DIFFERENTIAL ANALYSIS
  • STATISTICAL METHODS COMPARISON FOR SINGLE-CELL RNA SEQUENCING DIFFERENTIAL ANALYSIS
  • CONCLUSION
  • REFERENCES
• 7. Computational Epigenomics: From Fundamental Research to Disease Prediction and Risk Assessment
  Mohamed-Amin Choukrallah, Florian Martin, Nicolas Sierro, Julia Hoeng, Nikolai V. Ivanov, and Manuel C. Peitsch.
  • INTRODUCTION
  • DNA MODIFICATIONS
  • ASSESSMENT OF CYTOSINE MODIFICATIONS
  • CHROMATIN REGULATION
  • CONCLUSION
  • REFERENCES
• 8. Computational Approaches in Proteomics
  Karla Cervantes Gracia and Holger Husi.
  • INTRODUCTION
  • SAMPLE TYPES AND SAMPLE PROCESSING APPROACHES
  • DATA ACQUISITION
  • DATA HANDLING AND WORKFLOWS
  • DATA INTERPRETATION AND FUNCTIONAL ANALYSIS
  • CONCLUSION
  • REFERENCES
• 9. Cheminformatics and Computational Approaches in Metabolomics
  Marco Fernandes, Bela Sanches, and Holger Husi.
  • INTRODUCTION
  • METABOLOMICS DATA ACQUISITION AND PRE-PROCESSING
  • DATA MINING APPROACHES, STATISTICAL ANALYSIS AND ML METHODS
  • CONCLUSION
  • REFERENCES
• 10. Feature Selection in Microarray Data Using Entropy Information
  Ali Reza Soltanian, Niloofar Rabiei, and Fatemeh Bahreini.
  • INTRODUCTION
  • DATA NORMALISATION METHOD
  • SHANNON’S ENTROPY
  • APPLICATION
  • CONCLUSION
  • REFERENCES
• 11. Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining
  Xindi Wu, Xiangrui Zeng, Zhenxi Zhu, Xin Gao, and Min Xu.
  • INTRODUCTION
  • TEMPLATE-BASED STRUCTURAL PATTERN MINING
  • SUPERVISED SUBTOMOGRAM CLASSIFICATION AND SEGMENTATION
  • TEMPLATE-FREE STRUCTURAL PATTERN MINING
  • CRYO-ET BIOLOGICAL AND MEDICAL APPLICATIONS
  • CONCLUSION
  • REFERENCES

Computational Biology

ISBN: 978-0-9944381-9-5

DOI: http://dx.doi.org/10.15586/computationalbiology.2019

Edited by

Holger Husi, Dr sc nat, Division of Biomedical Science, University of the Highlands and Islands, UK

Published by

Codon Publications

Brisbane, Australia

Copyright© 2019 Codon Publications

Copyright of individual chapters belongs to the respective authors. The authors grant unrestricted publishing and distribution rights to the publisher. The electronic versions of the chapters are published under Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0). https://creativecommons.org/licenses/by-nc/4.0/. Users are allowed to share and adapt the chapters for any non-commercial purposes as long as the authors and the publisher are explicitly identified and properly acknowledged as the original source. The book in its entirety is subject to copyright by the publisher. The reproduction, modification, republication and display of the book in its entirety, in any form, by anyone, for commercial purposes are strictly prohibited without the written consent of the publisher.

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First Published in October 2019

Printed in Australia