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Computational Biology

Editor: Holger Husi , Dr sc nat.

Editors

Affiliations

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). 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.

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

• INTRODUCTION
• METHODS
• FIRST WORKFLOW: CELL BIOLOGY
• SECOND WORKFLOW: CANCER BIOLOGY
• THIRD WORKFLOW: BIOPRINTING
• OUTLOOK: EXPERIMENTS INSPIRED BY THE MATHEMATICAL MODELS
• CONCLUSION
• REFERENCES

• 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

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

• 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

• INTRODUCTION
• EARLY 2000 s : THE UNIVARIATE APPROACH
• LATE 2000 s : MULTIVARIATE APPROACHES
• EARLY 2010 s : MULTISET MULTIVARIATE APPROACHES
• LATE 2010 s : HIERARCHICAL MULTISET MULTIVARIATE APPROACHES
• CONCLUSION
• References

• 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

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

• INTRODUCTION
• SAMPLE TYPES AND SAMPLE PROCESSING APPROACHES
• DATA ACQUISITION
• DATA HANDLING AND WORKFLOWS
• DATA INTERPRETATION AND FUNCTIONAL ANALYSIS
• CONCLUSION
• REFERENCES

• INTRODUCTION
• METABOLOMICS DATA ACQUISITION AND PRE-PROCESSING
• DATA MINING APPROACHES, STATISTICAL ANALYSIS AND ML METHODS
• CONCLUSION
• REFERENCES

• INTRODUCTION
• DATA NORMALISATION METHOD
• SHANNON’S ENTROPY
• APPLICATION
• CONCLUSION
• REFERENCES

• 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

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

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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.

Notice to the user

The views and opinions expressed in this book are believed to be accurate at the time of publication. The publisher, editors or authors cannot be held responsible or liable for any errors, omissions or consequences arising from the use of the information contained in this book. The publisher makes no warranty, implicit or explicit, with respect to the contents of this book, or its use.

First Published in October 2019

Printed in Australia

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). 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.