Computational

Biology
Holger Husi
Editor
 Computational Biology

Cover image: A framework for integrative biology. See page 21, chapter 2 for details.
Computational Biology

Edited by

HOLGER HUSI, DR SC NAT

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

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First Published in October 2019

Printed in Australia
 Contents v

CONTENTS

Foreword vii
Preface ix
List of Contributors xiii

1 An Introduction to Image-Based Systems Biology of

Multicellular Spheroids for Experimentalists and
Theoreticians 1
Sabine C. Fischer

2 Integrative Biology Approaches Applied to

Human Diseases 19
Alysson H. Urbanski, José D. Araujo, Rachel Creighton,
Helder I. Nakaya

3 Deep Learning in Omics Data Analysis and

Precision Medicine 37
Jordi Martorell-Marugán, Siham Tabik, Yassir Benhammou,
Coral del Val, Igor Zwir, Francisco Herrera, Pedro Carmona-Sáez

4 Biological Sequence Analysis 55

Usman Saeed, Zainab Usman

5 Multivariate Statistical Methods for High-Dimensional

Multiset Omics Data Analysis 71
Attila Csala, Aeilko H. Zwinderman

6 Statistical Methods for RNA Sequencing Data Analysis 85

Dongmei Li
vi Contents

7 Computational Epigenomics: From Fundamental

Research to Disease Prediction and Risk Assessment 101
Mohamed-Amin Choukrallah, Florian Martin, Nicolas Sierro,
Julia Hoeng, Nikolai V. Ivanov, Manuel C. Peitsch

8 Computational Approaches in Proteomics 119

Karla Cervantes Gracia, Holger Husi

9 Cheminformatics and Computational

Approaches in Metabolomics 143
Marco Fernandes, Bela Sanches, Holger Husi

10 Feature Selection in Microarray Data Using Entropy

Information 161
Ali Reza Soltanian, Niloofar Rabiei, Fatemeh Bahreini

11 Template-Based and Template-Free Approaches

in Cellular Cryo-Electron Tomography
Structural Pattern Mining 175
Xindi Wu, Xiangrui Zeng, Zhenxi Zhu, Xin Gao, Min Xu

Index 187

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