Table Of ContentComputational Biology and Bioinformatics
Gene Regulation
Gene | Rna | Protein | Epigenetics
Computational Biology
and Bioinformatics
Gene Regulation
Gene | Rna | Protein | Epigenetics
Editor
Ka-Chun Wong
Department of Computer Science
City University of Hong Kong
Kowloon Tong, Hong Kong
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2016 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business
No claim to original U.S. Government works
Version Date: 20160419
International Standard Book Number-13: 978-1-4987-2500-2 (eBook - PDF)
This book contains information obtained from authentic and highly regarded sources. Reasonable efforts
have been made to publish reliable data and information, but the author and publisher cannot assume
responsibility for the validity of all materials or the consequences of their use. The authors and publishers
have attempted to trace the copyright holders of all material reproduced in this publication and apologize to
copyright holders if permission to publish in this form has not been obtained. If any copyright material has
not been acknowledged please write and let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmit-
ted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented,
including photocopying, microfilming, and recording, or in any information storage or retrieval system,
without written permission from the publishers.
For permission to photocopy or use material electronically from this work, please access www.copyright.
com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood
Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and
registration for a variety of users. For organizations that have been granted a photocopy license by the CCC,
a separate system of payment has been arranged.
Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used
only for identification and explanation without intent to infringe.
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com
Preface
The field of computational biology and bioinformatics has been rapidly
evolving in recent years. It holds tremendous potential to have a good impact
on understanding genetics, developing personalized medicine solutions.
Hundreds of books have been written on it. In particular, there are only few
bioinformatics books with a focus on gene regulation. Therefore, this book has
been compiled to fill the void. The book is an open-chapter-called collection
of peer-reviewed chapters contributed by international experts who have passed
through rigorous blind reviews. Following the central dogma of molecular
biology, the book content is divided into six sections: Genes (Chapters 1 to 3),
RNAs (Chapters 4 and 5), Proteins (Chapters 6 and 7), Epigenetics (Chapters
8 and 9), Case Study (Chapter 10), and Advanced Topics (Chapters 11
to 17).
(Section 1: Genes) In Chapter 1, Cao and Yip compile a comprehensive
survey on enhancers which are central to gene transcription. In Chapter 2, Wei
et al. introduce a software package for detecting differential gene expression. In
Chapter 3, Fujita et al. describe how Granger causality can be applied to infer
gene regulatory networks from gene expression data.
(Section 2: RNAs) In Chapter 4, Keservani et al. present a reader-friendly
tutorial on RNA sequencing and its relation to gene regulation. In Chapter 5,
Samantarrai et al. focus on non-coding RNAs and its network applications from
the view of system biology.
(Section 3: Proteins) In Chapter 6, Mishra et al. compare different algorithms
for the annotation of hypothetical proteins. In Chapter 7, Hahn and Muley review
the computational protein-protein functional linkage prediction methods. They
also propose a gene co-regulation based method for functional linkage prediction.
(Section 4: Epigenetics) In Chapter 8, Wang et al. give us a review on
bioinformatics methodologies and tools for performing epigenomic analysis of
chromatin organization and DNA methylation. In Chapter 9, Lou focuses on
the statistical modeling of DNA methylation with sharp insights into its role in
coding regions and gene regulation.
(Section 5: Case Study) In Chapter 10, Wang et al. describe a case study of
EGFR-related gene mutations which are linked to drug resistance in non-small-
cell lung carcinoma treatments.
(Section 6: Advanced Topics) In Chapter 11, Giannoulatou et al. review
contemporary approaches for quality assurance in genome-scale bioinformatics
analyses. In Chapter 12, Issa reports the recent trends in biological sequence
alignment methods. In Chapter 13, Mansouri et al. introduce a mathematical
book chapter on state estimation and process monitoring of nonlinear biological
vi Computational Biology and Bioinformatics
phenomena. In Chapter 14, Neelapu and Challa provide us a review on
metagenomics with an emphasis on gene regulation. In Chapter 15, Thukral and
Hasija describe how gene regulation can be altered in the context of metabolic
engineering. In Chapter 16, Gupta et al. review general bioinformatics tools
for phylogenetic analysis and ortholog identification which can shape gene
regulation mechanisms of different species throughout the evolutionary history.
In Chapter 17, Shikhin et al. have compiled a book chapter about protein model
ranking through topological assessment.
In summary, state-of-the-art computational biology and bioinformatics
studies are described and summarized in this book. This book provides updated
reviews on the computational biology and bioinformatics studies for gene
regulation. I hope that this book can help accelerate the advancement of the
scientific community in computational biology and bioinformatics, benefiting
the human beings and other species on the earth.
Ka-Chun Wong
City University of Hong Kong
July 2015
List of Reviewers
Alan Moses
André Fujita
Antonio Sze-To
Ashish Runthala
Bibekanand Mallick
Bjorn Wallner
Bo Hu
Carlos Lijeron
Daniel Alex
Debby D. Wang
Eleni Giannoulatou
Hafeez Ur Rehman
Harishchander Anandaram
Hong Yan
Huiluo Cao
Joshua Ho
Konstantinos Krampis
Salim Bougouffa
Shailendra K. Gupta
Shaoke Lou
Sun Jin
Vijaykumar Yogesh Muley
Wenye Li
Yanjie Wei
Yasha Hasija
Yingying Wei
Yu Chen
Yue Li
