Preface xix
List of Symbols xxi
About the Authors xxiii
Part One Introduction 1
1 Introduction to Bioinformatics 3
2 Computational Methods in Bioinformatics 9
Part Two Introduction to Molecular Biology 19
3 The Living Cell 21
4 Central Dogma of Molecular Biology 33
Part Three Data Acquisition and Pre-processing 53
5 High-throughput Technologies 55
6 Databases, Standards and Annotation 67
7 Normalisation 87
8 Feature Selection 109
9 Differential Expression 119
Part Four Clustering Methods 133
10 Clustering Forms 135
11 Partitional Clustering 143
12 Hierarchical Clustering 157
13 Fuzzy Clustering 167
14 Neural Network-based Clustering 181
15 Mixture Model Clustering 197
16 Graph Clustering 227
17 Consensus Clustering 247
18 Biclustering 265
19 Clustering Methods Discussion 283
Part Five Validation and Visualisation 303
20 Numerical Validation 305
21 Biological Validation 323
22 Visualisations and Presentations 339
Part Six New Clustering Frameworks Designed for Bioinformatics 363
23 Splitting-Merging Awareness Tactics (SMART) 365
24 Tightness-tunable Clustering (UNCLES) 385
Appendix 395
Index 409
Asoke K. Nandi, Department of Electronic & Computer
Engineering, Brunel University London, UK
Prof. Nandi is
Chair and Head of the Electronic and Computer Engineering
Department at Brunel University London, UK. He leads the Signal
Processing and Communications Research Group with interests in the
areas of signal processing, machine learning, and communications
research. He is a Finland Distinguished Professor at the University
of Jyvaskyla, Finland. In 1983 Professor Nandi was a member of the
UA1 team at CERN that discovered the three fundamental particles
known as W+, W- and Z0, providing the evidence for the unification
of the electromagnetic and weak forces, which was recognized by the
Nobel Committee for Physics in 1984. He has authored or co-authored
more than 190 journal papers, and 2 books. The Google Scholar
h-index of his publications is 54. In 2010 he received the Glory of
Bengal Award for his outstanding achievements in scientific
research, and in 2012 was awarded the IEEE Heinrich Hertz Award.
Prof. Nandi is a Fellow of the IEEE.
Rui Fa, Department of Electronic & Computer Engineering,
Brunel University London, UK
Dr. Fa is a Senior Reseach
Fellow in the Department of Electronic & Computer Engineering at
Brunel University London, UK. Prior to this, he held research
positions at the University of York and the University of Leeds
working in radar signal processing and wireless communication
projects. His current research interests include bioinformatics,
machine learning, Bayesian statistics, statistical signal
processing, and network science. Dr Rui Fa received his Bachelor
and Master degrees in electronic and electrical engineering from
Nanjing University of Science and Technology, China, in 2000 and in
2003, respectively, and his PhD degree in electrical engineering
from University of Newcastle, UK, in 2007.
Basel Abu-Jamous, Department of Electronic & Computer
Engineering, Brunel University London, UK
Basel Abu-Jamous
is currently studying for his PhD in electrical engineering &
electronics at Brunel University London, UK. His research interests
include bioinformatics, computational biology, and the broader
areas of information engineering and machine learning.Basel
Abu-Jamous received his B.Sc. degree in computer engineering from
the University of Jordan, Amman, Jordan, in 2010. He received his
M.Sc. degree in information and intelligence engineering from the
University of Liverpool, Liverpool, U.K., in 2011. He was awarded
the Sir Robin Saxby Prize of the 2010/2011 academic year based on
his performance in his M.Sc. degree.
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