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ENCYCLOPEDIA OF
BIOINFORMATICS AND
COMPUTATIONAL BIOLOGY
ENCYCLOPEDIA OF
BIOINFORMATICS AND
COMPUTATIONAL BIOLOGY
EDITORS IN CHIEF
Shoba Ranganathan
Macquarie University, Sydney, NSW, Australia
Michael Gribskov
Purdue University, West Lafayette, IN, United States
Kenta Nakai
The University of Tokyo, Tokyo, Japan
Christian Schönbach
Nazarbayev University, School of Science and Technology, Department of Biology,
Astana, Kazakhstan
VOLUME 1
Methods
Mario Cannataro
The Magna Græcia University of Catanzaro, Catanzaro, Italy
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Notices
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products, instructions, or ideas contained in the material herein.
ISBN 978-0-12-811414-8
Shoba Ranganathan holds a Chair in Bioinformatics at Macquarie University since 2004. She
has held research and academic positions in India, USA, Singapore and Australia as well as a
consultancy in industry. She hosted the Macquarie Node of the ARC Centre of Excellence in
Bioinformatics (2008–2013). She was elected the first Australian Board Director of the Inter-
national Society for Computational Biology (ISCB; 2003–2005); President of Asia-Pacific
Bioinformatics Network (2005–2016) and Steering Committee Member (2007–2012) of
Bioinformatics Australia. She initiated the Workshops on Education in Bioinformatics (WEB)
as an ISMB2001 Special Interest Group meeting and also served as Chair of ICSB's Educaton
Committee. Shoba currently serves as Co-Chair of the Computational Mass Spectrometry
(CompMS) initiative of the Human Proteome Organization (HuPO), ISCB and Metabolomics
Society and as Board Director, APBioNet Ltd.
Shoba's research addresses several key areas of bioinformatics to understand biological
systems using computational approaches. Her group has achieved both experience and
expertise in different aspects of computational biology, ranging from metabolites and small
molecules to biochemical networks, pathway analysis and computational systems biology. She
has authored as well as edited several books as well as articles for the 2013 Encyclopedia of
Systems Biology. She is currently an Editor-in-Chief of the Encyclopedia of Bioinformatics and
Computational Biology and the Bioinformatics Section Editor of the Reference Module in Life Science as well as an editorial board
member of several bioinformatics journals.
Dr. Gribskov graduated from Oregon State University in 1979 with a Bachelors of Science
degree (with Honors) in Biochemistry and Biophysics. He then moved to the University of
Wisconsin-Madison for graduate studies focused on the structure and function of the sigma
subunit of E. coli RNA polymerase, receiving his Ph.D. in 1985. Dr. Gribskov studied X-ray
crystallography as an American Cancer Society post-doctoral fellow at UCLA in the laboratory
of David Eisenberg, and followed this with both crystallographic and computational studies at
the National Cancer Institute. In 1992, Dr. Gribskov moved to the San Diego Supercomputer
Center at the University of California, San Diego where he was lead scientist in the area of
computational biology and an adjunct associate professor in the department of Biology. From
2003 to 2007, Dr. Gribskov was the president of the International Society for Computational
Biology, the largest professional society devoted to bioinformatics and computational biology.
In 2004, Dr. Gribskov moved to Purdue University where he holds an appointment as a full
professor in the Biological Sciences and Computer Science departments (by courtesy). Dr.
Gribskov's interests include genomic and transcriptomic analysis of model and non-model
organisms, the application of pattern recognition and machine learning techniques to biomolecules, the design and imple-
mentation of biological databases to support molecular and systems biology, development of methods to study RNA structural
patterns, and systems biology studies of human disease.
Kenta Nakai received the PhD degree on the prediction of subcellular localization sites of
proteins from Kyoto University in 1992. From 1989, he has worked at Kyoto University,
National Institute of Basic Biology, and Osaka University. From 1999 to 2003, he was an
Associate Professor at the Human Genome Center, the Institute of Medical Science, the Uni-
versity of Tokyo, Japan. Since 2003, he has been a full Professor at the same institute. His main
research interest is to develop computational ways for interpreting biological information,
especially that of transcriptional regulation, from genome sequence data. He has published
more than 150 papers, some of which have been cited more than 1,000 times.
v
vi Editors in Chief
Christian Schö nbach is currently Department Chair and Professor at Department of Biology,
School of Science and Technology, Nazarbayev University, Kazakhstan and Visiting Professor at
International Research Center for Medical Sciences at Kumamoto University, Japan. He is a
bioinformatics practitioner interfacing genetics, immunology and informatics conducting
research on major histocompatibility complex, immune responses following virus infection,
biomedical knowledge discovery, peroxisomal diseases, and autism spectrum disorder that
resulted in more than 80 publications. His previous academic appointments included Pro-
fessor at Kumamoto University (2016–2017), Nazarbayev University (2013–2016), Kazakh-
stan, Kyushu Institute of Technology (2009–2013) Japan, Associate Professor at Nanyang
Technological University (2006–2009), Singapore, and Team Leader at RIKEN Genomic Sci-
ences Center (2002–2006), Japan. Other prior positions included Principal Investigator at Kent
Ridge Digital Labs, Singapore and Research Scientist at Chugai Institute for Molecular Medi-
cine, Inc., Japan. In 2018 he became a member of International Society for Computational Biology (ISCB) Board of Directors.
Since 2010 he is serving Asia-Pacific Bioinformatics Network (APBioNet) as Vice-President (Conferences 2010–2016) and Pre-
sident (2016–2018).
VOLUME EDITORS
Bruno Gaeta is Senior Lecturer and Director of Studies in Bioinformatics in the School of
Computer Science and Engineering at UNSW Australia. His research interests cover multiple
areas of bioinformatics including gene regulation and protein structure, currently with a focus
on the immune system, antibody genes and the generation of antibody diversity. He is a
pioneer of bioinformatics education and has trained thousands of biologists and trainee
bioinformaticians in the use of computational tools for biological research through courses,
workshops as well as a book series. He has worked both in academia and in the bioinfor-
matics industry, and currently coordinates the largest bioinformatics undergraduate program
in Australia.
Mohammad Asif Khan, PhD, is an associate professor and the Dean of the School of Data
Sciences, as well as the Director of the Centre for Bioinformatics at Perdana University,
Malaysia. He is also a visiting scientist at the Department of Pharmacology and Molecular
Sciences, Johns Hopkins University School of Medicine (JHUSOM), USA. His research
interests are in the area of biological data warehousing and applications of bioinformatics to
the study of immune responses, vaccines, inhibitory drugs, venom toxins, and disease bio-
markers. He has published in these areas, been involved in the development of several novel
bioinformatics methodologies, tools, and specialized databases, and currently has three
patent applications granted. He has also led the curriculum development of a Postgraduate
Diploma in Bioinformatics programme and an MSc (Bioinformatics) programme at Perdana
University. He is an elected ExCo member of the Asia-Pacific Bioinformatics Network
(APBioNET) since 2010 and is currently the President of Association for Medical and Bio-
Informatics, Singapore (AMBIS). He has donned various important roles in the organization
of many local and international bioinformatics conferences, meetings and workshops.
vii
CONTENTS OF VOLUME 1
Editors in Chief v
Volume Editors vii
List of Contributors for Volume 1 xvii
Preface xxi
VOLUME 1
Algorithms Foundations
Nadia Pisanti 1
Techniques for Designing Bioinformatics Algorithms
Massimo Cafaro, Italo Epicoco, and Marco Pulimeno 5
Algorithms for Strings and Sequences: Searching Motifs
Francesco Cauteruccio, Giorgio Terracina, and Domenico Ursino 15
Algorithms for Strings and Sequences: Pairwise Alignment
Stefano Beretta 22
Algorithms for Strings and Sequences: Multiple Alignment
Pietro H Guzzi 30
Algorithms for Structure Comparison and Analysis: Prediction of Tertiary Structures of Proteins
Giuseppe Tradigo, Francesca Rondinelli, and Gianluca Pollastri 32
Algorithms for Structure Comparison and Analysis: Homology Modelling of Proteins
Marco Wiltgen 38
Ab initio Protein Structure Prediction
Rahul Kaushik, Ankita Singh, and B Jayaram 62
Algorithms for Structure Comparison and Analysis: Docking
Giuseppe Tradigo, Francesca Rondinelli, and Gianluca Pollastri 77
Algorithms for Graph and Network Analysis: Graph Indexes/Descriptors
Lo Giudice Paolo and Domenico Ursino 81
Algorithms for Graph and Network Analysis: Traversing/Searching/Sampling Graphs
Paolo Lo Giudice and Domenico Ursino 89
Algorithms for Graph and Network Analysis: Clustering and Search of Motifs in Graphs
Clara Pizzuti and Simona E Rombo 95
Algorithms for Graph and Network Analysis: Graph Alignment
Luigi Palopoli and Simona E Rombo 102
Bioinformatics Data Models, Representation and Storage
Mariaconcetta Bilotta, Giuseppe Tradigo, and Pierangelo Veltri 110
Data Storage and Representation
Antonella Guzzo 117
Experimental Platforms for Extracting Biological Data: Mass Spectrometry, Microarray, Next
Generation Sequencing
Barbara Calabrese 126
ix
x Contents of Volume 1
Introduction to Biostatistics
Antonella Iuliano and Monica Franzese 648
Descriptive Statistics
Monica Franzese and Antonella Iuliano 672
Measurements of Accuracy in Biostatistics
Haiying Wang, Jyotsna T Wassan, and Huiru Zheng 685
Hypothesis Testing
Claudia Angelini 691
Statistical Inference Techniques
Daniela De Canditiis 698
Correlation Analysis
Monica Franzese and Antonella Iuliano 706
Regression Analysis
Claudia Angelini 722
Nonlinear Regression Models
Audrone Jakaitiene 731
Parametric and Multivariate Methods
Luisa Cutillo 738
Stochastic Processes
Maria Francesca Carfora 747
Hidden Markov Models
Monica Franzese and Antonella Iuliano 753
Linkage Disequilibrium
Barbara Calabrese 763
Introduction to the Non-Parametric Bootstrap
Daniel Berrar 766
Population-Based Sampling and Fragment-Based De Novo Protein Structure Prediction
David Simoncini and Kam YJ Zhang 774
Ontology: Introduction
Gianluigi Greco, Marco Manna, and Francesco Ricca 785
Ontology: Definition Languages
Valeria Fionda and Giuseppe Pirrò 790
Ontology: Querying Languages and Development
Valeria Fionda and Giuseppe Pirrò 800
Ontology in Bioinformatics
Pietro Hiram Guzzi 809
Biological and Medical Ontologies: Introduction
Marco Masseroli 813
Biological and Medical Ontologies: GO and GOA
Marco Masseroli 823
Biological and Medical Ontologies: Protein Ontology (PRO)
Davide Chicco and Marco Masseroli 832
Biological and Medical Ontologies: Disease Ontology (DO)
Anna Bernasconi and Marco Masseroli 838
xiv Contents of Volume 1
Biological Pathways
Giuseppe Agapito 1047
Biological Pathway Data Formats and Standards
Ramakanth C Venkata and Dario Ghersi 1063
Biological Pathway Analysis
Ramakanth Chirravuri Venkata and Dario Ghersi 1067
Two Decades of Biological Pathway Databases: Results and Challenges
Sara Rahmati, Chiara Pastrello, Andrea EM Rossos, and Igor Jurisica 1071
Visualization of Biological Pathways
Giuseppe Agapito 1085
Integrative Bioinformatics
Marco Masseroli 1092
Integrative Bioinformatics of Transcriptome: Databases, Tools and Pipelines
Maria T Di Martino and Pietro H Guzzi 1099
Information Retrieval in Life Sciences
Pietro Cinaglia, Domenico Mirarchi, and Pierangelo Veltri 1104
LIST OF CONTRIBUTORS FOR VOLUME 1
xvii
xviii List of Contributors for Volume 1
FINE.
LA BISCIA AMOROSA
DANZA MILANESE
(ANNO 1580)