Advances in Bioinformatics and Big Data Analytics

Contents
Preface
	Overview
	Objective
	Organization
	Audiences for the Publication
Abbreviations
Part I: Application and Analysis of Omics Data
Chapter 1
The Value of Next-Generation Sequencing  and Multi-Omics Data for Clinical Diagnosis: Future Perspectives on Breast Cancer
	Abstract
	Introduction
	NGS Types, Workflow, and Its Potency in Cancer Research and Clinical Routine
	Driver and Passenger Mutations in Cancer, and Methods  for Differentiating In-between
		Strategies Relying on Differences in Biological Feature
		Strategies Relying on Machine-Learning Methods
		Methods Relating to the Effect of Mutations  on Their Functional Properties
	Pathway-Based and Network-Based Analysis
	Next-Generation Sequencing in the Era  of Breast Cancer Researches
	Multi-omics Data in Cancer Research
	Omics Data Repositories Databases
		Catalogue of Somatic Mutations in Cancer (COSMIC)
		Proteomics Identification Database (PRIDE)
		Genomic Expression Omnibus (GEO)
	Conclusion
	References
Chapter 2
Next-Generation Sequencing  and Omics Data Analysis Techniques
	Abstract
	Introduction
	Recent Advances in the Application of Next-Generation Sequencing and Omics Data Analysis Techniques
	Conclusion
	References
Chapter 3
In silico Approaches to Vaccine Design
	Abstract
	Introduction
	In silico Approaches for Vaccine Designing
	Numerous In silico Approaches for Vaccine Designing
	Conclusion
	References
Chapter 4
Evolution of Genomic Medicine
	Abstract
	Introduction
	Methodological Advancement
		DNA, the Genetic Material
		High Throughput Sequencing Technology
			Pre-Genomic Era
			First Generation Sequencing
			Second Generation Sequencing
			Third Generation Sequencing
	Computational Tools Development
		Whole Genome Analysis Tools
		Disease and Drug Target Tools
		Evolutionary Studies
		Structural Modelling
	Advent of Human Genome Projects
		A Brief History
		Significant Outcomes
			ENCODE
			GENCODE
		Development of Genomic Database
			Primary Databases
			Secondary Databases
			Composite Databases
		Genome Annotation and Comparison
	Paradigm Shift: Traditional to Genome Medicine
		Need of Genome Medicine: Broader Vision
			Genetic Diversity
			Shortcomings of Traditional Medicine
		GWAS and QTL Mapping
	Implementation of Genome Medicine
		Success, Challenges and Opportunities
			Cancer
			Sickle Cell Anaemia
			Lactose Intolerance
		Genomic Medicine and Its Financial Impact
		Ethical and Legal Issues
		Genome Medicine: Hope or Hype
	Conclusion
	References
Chapter 5
Bio-Inspired Computing
	Abstract
	Introduction
	P-System
		Informational Description
			Components of the P-System
				The Environment
				Membranes
				Symbols
				Catalysts
				Rules
		Computation Process
		Rule Application
		Non-Deterministic Application
		Maximally Parallel Application
			As a Computation Model
		Computation
			Step 1
			Step 2
			Step 3
			Step 4
			Step 5
			Step 6
		Computation Halts
	Bio-Inspired Swarm Optimization Algorithms
		Genetic Bee Colony (GBC) Algorithm
		Setting ABC Parameter
		Initialization of the Population of Solutions
		Evaluation of the Population Solutions
		Employer Bee
		Onlooker Bee
		Scout Bee
		Genetic Operators
	Cat Swarm Optimization (CSO)
		Seeking Mode
		The Tracing Mode
	Artificial Algae Algorithm (AAA)
		Helical Movement Phase
		Evolutionary Process Phase
		Adaptation Phase
	Elephant Search Algorithm (ESA)
	Chicken Swarm Optimization (CSO)
		Behavioral Understanding
		Mathematical Understanding
		Grey Wolf Optimization (GWO) Algorithm
		Mathematical Understanding
	Moth–Flame Optimization (MFO) Algorithm
		Algorithm
		Generating the Initial Population of Moths
		Updating the Positions of Moths
		Updating the Number of Flames
		Different Variants of MFO
		Multi-objective
		Binary
		Hybridization
		Applications
	Whale Optimization Algorithm (WOA)
		Mathematical Model
		Bubble-net Attacking Method (Exploitation Phase)
		Shrinking Encircling Mechanism
			Spiral Updating Position
			Search for Prey (Exploration Phase)
	Fish Swarm Optimization Algorithm (FSOA)
		Concept and Algorithm
			Individual Movement Operator
			Food Operator
			Instinctive Collective Movement Operator
			Non-Instinctive Collective Movement Operator
	Artificial Neural Network
	Artificial Bee Colony Algorithm
	Cuckoo Optimization Algorithm (COA)
	Bacterial Foraging Optimization Algorithm (BFOA)
	Flower Pollination Algorithm (FPA)
	Neuromorphic Engineering
	Neurological Inspiration
	Neuromorphic Prototypes
	Neuromorphic Sensors
	Conclusion
	References
Chapter 6
Feature Selection and Classification  of Microarray Cancer Dataset:  Review and Challenges
	Abstract
	Introduction
	Microarray Technology
	Feature Selection
		Methods
			Filter
			Wrapper
			Embedded
			Hybrid
	Classification
		Logistic Regression
		Naïve Bayes
		K-Nearest Neighbor (KNN)
		Support Vector Machine
		Random Forest
		Decision Trees
	Dataset
	Related Work
	Performance Evaluation Measures
	Result and Analysis
		Based on the Following
			Feature Selection
			Dataset
			Classifier
	Conclusion
	References
Part II: Application of Bioinformatics  Tools and Databases
Chapter 7
Machine Learning Methods in Bioinformatics
	Abstract
	Introduction
	Recent Trends in the Application of Machine Learning  in Bioinformatics Techniques
	Conclusion
	References
Chapter 8
Molecular Biomarkers as Health  and Disease Predictors
	Abstract
	Introduction
	Specific Authors That Have Worked on Molecular Biomarkers  as Health and Disease Predictors
	Conclusion
	References
Chapter 9
Systems Biology Applications and Bioinformatics
	Abstract
	Introduction
	System Biology
		Medicine
		Agriculture
		Bioremediation
	Current Techniques Involved Systems Biology Application  and Bioinformatics
	Conclusion
	References
Chapter 10
Genome Data Resources  and Tools for Sequence Analysis
	Abstract
	Introduction to Bioinformatics
	Role of Genomics
	Tools for Genomics Research
	FastQC
	GeneWise
	NCBI Prokaryotic Genomes Automatic Annotation Pipeline
	GenSAS
	Ori-Finder
	P2RP
	KAAS
	Simple Synteny
	MEGA11
	DNA Plotter
	SNP
	SNP2CAPS
	TASSEL
	STRUCTURE
	ClustalW
	Bioinformatics Databases
	GenBank
	Phytozome
	EMBL
	Swiss-Prot
	UniProtKB
	Gramene
	GrainGenes
	MaizeGDB
	Multiple Databases and Tools as Sources
	NCBI
	KEGG
	Conclusion
	References
Chapter 11
Bioinformatics Tools for Biomarker Discovery
	Abstract
	Introduction
	Typical Examples of Bioinformatics Tools  That Could Be Applied in the Discovery of Biomarkers
	Conclusion
	References
Chapter 12
A Review on Recent Advances  in Different Modelling Techniques, Algorithms,  and Software for Metabolic Pathways Analysis in System Biology
	Abstract
	Introduction
	Molecular Modeling in System Biology
	Concerns about Modeling and Simulation
	Classification of Models
	Structured Dynamical Systems
	Pathway Analysis in Biological Systems
	Interactions Flow through Biological Pathway
	Feedback Control
	Pathway Activation Measurement
	Future Aspects and Challenges
	Conclusion
	References
Chapter 13
Bioinformatics Tools and Databases for Genomics Research
	Abstract
	Introduction
	Relevance of Bioinformatics Tools and Databases for Genomics Research
	Databases for Genomics Research
	Conclusion
	References
Chapter 14
Computer Viruses and Their Defences in Computer Networks: An e-Epidemiological Model
	Abstract
	Introduction
	Simple SIVR Model
	SIVR Fuzzy Model
	Solution of Equilibrium Points
	Basic Reproduction Number R0
	Comparison R0 Versus
	Local Stability for Virus Free Equilibrium
	Global Stability Analysis
	Control Strategies for Virus
	Result and Discussion
		Example 1
	Conclusion
	References
Glossary
Index
About the Editors
About the Contributors
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