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Bioinformatics

Book Description

As a result of experimental techniques, the combination of biology and computer science was initiated to classify and process an expanding number of biological observations. Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the medical community with its innovations that change how we recognize and care for illnesses. This publication provides significant research and the most recent observations that are useful for researchers, practitioners, and academicians involved in the many aspects of bioinformatics.

Table of Contents

  1. Cover
  2. Title Page
  3. Copyright Page
  4. Editorial Advisory Board and List of Reviewers
    1. Editor-in-Chief
    2. Associate Editors
    3. Editorial Advisory Board
  5. Preface
  6. Section 1: Fundamental Concepts and Theories
    1. Chapter 1: Overview of Biomedical Engineering
      1. ABSTRACT
      2. INTRODUCTION
      3. HISTORY OF BIOMEDICAL ENGINEERING
      4. MAIN DUTIES OF BIOMEDICAL ENGINEER AND CLINICAL ENGINEER
      5. BIOMEDICAL ENGINEERING SPECIALIZATIONS
      6. CURRENT AND FUTURE DIRECTIONS OF BIOMEDICAL ENGINEERING
      7. CONCLUSION
      8. APPENDIX A: PROFESSIONAL SOCIETIES OF BIOMEDICAL ENGINEERING
      9. APPENDIX B: SOME OF THE MAJOR MANUFACTURERS OF MRI DEVICES
    2. Chapter 2: Evaluating a Genetics Concept Inventory
      1. ABSTRACT
      2. INTRODUCTION
      3. SURVEY PROCEDURES AND STUDENT PROFILE
      4. EXPERIMENTAL TECHNIQUES APPLIED TO ENCOURAGE LANGUAGE LEARNING
      5. QUANTITATIVE MEASURES AND STATISTICAL ANALYSIS
      6. STATISTICAL EVALUATION OF UCGenCI
      7. CONCLUSION
    3. Chapter 3: Overview of Knowledge Discovery in Databases Process and Data Mining for Surveillance Technologies and EWS
      1. ABSTRACT
      2. INTRODUCTION
      3. SOME DATA MINING APPLICATIONS FOR EWS DEVELOPMENT IN THE LITERATURE
      4. KNOWLEDGE DISCOVERY IN DATABASES PROCESS AND DATA MINING
      5. MINING ADVANCED DATA TYPES
      6. FUTURE RESEARCH DIRECTIONS
      7. CONCLUSION
    4. Chapter 4: A Review of Kernel Methods Based Approaches to Classification and Clustering of Sequential Patterns
      1. ABSTRACT
      2. INTRODUCTION
      3. DESIGN OF DYNAMIC KERNELS FOR DISCRETE SYMBOL SEQUENCES
      4. REVIEW OF KERNEL METHODS BASED APPROACHES TO CLASSIFICATION AND CLUSTERING OF DISCRETE SEQUENCES
      5. CONCLUSION
    5. Chapter 5: GO-Based Term Semantic Similarity
      1. ABSTRACT
      2. GENE ONTOLOGY AND GENE ONTOLOGY ANNOTATION
      3. SEMANTIC SIMILARITY BETWEEN GENE ONTOLOGY TERMS
      4. SEMANTIC SIMILARITY BETWEEN GENE PRODUCTS
      5. EVALUATION OF METHODS FOR COMPUTING SEMANTIC SIMILARITY BETWEEN GO TERMS
      6. PREVIOUS METHODS FOR COMPUTING SEMANTIC SIMILARITY BETWEEN GO TERMS
      7. A SEMANTIC SIMILARITY METHOD THAT DOES NOT RELY ON EXTERNAL DATA SOURCES
      8. DISCUSSION AND FUTURE DIRECTIONS
    6. Chapter 6: Parallel Evolutionary Computation in R
      1. ABSTRACT
      2. INTRODUCTION
      3. DIFFERENTIAL EVOLUTION
      4. DIFFERENTIAL EVOLUTION IN R
      5. PARALLEL EVOLUTIONARY COMPUTATION
      6. PACKAGES FOR EVOLUTIONARY COMPUTATION IN R
      7. CONCLUSION AND FUTURE DIRECTIONS
      8. APPENDIX 1: GETTING STARTED WITH R
      9. APPENDIX 2: A PARALLEL DE FUNCTION IN R
    7. Chapter 7: Developing a Library Collection in Bioinformatics
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. INFORMATION NEEDS OF BIOINFORMATICIANS
      5. LIBRARY USE IN BIOINFORMATICS
      6. BIOINFORMATICS COLLECTION DEVELOPMENT: RESOURCE TYPES, SELECTION CRITERIA, AND RECOMMENDATIONS
      7. EDUCATIONAL OPPORTUNITIES FOR BIOINFORMATICS LIBRARIANS
      8. CONCLUSION
      9. APPENDIX: KEY RESOURCES
    8. Chapter 8: Linking Interactome to Disease
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. INTERACTOME-TRANSCRIPTOME INTEGRATION
      5. RESULTS
      6. CONCLUSION AND FUTURE RESEARCH DIRECTIONS
    9. Chapter 9: Knowledge-Driven, Data-Assisted Integrative Pathway Analytics
      1. ABSTRACT
      2. INTRODUCTION
      3. PATHWAY AND NETWORK ANALYSIS TOOLS
      4. INTEGRATIVE ANALYSIS AND EXAMPLES OF ITS APPLICATION
      5. FUTURE DIRECTIONS
    10. Chapter 10: Medical Informatics and Bioinformatics
      1. ABSTRACT
      2. 1. CHAPTER OBJECTIVES
      3. 2. INTRODUCTION
      4. 3. DEFINITION OF MEDICAL INFORMATICS AND BIOINFORMATICS
      5. 4. HISTORICAL BACKGROUND AND LITERATURE OVERVIEW
      6. 5. MEDICAL INFORMATICS
      7. 6. BIOINFORMATICS
      8. 7. THE FUTURE OF MEDICAL INFORMATICS AND BIOINFORMATICS
      9. 8. PROFESSIONAL SOCIETIES, ORGANIZATIONS, AND TRAINING PROGRAMS
      10. 9. CHAPTER SUMMARY
    11. Chapter 11: An Overview of Graph Indexing and Querying Techniques
      1. ABSTRACT
      2. INTRODUCTION
      3. PRELIMINARIES
      4. SUBGRAPH QUERY PROCESSING
      5. SUPERGRAPH QUERY PROCESSING
      6. GRAPH SIMILARITY QUERIES
      7. GRAPH QUERY LANGUAGES
      8. DISCUSSION AND CONCLUSION
    12. Chapter 12: Genomics and Population Health
      1. ABSTRACT
      2. SOME PERTINENT QUESTIONS FROM THE SARS EPIDEMIC
      3. LESSONS FROM POPULATION HEALTH
      4. RE-EMERGENCE OF SOCIAL EPIDEMIOLOGY
    13. Chapter 13: Genomics and Genetic Engineering
      1. ABSTACT
      2. THE NEW DEVELOPMENTS IN GENETICS
      3. PLAYING GOD: THE MEANING
      4. PLAYING GOD: WE SHOULD NOT DO IT
      5. PLAYING GOD: WE MUST DO IT
      6. PLAYING GOD: AN ORIENTAL CHRISTIAN RESPONSE
      7. CAN HUMANS REALLY ‘PLAY GOD’?
      8. CONCLUSION
    14. Chapter 14: The Important Role of Lipids in Cognitive Impairment
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS
      5. DISCUSSION
      6. CONCLUSION
    15. Chapter 15: Virtual Worlds for Teaching
      1. ABSTRACT
      2. INTRODUCTION
      3. THE VIRTUAL WORLD ENVIRONMENT
      4. METHOD
      5. DISCUSSION
      6. CONCLUSION
    16. Chapter 16: Data Intensive Computing for Bioinformatics
      1. ABSTRACT
      2. INTRODUCTION
      3. INNOVATIONS IN ALGORITHMS FOR DATA INTENSIVE COMPUTING
      4. INNOVATIONS IN PROGRAMMING MODELS USING CLOUD TECHNOLOGIES
      5. ITERATIVE MAPREDUCE WITH TWISTER
      6. CONCLUSION
    17. Chapter 17: From Bench to Bedside
      1. I. ABSTRACT
      2. II. DISCOVERY AND CLONING OF BACE1
      3. III. PATHOLOGY OF BACE1 IN AD BRAINS
      4. IV. CLINICAL CSF STUDIES WITH BACE1 IN ALZHEIMER’S DISEASE
      5. V. PERSPECTIVES OF NEUROCHEMICAL BIOMARKER DEVELOPMENT IN ALZHEIMER’S DISEASE
  7. Section 2: Tools and Technologies
    1. Chapter 18: Analysis and Prediction of DNA-Recognition by Zinc Finger Proteins
      1. ABSTRACT
      2. INTRODUCTION
      3. PREDICTING THE RECOGNITION OF DNA BY ZINC FINGER PROTEINS COMPUTATIONALLY
      4. CONCLUSION
      5. FUTURE SCOPE
    2. Chapter 19: Web Services for Bioinformatics
      1. EXECUTIVE SUMMARY
      2. 1. INTRODUCTION
      3. 2. NATURE OF BIOLOGICAL RESEARCH
      4. 3. PREVIOUS EFFORTS AND EVOLVING SOLUTIONS
      5. 4. WEB SERVICES: APPLICABILITY AND LIMITATIONS
      6. 5. SEMANTIC WEB: THE FOUNDATION FOR SEMANTIC WEB SERVICE
      7. 6. BRINGING IT ALL TOGETHER
      8. 7. WEB SERVICES: THE ROLE OF SOFTWARE VENDORS
      9. 8. CONCLUSION AND FUTURE DIRECTIONS
    3. Chapter 20: Learning Binding Affinity from Augmented High Throughput Screening Data
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. DATASETS
      5. ALGORITHMS
      6. EXPERIMENTS
      7. CROSS CLASSIFIER AGREEMENT
      8. FUTURE RESEARCH DIRECTIONS
      9. CONCLUSION
    4. Chapter 21: Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism
      1. ABSTRACT
      2. INTRODUCTION
      3. REPRESENTATION SCHEME
      4. SCORING FUNCTION WITH NETWORK PROPERTIES
      5. SEARCH ALGORITHM
      6. CONCLUSION
    5. Chapter 22: Techniques for Named Entity Recognition
      1. ABSTRACT
      2. INTRODUCTION
      3. TAGGED DATASETS FOR NER
      4. EVALUATION OF NER ALGORITHMS
      5. RULE-BASED NER
      6. SUPERVISED LEARNING APPROACHES
      7. UNSUPERVISED LEARNING APPROACHES
      8. NER IN OTHER LANGUAGES
      9. CONCLUSION AND FUTURE RESEARCH DIRECTIONS
    6. Chapter 23: Neuroimaging in Alzheimer’s Disease
      1. ABSTRACT
      2. INTRODUCTION
      3. PET AND SPECT IMAGING
      4. NEW TRACERS FOR AD DIAGNOSIS
      5. LEWY BODY DISEASE AND PARKINSON’S DISEASE
      6. ALZHEIMER DISEASE NEUROIMAGING INITIATIVE
    7. Chapter 24: Neuronal Transcytosis of WGA Conjugated Protein
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS
      5. DISCUSSION
    8. Chapter 25: Noninvasive Detection of Misfolded Proteins in the Brain Using [11C]BF-227 PET
      1. ABSTRACT
      2. INTRODUCTION
      3. EXPERIMENT
      4. RESULTS
      5. DISCUSSION
    9. Chapter 26: Graph Mining Techniques
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. GRAPH GENERATORS
      5. GRAPH MINING: THE PROBLEM OF DISTINGUISHING REAL NETWORKS FROM SYNTHETIC ONES
      6. OBSERVATIONS
      7. SCALABILITY
      8. CONCLUSION
      9. FUTURE RESEARCH DIRECTIONS
    10. Chapter 27: Current Omics Technologies in Biomarker Discovery
      1. ABSTRACT
      2. INTRODUCTION
      3. GENETIC BIOMARKER
      4. TRANSCRIPTOMIC BIOMARKER
      5. MASS SPECTROMETRY-BASED QUANTITATIVE PROTEOMICS FOR BIOMARKER DISCOVERY
      6. METABONOMICS IN BIOMARKER DISCOVERY
      7. CONCLUSION
    11. Chapter 28: Prediction of Epigenetic Target Sites by Using Genomic DNA Sequence
      1. ABSTRACT
      2. INTRODUCTION
      3. METHODS TO PREDICT EPIGENETIC TARGETS
      4. DISCUSSION
    12. Chapter 29: Biclustering of DNA Microarray Data
      1. ABSTRACT
      2. INTRODUCTION
      3. BICLUSTERING OF DNA MICROARRAY DATA
      4. BICLUSTER MODELS, INTERPRETATIONS, AND EVALUATIONS
      5. ALGORITHMS FOR BICLUSTERS IDENTIFICATION
      6. BIOLOGICAL APPLICATIONS OF BICLUSTERING ALGORITHMS
      7. CONCLUSION, DISCUSSION AND FUTURE RESEARCH DIRECTIONS
      8. ADDITIONAL READING
    13. Chapter 30: Unsupervised Methods to Identify Cellular Signaling Networks from Perturbation Data
      1. ABSTRACT
      2. INTRODUCTION
      3. COMBINING MULTI-VARIATE MEASUREMENT DATA INTO QUANTITATIVE ESTIMATES OF SIGNAL TRANSDUCTION
      4. FUTURE RESEARCH DIRECTIONS
      5. CONCLUSION
      6. APPENDIX
    14. Chapter 31: Cross-Platform Microarray Data Integration Combining Meta-Analysis and Gene Set Enrichment Analysis
      1. ABSTRACT
      2. INTRODUCTION AND BACKGROUND
      3. MAIN FOCUS OF THE CHAPTER
      4. DISCUSSIONS AND CONCLUSION
    15. Chapter 32: Chemosensitivity Prediction of Tumours based on Expression, miRNA, and Proteomics Data
      1. ABSTRACT
      2. INTRODUCTION
      3. DATA AND PROBLEM DESCRIPTION
      4. IMPROVING THE ESTIMATION OF GI50
      5. COMPARISON OF FEATURE SELECTION TECHNIQUES
      6. COMPARISON OF REGRESSION VS. CLASSIFICATION
      7. A FULL ANALYSIS OF THE COMPLETE SET OF 120 DRUGS
      8. FOCUS ON THE MOST CLINICALLY RELEVANT SET OF DRUGS
      9. FURTHER REDUCING THE SELECTED VARIABLES BY EMPLOYING MULTI-TASK VARIABLE SELECTION
      10. CONCLUSION
    16. Chapter 33: FPGA-Based Accelerators for Bioinformatics Applications
      1. ABSTRACT
      2. 1. INTRODUCTION
      3. 2. PAIRWISE COMPARISON AND SEQUENCE-PROFILE ALIGNMENT
      4. 3. FPGA-BASED ACCELERATORS FOR PAIRWISE COMPARISON
      5. 4. FPGA-BASED ACCELERATORS FOR SEQUENCE-PROFILE COMPARISON
      6. 5. CONCLUSION AND PERSPECTIVES
  8. Section 3: Frameworks and Methodologies
    1. Chapter 34: Modules in Biological Networks
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL METHODS FOR MODULE IDENTIFICATION
      4. NOTATIONS AND DEFINITIONS
      5. MODULE-BASED APPLICATIONS IN BIOLOGICAL STUDIES
      6. CONCLUSION
    2. Chapter 35: A Framework for Networked Experiments in Global E-Science
      1. ABSTRACT
      2. INTRODUCTION
      3. SCIENCE, NETWORKS, AND COLLABORATION
      4. COLLABORATION AND E-SCIENCE
      5. DISTRIBUTED PROCESSES AND MUTUAL OBJECTIVES
      6. THE ARCHITECTURE OF PROJECTS
      7. MODULES
      8. ENHANCING FLEXIBILITY IN RESEARCH AND TEACHING
      9. DISCUSSION AND CONCLUDING REMARKS
    3. Chapter 36: Complexity and Modularity of MAPK Signaling Networks
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. DISCUSSION
      6. CONCLUSION
    4. Chapter 37: Using Systems Biology Approaches to Predict New Players in the Innate Immune System
      1. ABSTRACT
      2. INTRODUCTION
      3. METHODS
      4. RESULTS
      5. DISCUSSION
      6. CONCLUSION
      7. FUTURE WORK
      8. APPENDIX
    5. Chapter 38: Addressing the Challenges of Detecting Epistasis in Genome-Wide Association Studies of Common Human Diseases Using Biological Expert Knowledge
      1. ABSTRACT
      2. INTRODUCTION
      3. GENOME-WIDE ASSOCIATION STUDIES (GWAS)
      4. CHALLENGES OF DETECTING EPISTASIS IN GWAS
      5. BIOLOGICAL EXPERT KNOWLEDGE
      6. OUTLOOK/CONCLUDING REMARKS
    6. Chapter 39: Connecting Microbial Population Genetics with Microbial Pathogenesis
      1. ABSTRACT
      2. INTRODUCTION
      3. FUTURE DIRECTIONS AND DEVELOPMENTAL PROSPECTS
    7. Chapter 40: Hybrid Neural Genetic Architecture
      1. ABSTRACT
      2. INTRODUCTION
      3. RECOMMENDER SYSTEMS
      4. MOLECULAR BIOLOGY (SPLICE JUNCTION) DATASET
      5. EVOLUTIONARY ALGORITHMS
      6. FEATURE SELECTION
      7. HUMAN NATURE, INTERACTION, AND BEHAVIOUR: SOME FACTS
      8. LIMITATIONS OF EXISTING GA WORKS
      9. MOTIVATION FOR NEW DIRECTIONS
      10. NEW DIRECTIONS FOR GENETIC ALGORITHM DESIGN
      11. RESULT OF NEW DIRECTIONS: THE BUABIN ALGORITHM
      12. HUMAN BASED FEATURE SELECTION AND CLASSIFICATION
      13. JUSTIFICATION FOR HYBRID NEURAL INTEGRATION
      14. HYBRID RECURRENT NEURAL CLASSIFIER (HY-RNC)
      15. HYBRID NEURAL GENETIC ARCHITECTURE
      16. LIMITATIONS
      17. CONCLUSION
    8. Chapter 41: A Two-Layer Learning Architecture for Multi-Class Protein Folds Classification
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS
      4. METHOD
      5. RESULTS AND DISCUSSION
      6. CONCLUSION
      7. APPENDIX
    9. Chapter 42: The Mathematical Modeling and Computational Simulation for Error-Prone PCR
      1. ABSTRACT
      2. INTRODUCTION
      3. MODELING FOR ERROR-PRONE PCR
      4. DISCUSSION AND CONCLUSION
    10. Chapter 43: Using a Genetic Algorithm and Markov Clustering on Protein–Protein Interaction Graphs
      1. ABSTRACT
      2. INTRODUCTION
      3. RELATED WORK
      4. GENETIC ALGORITHMS
      5. OUR METHOD
      6. EXPERIMENTAL RESULTS
      7. CONCLUSION
    11. Chapter 44: Kernel Generative Topographic Mapping of Protein Sequences
      1. ABSTRACT
      2. INTRODUCTION
      3. FROM PROTEINS TO DRUGS
      4. ANALYZING PROTEIN SEQUENCES USING KERNEL METHODS
      5. RESULTS
      6. CONCLUSION
    12. Chapter 45: Incorporating Correlations among Gene Ontology Terms into Predicting Protein Functions
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. CHALLENGES IN NETWORK-BASED PROTEIN FUNCTION PREDICTION
      5. NETWORK-BASED PROTEIN FUNCTION PREDICTION
      6. FUNCTION PREDICTION WITH HIERARCHICALLY INDEPENDENT GENE ONTOLOGY TERMS
      7. CONCLUSION AND FUTURE DIRECTIONS
    13. Chapter 46: Bifurcation Analysis of a Model Accounting for the 14-3-3σ Signalling Compartmentalisation
      1. ABSTRACT
      2. INTRODUCTION
      3. MATHEMATICAL MODEL
      4. CONCLUSION
    14. Chapter 47: Engineering Gene Control Circuits with Allosteric Ribozymes in Human Cells as a Medicine of the Future
      1. ABSTRACT
      2. INTRODUCTION
      3. CONCLUSION
    15. Chapter 48: Computational Sequence Design Techniques for DNA Microarray Technologies
      1. ABSTRACT
      2. INTRODUCTION
      3. RELATED WORK
      4. DNA SEQUENCE DESIGN: PROBLEM DESCRIPTION
      5. STATE OF THE ART OF HEURISTIC ALGORITHMS
      6. COMPUTATIONAL EXPERIMENTS
      7. RESULTS
      8. CONCLUSION AND FUTURE RESEARCH DIRECTIONS
  9. Section 4: Cases and Applications
    1. Chapter 49: Can Activated Platelet Rich Plasma Combined with Adipose-Derived Stem Cells Be Used to Treat Skin Wrinkles?
      1. ABSTRACT
      2. INTRODUCTION
      3. ADSC ISOLATION AND VIABILITY
      4. ISOLATION AND CULTURE OF DERMAL FIBROBLAST
      5. PRP PREPARATION
      6. IN VITRO EFFECT OF ADSC AND FIBROBLAST CO-CULTURES SUPPLEMENTED WITH PRP
      7. IN VIVO EFFECT OF COMBINED ADSCS / PRP INJECTION ON PHOTO-AGED MOUSE MODELS
      8. DISCUSSION
      9. CONCLUSION
    2. Chapter 50: Analysis of Kinase Inhibitors and Druggability of Kinase-Targets Using Machine Learning Techniques
      1. ABSTRACT
      2. PATTERN DISCOVERY IN KINASES
      3. BACKGROUND
      4. DRUGGABILITY
      5. DISCUSSION AND CONCLUSION
    3. Chapter 51: In Silico Pharmaco-Gene-Informatic Identification of Insulin-Like Proteins in Plants
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. RESULTS OF IN SILICO INVESTIGATIONS
      5. COMMENT
      6. CONCLUSION
    4. Chapter 52: Molecular Network Analysis of Target RNAs and Interacting Proteins of TDP-43, a Causative Gene for the Neurodegenerative Diseases ALS/FTLD
      1. ABSTRACT
      2. INTRODUCTION
      3. METHODS
      4. RESULTS
      5. DISCUSSION
      6. CONCLUSION
    5. Chapter 53: Chemoinformatics on Metabolic Pathways
      1. ABSTRACT
      2. INTRODUCTION
      3. EC NUMBER CLASSIFICATION
      4. TRANSFORMATION PATTERN AND THE REACTION MECHANISM
      5. MANY HEURISTICS IN COMPUTATION
      6. ACTUAL RESEARCH EXAMPLES OF REACTION PREDICTION
      7. FUTURE RESEARCH DIRECTIONS
      8. CONCLUSION
      9. AVAILABILITY
    6. Chapter 54: Improving Prediction Accuracy via Subspace Modeling in a Statistical Geometry Based Computational Protein Mutagenesis
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS AND DISCUSSION
      5. CONCLUSION
    7. Chapter 55: Resolving Sample Traces in Complex Mixtures with Microarray Analyses
      1. ABSTRACT
      2. INTRODUCTION
      3. A BRIEF INTRODUCTION TO MICROARRAY DATA ANALYSIS
      4. HYBRIDIZATION DYNAMICS OF NUCLEIC ACIDS ON SOLID SURFACES
      5. THE MICRODISSECTION OF MICROARRAY DATA OR “SEARCHING NEEDLES IN THE HAYSTACK”
      6. CONCLUSION
      7. APPENDIX
    8. Chapter 56: Predictive Dynamical Modelling MicroRNAs Role in Complex Networks1
      1. ABSTRACT
      2. INTRODUCTION TO THE SPECIFIED SCOPE
      3. RECENT STUDIES ON ANALYSING MODULES OF CANCER NETWORKS
      4. ON THE ROLE OF MICRORNAS IN SOMITOGENESIS
      5. BISTABLE EQUATION WITH A DIFFUSION TERM
      6. POLARIZATION (DEPOLARIZATION)-DIFFUSION MODEL WITH ELASTIC TENSION
      7. ON THE ROBUSTNESS OF POLARIZATION (DEPOLARIZATION) WAVE FRONT PROPAGATION IN A TUMOR
      8. AN EXPERIMENTAL EVIDENCE OF THE CELL POLARIZATION ROLE IN TUMOROGENESIS
      9. SYNTHESIS OF DYNAMICAL MODEL OF MIRNA REGULATION OF A CANCER NETWORK
      10. ANALYSIS OF DYNAMICAL MODEL OF MIRNA REGULATION OF A CANCER NETWORK
      11. AN APPLICATION OF QUASI-STEADY-STATE APPROXIMATION TO MIRNA ROLE IN CANCER NETWORKS
      12. A MODIFIED MINIMAL MODEL OF miRNA-MEDIATED TARGET REGULATION
      13. APPLYING QSSA THEOREM TO DYNAMICAL SYSTEM (72-78)
      14. DISCUSSIONS AND UNRESOLVED PROBLEMS TO BE CONSIDERED IN THE FUTURE
    9. Chapter 57: Decision Support Systems in the Process of Improving Patient Safety
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. DECISION SUPPORT SYSTEMS: DESIGN, IMPLEMENTATION, AND VALIDATION
      5. POSITIVE AND NEGATIVE EFFECTS OF DECISION SUPPORT SYSTEMS ON PATIENT SAFETY
      6. DECISION SUPPORT SYSTEMS AND HIGH DIMENSIONAL DATA
      7. DECISION SUPPORT SYSTEMS: THEIR FUTURE AND RELATIONSHIP WITH OTHER E-HEALTH APPLICATIONS
      8. CONCLUSION
    10. Chapter 58: Graph Applications in Chemoinformatics and Structural Bioinformatics
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. NOTATION
      5. USE OF ALGORITHMS FROM GRAPH THEORY IN CHEMOINFORMATICS
      6. USE OF ALGORITHMS FROM GRAPH THEORY IN STRUCTURAL BIOINFORMATICS
      7. FUTURE RESEARCH DIRECTIONS
      8. CONCLUSION
    11. Chapter 59: Visualization of Protein 3D Structures in ‘Double-Centroid’ Reduced Representation
      1. ABSTRACT
      2. INTRODUCTION
      3. METHODS
      4. RESULTS AND DISCUSSION
      5. CONCLUSION AND FUTURE DIRECTIONS
    12. Chapter 60: JFeature
      1. ABSTRACT
      2. INTRODUCTION
      3. THE JFEATURE TOOLBOX
      4. APPLICATION
      5. CONCLUSION
    13. Chapter 61: Evaluation of Coupled Nuclear and Cytoplasmic p53 Dynamics
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. DISCUSSION
      6. CONCLUSION AND FUTURE WORK
    14. Chapter 62: Data Mining and Meta-Analysis on DNA Microarray Data
      1. ABSTRACT
      2. INTRODUCTION
      3. 1. PREREQUISITES FOR DATA MINING
      4. 2. DATA-MINING: DERIVING BIOLOGICAL INFORMATION FROM MICROARRAY EXPERIMENTS
      5. 3. META-ANALYSIS
      6. 4. CONCLUSION
      7. APPENDIX: ABBREVIATIONS
    15. Chapter 63: Efficient Computational Construction of Weighted Protein-Protein Interaction Networks Using Adaptive Filtering Techniques Combined with Natural Selection-Based Heuristic Algorithms
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. EXPERIMENTAL RESULTS
      5. CONCLUSION
    16. Chapter 64: BMP Signaling in Regenerative Medicine
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. SOLUTIONS AND RECOMMENDATIONS
      5. FUTURE RESEARCH DIRECTIONS
      6. CONCLUSION
  10. Section 5: Issues and Challenges
    1. Chapter 65: Certification and Security Issues in Biomedical Grid Portals
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. SECURITY REQUIREMENTS FOR BIOMEDICAL GRID PORTALS
      5. BASIC GRID SECURITY MECHANISMS
      6. THE GRISSOM PORTAL IN BRIEF
      7. SECURITY ASPECTS OF THE GRISSOM PORTAL
      8. SUMMARY AND CONCLUSION
      9. FUTURE WORK DIRECTIONS
      10. APPENDIX A
      11. APPENDIX B
    2. Chapter 66: A Comparative Study of an Unsupervised Word Sense Disambiguation Approach
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. RELATED WORK
      5. SENSATIONAL AND ITS APPLICATION
      6. EXPERIMENT AND RESULTS
      7. DISCUSSION AND FUTURE WORK
    3. Chapter 67: The Impact of Genetic Testing and Genetic Information on Ethical, Legal and Social Issues in North America
      1. ABSTRACT
      2. INTRODUCTION
      3. THE ETHICAL, LEGAL AND SOCIAL ISSUES FRAMEWORK
      4. FUTURE RESEARCH DIRECTIONS
      5. CONCLUSION
    4. Chapter 68: The Applications of Omics Technologies and the Challenges of Ethics in Nutritional Sciences
      1. ABSTRACT
      2. HUMAN GENOME TO APPLIED OMICS
      3. FUNCTIONAL FOODS
      4. ETHICAL ISSUES
      5. DEVELOPING COUNTRIES
      6. CONCLUSION
    5. Chapter 69: A Philosophical Exploration of the Concept of ‘Property’ in Genetics and Databanking
      1. ABSTRACT
      2. WHAT IS AT STAKE
      3. THE CONCEPTUAL DEBATE
      4. REVIS(IT)ING THE FRAMEWORK
      5. INTEGRATING DIVERSE NORMATIVE CULTURES TOWARDS AN ADVANCED FRAMEWORK
      6. WHAT CAN PHILOSOPHY DO TO CONTRIBUTE TO ETHICS OF GENETICS?
    6. Chapter 70: Genomics Perspectives of Bioethanol Producing Zymomonas Mobilis
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. SOLUTIONS AND RECOMMENDATIONS
      6. FUTURE RESEARCH DIRECTIONS
      7. CONCLUSION
    7. Chapter 71: Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine
      1. ABSTRACT
      2. INTRODUCTION
      3. PERSONALIZED MEDICINE: THE HISTORY
      4. SYSTEMS BIOLOGY AND PERSONALIZED MEDICINE
      5. PRIVACY AND ETHICAL DILEMMAS: A PROBLEM STATEMENT
      6. ETHICS ISSUES IN THE ERA OF PERSONALIZED MEDICINE
      7. PRIVACY CONSIDERATIONS IN THE ERA OF PERSONALIZED MEDICINE
      8. SUMMARY
      9. CONCLUSION
    8. Chapter 72: Ethics, Privacy, and the Future of Genetic Information in Healthcare Information Assurance and Security
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND OF PHARMACOGENOMICS
      4. EXISTING LAWS
      5. IMPLICATIONS FOR INFORMATION ASSURANCE AND SECURITY
      6. CONCLUSION
      7. APPENDIX: DISCUSSION QUESTIONS
    9. Chapter 73: Risk-Benefit Analysis of Combination vs. Unopposed HRT in Post-Menopausal Women
      1. ABSTRACT
      2. INTRODUCTION
      3. CONCLUSION
    10. Chapter 74: Plastika [Totipotenta]
      1. ABSTRACT
      2. INTRODUCTION
      3. VIRTUAL ORGANIC PLASTICINE
      4. FERTILE EVOLUTION
      5. PLASTIC PLASTICITY
      6. ELASTIC DIGITAL SOUNDS
      7. VIDEO STEM CELLS
      8. FLEXIBLE BIOMEDIA
      9. HYBRID WORLD
    11. Chapter 75: Pharmacovigilance
      1. ABSTRACT
      2. INTRODUCTION
      3. DEFINITION AND TERMINOLOGIES
      4. EPIDEMIOLOGY AND IMPLICATIONS OF ADRS
      5. CLASSIFICATION OF ADRS
      6. PREDISPOSING FACTORS FOR ADRS
      7. IMPORTANCE OF PHARMACOVIGILANCE
      8. SURVEILLANCE METHODS IN PHARMACOVIGILANCE
      9. EVALUATION OF INDIVIDUAL ADRS
      10. ROLES OF VARIOUS PROFESSIONALS IN PHARMACOVIGILANCE
      11. INTERNATIONAL REGULATORY AGENCIES ON PHARMACOVIGILANCE AND INFLUENCE OF PHARMACOINFORMATICS
      12. PHARMACOINFORMATICS: VARIOUS ARENAS
      13. TERMINOLOGIES
      14. FUTURE OF PHARMACOINFORMATICS IN IMPROVING PHARMACOVIGILANCE
      15. CONCLUSION
    12. Chapter 76: Language Focus for Genetics and Molecular Biology Students
      1. ABSTRACT
      2. INTRODUCTION
      3. LANGUAGE METHODS EMPLOYED TO SUPPORT LEARNING IN GENETICS
      4. IMPACT OF SCIENTIFIC LANGUAGE INTERVENTION ON STUDENT LEARNING IN GENETICS
      5. ASSESSING LANGUAGE CAPACITY IN EXPERIENCED SCIENCE STUDENTS: A FOCUS ON THE 2008-2009 GENETICS COHORT
      6. ANALYSIS OF LANGUAGE AND NON-LANGUAGE FACTORS THAT CONTRIBUTE TO STUDENT PERFORMANCE IN GENETICS
      7. ROLE OF MOTIVATION
      8. CONCLUSION
    13. Chapter 77: Data Analysis and Interpretation in Metabolomics
      1. ABSTRACT
      2. 1. INTRODUCTION
      3. 2: DATA ANALYSIS AND INTERPRETATION
      4. 3. FUTURE DIRECTIONS
      5. CONCLUDING REMARKS
      6. LIST OF ABBREVIATIONS
    14. Chapter 78: Promoter Structures Conserved between Homo Sapiens, Mus Musculus and Drosophila Melanogaster
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. METHODOLOGY
      5. RESULTS
      6. CONCLUSION
  11. Section 6: Emerging Trends
    1. Chapter 79: A New Approach for Sequence Analysis
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL ANALYSIS: INPUT
      4. COMPUTATIONAL ANALYSIS: METHOD
      5. COMPUTATIONAL ANALYSIS: OUTPUT
      6. CONCLUSION
    2. Chapter 80: Aβ Monomer, Oligomer and Fibril in Alzheimer’s Disease
      1. ABSTRACT
      2. INTRODUCTION
      3. A FAMILIAL CASE WITH THE EARLY ONSET ALZHEIMER’S DISEASE
      4. BEYOND AMYLOID PLAQUES
      5. PERSPECTIVE
    3. Chapter 81: BTISNet
      1. ABSTRACT
      2. INTRODUCTION
      3. MAJOR ACTIVITIES
      4. BTIS NETWORK AND ITS NODES
      5. BTIS IVRI
      6. DISCUSSION
    4. Chapter 82: Intelligent Classifiers Fusion for Enhancing Recognition of Genes and Protein Pattern of Hereditary Diseases
      1. ABSTRACT
      2. INTRODUCTION
      3. EXISTING WORKS
      4. REVIEW ON EXISTING CLASSIFIERS
      5. EVALUATION OF FUSION MODEL
      6. CONCLUDING REMARKS
    5. Chapter 83: Mining Statistically Significant Substrings based on the Chi-Square Measure
      1. ABSTRACT
      2. INTRODUCTION
      3. STATISTICAL MODELS AND TOOLS
      4. ALGORITHMS
      5. EXPERIMENTAL RESULTS
      6. CONCLUSION
    6. Chapter 84: Semi-Supervised Clustering for the Identification of Different Cancer Types Using the Gene Expression Profiles
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. FUTURE RESEARCH DIRECTIONS
      6. CONCLUSION
      7. APPENDIX
    7. Chapter 85: Cancer Gene Expression Data Analysis Using Rough Based Symmetrical Clustering
      1. ABSTRACT
      2. INTRODUCTION
      3. EXISTING WORKS
      4. ROUGH SETS THEORY
      5. SYMMETRY BASED CLUSTERING
      6. EXPERIMENTAL FRAMEWORK
      7. PERFORMANCE ANALYSIS
      8. TEST FOR STATISTICAL SIGNIFICANCE
      9. CONCLUSION
    8. Chapter 86: Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND INFORMATION ON VARIOUS DIFFERENT PARADIGMS FOR BIOSYNTHESIS OF POLYKETIDES AND NONRIBOSOMAL PEPTIDES
      4. DECIPHERING THE SECONDARY METABOLITE BIOSYNTHETIC CODE BY IN SILICO ANALYSIS
      5. PREDICTION OF DOMAIN ORGANIZATION IN PKS/NRPS GENE CLUSTERS
      6. PREDICTION OF SUBSTRATE SPECIFICITY OF VARIOUS CATALYTIC DOMAINS
      7. PREDICTION OF NUMBER OF ITERATIONS CATALYZED BY TYPE I ITERATIVE PKSs
      8. PREDICTION OF THE ORDER OF SUBSTRATE CHANNELING IN MODULAR PKS CLUSTERS
      9. PREDICTION OF SPECIFICITY OF THIOESTERASE DOMAINS AND TAILORING ENZYMES
      10. APPLICATION OF IN SILICO PREDICTIONS IN EXPERIMENTAL STUDIES INVOLVING DISCOVERY OF NEW SECONDARY METABOLITES AND REPROGRAMMING OF KNOWN BIOSYNTHETIC PATHWAYS
      11. FUTURE DIRECTIONS
      12. CONCLUSION
    9. Chapter 87: Improving PSI-BLAST’s Fold Recognition Performance through Combining Consensus Sequences and Support Vector Machine
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL MODELS AND METHODS
      4. RESULT
      5. DISCUSSION AND CONCLUSION
    10. Chapter 88: Towards Optimal Microarray Universal Reference Sample Designs
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND TO URR SAMPLE DESIGN
      4. TOWARDS OPTIMAL REFERENCE SAMPLE DESIGNS
      5. EXPERIMENTS
      6. RESULTS AND DISCUSSION
      7. CONCLUSION
    11. Chapter 89: Gene Expression Regulation underlying Osteo-, Adipo-, and Chondro-Genic Lineage Commitment of Human Mesenchymal Stem Cells
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS
      5. DISCUSSION
    12. Chapter 90: Quantum Computing Approach for Alignment-Free Sequence Search and Classification
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS: SEQUENCE ANALYSIS
      5. SOLUTIONS AND RECOMMENDATIONS
      6. FUTURE RESEARCH DIRECTIONS
      7. CONCLUSION
      8. APPENDIX A: COMPLEXITY ANALYSIS
      9. APPENDIX B
    13. Chapter 91: An Approach for Biological Data Integration and Knowledge Retrieval Based on Ontology, Semantic Web Services Composition, and AI Planning
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. SEMANTIC WEB APPROACH FOR DATA INTEGRATION
      5. WEB SERVICES COMPOSITION TO KNOWLEDGE RETRIEVAL
      6. CONCLUSION AND FUTURE RESEARCH DIRECTION
    14. Chapter 92: An Optimization to Protein Coding Regions Identification in Eukaryotes
      1. ABSTRACT
      2. INTRODUCTION
      3. RELATED WORK
      4. PROPOSED SOLUTION
      5. RESULTS AND DISCUSSION
      6. CONCLUSION
    15. Chapter 93: Use of SciDBMaker as Tool for the Design of Specialized Biological Databases
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. SCIENTIFIC DATABASE MAKER, A COMPREHENSIVE TOOL FOR THE DESIGN OF SPECIALIZED BIOLOGICAL DATABASES
      5. WHAT NEXT: WEB INTERFACE DESIGN AND TOOLS IMPLEMENTATION
      6. CONCLUSION
    16. Chapter 94: Emerging Web Tools and Their Applications in Bioinformatics
      1. ABSTRACT
      2. INTRODUCTION TO BIOINFORMATICS
      3. APPLICATIONS OF BIOINFORMATICS
      4. EMERGING APPLICATIONS
      5. WEB
      6. CHALLENGES IN BIOINFORMATICS
      7. WEB IN BIOINFORMATICS
      8. WEB TOOLS IN SEQUENCE, STRUCTURE AND FUNCTION CATEGORY
      9. CASE STUDY OF WEB BASED TOOLS
      10. CONCLUSION