Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology

Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology

by Hamid R Arabnia, Quoc Nam Tran
Released August 2015
Publisher(s): Morgan Kaufmann
ISBN: 9780128026465

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Book description

Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology discusses the latest developments in all aspects of computational biology, bioinformatics, and systems biology and the application of data-analytics and algorithms, mathematical modeling, and simu- lation techniques.

• Discusses the development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques to the study of biological and behavioral systems, including applications in cancer research, computational intelligence and drug design, high-performance computing, and biology, as well as cloud and grid computing for the storage and access of big data sets.

• Presents a systematic approach for storing, retrieving, organizing, and analyzing biological data using software tools with applications to general principles of DNA/RNA structure, bioinformatics and applications, genomes, protein structure, and modeling and classification, as well as microarray analysis.

• Provides a systems biology perspective, including general guidelines and techniques for obtaining, integrating, and analyzing complex data sets from multiple experimental sources using computational tools and software. Topics covered include phenomics, genomics, epigenomics/epigenetics, metabolomics, cell cycle and checkpoint control, and systems biology and vaccination research.

• Explains how to effectively harness the power of Big Data tools when data sets are so large and complex that it is difficult to process them using conventional database management systems or traditional data processing applications.

  • Discusses the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological and behavioral systems.
  • Presents a systematic approach for storing, retrieving, organizing and analyzing biological data using software tools with applications.
  • Provides a systems biology perspective including general guidelines and techniques for obtaining, integrating and analyzing complex data sets from multiple experimental sources using computational tools and software.

Table of contents

  1. Cover image
  2. Title page
  3. Table of Contents
  4. Copyright
  5. Contributors
  6. Preface
  7. Acknowledgments
  8. Introduction
  9. Chapter 1: Supervised Learning with the Artificial Neural Networks Algorithm for Modeling Immune Cell Differentiation
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Related work
    5. 3 Modeling immune cell differentiation
    6. 4 Discussion
    7. 5 Conclusion
  10. Chapter 2: Accelerating Techniques for Particle Filter Implementations on FPGA
    1. Abstract
    2. 1 Introduction
    3. 2 PF and SLAM algorithms
    4. 3 Computational bottleneck identification and hardware/software partitioning
    5. 4 PF acceleration techniques
    6. 5 Hardware implementation
    7. 6 Hardware/software Architecture
    8. 7 Results and discussion
    9. 8 Conclusions
  11. Chapter 3: Biological Study on Pulsatile Flow of Herschel-Bulkley Fluid in Tapered Blood Vessels
    1. Abstract
    2. 1 Introduction
    3. 2 Formulation of the problem
    4. 3 Solution
    5. 4 Discussion
    6. 5 Conclusion
  12. Chapter 4: Hierarchical k-Means: A Hybrid Clustering Algorithm and Its Application to Study Gene Expression in Lung Adenocarcinoma
    1. Abstract
    2. 1 Introduction
    3. 2 Methods
    4. 3 Data set
    5. 4 Results and Discussion
    6. 5 Conclusions
    7. Supplementary materials
  13. Chapter 5: Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Computational method
    5. 3 Classification algorithm
    6. 4 Information entropy
    7. 5 The EC of entropy production
    8. 6 Learning procedure
    9. 7 Calculation results and discussion
    10. 8 Conclusions
  14. Chapter 6: Review of Recent Protein-Protein Interaction Techniques
    1. Abstract
    2. 1 Introduction
    3. 2 Technical challenges and open issues
    4. 3 Performance measures
    5. 4 Computational approaches
    6. 5 Conclusion
  15. Chapter 7: Genetic Regulatory Networks: Focus on Attractors of Their Dynamics
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Immunetworks
    5. 3 The iron control network
    6. 4 Morphogenetic networks
    7. 5 Biliary atresia control network
    8. 6 Conclusion and perspectives
    9. Mathematical Annex
  16. Chapter 8: Biomechanical Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement or not?
    1. Abstract
    2. 1 Introduction
    3. 2 Materials and methods
    4. 3 Results
    5. 4 Discussion
    6. 5 Conclusion
    7. 6 Disclaimer
  17. Chapter 9: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?
    1. Abstract
    2. Acknowledgments
    3. Graphical Abstract
    4. 1 Introduction
    5. 2 Computational methods
    6. 3 Results and discussion
    7. 4 Conclusions
    8. Supplementary Material: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?
    9. 1 Conformational analysis of macrocyclic lactone (4)
    10. 2 Modelling of a theozyme for the conversion of macrocyclic lactone (4) into tricyclic compound (5)
    11. 3 ELF bonding analysis of the conversion of macrocyclic lactone (4) into the tricyclic compound (5)
  18. Chapter 10: CLAST: Clustering Biological Sequences
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Methods
    5. 3 Evaluation and discussion
    6. 4 Conclusions
  19. Chapter 11: Computational Platform for Integration and Analysis of MicroRNA Annotation
    1. Abstract
    2. 1 Introduction
    3. 2 Material
    4. 3 MIRIA Database
    5. 4 MiRNA CFSim
    6. 5 Web Framework
    7. 6 Results
    8. 7 Conclusions
  20. Chapter 12: Feature Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear Programming
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 LP formulation of separability
    5. 3 Offline approach
    6. 4 Incremental approach
    7. 5 Gene selection
    8. 6 A new methodology for gene selection
    9. 7 Results and discussion
    10. 8 Conclusions
  21. Chapter 13: The Big ORF Theory: Algorithmic, Computational, and Approximation Approaches to Open Reading Frames in Short- and Medium-Length dsDNA Sequences
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Molecular genetic and bioinformatic considerations
    5. 3 Algorithmic and programming considerations
    6. 4 Analytical and random sampling solutions to L > 25 sequences: Triplet-based approximations
    7. 5 Alternative genetic codes
    8. 6 Implications for the evolution of ORF size
  22. Chapter 14: Intentionally Linked Entities: A Detailed Look at a Database System for Health Care Informatics
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Introducing ILE for Health Care Applications
    5. 3 ILE and epidemiological data modeling
    6. 4 Other nonrelational approaches to keeping medical records
    7. 5 Inside the ILE database system
    8. 6 An example of the Importance of an EHR implemented in ILE
    9. 7 Conclusions
  23. Chapter 15: Region Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction
    1. Abstract
    2. 1 Introduction
    3. 2 Related works
    4. 3 Basic foundation
    5. 4 Methodology
    6. 5 Empirical results
    7. 6 Conclusions and future research
  24. Chapter 16: Contribution of Noise Reduction Algorithms: Perception Versus Localization Simulation in the Case of Binaural Cochlear Implant (BCI) Coding
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Materials and Methods
    5. 3 Results
    6. 4 Discussion
    7. 5 Conclusions
  25. Chapter 17: Lowering the Fall Rate of the Elderly from Wheelchairs
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Current solutions
    5. 3 A systems solution
    6. 4 The sparrow design
    7. 5 Assessment algorithm
    8. 6 Assessment decision algorithm
    9. 7 The future
    10. 8 Conclusion
  26. Chapter 18: Occipital and Left Temporal EEG Correlates of Phenomenal Consciousness
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Participants
    5. 3 Apparatus and stimuli
    6. 4 Procedure
    7. 5 EEG recording
    8. 6 Experiment I
    9. 7 Experiment II
    10. 8 The grand average occipital and temporal electrical activity correlated with a contrast in access
    11. 9 Behavioral data
    12. 10 The grand average occipital and temporal electrical activity correlated with a contrast in phenomenology
    13. 11 The grand average occipital and temporal electrical activity co-occurring with unconsciousness
  27. Chapter 19: Chaotic Dynamical States in the Izhikevich Neuron Model
    1. Abstract
    2. 1 Introduction
    3. 2 Fundamental description
    4. 3 Chaotic properties of Izhikevich neuron model
    5. 4 Response efficiency in chaotic resonance
    6. 5 Conclusions
  28. Chapter 20: Analogy, Mind, and Life
    1. Abstract
    2. Acknowledgements
    3. 1 Introduction
    4. 2 The artificial mind and cognitive science
    5. 3 Consciousness
    6. 4 The classic watchmaker analogy
    7. 5 The classic watchmaker analogy is fragile, remote and reductive
    8. 6 The analogy between life and information seems to suggest some type of reductionism
    9. 7 Conclusion
  29. Chapter 21: Copy Number Networks to Guide Combinatorial Therapy of Cancer and Proliferative Disorders
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 A diminishing drug pipeline
    5. 3 Using genome data to replenish the pipeline by drug repositioning
    6. 4 The small-world properties of networks expedite combination therapies
    7. 5 Molecular networks can be used to guide drug combinations
    8. 6 Copy number alterations as a disease driver
    9. 7 Using correlated copy number alterations to construct survival networks
    10. 8 A pan-cancer CNA interaction network
    11. 9 Mapping genetic survival networks using correlated CNAs in radiation hybrid cells
    12. 10 A survival network for GBM at single-gene resolution
    13. 11 Using CNA networks to guide combination therapies
    14. 12 Targeting multiple drugs to single-disease genes in cancer
    15. 13 Targeting multiple drugs to a single-disease gene in autoimmunity
    16. 14 Targeting multiple genes in a single pathway for cancer
    17. 15 Targeting genes in parallel pathways converging on atherosclerosis
    18. 16 Using CNA networks to synergize drug combinations and minimize side effects
    19. 17 Disclaimer
  30. Chapter 22: DNA Double-Strand Break–Based Nonmonotonic Logic
    1. Abstract
    2. 1 Introduction
    3. 2 DNA DSBs
    4. 3 Logical model for system biology
    5. 4 Completing the signaling pathways by default abduction
    6. 5 Logic representation of a signaling pathway with the goal of reducing computational complexity
    7. 6 Algorithm and implementation
    8. 7 Results
    9. 8 Conclusions
  31. Chapter 23: An Updated Covariance Model for Rapid Annotation of Noncoding RNA
    1. Abstract
    2. 1 Introduction
    3. 2 Method
    4. 3 Test results
    5. 4 Conclusions
  32. Chapter 24: SMIR: A Web Server to Predict Residues Involved in the Protein Folding Core
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Methods
    5. 3 Results
    6. 4 Conclusion
  33. Chapter 25: Predicting Extinction of Biological Systems with Competition
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 A Model of Competing Species
    5. 3 Density function of extinction time
    6. 4 Estimation of parameters
    7. 5 Numerical results
    8. 6 Summary
  34. Chapter 26: Methodologies for the Diagnosis of the Main Behavioral Syndromes for Parkinson’s Disease with Bayesian Belief Networks
    1. Abstract
    2. 1 Introduction
    3. 2 Diagnosis of FoG
    4. 3 Diagnosis of handwriting and speech
    5. 4 Toward a global methodology for PD
    6. 5 Conclusions and future work
  35. Chapter 27: Practical Considerations in Virtual Screening and Molecular Docking
    1. Abstract
    2. 1 Introduction
    3. 2 Receptor structure preparation
    4. 3 Accurately predicting the pose of solved crystal structures and differentiating decoys from actives
    5. 4 Side-chain flexibility and ensemble docking
    6. 5 Consensus docking
    7. 6 MM-GBSA
    8. 7 Incorporating pharmacophoric constraints within the virtual screen
    9. 8 Conclusion
  36. Chapter 28: Knowledge Discovery in Proteomic Mass Spectrometry Data
    1. Abstract
    2. 1 Introduction
    3. 2 Technical background
    4. 3 Computational workflow
    5. 4 Analysis tool
    6. 5 Conclusion
  37. Chapter 29: A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data
    1. Abstract
    2. 1 Introduction
    3. 2 Mapping and calling software
    4. 3 Methods
    5. 4 Real data
    6. 5 Results and discussion
    7. 6 Conclusions
  38. Chapter 30: Two-Stage Evolutionary Quantification of In Vivo MRS Metabolites
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Proposed methodology
    5. 3 Experiment
    6. 4 Conclusions
  39. Chapter 31: Keratoconus Disease and Three-Dimensional Simulation of the Cornea throughout the Process of Cross-Linking Treatment
    1. Abstract
    2. Acknowledgments
    3. 1 Introduction
    4. 2 Methodology
    5. 3 Conclusions and Recommendations
  40. Chapter 32: Emerging Business Intelligence Framework for a Clinical Laboratory Through Big Data Analytics
    1. Abstract
    2. 1 Introduction
    3. 2 Motivation
    4. 3 Material and methods
    5. 4 Use-cases
    6. 5 Case Study 1: Clinical laboratory test usage patterns visualization
    7. 6 Data source and methodology
    8. 7 Results and discussion
    9. 8 Limitations
    10. 9 Case Study 2: Provincial laboratory clinical test volume estimation
    11. 10 Data source and methodology
    12. 11 Results and discussion
    13. 12 Limitations
    14. 13 Conclusion and future work
  41. Chapter 33: A Codon Frequency Obfuscation Heuristic for Raw Genomic Data Privacy
    1. Abstract
    2. 1 Introduction
    3. 2 Background
    4. 3 Related work
    5. 4 Methodology
    6. 5 Experiment and results
    7. 6 Conclusion
  42. Index

Product information

  • Title: Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology
  • Author(s): Hamid R Arabnia, Quoc Nam Tran
  • Release date: August 2015
  • Publisher(s): Morgan Kaufmann
  • ISBN: 9780128026465