Title page
by Quoc Nam Tran, Hamid R Arabnia
Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology
- Cover image
- Title page
- Table of Contents
- Copyright
- Contributors
- Preface
- Acknowledgments
- Introduction
- Chapter 1: Supervised Learning with the Artificial Neural Networks Algorithm for Modeling Immune Cell Differentiation
- Chapter 2: Accelerating Techniques for Particle Filter Implementations on FPGA
- Chapter 3: Biological Study on Pulsatile Flow of Herschel-Bulkley Fluid in Tapered Blood Vessels
- Chapter 4: Hierarchical k-Means: A Hybrid Clustering Algorithm and Its Application to Study Gene Expression in Lung Adenocarcinoma
- Chapter 5: Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors
- Chapter 6: Review of Recent Protein-Protein Interaction Techniques
- Chapter 7: Genetic Regulatory Networks: Focus on Attractors of Their Dynamics
- Chapter 8: Biomechanical Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement or not?
- Chapter 9: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?
- Abstract
- Acknowledgments
- Graphical Abstract
- 1 Introduction
- 2 Computational methods
- 3 Results and discussion
- 4 Conclusions
- Supplementary Material: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?
- 1 Conformational analysis of macrocyclic lactone (4)
- 2 Modelling of a theozyme for the conversion of macrocyclic lactone (4) into tricyclic compound (5)
- 3 ELF bonding analysis of the conversion of macrocyclic lactone (4) into the tricyclic compound (5)
- Chapter 10: CLAST: Clustering Biological Sequences
- Chapter 11: Computational Platform for Integration and Analysis of MicroRNA Annotation
- Chapter 12: Feature Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear Programming
- Chapter 13: The Big ORF Theory: Algorithmic, Computational, and Approximation Approaches to Open Reading Frames in Short- and Medium-Length dsDNA Sequences
- Abstract
- Acknowledgments
- 1 Introduction
- 2 Molecular genetic and bioinformatic considerations
- 3 Algorithmic and programming considerations
- 4 Analytical and random sampling solutions to L > 25 sequences: Triplet-based approximations
- 5 Alternative genetic codes
- 6 Implications for the evolution of ORF size
- Chapter 14: Intentionally Linked Entities: A Detailed Look at a Database System for Health Care Informatics
- Chapter 15: Region Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction
- Chapter 16: Contribution of Noise Reduction Algorithms: Perception Versus Localization Simulation in the Case of Binaural Cochlear Implant (BCI) Coding
- Chapter 17: Lowering the Fall Rate of the Elderly from Wheelchairs
- Chapter 18: Occipital and Left Temporal EEG Correlates of Phenomenal Consciousness
- Abstract
- Acknowledgments
- 1 Introduction
- 2 Participants
- 3 Apparatus and stimuli
- 4 Procedure
- 5 EEG recording
- 6 Experiment I
- 7 Experiment II
- 8 The grand average occipital and temporal electrical activity correlated with a contrast in access
- 9 Behavioral data
- 10 The grand average occipital and temporal electrical activity correlated with a contrast in phenomenology
- 11 The grand average occipital and temporal electrical activity co-occurring with unconsciousness
- Chapter 19: Chaotic Dynamical States in the Izhikevich Neuron Model
- Chapter 20: Analogy, Mind, and Life
- Chapter 21: Copy Number Networks to Guide Combinatorial Therapy of Cancer and Proliferative Disorders
- Abstract
- Acknowledgments
- 1 Introduction
- 2 A diminishing drug pipeline
- 3 Using genome data to replenish the pipeline by drug repositioning
- 4 The small-world properties of networks expedite combination therapies
- 5 Molecular networks can be used to guide drug combinations
- 6 Copy number alterations as a disease driver
- 7 Using correlated copy number alterations to construct survival networks
- 8 A pan-cancer CNA interaction network
- 9 Mapping genetic survival networks using correlated CNAs in radiation hybrid cells
- 10 A survival network for GBM at single-gene resolution
- 11 Using CNA networks to guide combination therapies
- 12 Targeting multiple drugs to single-disease genes in cancer
- 13 Targeting multiple drugs to a single-disease gene in autoimmunity
- 14 Targeting multiple genes in a single pathway for cancer
- 15 Targeting genes in parallel pathways converging on atherosclerosis
- 16 Using CNA networks to synergize drug combinations and minimize side effects
- 17 Disclaimer
- Chapter 22: DNA Double-Strand Break–Based Nonmonotonic Logic
- Chapter 23: An Updated Covariance Model for Rapid Annotation of Noncoding RNA
- Chapter 24: SMIR: A Web Server to Predict Residues Involved in the Protein Folding Core
- Chapter 25: Predicting Extinction of Biological Systems with Competition
- Chapter 26: Methodologies for the Diagnosis of the Main Behavioral Syndromes for Parkinson’s Disease with Bayesian Belief Networks
- Chapter 27: Practical Considerations in Virtual Screening and Molecular Docking
- Abstract
- 1 Introduction
- 2 Receptor structure preparation
- 3 Accurately predicting the pose of solved crystal structures and differentiating decoys from actives
- 4 Side-chain flexibility and ensemble docking
- 5 Consensus docking
- 6 MM-GBSA
- 7 Incorporating pharmacophoric constraints within the virtual screen
- 8 Conclusion
- Chapter 28: Knowledge Discovery in Proteomic Mass Spectrometry Data
- Chapter 29: A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data
- Chapter 30: Two-Stage Evolutionary Quantification of In Vivo MRS Metabolites
- Chapter 31: Keratoconus Disease and Three-Dimensional Simulation of the Cornea throughout the Process of Cross-Linking Treatment
- Chapter 32: Emerging Business Intelligence Framework for a Clinical Laboratory Through Big Data Analytics
- Abstract
- 1 Introduction
- 2 Motivation
- 3 Material and methods
- 4 Use-cases
- 5 Case Study 1: Clinical laboratory test usage patterns visualization
- 6 Data source and methodology
- 7 Results and discussion
- 8 Limitations
- 9 Case Study 2: Provincial laboratory clinical test volume estimation
- 10 Data source and methodology
- 11 Results and discussion
- 12 Limitations
- 13 Conclusion and future work
- Chapter 33: A Codon Frequency Obfuscation Heuristic for Raw Genomic Data Privacy
- Index
Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology
Algorithms and Software Tools
First Edition
Quoc Nam Tran
Hamid Arabnia
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