Home Page Icon
Home Page
Table of Contents for
Cover image
Close
Cover image
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
Abstract
Acknowledgments
1 Introduction
2 Related work
3 Modeling immune cell differentiation
4 Discussion
5 Conclusion
Chapter 2: Accelerating Techniques for Particle Filter Implementations on FPGA
Abstract
1 Introduction
2 PF and SLAM algorithms
3 Computational bottleneck identification and hardware/software partitioning
4 PF acceleration techniques
5 Hardware implementation
6 Hardware/software Architecture
7 Results and discussion
8 Conclusions
Chapter 3: Biological Study on Pulsatile Flow of Herschel-Bulkley Fluid in Tapered Blood Vessels
Abstract
1 Introduction
2 Formulation of the problem
3 Solution
4 Discussion
5 Conclusion
Chapter 4: Hierarchical k-Means: A Hybrid Clustering Algorithm and Its Application to Study Gene Expression in Lung Adenocarcinoma
Abstract
1 Introduction
2 Methods
3 Data set
4 Results and Discussion
5 Conclusions
Supplementary materials
Chapter 5: Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors
Abstract
Acknowledgments
1 Introduction
2 Computational method
3 Classification algorithm
4 Information entropy
5 The EC of entropy production
6 Learning procedure
7 Calculation results and discussion
8 Conclusions
Chapter 6: Review of Recent Protein-Protein Interaction Techniques
Abstract
1 Introduction
2 Technical challenges and open issues
3 Performance measures
4 Computational approaches
5 Conclusion
Chapter 7: Genetic Regulatory Networks: Focus on Attractors of Their Dynamics
Abstract
Acknowledgments
1 Introduction
2 Immunetworks
3 The iron control network
4 Morphogenetic networks
5 Biliary atresia control network
6 Conclusion and perspectives
Mathematical Annex
Chapter 8: Biomechanical Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement or not?
Abstract
1 Introduction
2 Materials and methods
3 Results
4 Discussion
5 Conclusion
6 Disclaimer
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
Abstract
Acknowledgments
1 Introduction
2 Methods
3 Evaluation and discussion
4 Conclusions
Chapter 11: Computational Platform for Integration and Analysis of MicroRNA Annotation
Abstract
1 Introduction
2 Material
3 MIRIA Database
4 MiRNA CFSim
5 Web Framework
6 Results
7 Conclusions
Chapter 12: Feature Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear Programming
Abstract
Acknowledgments
1 Introduction
2 LP formulation of separability
3 Offline approach
4 Incremental approach
5 Gene selection
6 A new methodology for gene selection
7 Results and discussion
8 Conclusions
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
Abstract
Acknowledgments
1 Introduction
2 Introducing ILE for Health Care Applications
3 ILE and epidemiological data modeling
4 Other nonrelational approaches to keeping medical records
5 Inside the ILE database system
6 An example of the Importance of an EHR implemented in ILE
7 Conclusions
Chapter 15: Region Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction
Abstract
1 Introduction
2 Related works
3 Basic foundation
4 Methodology
5 Empirical results
6 Conclusions and future research
Chapter 16: Contribution of Noise Reduction Algorithms: Perception Versus Localization Simulation in the Case of Binaural Cochlear Implant (BCI) Coding
Abstract
Acknowledgments
1 Introduction
2 Materials and Methods
3 Results
4 Discussion
5 Conclusions
Chapter 17: Lowering the Fall Rate of the Elderly from Wheelchairs
Abstract
Acknowledgments
1 Introduction
2 Current solutions
3 A systems solution
4 The sparrow design
5 Assessment algorithm
6 Assessment decision algorithm
7 The future
8 Conclusion
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
Abstract
1 Introduction
2 Fundamental description
3 Chaotic properties of Izhikevich neuron model
4 Response efficiency in chaotic resonance
5 Conclusions
Chapter 20: Analogy, Mind, and Life
Abstract
Acknowledgements
1 Introduction
2 The artificial mind and cognitive science
3 Consciousness
4 The classic watchmaker analogy
5 The classic watchmaker analogy is fragile, remote and reductive
6 The analogy between life and information seems to suggest some type of reductionism
7 Conclusion
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
Abstract
1 Introduction
2 DNA DSBs
3 Logical model for system biology
4 Completing the signaling pathways by default abduction
5 Logic representation of a signaling pathway with the goal of reducing computational complexity
6 Algorithm and implementation
7 Results
8 Conclusions
Chapter 23: An Updated Covariance Model for Rapid Annotation of Noncoding RNA
Abstract
1 Introduction
2 Method
3 Test results
4 Conclusions
Chapter 24: SMIR: A Web Server to Predict Residues Involved in the Protein Folding Core
Abstract
Acknowledgments
1 Introduction
2 Methods
3 Results
4 Conclusion
Chapter 25: Predicting Extinction of Biological Systems with Competition
Abstract
Acknowledgments
1 Introduction
2 A Model of Competing Species
3 Density function of extinction time
4 Estimation of parameters
5 Numerical results
6 Summary
Chapter 26: Methodologies for the Diagnosis of the Main Behavioral Syndromes for Parkinson’s Disease with Bayesian Belief Networks
Abstract
1 Introduction
2 Diagnosis of FoG
3 Diagnosis of handwriting and speech
4 Toward a global methodology for PD
5 Conclusions and future work
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
Abstract
1 Introduction
2 Technical background
3 Computational workflow
4 Analysis tool
5 Conclusion
Chapter 29: A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data
Abstract
1 Introduction
2 Mapping and calling software
3 Methods
4 Real data
5 Results and discussion
6 Conclusions
Chapter 30: Two-Stage Evolutionary Quantification of In Vivo MRS Metabolites
Abstract
Acknowledgments
1 Introduction
2 Proposed methodology
3 Experiment
4 Conclusions
Chapter 31: Keratoconus Disease and Three-Dimensional Simulation of the Cornea throughout the Process of Cross-Linking Treatment
Abstract
Acknowledgments
1 Introduction
2 Methodology
3 Conclusions and Recommendations
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
Abstract
1 Introduction
2 Background
3 Related work
4 Methodology
5 Experiment and results
6 Conclusion
Index
Search in book...
Toggle Font Controls
Playlists
Add To
Create new playlist
Name your new playlist
Playlist description (optional)
Cancel
Create playlist
Sign In
Email address
Password
Forgot Password?
Create account
Login
or
Continue with Facebook
Continue with Google
Sign Up
Full Name
Email address
Confirm Email Address
Password
Login
Create account
or
Continue with Facebook
Continue with Google
Next
Next Chapter
Title page
Add Highlight
No Comment
..................Content has been hidden....................
You can't read the all page of ebook, please click
here
login for view all page.
Day Mode
Cloud Mode
Night Mode
Reset