book

Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology

Name: Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology
ISBN: 9780128026465

by Hamid R Arabnia, Quoc Nam Tran

August 2015

Intermediate to advanced

670 pages

21h 9m

English

Morgan Kaufmann

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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
AbstractAcknowledgments1 Introduction2 Related work3 Modeling immune cell differentiation4 Discussion5 Conclusion
Chapter 2: Accelerating Techniques for Particle Filter Implementations on FPGA
Abstract1 Introduction2 PF and SLAM algorithms3 Computational bottleneck identification and hardware/software partitioning4 PF acceleration techniques5 Hardware implementation6 Hardware/software Architecture7 Results and discussion8 Conclusions

Chapter 3: Biological Study on Pulsatile Flow of Herschel-Bulkley Fluid in Tapered Blood Vessels
Abstract1 Introduction2 Formulation of the problem3 Solution4 Discussion5 Conclusion
Chapter 4: Hierarchical k-Means: A Hybrid Clustering Algorithm and Its Application to Study Gene Expression in Lung Adenocarcinoma
Abstract1 Introduction2 Methods3 Data set4 Results and Discussion5 ConclusionsSupplementary materials
Chapter 5: Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors
AbstractAcknowledgments1 Introduction2 Computational method3 Classification algorithm4 Information entropy5 The EC of entropy production6 Learning procedure7 Calculation results and discussion8 Conclusions
Chapter 6: Review of Recent Protein-Protein Interaction Techniques
Abstract1 Introduction2 Technical challenges and open issues3 Performance measures4 Computational approaches5 Conclusion
Chapter 7: Genetic Regulatory Networks: Focus on Attractors of Their Dynamics
AbstractAcknowledgments1 Introduction2 Immunetworks3 The iron control network4 Morphogenetic networks5 Biliary atresia control network6 Conclusion and perspectivesMathematical Annex
Chapter 8: Biomechanical Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement or not?
Abstract1 Introduction2 Materials and methods3 Results4 Discussion5 Conclusion6 Disclaimer
Chapter 9: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?
AbstractAcknowledgmentsGraphical Abstract1 Introduction2 Computational methods3 Results and discussion4 ConclusionsSupplementary 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
AbstractAcknowledgments1 Introduction2 Methods3 Evaluation and discussion4 Conclusions
Chapter 11: Computational Platform for Integration and Analysis of MicroRNA Annotation
Abstract1 Introduction2 Material3 MIRIA Database4 MiRNA CFSim5 Web Framework6 Results7 Conclusions
Chapter 12: Feature Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear Programming
AbstractAcknowledgments1 Introduction2 LP formulation of separability3 Offline approach4 Incremental approach5 Gene selection6 A new methodology for gene selection7 Results and discussion8 Conclusions
Chapter 13: The Big ORF Theory: Algorithmic, Computational, and Approximation Approaches to Open Reading Frames in Short- and Medium-Length dsDNA Sequences
AbstractAcknowledgments1 Introduction2 Molecular genetic and bioinformatic considerations3 Algorithmic and programming considerations4 Analytical and random sampling solutions to L > 25 sequences: Triplet-based approximations5 Alternative genetic codes6 Implications for the evolution of ORF size
Chapter 14: Intentionally Linked Entities: A Detailed Look at a Database System for Health Care Informatics
AbstractAcknowledgments1 Introduction2 Introducing ILE for Health Care Applications3 ILE and epidemiological data modeling4 Other nonrelational approaches to keeping medical records5 Inside the ILE database system6 An example of the Importance of an EHR implemented in ILE7 Conclusions
Chapter 15: Region Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction
Abstract1 Introduction2 Related works3 Basic foundation4 Methodology5 Empirical results6 Conclusions and future research
Chapter 16: Contribution of Noise Reduction Algorithms: Perception Versus Localization Simulation in the Case of Binaural Cochlear Implant (BCI) Coding
AbstractAcknowledgments1 Introduction2 Materials and Methods3 Results4 Discussion5 Conclusions
Chapter 17: Lowering the Fall Rate of the Elderly from Wheelchairs
AbstractAcknowledgments1 Introduction2 Current solutions3 A systems solution4 The sparrow design5 Assessment algorithm6 Assessment decision algorithm7 The future8 Conclusion
Chapter 18: Occipital and Left Temporal EEG Correlates of Phenomenal Consciousness
AbstractAcknowledgments1 Introduction2 Participants3 Apparatus and stimuli4 Procedure5 EEG recording6 Experiment I7 Experiment II8 The grand average occipital and temporal electrical activity correlated with a contrast in access9 Behavioral data10 The grand average occipital and temporal electrical activity correlated with a contrast in phenomenology11 The grand average occipital and temporal electrical activity co-occurring with unconsciousness
Chapter 19: Chaotic Dynamical States in the Izhikevich Neuron Model
Abstract1 Introduction2 Fundamental description3 Chaotic properties of Izhikevich neuron model4 Response efficiency in chaotic resonance5 Conclusions
Chapter 20: Analogy, Mind, and Life
AbstractAcknowledgements1 Introduction2 The artificial mind and cognitive science3 Consciousness4 The classic watchmaker analogy5 The classic watchmaker analogy is fragile, remote and reductive6 The analogy between life and information seems to suggest some type of reductionism7 Conclusion
Chapter 21: Copy Number Networks to Guide Combinatorial Therapy of Cancer and Proliferative Disorders
AbstractAcknowledgments1 Introduction2 A diminishing drug pipeline3 Using genome data to replenish the pipeline by drug repositioning4 The small-world properties of networks expedite combination therapies5 Molecular networks can be used to guide drug combinations6 Copy number alterations as a disease driver7 Using correlated copy number alterations to construct survival networks8 A pan-cancer CNA interaction network9 Mapping genetic survival networks using correlated CNAs in radiation hybrid cells10 A survival network for GBM at single-gene resolution11 Using CNA networks to guide combination therapies12 Targeting multiple drugs to single-disease genes in cancer13 Targeting multiple drugs to a single-disease gene in autoimmunity14 Targeting multiple genes in a single pathway for cancer15 Targeting genes in parallel pathways converging on atherosclerosis16 Using CNA networks to synergize drug combinations and minimize side effects17 Disclaimer
Chapter 22: DNA Double-Strand Break–Based Nonmonotonic Logic
Abstract1 Introduction2 DNA DSBs3 Logical model for system biology4 Completing the signaling pathways by default abduction5 Logic representation of a signaling pathway with the goal of reducing computational complexity6 Algorithm and implementation7 Results8 Conclusions
Chapter 23: An Updated Covariance Model for Rapid Annotation of Noncoding RNA
Abstract1 Introduction2 Method3 Test results4 Conclusions
Chapter 24: SMIR: A Web Server to Predict Residues Involved in the Protein Folding Core
AbstractAcknowledgments1 Introduction2 Methods3 Results4 Conclusion
Chapter 25: Predicting Extinction of Biological Systems with Competition
AbstractAcknowledgments1 Introduction2 A Model of Competing Species3 Density function of extinction time4 Estimation of parameters5 Numerical results6 Summary
Chapter 26: Methodologies for the Diagnosis of the Main Behavioral Syndromes for Parkinson’s Disease with Bayesian Belief Networks
Abstract1 Introduction2 Diagnosis of FoG3 Diagnosis of handwriting and speech4 Toward a global methodology for PD5 Conclusions and future work
Chapter 27: Practical Considerations in Virtual Screening and Molecular Docking
Abstract1 Introduction2 Receptor structure preparation3 Accurately predicting the pose of solved crystal structures and differentiating decoys from actives4 Side-chain flexibility and ensemble docking5 Consensus docking6 MM-GBSA7 Incorporating pharmacophoric constraints within the virtual screen8 Conclusion
Chapter 28: Knowledge Discovery in Proteomic Mass Spectrometry Data
Abstract1 Introduction2 Technical background3 Computational workflow4 Analysis tool5 Conclusion
Chapter 29: A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data
Abstract1 Introduction2 Mapping and calling software3 Methods4 Real data5 Results and discussion6 Conclusions
Chapter 30: Two-Stage Evolutionary Quantification of In Vivo MRS Metabolites
AbstractAcknowledgments1 Introduction2 Proposed methodology3 Experiment4 Conclusions
Chapter 31: Keratoconus Disease and Three-Dimensional Simulation of the Cornea throughout the Process of Cross-Linking Treatment
AbstractAcknowledgments1 Introduction2 Methodology3 Conclusions and Recommendations
Chapter 32: Emerging Business Intelligence Framework for a Clinical Laboratory Through Big Data Analytics
Abstract1 Introduction2 Motivation3 Material and methods4 Use-cases5 Case Study 1: Clinical laboratory test usage patterns visualization6 Data source and methodology7 Results and discussion8 Limitations9 Case Study 2: Provincial laboratory clinical test volume estimation10 Data source and methodology11 Results and discussion12 Limitations13 Conclusion and future work
Chapter 33: A Codon Frequency Obfuscation Heuristic for Raw Genomic Data Privacy
Abstract1 Introduction2 Background3 Related work4 Methodology5 Experiment and results6 Conclusion
Index

Content preview from Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology

Chapter 1: Supervised Learning with the Artificial Neural Networks Algorithm for Modeling Immune Cell Differentiation

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 ...

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Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology

by Hamid R Arabnia, Quoc Nam Tran

Table of Contents

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