Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology

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?ased 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? 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

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