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Emerging trends in computational biology, bioinformatics, and systems biology : algorithms and software tools / edited by Quoc Nam Tran, Hamid Arabnia. -- Waltham, MA : Elsevier : Morgan Kaufman, 2015. – (58.17115 /E53) |
Contents
Contributors
xix
Preface
xxvii
Acknowledgments
xxxiii
Introduction
xxxv
CHAPTER 1
Supervised Learning with the Artificial Neural Networks Algorithm for
Modeling Immune Cell Differentiation 1
1 Introduction 1
2 Related
Work 5
3 Modeling
Immune Cell Differentiation 9
4 Discussion 14
5 Conclusion 15
Acknowledgments
15
References
16
CHAPTER 2 Accelerating Techniques for Particle
Filter Implementations on FPGA 19
1 Introduction 19
2 PF and
SLAM Algorithms 21
3 Computational
Bottleneck Identification and Hardware/software Partitioning 25
4 PF
Acceleration Techniques 26
5 Hardware
Implementation 30
6
Hardware/Software Architecture 31
7 Results
and Discussion 34
8
Conclusions 35
References
35
CHAPTER 3 Biological
Study on Pulsatile Flow of HerscheI-Bulkley Fluid in Tapered Blood Vessels 39
1 Introduction 39
2 Formulation
of the Problem 41
3 Solution 43
4 Discussion 45
5 Conclusion 48
References
49
CHAPTER 4 Hierarchical
k-Means: A Hybrid Clustering Algorithm and its Application to Study Gene Expression
in Lung Adenocarcinoma 51
1 Introduction 5l
2 Methods 53
3 Data
Set 57
4 Results
and Discussion 57
5 Conclusions 64
References
65
Supplementary Materials 67
CHAPTER 5 Molecular
Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency
Virus Protease Inhibitors 69
1 Introduction 69
2 Computational
Method 71
3 Classification
Algorithm 71
4 Information
Entropy 73
5 The EC of
Entropy Production 74
6 Learning
Procedure 74
7 Calculation
Results and Discussion 75
8 Conclusions 93
Acknowledgments
94
References
94
CHAPTER 6 Review
of Recent Protein-Protein Interaction Techniques 99
1 Introduction 99
2 Technical
Challenges and Open Issues 100
3 Performance
Measures 101
4 Computational
Approaches 102
5 Conclusion 115
References
116
CHAPTER 7 Genetic
Regulatory Networks: Focus on Attractors Of Their Dynamics 123
1 Introduction 123
2 Immunetworks 124
3 The Iron
Control Network 127
4 Morphogenetic
Networks 130
5 Biliary
Atresia Control Network 133
6 Conclusion
and Perspectives 137
Mathematical Annex
138
A1 Definitions
138
A2 First Propositions 140
A3 Tangent and Intersecting Circuits 142
A4 State-dependent Updating Schedule 145
A5 the Circular Hamming Distance 146
A6 the ArchetypaL Sequence AL 147
Acknowledgments
149
References
149
CHAPTER 8 Biomechanical
Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement
or Not? 155
1 Introduction 155
2 Materials
and Methods 156
3 Resuits 159
4 Discussion 164
5 Conclusion 165
6 Disclaimer 165
References
165
CHAPTER 9 Diels-Alderase
Catalyzing the Cyclization Step In the Biosynthesis of Spinosyn A: Reality or
Fantasy? 169
1 Introduction 170
2 Computational
Methods 174
3 Results
and Discussion 174
4 Conclusions 179
Acknowledgments
181
References
181
Supplementary Material: Diels-Alderase Catalyzing
the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or
Fantasy? 183
1 Conformational
Analysis of Macrocyclic Lactone (4) 183
2 Modelling
of a Theozyme for the Conversion of Macrocyclic Lactone (4) into Tricyclic
Compound (5) 184
3 ELF
Bonding Analysis of the Conversion of Macrocyclic Lactone (4) Into the
Tricyclic Compound (5) 186
References
201
CHAPTER 10 CLAST: Clustering Biological
Sequences 203
1
Introduction 203
2
Methods 205
3 Evaluation
and Discussion 211
4
Conclusions 219
Acknowledgments
220
References
220
CHAPTER 11 Computational
Platform for Integration and Analysis of MicroRNA Annotation 221
1 Introduction 221
2 Material 223
3 MIRIA
Database 225
4 MiRNA
CFSim 226
5 Web
Framework 227
6 Results 227
7 Conclusions 231
References
232
CHAPTER 12 Feature
Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear
Programming 235
1 Introduction 235
2 LP
Formulation of Separability 237
3 Offline
Approach 239
4 Incremental
Approach 240
5 Gene
Selection 247
6 A New
Methodology for Gene Selection 248
7 Results
and Discussion 249
8 Conclusions 262
Acknowledgments
263
References
263
CHAPTER 13 The Big ORF Theory: Algorithmic,
Computational, and Approximation Approaches to Open Reading Frames in Short-
and Medium-Length dsDNA Sequences 265
1 Introduction 265
2 Molecular
Genetic and Bioinformatic Considerations
266
3 Algorithmic
and Programming Considerations 267
4 Analytical
and Random Sampling Solutions to L>25 Sequences: Triplet-based
Approximations 269
5 Alternative
Genetic Codes 271
6 Implications
for the Evolution of ORF Size 272
Acknowledgments
273
References
273
CHAPTER 14 Intentionally
Linked Entities: A Detailed Look At a Database System for Health Care
Informatics 275
1 Introduction 275
2 Introducing
ILE for Health Care Applications 278
3 ILE and
Epidemiological Data Modeling 281
4 Other
Nonrelational Approaches to Keeping Medical Records 283
5 Inside the
ILE Database System 286
6 An Example
of the Importance of An EHR Implemented in ILE
292
7 Conclusions 292
Acknowledgments
293
References
293
CHAPTER 15 Region
Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction 295
1 Introduction 295
2 Related
Works 296
3 Basic
Foundation 296
4 Methodology 298
5 Empirical
Results 302
6 Conclusions
and Future Research 304
References
305
CHAPTER 16 Contribution
of Noise Reduction Algorithms: Perception Versus Localization Simulation in the
Case of Binaural Cochlear Implant (BCI) Coding
307
1 Introduction 307
2 Materials
and Methods 309
3 Results 316
4 Discussion 317
5 Conclusions 322
Acknowledgments
322
References
323
CHAPTER 17 Lowering
the Fall Rate of the Elderly From Wheelchairs
325
1 Introduction 325
2 Current
Solutions 326
3 A Systems
Solution 328
4 The
Sparrow Design 329
5 Assessment
Algorithm 331
6 Assessment
Decision Algorithm 331
7 The
Future 332
8
Conclusion 333
Acknowledgments
333
References
333
CHAPTER 18 Occipital and Left Temporal EEG
Correlates of Phenomenal Consciousness
335
1
Introduction 335
2
Participants 335
3 Apparatus
and Stimuli 335
4
Procedure 336
5 EEG
Recording 337
6 Experiment
I 337
7 Experiment
II 338
8 The Grand
Average Occipital and Temporal Electrical Activity Correlated with a Contrast
in Access 340
9 Behavioral
Data 342
10 The Grand
Average Occipital and Temporal Electrical Activity Correlated with a Contrast
in Phenomenology 344
11 The Grand
Average Occipital and Temporal Electrical Activity Co-occurring with
Unconsciousness 350
Acknowledgments
354
References
354
CHAPTER 19 Chaotic
Dynamical States in the Izhikevich Neuron Model
355
1 Introduction 355
2 Fundamental
Description 356
3 Chaotic
Properties of Izhikevich Neuron Model
361
4 Response
Efficiency in Chaotic Resonance 366
5 Conclusions 372
References
373
CHAPTER 20 Analogy, Mind, and Life 377
1
Introduction 377
2 The
Artificial Mind and Cognitive Science
377
3
Consciousness 378
4 The
Classic Watchmaker Analogy 382
5 The
Classic Watchmaker Analogy Is Fragile, Remote and Reductive 383
6 The
Analogy Between Life and Information Seems to Suggest Some Type of
Reductionism 384
7
Conclusion 385
Acknowledgements
387
References
387
CHAPTER 21 Copy
Number Networks to Guide Combinatorial Therapy of Cancer and Proliferative
Disorders 389
1 Introduction 389
2 A
Diminishing Drug Pipeline 389
3 Using
Genome Data to Replenish the Pipeline by Drug Repositioning 390
4 The
Small-world Properties of Networks Expedite Combination Therapies 390
5 Molecular
Networks can be Used to Guide Drug Combinations
391
6 Copy
Number Alterations as a Disease Driver
391
7 Using
Correlated Copy Number Alterations to Construct Survival Networks 392
8 A
Pan-cancer CNA Interaction Network 392
9 Mapping
Genetic Survival Networks Using Correlated CNAs in Radiation Hybrid Cells 393
10 A
Survival Network for GBM At Single-gene Resolution 393
11 Using CNA
Networks to Guide Combination Therapies
394
12 Targeting
Multiple Drugs to Single-disease Genes in Cancer 395
13 Targeting
Multiple Drugs to a Single-disease Gene in Autoimmunity 398
14 Targeting
Multiple Genes in a Single Pathway for Cancer
399
15 Targeting
Genes in Parallel Pathways Converging on Atherosclerosis 400
16 Using CNA
Networks to Synergize Drug Combinations and Minimize Side Effects 401
17 Disclaimer 401
Acknowledgments
401
References
401
CHAPTER 22 DNA
Double-Strand Break-Based Nonmonotonic Logic
409
1 Introduction 409
2 DNA
DSBs 410
3 Logical
Model for System Biology 412
4 Completing
the Signaling Pathways by Default Abduction
417
5 Logic
Representation of a Signaling Pathway with the Goal of Reducing Computational
Complexity 418
6 Algorithm
and Implementation 422
7 Results 423
8 Conclusions 425
References
426
CHAPTER 23 An Updated Covariance Model for Rapid
Annotation of Noncoding RNA 429
1
Introduction 429
2
Method 430
3 Test
Results 432
4
Conclusions 433
References
434
CHAPTER 24 SMIR: A Web Server to Predict Residues
Involved in the Protein Folding Core 437
1
Introduction 437
2
Methods 439
3
Results 441
4
Conclusion 451
Acknowledgments
452
References
452
CHAPTER 25 Predicting
Extinction of Biological Systems with Competition 455
1 Introduction 455
2 A Model of
Competing Species 457
3 Density
Function of Extinction Time 458
4 Estimation
of Parameters 460
5 Numerical
Results 461
6
Summary 464
Acknowledgments
464
References
464
CHAPTER 26 Methodologies for the Diagnosis of the
Main Behavioral Syndromes for Parkinson's Disease with Bayesian Belief
Networks 467
1 Introduction 467
2 Diagnosis
of FoG 468
3 Diagnosis
of Handwriting and Speech 475
4 Toward a
Global Methodology for PD 478
5 Conclusions
and Future Work 481
References
482
CHAPTER 27 Practical Considerations in Virtual
Screening and Molecular Docking 487
1 Introduction 487
2 Receptor
Structure Preparation 488
3 Accurately
Predicting the Pose of Solved Crystal Structures and Differentiating Decoys
From Actives 491
4 Side-chain
Flexibility and Ensemble Docking 492
5 Consensus
Docking 493
6 MM-GBSA 494
7 Incorporating
Pharmacophoric Constraints Within the Virtual Screen 496
8 Conclusion 496
References
497
CHAPTER 28 Knowledge Discovery in Proteomic Mass
Spectrometry Data 503
1
Introduction 503
2 Technical
Background 504
3
Computational Workflow 505
4 Analysis
Tool 513
5
Conclusion 517
References
517
CHAPTER 29 A Comparative Analysis of Read Mapping
and Indel Calling Pipelines for Next-Generation Sequencing Data 521
1
Introduction 521
2 Mapping
and Calling Software 522
3
Methods 524
4 Real
Data 527
5 Results
and Discussion 528
6
Conclusions 534
References
534
CHAPTER 30 Two-Stage Evolutionary Quantification of
In Vivo MRS Metabolites 537
1
Introduction 537
2 Proposed
Methodology 538
3
Experiment 546
4
Conclusions 558
Acknowledgments
559
References
559
CHAPTER 31 Keratoconus Disease and
Three-Dimensional Simulation of the Cornea Throughout the Process of
Cross-Linking Treatment 561
1 Introduction 561
2 Methodology 564
3 Conclusions
and Recommendations 571
Acknowledgments
574
References
574
CHAPTER 32 Emerging
Business Intelligence Framework for a Clinical Laboratory Through Big Data
Analytics 577
1 Introduction 577
2 Motivation 578
3 Material
and Methods 579
4 Use-cases 584
5 Case Study
1: Clinical Laboratory Test Usage Patterns Visualization 585
6 Data
Source and Methodology 585
7 Results
and Discussion 587
8 Limitations 588
9 Case Study
2: Provincial Laboratory Clinical Test Volume Estimation 589
10 Data
Source and Methodology 589
11 Results
and Discussion 594
12 Limitations 598
13 Conclusion
and Future Work 598
References
599
CHAPTER 33 A Codon Frequency Obfuscation Heuristic
for Raw Genomic Data Privacy 603
1
Introduction 603
2
Background 603
3 Related
Work 604
4
Methodology 606
5 Experiment
and Results 610
6
Conclusion 616
References
618
Index 621