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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