فهرست مطالب:

Contents

ProtRet: A Web Server for Retrieving Proteins

in a Functional Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Proposal of a New Bioinformatics Pipeline for Metataxonomics

in Precision Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Systems Toxicology Approach to Unravel Early Indicators

of Squamous Cell Carcinoma Rate in Rat Nasal Epithelium

Induced by Formaldehyde Exposure . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Moment Vector Encoding of Protein Sequences

for Supervised Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

A Hybrid of Particle Swarm Optimization and Minimization

of Metabolic Adjustment for Ethanol Production

of Escherichia Coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Cache-Efficient FM-Index Variants for Mapping of DNA Sequences . . . 45

A Parallel Implementation for Cellular Potts Model with Software

Transactional Memory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Inferring Positive Selection in Large Viral Datasets . . . . . . . . . . . . . . . .       61

Data-Driven Extraction of Quantitative Multi-dimensional

Associations of Cardiovascular Drugs and Adverse Drug Reactions . . .

An Identical String Motif Finding Algorithm Through

Dynamic Programming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .            70

78          

Parallel Density-Based Downsampling of Cytometry Data . . . . . . . . . . .

Signaling Transduction Networks in Choroidal Melanoma:

A Symbolic Model Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .          87

96          

Predicting Promoters in Phage Genomes Using Machine

Learning Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

Detection and Characterization of Local Inverted

Repeats Regularities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

An Efficient and User-Friendly Implementation of the Founder

Analysis Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

Visualization of Similar Primer and Adapter Sequences

in Assembled Archaeal Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

GeCo2: An Optimized Tool for Lossless Compression and Analysis

of DNA Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Troppo - A Python Framework for the Reconstruction

of Context-Specific Metabolic Models . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

Deterministic Classifiers Accuracy Optimization for Cancer

Microarray Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154

Artificial Intelligence in Biological Activity Prediction . . . . . . . . . . . . . . 164

Towards the Reconstruction of Integrated Genome-Scale Models

of Metabolism and Gene Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . 173

Author Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

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