Advances in Bioinformatics and Computational Biology

Name: Advances in Bioinformatics and Computational Biology | 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012, Proceedings
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7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012, Proceedings

Marcilio C.P. de Souto Maricel G. Kann(Herausgeber*in)

Springer (Verlag)

Erschienen am 10. August 2012

XII, 204 Seiten

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978-3-642-31927-3 (ISBN)

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Inhalt

Title
Preface
Organization
Table of Contents
Transposition Diameter and Lonely Permutations
Introduction
Background
Nonexistence of Super-Bad Permutations
Further Remarks about Unions of Lonely Permutations
References
Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes
Introduction
Algebraic Rearrangement Theory
Basic Concepts
Modeling Genomes with Algebraic Theory
Adjacency Algebraic Theory
Sorting by Algebraic Operations
Characterizing -1 and Finding Sorting Operations
Algebraic Sorting with 2-Break (DCJ) Operations
Comparing the Algebraic with DCJ Distance
Conclusions
References
On the Approximation Ratio of Algorithms for Sorting by Transpositions without Using Cycle Graphs
Introduction
Preliminaries
Approximation Ratio Results
Experimental Results and Discussion
Conclusions
References
A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats
Introduction
Definitions and Background
A Duplication Model for Tandem Repeats
The Importance of the Parsing Problem
Heuristic Methods to Estimate Tandem Repeat Parsing
PAIR - The Adjacent Pairs Method
VAR - The Number of Variants Method
MST - The Minimum Spanning Tree Method
Results and Discussion
References
RNA Folding Algorithms with G-Quadruplexes
Introduction
Energy Model for RNA Quadruplexes
Combinatorics of Structures with Quadruplexes
RNA Folding Algorithms
Evaluation
Discussion
References
Molecular Dynamics for Simulating the Protein Folding Process Using the 3D AB Off-Lattice Model
Introduction
The Protein Folding Problem
The AB Off-Lattice Model
Molecular Dynamics
Methodology
Computational Experiments and Results
Temperature Dependence
Results
Conclusions and Future Works
References
A Bioconductor Based Workflow for Z-DNA Region Detection and Biological Inference
Introduction
The Structure of Z-DNA
Z-DNA Prediction Softwares: Z-Catcher and Z-Hunt
R and Bioconductor
Workflow Overview
ZDR Distribution Analysis
ZDRs and Differential RNA Polymerase Occupation Data
ZDRs and Genomic Features
Case Study: Human Chromosome 14
Genomic Feature Analysis
Differential Occupation Analysis
Conclusions
References
A Probabilistic Model Checking Approach to Investigate the Palytoxin Effects on the Na+/K+-ATPase
Introduction
Preliminaries
Transmembrane Ionic Transport Systems
Related Work
Experimental and Simulational Techniques
Model Checking
The Na+/K+-ATPase Model
Discrete Chemistry
The Palytoxin Model
Experimental Results
Parameters and Model Complexity
PTX Inhibition by High Doses of ATP
Conclusions and Future Work
References
RFMirTarget: A Random Forest Classifier for Human miRNA Target Gene Prediction
Introduction
Materials and Methods
Random Forest
Data Set
Data Preparation
Features
Performance Assessment
Results
RFMirTarget Prediction Performance Based on 28 Features
RFMirTarget Prediction Performance Based on 34 Features
Conclusion and Future Work
References
Prediction of Transcription Factor Binding Sites by Integrating DNase Digestion and Histone Modification
Introduction
Related Work
Materials and Methods
Motif Matching
DNase and Histone Modification High-Resolution Signal Generation
Detection of Footprints with HMMs
TFBS Gold Standard
Results and Discussion
Final Remarks
References
Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer
Introduction
Correlation Coefficients
Pearson
Jackknife
Spearman
Kendall
Rank-Magnitude
Evaluating Proximity Measures
Intrinsic Separation Ability
Predictive Clustering Ability
Statistical Significance
Results and Discussion
Intrinsic Separation Ability
Predictive Clustering Ability
Relation between Intrinsic Separation and Predictive Ability
Discussion
Conclusions and Future Work
References
Associating Genotype Sequence Properties to Haplotype Inference Errors
Introduction
Experiments Design
Data Bases Used
Multiple Linear Regression Models
Statistical Analysis of Results
Results
Selected Regression Variables
Regression Models Accuracy
Comparison of Regression and Neural Net Models
Final Discussion and Conclusions
References
Design and Implementation of ProteinWorldDB
Introduction
Motivation
Database Conceptual Modeling
Relational Implementation and Queries
Conclusions
References
A Comparative Analysis of Public Ligand Databases Based on Molecular Descriptors
Introduction
Methods
Ligand Databases
Target Protein and Ligands
Evaluation of Public Ligand Databases
Evaluation of Data Source
Results and Discussion
Lessons Learned
Conclusions
References
Phylogenetic Distance Computation Using CUDA
Introduction
GPU Implementation
Experimental Results
Conclusions and Future Works
References
Exploring Molecular Evolution Reconstruction Using a Parallel Cloud Based Scientific Workflow
Introduction
Background on Adaptive Molecular Evolution Reconstruction
SciEvol: A Workflow for Molecular Evolution Reconstruction
Experimental Results
Related Work
Final Remarks
References
How Bioinformatics Enables Livestock Applied Sciences in the Genomic Era
Introduction
Genomic Selection: Increasing Accuracy of Genetic Predictions in Cattle
Genome Wide Association Study for Disease Resistance and Complex Traits in Cattle
Signatures of Selection and Their Role in Unraveling Traits under Selection in Livestock
Concluding Remarks
References
Author Index

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