Bioinformatics Research and Application

Name: Bioinformatics Research and Application | 7th International Symposium, ISBRA 2011, Changsha, China, May 27-29, 2011, Proceedings
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7th International Symposium, ISBRA 2011, Changsha, China, May 27-29, 2011, Proceedings

Jianer Chen Jianxin Wang Alexander Zelikovsky(Editor)

Springer (Publisher)

Published on 29. April 2011

XIV, 454 pages

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978-3-642-21260-4 (ISBN)

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Content

Title Page
Preface
Symposium Organization
Table of Contents
Phylogenetics of Heterogeneous Samples
OMG! Orthologs for Multiple Genomes - Competing Formulations
Phylogenetic Analysis of Whole Genomes
Introduction
Some Extant Problems
Some Encouraging Results from My Group
Conclusions
Genetic and Pharmacogenetic Studies of Neuropsychiatric Disorders: Increasingly Critical Roles of Bioinformatics Research and Applications(Keynote Talk)
Genome-Phenome Association Analysis of Complex Diseases a Structured Sparse Regression Approach
Prediction of Essential Proteins by Integration of PPI Network Topology and Protein Complexes Information
Introduction
Method
Six Centrality Measures
The Correlation of Protein Complexes and Essential Proteins
Algorithm ECC
Results
Identification of Essential Proteins by Integration of PPI Network Topology and Protein Complexes Information
Comparison with Six Centrality Methods in Identifying Essential Proteins
Comparison with Six Centrality Methods in Identifying Low-Connectivity Essential Proteins
Conclusions and Future Work
References
Computing the Protein Binding Sites
Introduction
Methods
Step 1: Local Sequence Alignment
Step 2: Identifying Surface Segments
Step 3: Computing Rigid Transformations to Match Candidate Binding Sites
Implementation
Results
Comparison with Existing Methods
Evaluation of Prediction
Comparison of Running Time
Performance of Programs for Different Families
Search a Binding Site in PDB
Discussion
Conclusion
SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm
Introduction
Method Principles
Single GSSU Pairwise Comparison
Multiple GSSU Structure Comparison
Speed Up
Experimental Results
Conclusion
Prediction of Essential Genes by Mining Gene Ontology Semantics
Introduction
Related Work
Essential Gene Prediction
Association Rule Mining
Frequent Closed Itemset Mining
Classification Based on Associations
Materials and Methods
GO Association Rule Classifier
Features GOARC and GOCBA
Data for Evaluation
Evaluation Method
Results and Discussion
Evaluation of Individual Features
Performance Enhancement by GOARC and GPCBA
Classifier Evaluation
Discussion of GO Association Rules
Conclusions and Future Work
References
High-Performance Blob-Based Iterative Reconstruction of Electron Tomography on Multi-GPUs
Introduction
Related Work
Blob-Based Iterative Reconstruction Methods
GPU Computation Model
Multilevel Parallel Strategy for Blob-Based Iterative Reconstruction
Coarse-Grained Parallel Scheme Using OpenMP
Fine-Grained Parallel Scheme Using CUDA
Asynchronous Communication Scheme
Blob-ELLR Format with Symmetric Optimization Techniques
Result
Conclusion
Component-Based Matching for Multiple Interacting RNA Sequences
Introduction
Backtracking Approach
Simple Structure for Patterns
Backtracking Algorithm
Component-Based Structure for Patterns
Trie-Based LLP Structure for Sequences
The LLP Approach
Updating the LLP Structure for INTRAM Components
Updating the LLP Structure for INTERM Components
Pruning Search Space in LLP
Experimental Setup
Results and Discussion
Conclusion
A New Method for Identifying Essential Proteins Based on Edge Clustering Coefficient
Introduction
Materials and Methods
Experimental Data
Centrality Measures
Degree Centrality (DC).
Betweenness Centrality (BC).
Closeness Centrality (CC).
Subgraph Centrality (SC).
Eigenvector Centrality (EC).
Information Centrality (IC).
Edge Clustering Coefficient
Evaluation Methods
Sensitivity (SN).
Specificity (SP).
Positive Predictive Value (PPV).
Negative Predictive Value (NPV).
F-measure (F).
Accuracy (ACC).
Results and Discussion
Conclusions
Gene Order in Rosid Phylogeny, Inferred from Pairwise Syntenies among Extant Genomes
Introduction
Six Eudicotyledon Sequences
Formal Background
Rearrangement Distance
The Median Problem and Small Phylogeny Problem
The OMG Problem
Pairwise Orthologies
Multi-genome Orthology Sets
PATHGROUPS
Inferring the Gene Content of Ancestral Genomes
Median and Small Phylogeny Problems with Unequal Genomes
Results on Rosid Evolution
Properties of the Solution as a Function of Synteny Block Size
Block Validation
Discussion and Future Work
Algorithms to Detect Multiprotein Modularity Conserved during Evolution
Introduction
Algorithms
Biologically Motivated Algorithm Goals
Experiments and Results
Conclusion
The Kernel of Maximum Agreement Subtrees
Introduction
Definitions
Properties of a MAST and the KAST
A Dynamic Programming Algorithm to Find the MAST
Finding the KAST
Experiments
Applications
Analyses on Flatworm Phylogenies
Analyses on -Proteobacteria Phylogenies
Conclusion
A consensus approach to predicting protein contact map via logistic regression
Introduction
Materials and Methods
Datasets
Contact Definition
Performance Evaluation
Consensus Prediction via Logistic Regression
Overall Architecture
Selection of Residue Pairs
Results
Results on the CASP9 Dataset
Results on the D856 Dataset
Discussions
The Impact of Residue Pair Selection
The Impact of Individual Predictors
The Impact of Classification Algorithm
Conclusions
A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees
Introduction
Duplication-Loss Model
Introduction to Unrooted Reconciliation
Algorithm
General Reconstruction Problems
Experiments
Discussion
References
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation
Introduction
Method
Corticosteroid Pharmacokinetic and Pharmacogenomics Models
Data Assimilation for Parameter Estimation and Model Selection
Pharmacogenomic Pathway Screening for Corticosteroid 58 Models
Time-Course Gene Expressions
Results of Pathway Screening with Data Assimilation
Discussion
The Deep Coalescence Consensus Tree Problem is Pareto on Clusters
Introduction
Preliminaries
Basic Definitions
Deep Coalescence
Consensus Tree
Cluster and Pareto
Theorem Overview
Supporting Lemmata
Shallowest Regrouping Operation
Properties of the Shallowest Regrouping Operation
Counting the Number of Degree-Two Nodes
Main Theorem
Algorithm for Improving a Candidate Solution
Experiment
Discussion
Conclusion and Future Work
Fast Local Search for Unrooted Robinson-Foulds Supertrees
Introduction
Preliminaries
Basic Notations and Problem Definition
Local Search Problems
Structural Properties
Preprocessing
Solving the NNI Search Problem
Solving the 2-ECR Search Problem
Experimental Results
Conclusion
A Metric for Phylogenetic Trees Based on Matching
Introduction
Background
Similarity, Editing, and Distance
Tree Similarity Measures
Tree Editing
The Robinson-Foulds Distance
Our Matching Distance
Basic Properties
Sensitivity to Tree Editing
Experimental Results
Distribution of the Tree Distance Metrics
Tree Distance Metrics Under Tree Editing Operations
Clustering Trees: An Application
Conclusion
Describing the Orthology Signal in a PPI Network at a Functional, Complex Level
Introduction
Other Related Work
Method
Inferring Putative Complexes and their Functional Categories.
Estimating the Frequency of a Functional Category.
Identifying Orthology-Related Categories.
Experimental Settings
Data Collection
Yeast Protein Function Annotations and Gene Ontology Files
Clustering
Results
Orthology-Related Functional Categories
Orthology-Related Putative Protein Complexes
Conclusions
Algorithms for Rapid Error Correction for the Gene Duplication Problem
Introduction
Basic Notations and Preliminaries
Basic Definitions and Notations
The Gene Duplication Cost Model
The Error-Correction Problems
Solving the SEC Problem
Structural Properties
Characterizing Duplications
The Algorithm
Solving the TEC Problem
Experimental Results
Conclusion
TransDomain: A Transitive Domain-Based Method in Protein-Protein Interaction Prediction
Introduction
Method
Overall Architecture of TransDomain
Transitive Role Feature Generation Step
Transitive Domain Pattern Generation Step
Two Stages PPIs Prediction Step
Results and Discussions
Datasets Generation
Performance Evaluation of Predicting Combined Protein Interactions
Performance Evaluation of Predicting Direct Protein Interactions
Case Studies
Conclusion
References
Rapid and Accurate Generation of Peptide Sequence Tags with a Graph Search Approach
Introduction
Algorithms
Experiments and Results
Conclusions
References
In Silico Evolution of Multi-scale Microbial Systems in the Presence of Mobile Genetic Elements and Horizontal Gene Transfer
Introduction
Biological Model
Parallel Simulation Framework
Application: Horizontal Gene Transfer
Evolution in Coupled Environments of Increasing Complexity
Effect of Horizontal Gene Transfer on the Network Organization
Distribution of Fitness Effect of Mutational and HGT Events
Discussion
References
Comparative Evaluation of Set-Level Techniques in Microarray Classification
Introduction
Methods and Data
Gene Set Ranking
Expression Aggregation
Machine Learning
Expression and Gene Sets
Experimental Protocol
Results
Conclusions and Future Work
Gene Network Modules-Based Liner Discriminant Analysis of Microarray Gene Expression Data
Introduction
Methods
MLDA Algorithm
Comparisons of Different Classification Methods
Cross-Validation
Results
Discussions and Conclusions
References
A Polynomial Algebra Method for Computing Exemplar Breakpoint Distance
Introduction
Notations
A Simple Algorithm
Polynomial Algebra Method
Breakpoint Distance for One Sequence without Repetition
Exemplar Breakpoint Distance between Arbitrary Genomes
Conclusions
The Maximum Clique Enumeration Problem: Algorithms, Applications and Implementations
Introduction
Implementation Environment
Fundamental Approaches to MCE
Basic Backtracking
Backtracking with Knowledge of Maximum Clique Size
Intelligent Backtracking.
Parameterized Enumeration.
Maximum Clique Covers
Essential Vertex Sets
Analysis and Discussion
Contrast to Random Graphs
Future Research Directions
Query-Adaptive Ranking with Support Vector Machines for Protein Homology Prediction
Introduction
Algorithm
K Nearest Blocks (KNB)
KNB Ensemble Ranking
Experiments
Data Set
Performance Evaluation
Results
Conclusion and Future Work
A Novel Core-Attachment Based Greedy Search Method for Mining Functional Modules in Protein Interaction Networks
Introduction
Methods
Definitions
Greedy Search Method (GSM)
Generation of Overlapping Clusters
Experiments and Results
Conclusions
References
ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks
Introduction
Background
Base Network Inference Methods
Reconciliation of Species Tree and Gene Trees
Models and Methods
Network Evolutionary Models
The ProPhyC Framework
ProPhyC Under the Basic Model
ProPhyC Under the Extended Model
Refinement Algorithm ProPhyCC Using Confidence Values
Experimental Design
Biological Data Collection
Data Simulation
Measurements
Results and Analysis
Performance Under the Basic Model on Simulated Data
Performance Under the Basic Model on Biological Data
Performance Under the Extended Model on Simulated Data
Conclusions
Prediction of DNA-Binding Propensity of Proteins by the Ball-Histogram Method
Introduction
Data
Method
Ball Histograms
Ball-Histogram Construction
Predictive Classification Using Ball Histograms
Results
Conclusion
Multi-label Correlated Semi-supervised Learning for Protein Function Prediction
Introduction
Multi-label Correlated Semi-supervised Learning
Algorithm, Justification and Extension
Iterative Algorithm
Justification and Extensions
Experiment
Setup
Evaluation Metrics
Construct Functional Category Network
5-Fold Cross Validation
Predict Function for Uncharacterized Proteins
Concluding Remarks
Regene: Automatic Construction of a Multiple Component Dirichlet Mixture Priors Covariance Model to Identify Non-coding RNA
Introduction
Covariance Models
Dirichlet Mixture Priors
Obtaining the Mixture Prior
Conjugate Gradient Method
Multiple Component Dirichlet Mixture Priors
Regene Method
Regene Implementation Details
Results and Discussion
Conclusions and Future Work
Accurate Estimation of Gene Expression Levels from DGE Sequencing Data
Introduction
DGE Protocol
DGE-EM Algorithm
E-Step
M-Step
Inferring p
Implementation
Results
Experimental Setup
DGE-EM Outperforms Uniq
Comparison of DGE and RNA-Seq Protocols
Possible DGE Assay Optimizations
Conclusions
An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes
Introduction
Materials and Methods
Dataset
Computational Framework
Feature Extraction
Model Construction
Genome-Scale Genomic Island Prediction
Performance Evaluation
Experimental Results
Feature Analysis
GI Structural Model
Prediction Accuracy
Conclusion and Discussion
A Systematic Comparison of Genome Scale Clustering Algorithms
Background
Results
Discussion
Conclusions
Materials and Methods
Data
Clustering Methods
Comparison Metrics
References
Mining Biological Interaction Networks Using Weighted Quasi-Bicliques
Introduction
Basic Notation, Definitions and Preliminaries
Maximum Weighted Quasi-Biclique (,-WQB) Problem
Query Problem
Time Complexity Results
IP Formulations for the ,-WQB Problem
Results and Discussion
Genetic Interaction Networks
Conclusions and Outlook
Towards a Characterisation of the Generalised Cladistic Character Compatibility Problem for Non-branching Character Trees
Introduction
Generalised Cladistic Character Compatibility Problem
Ordering Problems
Tractability Results
An Algorithm for Cases of the SB-GCCC Problem
The {{1},{2},{0,2}}-P-GCCC-NB Problem
Hardness Results
Conclusions and Open Problems

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Bioinformatics Research and Application

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