Bioinformatics Research and Applications

Name: Bioinformatics Research and Applications | 8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings
Brand: Springer
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8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings

Leonidas Bleris Ion Mandoiu Russell Schwartz Jianxin Wang(Herausgeber*in)

Springer (Verlag)

Erschienen am 10. Mai 2012

XIII, 332 Seiten

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Inhalt

Title Page
Preface
Organization
Table of Contents
Trie-based Apriori Motif Discovery Approach
Introduction
Problem Definition
Contribution
Background
Computational Approaches in Common Motifs Discovery
Suffix Trees in Common Motifs Discovery
Apriori Approach in Motif Discovery
The Proposed Trie-based Apriori Approach
Window-Based Trie Construction
Trie-based 2-mer Extraction
Trie-based Candidate Generation
Measures for Frequent Motifs
Algorithm
Empirical Results
Experimental Setup
Results and Discussion
Conclusion and Future Work
References
Inapproximability of (1, 2)-Exemplar Distance
Introduction
MAD Distance
SAD Distance
Signed Reversal Distance
Edit Distance
Concluding Remarks
References
A Mixed Integer Programming Model for the Parsimonious Loss of Heterozygosity Problem
Introduction
Notation and Problem Formulation
The LOH Graph
The Complexity of the PLOHP
A Mixed Integer Programming Model for the PLOHP
Experiments
Numerical Results
References
Reconstruction of Transcription Regulatory Networksby Stability-Based Network Component Analysis
Introduction
Motif-directed NCA and Stability Analysis
Motif-directed NCA
Stability Analysis
Simulation and Experiment Results
Simulation Data
Breast Cancer Expression Data
Conclusions
References
A Transcript Perspective on Evolution
Introduction
A Model of Transcript Evolution
Results
Transcriptome Reconstruction
Functional Study on Transcripts
Reconstruction of Transcript Phylogenies
TrEvoR Algorithm
Conclusion
References
A Fast Algorithm for Computing the Quartet Distance for Large Sets of Evolutionary Trees
Introduction
Previous Work: QDist
The QuickQuartet Algorithm
Experimental Methodology
Experimental Results
Conclusions
References
Error Propagation in Sparse Linear Systems with Peptide-Protein Incidence Matrices
Introduction
Error Bounds through Linear Programming
Unit Vectors and Rows with Two Variables
Properties of Optimal Combinations of Rows
Approximate Solutions with Two Variables Per Row
Some Experimental Results and Conclusions
References
Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions
References
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms
Introduction
Preliminaries
The Reduced Consensus Problem Is NP-Complete
Fixed Parameter Tractability
ILP Formulations
Experiments and Results
References
Analytics Approaches for the Era of 10,000* Genomes*and Counting
The Impact of High-Throughput Sequencing
The Role of Analytic Provenance in Genomics
Visual Analytic Approaches to Fast-Growing Data
References
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches
Introduction
Definitions
Unrooted Reconciliation
Methods
Algorithms
Experimental Results and Discussion
Outlook and Conclusion
References
A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees
Introduction
Basic Definitions and Preliminaries
New RF Measure for Comparing Unrooted with Rooted Trees
Methods
Transforming Gene Tree
RF Cost and the Star Topologies
Algorithm and the Properties of urRF
Relations between urRF and DL
Experiment
Discussion and Conclusion
References
P-Binder: A System for the Protein-Protein Binding Sites Identification
Introduction
Methods
Selecting Fragments on a Single Protein
Side-Chain Conformation and Side-Chain Energy
Atomic Contact Energy
Secondary Structure Energy
Combination of Energy Scores
Results
Comparison to Existing Methods
Evaluation on Benchmark v4.0
Assessment of the Energy Items
Conclusions and Discussion
References
Non-identifiable Pedigrees and a Bayesian Solution
Introduction
Background
Methods
Examples
A Potential Solution
Discussion
References
Iterative Piecewise Linear Regressionto Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis
Background
Methods
Re-estimate the Expected Statistics
Iterative Piecewise Linear Regression (iPLR)
iPLR for One-Sided Test
Results
Two-Class Simulations
Multi-class Simulations
Fission Yeast Data
Human Ewing Tumor Data
Conclusions
References
Reconstruction of Network EvolutionaryHistory from Extant Network Topology and Duplication History
Introduction
Methods
Modeling Network Evolution
History Reconstruction
Duplication Forest
Backward Operator
Growth History with Known Duplication Forest
Theoretical Results
Reconstruction Algorithms
Estimating Parameters
Results
Simulation Validation
Comparison with Existing Methods
Application to Real PPI Networks
Discussion
References
POPE: Pipeline of Parentally-Biased Expression
Introduction
POPE Pipeline Structure
Filtering Out Loci with High Genome Mapping Bias
Theory of POPE
Modeling
Detecting the Presence and Absence of cis and trans Effects
Applying the Definition of Additivity
Illustration of the Pipeline
Detecting Additivity from the Absence of cis and trans Effects
Case Study
Discussion
Conclusion
References
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering
Introduction
Computational Methods
Metric Access Methods (MAMs)
Spectrum Similarity
Original Method
Improvements
Preprocessing.
Query Phase.
Postprocessing.
Experiments
Clustering of Spectra from Two Spectrometer Runs
Effectiveness and Efficiency of Peptide Sequences Identification
Clustering of Spectra Merged from More Spectrometer Runs
Impact of Distance Threshold on Clustering
Conclusions
References
On the Comparison of Sets of Alternative Transcripts
Introduction
Basic Representations of Transcripts
Integrating Coding Information
Multi-species Comparisons
Comparison with Other Formalisms
Formalities of Block Construction
Conclusion
References
MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees
Introduction
Phylogenetic Networks and Trees
Pairwise and Set-Wise Reconciliation of Trees
MURPAR
Experimental Evaluation
Data
Methods and Accuracy Measure
Results on Simulated Data
Results on Biological Data
Conclusions
References
Large Scale Ranking and Repositioning of Drugs with Respectto Drug Bank Therapeutic Categories
Introduction
Methods
Bipartite Networks Projection and Integration
Construction of Pharmacological Networks
Ranking Methods for Drug Therapeutic Category Prediction
Experiments
Experimental Setup
Results
Conclusions
References
Score Based Aggregation of microRNA Target Orderings
Background
Foundation
The General Goal of Rank Aggregation and Logic Behind Consideration of Scores
Rank Aggregation
Distance Functions with Their Score Based Analogs
Formulation of the Proposed Algorithm
Extension of the Local Kemenization Technique for Allowing Scores
Results
An Artificial Simulation
Application on miRNA Target Prediction
Conclusion
References
Modeling Complex Diseases Using Discriminative Network Fragments
Novel Multi-sample Scheme for Inferring Phylogenetic Markersfrom Whole Genome Tumor Profiles
Introduction
Approach
Experimental Methods
Synthetic Data
Experiments: Real Data
Results and Discussion
Synthetic Data
Real Data
Conclusion
References
Algorithms for Knowledge-Enhanced Supertrees
Introduction
Basic Notation and Preliminaries
Structural Properties of the c-Similarity Problems
Dynamic Programming for RF and c-Similarity Supertree Problems
Experiments
Conclusion
References
Improvement of BLASTp on the FPGA-Based High-Performance Computer RIVYERA
Introduction
BLAST
RIVYERA Architecture
Application Structure and Implementation
Modified BLASTp Hardware Pipeline
Software Control
Performance Evaluation
Discussion
Conclusion
References
A Polynomial Time Solution for Protein Chain Pair Simplification under the Discrete Fr´echet Distance
Introduction
Background
Polynomial Time Solution for CPS-3F+
CPS-3F+ $\in $ P
Time Complexity
Dynamic Programming Algorithm
Comparison of Results
Concluding Remarks
References
Designing RNA Secondary Structures in Coding Regions
Introduction
Preliminaries
Heuristics for Inverse RNA Folding
Structure Maximization
Structure Minimization
Algorithmic Variants
Experimental Results
Parameter Optimization
Conclusion
References
Phylogenetic Tree Reconstruction with Protein Linkage
Introduction
Different Versions of Linkage Distance
Whole Block Linkage Distance
Partial Block Linkage Distance
Pairwise Linkage Distance
General Algorithm for the PTRPL Problem
Experiments and Results
Conclusion
References
Protein Structure Prediction and Clustering Using MUFOLD
References
Computational Modeling of Mammalian Promoters
Author Index

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