Bioinformatics Research and Applications
8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings
Published on 10. May 2012
XIII, 332 pages
978-3-642-30191-9 (ISBN)
Description
This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012.
The 26 revised full papers presented together with five invited talks were carefully reviewed and
selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.
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Leonidas Bleris | Ion Mandoiu | Russell Schwartz
Bioinformatics Research and Applications
8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings
Book
05/2012
Springer
€53.49
Shipment within 7-9 days
Content
- 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
