Research in Computational Molecular Biology

Name: Research in Computational Molecular Biology | 16th Annual International Conference, RECOMB 2012, Barcelona, Spain, April 21-24, 2012. Proceedings
Brand: Springer
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16th Annual International Conference, RECOMB 2012, Barcelona, Spain, April 21-24, 2012. Proceedings

Benny Chor(Herausgeber*in)

Springer (Verlag)

Erschienen am 13. April 2012

XVI, 372 Seiten

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Inhalt

7262
Preface
Organization
Table of Contents
Protein Structure by Semidefinite Facial Reduction
Introduction
Gram Matrix Methods
Contributions of the Proposed SPROS Method
The SPROS Method
Euclidean Distance Geometry
The SDP Formulation
Cliques in a Protein Molecule
Algorithm for Finding the Face of the Structure
The Face of a Protein Molecule
Solving and Refining the Reduced SDP Problem
Results
Implementation
Determined Structures
Discussion
References
Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models
Introduction
Methods
Results
Discussion
References
Charge Group Partitioning in Biomolecular Simulation
Introduction
Problem Statement and Complexity
Dynamic Programming for Bounded Treewidth
Experimental Evaluation
Hydration Free Energy of Amino Acid Side Chains
Adenosine Tri-Phosphate (ATP)
Discussion
References
Increased Methylation Variation in Epigenetic Domains across Cancer Types
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising
Introduction
Accuracy Estimators
Learning the Estimator from Examples
Estimator Features
Application to Parameter Advising
Experimental Results
Conclusion
References
Quantifying the Dynamics of Coupled Networks of Switches and Oscillators
lobSTR: A Short Tandem Repeat Profiler for Personal Genomes
References
Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data
Introduction
Likelihood Model
Overview
Likelihood with Respect to Sequence Reads
Likelihood with Respect to Reference Dataset
Hap-seq
Transition Probability
Emission Probability
Recursions
Complexity
Read Length
Illustrative Example
Experimental Results
Discussion
References
Ballast: A Ball-Based Algorithm for Structural Motifs
Introduction
Problem Statement, Algorithm, and Analysis
Results
Enolase Superfamily
SOIPPA-Derived Motifs
Catalytic Site Atlas
Conclusion
References
Evolution of Genome Organization by Duplication and Loss: An Alignment Approach
Introduction
Research Context
The Duplication and Loss Model of Evolution
Method
The Pseudo-Boolean Linear Program
Applications
Evolution of Stable RNA Gene Content and Organization in Bacillus
Execution Time
Simulations
Conclusion
References
LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins
Problem Definition
Related Work
Method Overview
Results
Test Sets
Other Methods
Scores
Consensus Scores
Method Details
Database Matches
Fitting the Loop
Clashes
Ranking and Selection
Conclusions
References
A Robust Method for Transcript Quantification with RNA-seq Data
Introduction
Related Work
Method
MultiSplice
Expected Coverage and Observed Coverage
A Generalized Linear Model for Transcript Quantification
Bias Correction
Solving the Generalized Linear Models with Bias Correction
Experimental Results
Transcriptome Identifiability with Increasing Read Length
Simulated Human RNA-seq Experiment
Real Human RNA-seq Experiment
Conclusion
References
Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics
Introduction
Formalizing the BFB Schedule
Algorithms for BFB
Results
Discussion
References
TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq
Introduction
Methods
Results
Conclusions
References
Synthetic Sequence Design for Signal Location Search
Introduction
Signal Location Search Experience
Biological Signal Search
Practical Experience
Lessons Learned: Design Criteria for Sequence Signal Search
Group Testing Designs
Maximal Cycles Crossing Adjacent Levels of the Hasse Diagram
Consecutive Positives Detectable Matrices
Optimizing Experimental Design
Conclusion
References
The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing
Network-Based Prediction and Analysis of HIV Dependency Factors
Structure-Guided Deimmunization of Therapeutic Proteins
Introduction
Methods
Sweep Algorithm
Preprocessing Filters
Postprocessing Energy Minimization
Results
Staphylokinase (SakSTAR) Peptides
Erythropoietin (Epo) Peptides
SakSTAR Full-Protein Design
Conclusion
References
Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly
Introduction
Methods
De Bruijn Graphs
From k-mer Pairs to Edge-Pair Histograms
From Edge-Pair Intervals to Pathsets
Removing Phantom Paths from Pathsets
Splitting Pathsets
Identifying Essential Edges
Pathset Graph
Results
From Mate-Pairs to Edge-Pair Intervals
From Edge-Pair Intervals to Pathsets
Comparing Pathset with Other Genome Assemblers
Discussion
References
Finding Maximum Colorful Subtrees in Practice
Introduction
Computing Fragmentation Trees
Complexity Results and Algorithms
Exact Methods
Heuristics
Evaluation Results
Conclusions
References
Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
Introduction
Model and Main Results
Stochastic Model of LGT
Recovering a Tree-like Trend: Main Results
Probabilistic Analysis
Algorithm
A General Formula
Bounded-Rates and Yule Models
Highways of LGT
Model
Building the Species Tree in the Presence of Highways
Inferring Highways
Discussion
References
RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract)
Introduction
Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies
References
A Model for Biased Fractionation after Whole Genome Duplication
Exact Pattern Matching for RNA Structure Ensembles
Introduction
Preliminaries
Exact Pattern Matchings in RNA Structure Ensembles
The Algorithm ExpaRNA-P
Evaluation
Conclusion
References
Reconstructing Boolean Models of Signaling
Introduction
Preliminaries
Logic Learning via ILP
Symmetric Threshold Functions
Experimental Design
Learning Read-Once Functions
An Information-Theoretic Experimental Design Algorithm
Results
Implementation and Evaluation
The EGFR System
IL-1 Signaling
Conclusions
References
Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract
Introduction
Materials and Methods
Extending the D2, D2* and D2S Statistics to the NGS Read Data
Modeling the Long Underlying Sequences and the Samplingof Reads Using NGS
The Mean and Covariance of the Numbers of Occurrencesof Word Patterns in a Read Set
The Approximate Distributions of D2, D2* and D2S under the Null and the Alternative Models
New Distance Measures for Clustering Genome Sequences Based on k-tuple Distributions
Results
Clustering of Five Mammalian Species Using d2, d2* and d2S Based on Pseudo-NGS Reads
Applications to the Detection of the Relationship among Different Tree Species Using NGS Data
Discussion
References
Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem
Introduction
Methods
Datasets
Prize-collecting Steiner Tree Problem
Prize-collecting Steiner Forest (PCSF) Problem
Results
The PCSF Approach Reveals Parallel Working Pathways in Additionto Hidden Individual Proteins or Genes in Yeast Pheromone Response
The PCSF Algorithm Reveals Coordinately Acting Receptor Molecules Functioning in Human GBM by Integrating Receptome, Interactome and Proteomics Data
Discussion
References
Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks
Introduction
Network Based Protein Function Prediction
Multi-Label Correlated Protein Function Prediction
Methods
Notations and Problem Formalization
Protein Function Prediction Using the Green's Function over a Graph
Function-Function Correlated RKHS Approach for Multi-Label Classification
Correlation Augmented Interaction Network
Materials and Data Sets
Results and Discussions
Evaluation of the Function-Function Correlations
Improved Function Prediction in Cross-Validation
Conclusions
References
Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization
Introduction
Methods
Predict New Protein Interactions via PPI Networks
Predict New Protein Interactions from Multimodal Biological Data
Experimental Results and Discussions
Materials and Data Sources
Improved Prediction Capability in Cross-Validation
Improved Protein Function Prediction Using Predicted PPI Networks
Conclusions
References
CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping
Introduction
Methods
A Motivating Example
The Generative Model
Optimization
Implementation
GC-Bias Correction
Results
Simulation Results
Results on Real Data
Conclusion and Discussions
References
Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs
Probabilistic Inference of Viral Quasispecies Subject to Recombination
Introduction
Methods
Hidden Markov Model
EM Algorithm (Baum-Welch)
Sparse Recombination Rates
Estimating the Haplotype Distribution
Results
Simulated Datasets
Real HIV Dataset
Discussion
References
Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm
Introduction
SEME Algorithm
Identifying Over-represented l-mers.
Extending EM.
Re-sampling EM.
Sorting and Redundancy Filtering.
Result
Profiling Two Novel EM Procedures
SEME Significantly Outperforms MEME in Recovering the Planted PWM.
SEME Is More Suitable in Handling Large Scale Data.
Comparing TF Motif Finding in Large Scale Real Datasets
The Metazoan Compendium Datasets.
ChIP-Seq Experimental Datasets: Discovery of the ChIPed TF Motif from ChIP-Seq Data.
Discovery of co-TF Motifs from ChIP-Seq Data.
Conclusion
References
Author Index

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