Research in Computational Molecular Biology

Name: Research in Computational Molecular Biology | 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings
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15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings

Vineet Bafna S. Cenk Sahinalp(Herausgeber*in)

Springer (Verlag)

Erschienen am 24. März 2011

XVII, 580 Seiten

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Inhalt

Title
Preface
Organization
Table of Contents
Bacterial Community Reconstruction Using Compressed Sensing
Introduction
The BCS Algorithm
Results
Simulation Results
Reconstruction of an Experimental Mixture
Discussion
References
Constrained De Novo Sequencing of Peptides with Application to Conotoxins
Introduction
Problem Formulation
Constraints and Algorithms for Constrained De Novo Search
Multiset Constraint
An Algorithm for Generating Multiset-Constrained Candidates
Acyclic Regular Expression Constraint
An Algorithm for Generating Regex-Constrained Candidates
Constrained Spectral Search and Clustering
Application to Conotoxins
Validation on Known Sequences
Discovery of Novel Conotoxins
Discussion
References
Metabolic Network Analysis Demystified
References
Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes (Extended Abstract)
Introduction
Methods
Validation and Results
References
Hapsembler: An Assembler for Highly Polymorphic Genomes
Introduction
Methods
Overlap Computation
Error Correction
Building the Overlap Graph
Finding Paths between Mate Pairs
Building the Mate Pair Graph
Processing the Mate Pair Graph
Polymorphism and Repeat Resolution with the Mate Pair Graph
Results
Error Correction
Assembly
Discussion
References
Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome
Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks
Introduction
Methods
Disease Gene Prioritization Problem
Topological Similarity of Proteins in a PPI Network
Using Topological Similarity to Prioritize Candidate Genes
Results
Datasets
Experimental Setting
Performance Evaluation
Conclusion
References
Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast
Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways
Introduction
Previous Work
BPAT-M: Branched Pathfinding by Merging Linear Pathways
Construction of Q, C and M from Target Atom Markings (TAMs)
Finding Branched Pathways Using Q, C and M
Results
Experimental Setup
-d-Glucose 6-Phosphate to Lycopene
-d-Glucose 6-Phosphate to Cephalosporin C
Discussion
References
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels
Introduction
TAG Indel Model
Pairwise Alignment and Parameter Estimation
Results and Discussion
References
Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes
References
Variable Selection through Correlation Sifting
Introduction
The Problems Caused by Correlations
Datasets
Sifting through HIV Epitopes to Explain Viral Load
The Analysis of the Seasonal Variation in Influenza Genomic Sites and Their Relationship with the Pneumonia and Influenza Index for the Subsequent Season
Correlation Sifting
The Effect of Removing Correlations
Results
Empirical Analysis of the Algorithm Using Synthetic Data
Identifying HIV-Gag Epitopes That Are Predictive of Viral Load
Discovering the Effect of Diversifying Selection on Seasonal Influenza Epidemics
Discussion
References
Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions
Introduction
Multi-break Rearrangements and Breakpoint Graphs
Breakages and Optimal Transformations
Weighted Multi-break Distance
Discussion
References
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling
Introduction
Methods
Results
Conclusion
References
Pedigree Reconstruction Using Identity by Descent
Introduction
Background
A Lower Bound for Pair-Wise Relationships with Out-Breeding
Algorithms for Constructing Pedigrees
IBD Model for Constructing Outbred Pedigrees (COP)
IBD Model for Constructing Inbred Pedigrees (CIP)
Heuristic Graph Partitioning Method
Results
Discussion
References
A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription
Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut
Introduction
Related work
Data
Results
Discussion
Methods
The Graph Model
The Algorithm
Removing BPM Redundancies
References
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly
Introduction
Methods
Enumerating Candidate Isoforms
The LASSO Approach of Estimating Isoform Expression Levels
Completeness Requirement
Experimental Results
Simulated Mouse RNA-Seq Data
Comparisons between IsoLasso, IsoInfer, Cufflinks, and Scripture
Real RNA-Seq Data
Conclusion
References
Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals
Introduction
Methods
Inference of Pairwise IBD
From Pairwise IBD to Global IBD
Haplotype Reconstruction
Experiments
Discussions
References
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs
Introduction
Methods
Modeling Targeting Pathway by Hidden Markov Models
A HMM for the Targeting Pathways Problem
Defining the Emission and Transition Probabilities for Our Model
Approximation and Feature Levels
Structure Learning
Results
Simulated Data
Predicting Protein Locations.
Recovering the True Structure.
Yeast Data
Predicting Protein Locations.
Evaluation of the Learned Structure.
Discussion
References
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs
Introduction
Methods
Solving for Protein Orientation
Solving for the Symmetry Axis Position
Analysis of Multiple Distance Restraints
Evaluation
Extensions to disco
Results
DAGK with Subunit Ambiguity
GB1 with Simulated Atom Ambiguity
Conclusion
References
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers
Introduction
From de Bruijn Graphs to Paired de Bruijn Graphs
Preliminaries
De Bruijn Graphs (Modelling Unpaired Reads)
Graph Complexity
Paired de Bruijn Graphs (Modelling Paired Reads with Exact Distance)
Approximate Paired de Bruijn Graphs (Modelling Inexact Distance)
Results
Towards a Practical Paired de Bruijn Graph Assembler
Conclusion
References
An Optimization-Based Sampling Scheme for Phylogenetic Trees
Introduction
Notation
Likelihood Model
ILP for Solving the Degree Constrained Spanning Tree Problem
Mixing Time for the Cavender-Farris-Neyman Model
Experiments
Data Sets
Results
Discussion
Conclusions
References
Multiplex De Novo Sequencing of Peptide Antibiotics
Introduction
Results
Methods
References
Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk
AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization
Introduction
Methods
Notations
Mixture Model
Parameter Estimation
Expectation-Maximization Algorithm
Implementation of E-M Updates
Results
AREM Identifies Additional Binding Sites
AREM's Sensitivity Is Increased with Ambiguous Reads
AREM Is Sensitive to Repeat Regions
Discussion
References
Blocked Pattern Matching Problem and Its Applications in Proteomics
Introduction
The Blocked Pattern Matching Problem
BPM Algorithms
BPM Algorithms without Text Indexing
BPM Indexing for Length-1 Patterns
MBPM Algorithms
Transforming the Text into a Set of Patterns
Matching the Keyword Tree of Patterns against the Text
Mutation-Tolerant Peptide Identification
Results
Discussion
References
A Three-Dimensional Model of the Yeast Genome
Optimization of Combinatorial Mutagenesis
Introduction
Methods
Results
Discussion and Conclusion
References
Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets
T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome
Introduction
References
Experiment Specific Expression Patterns
Introduction
Related Work
Material and Methods
Data Sets
Basic Protocol
Differential Analysis
Support Vector Regression
Model Building
Fold-Change Prediction
Scoring Performance Deviation
Permutation Test for the Evaluation of Padesco
Results
Discussion
References
Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles
References
A Ribosome Flow Model for Analyzing Translation Elongation
References
Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm
Introduction
Protein Design and K*
CFTR and CAL
Previous Work
Methods
K* Algorithm
Extension of K* to Mutations/Flexibility on Two Protein Strands
Results
Computational Designs with K*
Training of Energy Function Weights
Retrospective Test against Peptide Array Data
Prospective validation of the K* Algorithm
Conclusions
References
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data
Introduction
Constructing Fragmentation Trees from MS2 and MSn Data
Hardness Results
An Exact Algorithm for the Combined Colorful Subtree Problem
Scoring
Results
Conclusion
References
Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction
Introduction
Metric Labeling for Function Prediction
Constructing a Metric Distance between GO Functions
Improvement in Function Prediction
Our Contributions
Methods
The Metric Labeling Problem
Integer Programming Formulation of Metric Labeling
Metric Approximation via Least Square Distortion Minimization
Metrics and Semimetrics
Network Data
Comparison to Other Methods
Evaluating Performance
Results
Function Prediction in Yeast Using a PPI Network
Trade-off between GO-Distances and Network Distances
Robustness on the Yeast PPI Network
Performance on Other Networks
Conclusions
References
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models
Introduction
Methods
Predicting Folding Dynamics
Results
Discussion
References
Optimally Orienting Physical Networks
Introduction
Preliminaries
An ILP Algorithm for Orienting Mixed Graphs
A Reduction to a Mixed Acyclic Graph
An ILP Formulation for Mixed Acyclic Graphs
Implementation Details
Experimental Results
Data Acquisition and Integration
Application and Performance Evaluation
Comparison to Layman Approaches
Conclusions
References
Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
Introduction
Methods
Definitions
Scaffold Graph
Fixed-Parameter Tractability
Minimizing Discordant Edges
Graph Contraction
Handling of Repeat Contigs
Determination of Gap Sizes
Experimental Results
Datasets
Scaffold Contiguity
Scaffold Correctness
Running Time and Gaps
Discussion
References
Increasing Power of Groupwise Association Test with Likelihood Ratio Test
Introduction
Material and Methods
Computation of Likelihoods of Haplotypes
Computation of Likelihoods of Variants
Efficient Permutation Test for LRT
Power Simulation Framework
Estimating PAR of a Group of Variants Using LRT
Results
Type I Error Rate of LRT
Power Comparison between LRT and Previous Grouping Methods
LRT on Real Mutation Screening Data of ATM
Discussion
References
Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection
Desiderata for Linkage Disequilibrium Measures
Axiom 1: The Extendability of LD Measures to Multi-loci as a Unique Conservative Extension of the Pairwise Values
Axiom 2: The Interpretability of Intermediary Values
Directed Informativeness and the Minimum Informative Subset Tagging SNPs Problem
Informativeness
Directed Informativeness
Directed Informativeness and the Conservative Extension to Multi-loci Axiom
Directed Informativeness and the Interpretability of Intermediary Values Axiom
Formalizing LD-Select/Tagger
LD Measure Assumptions
SNP Selection Graph Properties
Minimum Dominating Set Algorithm
Comparison of LD-Select/Tagger vs. Optimal
Tagger ``Best N''
Comparison of Directed Informativeness with (Undirected) Informativeness
Prediction vs. Distinguishability
Non-monotonicity vs. Monotonicity
Empirical Results
Haplotype Discrimination
Haplotype Imputation
Computational Complexity of the Minimum Directed Informative Set of SNPs/Tagging SNPs Problem
References
Protein Loop Closure Using Orientational Restraints from NMR Data
Introduction
Theory and Methods
Overview
RDC Sphero-Conics
Analytic Solutions for Peptide Plane Orientations from -Defining and -Defining RDCs in One Alignment Medium
Analytic Solutions for the Angle of Glycine from C-H RDC
Sampling the DOFs When RDCs Are Missing
Pruning with Conformation Filters
Results and Discussion
Tests on Experimental NMR Data
Comparison vs. Traditional Structure Determination Protocols
Comparison with Loop Prediction Algorithms
Conclusions
References
De Novo Discovery of Mutated Driver Pathways in Cancer
References
An Unbiased Adaptive Sampling Algorithm forthe Exploration of RNA Mutational Landscapes under Evolutionary Pressure
Introduction
Methods
Results
Conclusion
References
Nonparametric Combinatorial Sequence Models
Introduction
Model
Chinese Restaurant Process Linkage Model
Chinese Restaurant Franchise Observation Model
Inference
Resampling Site Groupings zsite
Resampling zclust and zprof
Results
MHC Class I Binding Prediction
Conclusion
References
Algorithms for MDC-Based Multi-locus Phylogeny Inference
Introduction
Preliminary Material
The MDC Problem: Rooted, Binary Gene Trees
MDC on Estimated Gene Trees
Unrooted, Binary Gene Trees
Rooted, Non-binary Gene Trees
Unrooted, Non-binary Gene Trees
Experimental Evaluation
Methods
Results
References
Rich Parameterization Improves RNA Structure Prediction
Introduction
Preliminaries and Problem Definition
Feature Representations
Learning Algorithm
Experiments
Experiment Settings
Results
Discussion
References
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data
Introduction
Related Work
Methods
Backbone Structure Determination from Residual Dipolar Couplings
Using Markov Random Fields for Rotamer Assignment
Deriving the Prior Probability
Deriving the Likelihood Function and the Scoring Function
Estimation of Experimental Noise in the NOESY Data
Results
Parameter Estimation
Accuracy of Determined Side-Chain Rotamer Conformations
Improvement on Our Previous Approaches hana and Nasca
Comparisons with Scwrl4
Conclusions
References

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