دانلود کتاب Comparative Genomics: RECOMB 2007, International Workshop, RECOMB-CG 2007, San Diego, CA, USA, September 16-18, 2007, Proceedings (Lecture Notes in Computer Science, 4751)

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Title Page
Preface
Organization
Table of Contents
Multi-break Rearrangements: From Circular to Linear Genomes
Introduction
Multi-break Rearrangements in Circular Genomes
Multi-break Distance Between Circular Genomes
Breakpoint Re-Use in Circular Genomes
Rearrangements in Linear Genomes
Rearrangement Distance Between Linear Genomes
Breakpoint Re-Use in Linear Genomes
References
A Pseudo-boolean Programming Approach for Computing the Breakpoint Distance Between Two Genomes with Duplicate Genes
Introduction
Preliminaries
An Exact Algorithm
Pseudo-boolean Problem
Maximizing the Number of Adjacencies
Speeding-Up the Program
Experimental Results
Conclusion
References
Improving Inversion Median Computation Using Commuting Reversals and Cycle Information
Introduction
Backgrounds
Genome Rearrangements
Distance Computation
Sorting and Commuting Reversals
Inversion Median Problem
Inversion Median Computation Using Commuting Reversals
A Naive Approach
An Improved Algorithm
Parallel and Perpendicular Sorting Reversals
The Final Algorithm
Experimental Results
Setup of Simulations
Accuracy
Speed
Medians of Larger Genomes
Discussion
Conclusions and Future Work
References
Inferring a Duplication, Speciation and Loss History from a Gene Tree
Introduction
Duplication/Speciation History and Reconciliation
Recognizing a DS-Tree
Inferring Gene Losses in a Non DS-Tree
Problem Statements
A Heuristic for the Subtrees Insertion Problem
Experimental Results
Conclusion
References
How to Achieve an Equivalent Simple Permutation in Linear Time
Introduction
Preliminaries
Creating Equivalent Simple Permutations Revisited
The Data Structure
The Algorithm
References
Baculovirus Phylogeny Based on Genome Rearrangements
Introduction
Phylogenomics and Genome Rearrangement
Application to Viral Genomes
Finding Shared Genes Presents Key Challenge
Baculoviridae
Materials and Methods
Detection of Orthologous Gene Clusters
Cluster Pruning
Gene Order and Phylogeny
MULGOR Software
Using MULGOR Iteratively on Baculovirus
Results
Baculovirus Phylogeny of Nine Species
Baculovirus Phylogeny of Twelve Species
Updated Phylogeny of Thirty-two Genomes
Discussion
Gene Deletions and Low Sequence Homology
Deviations from Parsimony
Strong Gene Order Conservation vs. Lack of Shared Genes
Improvements and Future Work
Conclusion
References
Learning Gene Regulatory Networks via Globally Regularized Risk Minimization
Introduction
Method
Linear Modeling
Coping with Time Lags via Time Shifting
Feature Selection via L1 Regularized Risk Minimization
Regulation Sharing via Globally Regularized Risk Minimization
Optimization Procedure
Experiments and Results
Experiments on Synthetic Data
Experiments on Real Data
Conclusions
References
Evolution of Tandemly Arrayed Genes in Multiple Species
Introduction
The Evolutionary Model
An Inference Problem
The Generalized Minimum-DI Problem
A General Method Using the Median Problem
A Branch-and-Bound Algorithm for the Median Problem
Results
Branch-and-Bound Efficiency
Application on Biological Data
Conclusion
References
Selecting Genomes for Reconstruction of Ancestral Genomes
Introduction
Parsimony Methods and Its Accuracy
A Simple Jukes-Cantor Evolutionary Model
Parsimony Reconstruction Method
Reconstruction Accuracy
More Genomes Are Not Necessarily Better
Algorithms for Genome Selection
Forward Greedy Algorithm
Backward Greedy Algorithm
Simulation Test
A Biological Example
Conclusion
References
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications
Introduction
Methods
Definitions
Species Tree, Gene Tree, and Reconciled Tree
Reconstructing Ancestral Adjacency
From Ancestral Adjacency to Ancestral Gene Order
Summary
Results
Simulation Results
Application to Real Data
Discussion
References
Reconstructing an Inversion History in the $\\it{AnophelesGambiae}$ Complex
Introduction
Materials and Methods
Results
Conclusion
References
Recovering True Rearrangement Events on Phylogenetic Trees
Introduction
Basic Concepts
Methods and Algorithms
A Naive Algorithm: All Versus All
Extension: EMRAE
Simulations
Random Breakage Model
Fragile Regions Model
Result on Real Data
Discussion
References
Parts of the Problem of Polyploids in Rearrangement Phylogeny
Introduction
Terminology and Scope
Generation and Inference of Polyploidy
Existing Resources
Parts Already in Place
The Case of Two Doubling Descendants
Halving
Doubling First
Speciation First
Simulations
Genome Doubling in Yeast
Conclusions
References
A Rigorous Analysis of the Pattern of Intron Conservation Supports the $\\it{Coelomata}$ Clade of Animals
Introduction
Materials and Methods
Results
The Dependence of Intron Loss Rate in a Branch on Intron Conservation in Other Branches
Parsimony Analysis of Conserved Introns Supports the Coelomata Topology
Three Additional Tests to Resolve the Coelomata/Ecdysozoa Dilemma
Discussion and Conclusions
References
Author Index