This book constitutes the proceedings of the 7th RECOMB International Satellite Workshop on Comparative Genomics, RECOMB-CG 2009, Budapest, Hungary, in September 2009.
This workshop is devoted to bringing together scientists working on all aspects of comparative genomics, from computer scientists, mathematicians and statisticians working on novel computational approaches for genome analysis and comparison, to biologists applying these computational tools to study the structure and the evolution of prokaryotic and eukaryotic genomes.
The 19 papers presented were carefully reviewed and selected from 31 submissions. The papers illustrate the crucial role of comparative genomics in understanding genome function and address a broad variety of aspects, ranging from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication events and to the importance of new computational approaches to unraveling the structural evolution of genomes.
Author(s): Eric Tannier (auth.), Francesca D. Ciccarelli, István Miklós (eds.)
Series: Lecture Notes in Computer Science 5817 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2009
Language: English
Pages: 241
Tags: Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Bioinformatics; Symbolic and Algebraic Manipulation; Discrete Mathematics in Computer Science; Algorithm Analysis and Problem Complexity
Front Matter....Pages -
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods....Pages 1-12
Natural Parameter Values for Generalized Gene Adjacency....Pages 13-23
Parking Functions, Labeled Trees and DCJ Sorting Scenarios....Pages 24-35
Counting All DCJ Sorting Scenarios....Pages 36-47
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction....Pages 48-58
Finding Nested Common Intervals Efficiently....Pages 59-69
DCJ Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions....Pages 70-83
Rearrangement Models and Single-Cut Operations....Pages 84-97
Aligning Two Genomic Sequences That Contain Duplications....Pages 98-110
Inferring the Recent Duplication History of a Gene Cluster....Pages 111-125
Pseudo Boolean Programming for Partially Ordered Genomes....Pages 126-137
Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes Using Pseudo-Boolean Optimization....Pages 138-149
Reconstructing Histories of Complex Gene Clusters on a Phylogeny....Pages 150-163
Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples....Pages 164-180
Whole-Genome Analysis of Gene Conversion Events....Pages 181-192
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances....Pages 193-204
Comparative Genomics and Extensive Recombinations in Phage Communities....Pages 205-216
Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana ....Pages 217-228
Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of Functional Regulatory Targets....Pages 229-240
Back Matter....Pages -
