Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings / Edition 1

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This book constitutes the refereed proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2005, held in Cambridge, MA, USA in May 2005.

The 39 revised full papers presented together with abstracts of keynote talks were carefully reviewed and selected from 217 submissions. As the top conference in computational molecular conference, RECOMB addresses all current issues in algorithmic and theoretical bioinformatics.

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Table of Contents

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.- Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.- Towards an Integrated Protein-Protein Interaction Network.- The Factor Graph Network Model for Biological Systems.- Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution.- Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model.- Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis.- Keynote.- A Regulatory Network Controlling Drosophila Development.- Keynote.- Yeast Cells as a Discovery Platform for Neurodegenerative Disease.- RIBRA–An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem.- Avoiding Local Optima in Single Particle Reconstruction.- A High-Throughput Approach for Associating microRNAs with Their Activity Conditions.- RNA-RNA Interaction Prediction and Antisense RNA Target Search.- Consensus Folding of Unaligned RNA Sequences Revisited.- Keynote.- Discovery and Annotation of Genetic Modules.- Efficient q-Gram Filters for Finding All—-Matches over a Given Length.- A Polynomial Time Solvable Formulation of Multiple Sequence Alignment.- A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters.- Reconstruction of Reticulate Networks from Gene Trees.- A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction.- Constructing a Smallest Refining Galled Phylogenetic Network.- Keynote.- Mapping Molecular Landscapes Inside Cells.- Information Theoretic Approaches to Whole Genome Phylogenies.- Maximum Likelihood of Evolutionary Trees Is Hard.- Graph Theoretical Insights into Evolution of Multidomain Proteins.- Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry.- A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search.- EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning.- Keynote.- Biology as Information.- Using Multiple Alignments to Improve Gene Prediction.- Learning Interpretable SVMs for Biological Sequence Classification.- Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition.- Rapid Protein Side-Chain Packing via Tree Decomposition.- Recognition of Binding Patterns Common to a Set of Protein Structures.- Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions.- Keynote.- Amino Acid Sequence Control of the Folding of the Parallel—-Helix, the Simplest—-Sheet Fold.- A Practical Approach to Significance Assessment in Alignment with Gaps.- Alignment of Optical Maps.- Keynote.- Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology.- Modeling the Combinatorial Functions of Multiple Transcription Factors.- Predicting Transcription Factor Binding Sites Using Structural Knowledge.- Motif Discovery Through Predictive Modeling of Gene Regulation.- HAPLOFREQ – Estimating Haplotype Frequencies Efficiently.- Improved Recombination Lower Bounds for Haplotype Data.- A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem.- Keynote.- Human Genome Sequence Variation and the Inherited Basis of Common Disease.- Stability of Rearrangement Measures in the Comparison of Genome Sequences.- On Sorting by Translocations.

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