Algorithms in Bioinformatics

7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings

By: Sridhar Hannenhalli (Editor), Raffaele Giancarlo (Editor)

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Paperback | 22 August 2007

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The refereed proceedings from the 7th International Workshop on Algorithms in Bioinformatics are provided in this volume. Papers address current issues in algorithms in bioinformatics, ranging from mathematical tools to experimental studies of approximation algorithms to significant computational analyses. Biological problems examined include genetic mapping, sequence alignment and analysis, phylogeny, comparative genomics, and protein structure.

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Shotgun Protein Sequencing (Keynote)	p. 1
Locality Kernels for Protein Classification	p. 2
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features	p. 12
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps	p. 25
Bringing Folding Pathways into Strand Pairing Prediction	p. 38
A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage	p. 49
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies	p. 61
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity	p. 73
Haplotype Inference Via Hierarchical Genotype Parsing	p. 85
Seeded Tree Alignment and Planar Tanglegram Layout	p. 98
Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion (Extended Abstract)	p. 111
An [Omega](n[superscript 2]/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem	p. 124
Incremental Discovery of Irredundant Motif Bases in Time O([vertical bar Sigma vertical bar]n[superscript 2] log n) (Extended Abstract)	p. 136
A Graph Clustering Approach to Weak Motif Recognition	p. 149
Informative Motifs in Protein Family Alignments	p. 161
Topology Independent Protein Structural Alignment	p. 171
Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction	p. 183
Alignment-Free Local Structural Search by Writhe Decomposition	p. 194
Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment	p. 196
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding	p. 208
Genomic Signatures in De Bruijn Chains	p. 216
Fast Kernel Methods for SVM Sequence Classifiers	p. 228
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences	p. 240
Predicting Protein Folding Kinetics Via Temporal Logic Model Checking (Extended Abstract)	p. 252
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops	p. 265
Algorithms for the Extraction of Synteny Blocks from Comparative Maps	p. 277
Computability of Models for Sequence Assembly	p. 289
Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data	p. 302
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound	p. 310
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding	p. 323
Homology Search with Fragmented Nucleic Acid Sequence Patterns	p. 335
Fast Computation of Good Multiple Spaced Seeds	p. 346
Inverse Sequence Alignment from Partial Examples	p. 359
Novel Approaches in Psychiatric Genomics (Keynote)	p. 371
The Point Placement Problem on a Line - Improved Bounds for Pairwise Distance Queries	p. 372
Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach	p. 383
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data	p. 395
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence	p. 407
Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation	p. 420
Author Index	p. 431
Table of Contents provided by Ingram. All Rights Reserved.

Algorithms in Bioinformatics

7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings

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