Algorithms in Bioinformatics: 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings

Front Matter....Pages -
Minimum Factorization Agreement of Spliced ESTs....Pages 1-12
Annotating Fragmentation Patterns....Pages 13-24
biRNA: Fast RNA-RNA Binding Sites Prediction....Pages 25-36
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks....Pages 37-48
PMFastR: A New Approach to Multiple RNA Structure Alignment....Pages 49-61
On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices....Pages 62-72
Constructing Majority-Rule Supertrees....Pages 73-84
SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy....Pages 85-96
A Simple, Practical and Complete $O(\\frac{n^3}{ \\log n})$ -Time Algorithm for RNA Folding Using the Four-Russians Speedup....Pages 97-107
Back-Translation for Discovering Distant Protein Homologies....Pages 108-120
A Markov Classification Model for Metabolic Pathways....Pages 121-132
Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction....Pages 133-144
Phylogenetic Comparative Assembly....Pages 145-156
K-Partite RNA Secondary Structures....Pages 157-168
Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes....Pages 169-180
Predicting Gene Structures from Multiple RT-PCR Tests....Pages 181-193
A Tree Based Method for the Rapid Screening of Chemical Fingerprints....Pages 194-205
Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters....Pages 206-219
Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes....Pages 220-232
A General Framework for Local Pairwise Alignment Statistics with Gaps....Pages 233-245
 mpscan : Fast Localisation of Multiple Reads in Genomes....Pages 246-260
Fast Prediction of RNA-RNA Interaction....Pages 261-272
FlexSnap: Flexible Non-sequential Protein Structure Alignment....Pages 273-285
A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures....Pages 286-297
Exact Score Distribution Computation for Similarity Searches in Ontologies....Pages 298-309
Linear-Time Protein 3-D Structure Searching with Insertions and Deletions....Pages 310-320
Visualizing Phylogenetic Treespace Using Cartographic Projections....Pages 321-332
A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen....Pages 333-344
Aligning Biomolecular Networks Using Modular Graph Kernels....Pages 345-361
MADMX: A Novel Strategy for Maximal Dense Motif Extraction....Pages 362-374
Large-Scale Neighbor-Joining with NINJA....Pages 375-389
A Unifying View on Approximation and FPT of Agreement Forests....Pages 390-402
Structural Alignment of RNA with Complex Pseudoknot Structure....Pages 403-414
Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models....Pages 415-428
Back Matter....Pages -