Bioinformatics Research and Applications: 8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings

Front Matter....Pages -
Trie-based Apriori Motif Discovery Approach....Pages 1-12
Inapproximability of (1,2)-Exemplar Distance....Pages 13-23
A Mixed Integer Programming Model for the Parsimonious Loss of Heterozygosity Problem....Pages 24-35
Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis....Pages 36-47
A Transcript Perspective on Evolution....Pages 48-59
A Fast Algorithm for Computing the Quartet Distance for Large Sets of Evolutionary Trees....Pages 60-71
Error Propagation in Sparse Linear Systems with Peptide-Protein Incidence Matrices....Pages 72-83
Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions....Pages 84-86
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms....Pages 87-98
Analytics Approaches for the Era of 10,000* Genomes *and Counting....Pages 99-101
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches....Pages 102-114
A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees....Pages 115-126
P-Binder: A System for the Protein-Protein Binding Sites Identification....Pages 127-138
Non-identifiable Pedigrees and a Bayesian Solution....Pages 139-152
Iterative Piecewise Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis....Pages 153-164
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History....Pages 165-176
POPE: Pipeline of Parentally-Biased Expression....Pages 177-188
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering....Pages 189-200
On the Comparison of Sets of Alternative Transcripts....Pages 201-212
MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees....Pages 213-224
Large Scale Ranking and Repositioning of Drugs with Respect to DrugBank Therapeutic Categories....Pages 225-236
Score Based Aggregation of microRNA Target Orderings....Pages 237-248
Modeling Complex Diseases Using Discriminative Network Fragments....Pages 249-249
Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles....Pages 250-262
Algorithms for Knowledge-Enhanced Supertrees....Pages 263-274
Improvement of BLASTp on the FPGA-Based High-Performance Computer RIVYERA....Pages 275-286
A Polynomial Time Solution for Protein Chain Pair Simplification under the Discrete Fréchet Distance....Pages 287-298
Designing RNA Secondary Structures in Coding Regions....Pages 299-314
Phylogenetic Tree Reconstruction with Protein Linkage....Pages 315-327
Protein Structure Prediction and Clustering Using MUFOLD....Pages 328-329
Computational Modeling of Mammalian Promoters....Pages 330-330
Back Matter....Pages -