Bioinformatics Research and Applications: 5th International Symposium, ISBRA 2009 Fort Lauderdale, FL, USA, May 13-16, 2009 Proceedings

Front Matter....Pages -
Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk)....Pages 1-4
Integrating Multiple-Platform Expression Data through Gene Set Features....Pages 5-17
Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression....Pages 18-27
Mean Square Residue Biclustering with Missing Data and Row Inversions....Pages 28-39
Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks....Pages 40-51
Querying Protein-Protein Interaction Networks....Pages 52-62
Integrative Approach for Combining TNFα-NFκB Mathematical Model to a Protein Interaction Connectivity Map....Pages 63-74
Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient....Pages 75-86
Bioinformatics Challenges in Translational Research....Pages 87-87
Untangling Tanglegrams: Comparing Trees by Their Drawings....Pages 88-99
An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections....Pages 100-111
Counting Faces in Split Networks....Pages 112-123
Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns....Pages 124-134
Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots....Pages 135-147
Efficient Algorithms for Self Assembling Triangular and Other Nano Structures....Pages 148-158
Motif Construction from High–Throughput SELEX Data....Pages 159-159
Rearrangement Phylogeny of Genomes in Contig Form....Pages 160-172
Prediction of Contiguous Regions in the Amniote Ancestral Genome....Pages 173-185
Pure Parsimony Xor Haplotyping....Pages 186-197
A Decomposition of the Pure Parsimony Haplotyping Problem....Pages 198-208
Exact Computation of Coalescent Likelihood under the Infinite Sites Model....Pages 209-220
Imputation-Based Local Ancestry Inference in Admixed Populations....Pages 221-233
Interpreting Population Sequencing Data....Pages 234-235
Modeling and Visualizing Heterogeneity of Spatial Patterns of Protein-DNA Interaction from High-Density Chromatin Precipitation Mapping Data....Pages 236-247
A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation....Pages 248-259
Mining of cis -Regulatory Motifs Associated with Tissue-Specific Alternative Splicing....Pages 260-271
Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates....Pages 272-283
A Class of Evolution-Based Kernels for Protein Homology Analysis: A Generalization of the PAM Model....Pages 284-296
Irreplaceable Amino Acids and Reduced Alphabets in Short-Term and Directed Protein Evolution....Pages 297-309
A One-Class Classification Approach for Protein Sequences and Structures....Pages 310-322
Prediction and Classification of Real and Pseudo MicroRNA Precursors via Data Fuzzification and Fuzzy Decision Trees....Pages 323-334
Back Matter....Pages -