Bioinformatics Research and Applications

Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk).- Integrating Multiple-Platform Expression Data through Gene Set Features.- Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression.- Mean Square Residue Biclustering with Missing Data and Row Inversions.- Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks.- Querying Protein-Protein Interaction Networks.- Integrative Approach for Combining TNF?-NF?B Mathematical Model to a Protein Interaction Connectivity Map.- Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient.- Bioinformatics Challenges in Translational Research.- Untangling Tanglegrams: Comparing Trees by Their Drawings.- An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections.- Counting Faces in Split Networks.- Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns.- Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots.- Efficient Algorithms for Self Assembling Triangular and Other Nano Structures.- Motif Construction from High–Throughput SELEX Data.- Rearrangement Phylogeny of Genomes in Contig Form.- Prediction of Contiguous Regions in the Amniote Ancestral Genome.- Pure Parsimony Xor Haplotyping.- A Decomposition of the Pure Parsimony Haplotyping Problem.- Exact Computation of Coalescent Likelihood under the Infinite Sites Model.- Imputation-Based Local Ancestry Inference in Admixed Populations.- Interpreting Population Sequencing Data.- Modeling and Visualizing Heterogeneity of Spatial Patterns of Protein-DNA Interaction from High-Density Chromatin Precipitation Mapping Data.- A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation.- Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing.- Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates.- A Class of Evolution-Based Kernels for Protein Homology Analysis: A Generalization of the PAM Model.- Irreplaceable Amino Acids and Reduced Alphabets in Short-Term and Directed Protein Evolution.- A One-Class Classification Approach for Protein Sequences and Structures.- Prediction and Classification of Real and Pseudo MicroRNA Precursors via Data Fuzzification and Fuzzy Decision Trees.