Bioinformatics Research and Applications

Tracing the Early Cell Divisions of Mouse Embryos by Single Cell RNA-Seq.- Successes and Failures of Elegant Algorithms in Computational Biology.- Modeling without Borders: Creating and Annotating VCell Models Using the Web.- Touring Protein Space with Matt.- Fixed-Parameter Algorithm for General Pedigrees with a Single Pair of Sites.- Analysis of Temporal-spatial Co-variation within Gene Expression Microarray Data in an Organogenesis Model.- Human Genome Annotation.- Extensions and Improvements to the Chordal Graph Approach to the Multi-state Perfect Phylogeny Problem.- Analysis of Gene Interactions Using Restricted Boolean Networks and Time-Series Data.- Residue Contexts: Non-sequential Protein Structure Alignment Using Structural and Biochemical Features.- Essential Proteins Discovery from Weighted Protein Interaction Networks.- Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets.- A Novel Approach for Compressing Phylogenetic Trees.- Structure of Proximal and Distant Regulatory Elements in the Human Genome.- Combinatorics in Recombinational Population Genomics.- Uncovering Hidden Phylogenetic Consensus.- An Agglomerate Algorithm for Mining Overlapping and Hierarchical Functional Modules in Protein Interaction Networks.- Fast Protein Structure Alignment.- Predicting and Analyzing Cellular Networks.- A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure.- Inferring Evolutionary Scenarios for Protein Domain Compositions.- Local Structural Alignment of RNA with Affine Gap Model.- Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees.- "Master-Slave" Biological Network Alignment.- Deciphering Transcription Factor Binding Patterns from Genome-Wide High Density ChIP-chip Tiling Array Data.- The Expected Fitness Cost of a Mutation Fixation under the One-Dimensional Fisher Model.