Bioinformatics Research and Applications

Peptide Identification from Mass Spectrometry.- Identifying Critical Transitions of Biological Processes by Dynamical Network Biomarkers.- Computational Behavioral Ecology.- Unusual RNA Structures: Information Content in RNAs from the “Prebiotic Ribosome” to Modern Viruses.- The Radiation Hybrid Map Construction Problem Is FPT.- Reconstructing Ancestral Genomic Orders Using Binary Encoding and Probabilistic Models.- Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale.- A Tool for Non-binary Tree Reconciliation.- Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis.- Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression.- A Simulation of Synthetic agr System in E.coli.- Gene Regulatory Networks from Gene Ontology.- Partitioning Biological Networks into Highly Connected Clusters with Maximum Edge Coverage.- Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees.- LCR Finder: A de Novo Low Copy Repeat Finder for Human Genome.- Heuristic Algorithms for the Protein Model Assignment Problem.- Alignment of DNA Mass-Spectral Profiles Using Network Flows.- A Context-Driven Gene Prioritization Method for Web-Based Functional Genomics .- Exploiting Dependencies of Patterns in Gene Expression Analysis Using Pairwise Comparisons.- Cloud Computing for De Novo Metagenomic Sequence Assembly.- Protein Closed Loop Prediction from Contact Probabilities.- A Graph Approach to Bridge the Gaps in Volumetric Electron Cryo-Microscopy Skeletons.- Measure the Semantic Similarity of GO Terms Using Aggregate Information Content.- Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data.- POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria.- Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication.- Ellipsoid-Weighted Protein Conformation Alignment.- Construction of Uncertain Protein-Protein Interaction Networks and Its Applications.- Does Accurate Scoring of Ligands against Protein Targets Mean Accurate Ranking?.