Research in Computational Molecular Biology

Integrated Protein Interaction Networks for 11 Microbes.- Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination.- Biological Networks: Comparison, Conservation, and Evolutionary Trees.- Assessing Significance of Connectivity and Conservation in Protein Interaction Networks.- Clustering Short Gene Expression Profiles.- A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies.- Global Interaction Networks Probed by Mass Spectrometry.- Statistical Evaluation of Genome Rearrangement.- An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets.- Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization.- Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data.- RNA Secondary Structure Prediction Via Energy Density Minimization.- Structural Alignment of Pseudoknotted RNA.- Stan Ulam and Computational Biology.- CONTRAlign: Discriminative Training for Protein Sequence Alignment.- Clustering Near-Identical Sequences for Fast Homology Search.- New Methods for Detecting Lineage-Specific Selection.- A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer.- A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric.- Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations.- Inferring Common Origins from mtDNA.- Efficient Enumeration of Phylogenetically Informative Substrings.- Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes.- Maximal Accurate Forests from DistanceMatrices.- Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction.- Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence.- An Important Connection Between Network Motifs and Parsimony Models.- Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome.- Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data.- Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes.- A New Approach to Protein Identification.- Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics.- Simulating Protein Motions with Rigidity Analysis.- Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation.- An Outsider's View of the Genome.- Alignment Statistics for Long-Range Correlated Genomic Sequences.- Simple and Fast Inverse Alignment.- Revealing the Proteome Complexity by Mass Spectrometry.- Motif Yggdrasil: Sampling from a Tree Mixture Model.- A Study of Accessible Motifs and RNA Folding Complexity.- A Parameterized Algorithm for Protein Structure Alignment.- Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction.- A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem.- A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles.- 10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB).- Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions.- A ParsimonyApproach to Genome-Wide Ortholog Assignment.- Detecting the Dependent Evolution of Biosequences.- Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data.