Research in Computational Molecular Biology

Searching Protein 3-D Structures in Linear Time.- Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification.- Boosting Protein Threading Accuracy.- New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees.- A Probabilistic Graphical Model for Ab Initio Folding.- Topology-Free Querying of Protein Interaction Networks.- Cross Species Expression Analysis of Innate Immune Response.- Haplotype Inference in Complex Pedigrees.- Storage and Retrieval of Individual Genomes.- An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations.- Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology.- Spatial Clustering of Multivariate Genomic and Epigenomic Information.- How Many Bootstrap Replicates Are Necessary?.- A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series.- Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation.- Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes.- Optimizing PCR Assays for DNA Based Cancer Diagnostics.- The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory.- COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study.- Overlapping Pools for High Throughput Targeted Resequencing.- Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction.- Lifting Prediction to Alignment of RNA Pseudoknots.- Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks.- Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination.- Simultaneous Alignment and Folding of Protein Sequences.- Shared Peptides in Mass Spectrometry Based Protein Quantification.- Evaluating Between-Pathway Models with Expression Data.- Sorting Signed Permutations by Inversions in O(nlogn) Time.- Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information.- Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data.- On the Relationship between DNA Periodicity and Local Chromatin Structure.- Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep.- Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples.- An Adaptive and Memory Efficient Algorithm for Genotype Imputation.- A Statistical Framework for the Functional Analysis of Metagenomes.- Learning Models for Aligning Protein Sequences with Predicted Secondary Structure.