Research in Computational Molecular Biology

Computational Biology: Its Challenges Past, Present, and Future.- Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast.- CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads.- Reconstructing the Evolutionary History of Complex Human Gene Clusters.- Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads.- Orchestration of DNA Methylation.- BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes.- A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors.- A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery.- The Statistical Power of Phylogenetic Motif Models.- Transcriptional Regulation and Cancer Genomics.- Automatic Recognition of Cells (ARC) for 3D Images of C. elegans.- Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing.- A Fragmentation Event Model for Peptide Identification by Mass Spectrometry.- A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics.- De Novo Sequencing of Nonribosomal Peptides.- Systems Metabolic Engineering.- Protein Function Prediction Based on Patterns in Biological Networks.- Automatic Parameter Learning for Multiple Network Alignment.- An Integrative Network Approach to Map the Transcriptome to the Phenome.- Fast and Accurate Alignment of Multiple Protein Networks.- High-Resolution Modeling of Cellular Signaling Networks.- At the Origin of Life: How Did Folded Proteins Evolve?.- Locating Multiple Gene Duplications through Reconciled Trees.- Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information.- Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins.- DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework.- Computation of Median Gene Clusters.- BCL-2: From Translocation to Therapy.- Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles.- Constructing Treatment Portfolios Using Affinity Propagation.- Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs.- More Efficient Algorithms for Closest String and Substring Problems.- Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia.- Accounting for Non-genetic Factors Improves the Power of eQTL Studies.- Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA.- On the Inference of Ancestries in Admixed Populations.- Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information.- Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information.- Constructing Level-2 Phylogenetic Networks from Triplets.- Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony.