Research in Computational Molecular Biology

Efficient Alignment Free Sequence Comparison with Bounded Mismatches.- DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes.- CRISPR Detection from Short Reads Using Partial Overlap Graphs.- Hap Tree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data.- Read Clouds Uncover Variation in Complex Regions of the Human Genome.- Learning Microbial Interaction Networks from Metagenomic Count Data.- Immunoglobulin Classification Using the Colored Antibody Graph.- CIDANE: Comprehensive Isoform Discovery and Abundance Estimation.- Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.- Fragmentation Trees Reloaded.- KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids.- Locating a Tree in a Phylogenetic Network in Quadratic Time.- Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data.- COMETS (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.- Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure.- BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design.- An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations.- Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models.- CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer.- Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.- Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning.- ScaffMatch: Scaffolding Algorithm Basedon Maximum Weight Matching.- Symmetric Length-Aware Enrichment Test.- Functional Alignment of Metabolic Networks.- Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples.- Ultra-Large Alignments Using Ensembles of Hidden Markov Models.- Topological Signatures for Population Admixture.- Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele.- Gap Filling as Exact Path Length Problem.- Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.- A Fast and Exact Algorithm for the Exemplar Breakpoint Distance.- Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions.- On the Sample Complexity of Cancer Pathways Identification.- A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks.- Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.- Computational Protein Design Using AND/OR Branch-and-Bound Search.