Research in Computational Molecular Biology

Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts.- Hap Tree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.- Change point Analysis for Efficient Variant Calling.- On the Representation of de Bruijn Graphs.- Exact Learning of RNA Energy Parameters from Structure.- An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data.- The Generating Function Approach for Peptide Identification in Spectral Networks.- Decoding Coalescent Hidden Markov Models in Linear Time.- AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application.- Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models.- On Sufficient Statistics of Least-Squares Superposition of Vector Sets.- IDBA-MTP: A Hybrid Meta Transcriptomic Assembler Based on Protein Information.- MRFalign: Protein Homology Detection through Alignment of Markov Random Fields.- An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.- PASTA: Ultra-Large Multiple Sequence Alignment.- Fast Flux Module Detection Using Matroid Theory.- Building a Pangenome Reference for a Population.-CSAX: Characterizing Systematic Anomalies in eXpression Data.-Whats Hap: Haplotype Assembly for Future-Generation Sequencing Reads.- Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data.- dip SPA des: Assembler for Highly Polymorphic Diploid Genomes.- An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes.- HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time.- Modeling Mutual Exclusivity of Cancer Mutations.-Viral Quasispecies Assembly via Maximal Clique Enumeration.-Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency.- Bayesian Multiple Protein StructureAlignment.- Gene-Gene Interactions Detection Using a Two-Stage Model.- A Geometric Clustering Algorithm and Its Applications to Structural Data.- A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation.- Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification.-Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.- Reconciliation with Non-binary Gene Trees Revisited.- Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models.-Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion.