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