Algorithms for Computational Biology

- Comparative Genomics Approaches to Identifying Functionally Related Genes

- A Greedy Algorithm for Hierarchical Complete Linkage Clustering

- Vester's Sensitivity Model for Genetic Networks with Time-Discrete Dynamics

- Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem

- Heuristics for the Sorting by Length-Weighted Inversions Problem on Signed Permutations

- On Low Treewidth Graphs and Supertrees

- On Optimal Read Trimming in Next Generation Sequencing and Its Complexity

- On the Implementation of Quantitative Model Refinement

- HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads

- Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads

- Modeling the Geometry of the Endoplasmic Reticulum Network

- On Sorting of Signed Permutations by Prefix and Suffix Reversals and Transpositions

- On the Diameter of Rearrangement Problems

- Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network

- On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

- A Closed-Form Solution for Transcription Factor Activity Estimation Using Network Component Analysis

- SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints

- Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures

- Inference of Boolean Networks from Gene Interaction Graphs Using a SAT Solver

- RRCA: Ultra-Fast Multiple In-species Genome Alignments

- Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric