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MOTIVATION Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. RESULTS Here, we present a novel(More)
We consider the interval constrained coloring problem, which appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy experiments is a method used in that field to obtain information about protein tertiary structure. The output of these experiments provides data about the exchange(More)
MOTIVATION A large and rapidly growing number of bacterial organisms have been sequenced by the newest sequencing technologies. Cheaper and faster sequencing technologies make it easy to generate very high coverage of bacterial genomes, but these advances mean that DNA preparation costs can exceed the cost of sequencing for small genomes. The need to(More)
Determining the hydrogen-deuterium exchange speeds of single residues from data for peptic fragments obtained by FT-ICS MS is currently mainly done by manual interpretation. We provide an automated method based on combinatorial optimization. More precisely, we present an algorithm that enumerates all possible exchange speeds for single residues that explain(More)
Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by a dramatic reduction in cost since its introduction in 2004, NGS technology has provided a new way of addressing a wide range of biological and biomedical questions, from the study(More)
Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here, we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter to characterize the(More)
Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or(More)
Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields to represent the intermolecular interactions. There are many different force fields available--each based on a different set of assumptions and thus requiring different parametrization procedures.(More)
We present a branch-and-bound (bb) algorithm for the multiple sequence alignment problem (MSA), one of the most important problems in computational biology. The upper bound at each bb node is based on a Lagrangian relaxation of an integer linear programming formulation for MSA. Dualizing certain inequalities, the Lagrangian sub-problem becomes a pairwise(More)
We consider the following Tree-Constrained Bipartite Matching problem: Given a bipartite graph G=(V 1,V 2,E) with edge weights $w:E \mapsto\mathbb{R}_{+}$ , a rooted tree T 1 on the set V 1 and a rooted tree T 2 on the set V 1, find a maximum weight matching $\mathcal{M}$ in G, such that none of the matched nodes is an ancestor of another matched node in(More)