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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)
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)
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)
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)
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)
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)
This thesis is devoted to two N P-complete combinatorial optimization problems arising in computational biology, the well-studied multiple sequence alignment problem and the new formulated interval constraint coloring problem. It shows that advanced mathematical programming techniques are capable of solving large scale real-world instances from biology to(More)
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the small phylogeny problem to be formulated as an alignment problem. In this work we present a branch-and-cut algorithm(More)