Let P be a point set in ℝ^d, and let M be a function that maps any subset of P to a positive real. We examine the problem of computing the mean and variance of M when a subset in P is selected according to a random distribution. We consider two ...

We consider approximate string matching of a circular pattern consisting of the rotations of a pattern of length m. From SBNDM and Tuned Shift-Add, we derive a sublinear-time algorithm for searching a noncircular pattern with k allowed mismatches, which ...

We study the interval constrained coloring problem, a combinatorial problem arising in the interpretation of data on protein structure emanating from experiments based on hydrogen/deuterium exchange and mass spectrometry. The problem captures the ...

This article presents a new algorithm for finding oligonucleotide signatures that are specific and sensitive for organisms or groups of organisms in large-scale sequence datasets. We assume that the organisms have been organized in a hierarchy, for ...

The development of cancer is largely driven by the gain or loss of subsets of the genome, promoting uncontrolled growth or disabling defenses against it. Denoising array-based Comparative Genome Hybridization (aCGH) data is an important computational ...

The generation of random graphs using edge swaps provides a reliable method to draw uniformly random samples of sets of graphs respecting some simple constraints (e.g., degree distributions). However, in general, it is not necessarily possible to access ...

As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome evolves through insertions, duplications, deletions, and movements of genes ...

We present a novel graph model and an efficient algorithm for solving the “threshold all against all” problem, which involves searching two strings (with length M and N, respectively) for all maximal approximate substring matches of length at least S, ...

In the next century, virtual laboratories will play a key role in biotechnology. Computer experiments will not only replace some of the time-consuming and expensive real-world experiments, but they will also provide insights that cannot be obtained ...

A major computational problem in biology is the reconstruction of evolutionary trees for species sets, and accuracy is measured by comparing the topologies of the reconstructed tree and the model tree. One of the major debates in the field is whether ...