Michael Kaufmann

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The existing literature gives efficient algorithms for mapping trees or less restrictively outerplanar graphs on a given set of points in a plane, so that the edges are drawn planar and as straight lines. We relax the latter requirement and allow very few bends on each edge while considering general plane graphs. Our results show two algorithms for mapping(More)
DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to(More)
We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods(More)
In this paper, we present boundary labeling, a new approach for labeling point sets with large labels. We first place disjoint labels around an axis-parallel rectangle that contains the points. Then we connect each label to its point such that no two connections intersect. Such an approach is common e.g. in technical drawings and medical atlases, but so far(More)
High-throughput methods that allow for measuring the expression of thousands of genes or proteins simultaneously have opened new avenues for studying biochemical processes. While the noisiness of the data necessitates an extensive pre-processing of the raw data, the high dimensionality requires effective statistical analysis methods that facilitate the(More)
We describe a new technique that can be used to derandomize a number of randomized algorithms for routing and sorting on meshes. We demonstrate the power of this technique by deriving improved deterministic algorithms for a variety of routing and sorting problems. Our main results are an optimal algorithm for k-k routing on multi-dimensional meshes, a(More)
Triangulation of planar graphs under constraints is a fundamental problem in the representation of objects. Related keywords are graph augmentation from the field of graph algorithms and mesh generation from the field of computational geometry. We consider the triangulation problem for planar graphs under the constraint to satisfy 4-connectivity. A(More)
In this paper we present a paradigm for solving external-memory problems, and illustrate it by algorithms for matrix multiplication, sorting and list ranking. Our paradigm is based on the use of BSP algorithms. The correspondence is almost perfect, and especially the notion of x-optimality carries over to algorithms designed according to our paradigm. The(More)