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- Michael Kaufmann, Roland Wiese
- J. Graph Algorithms Appl.
- 1999

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)

- Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
- Algorithms for Molecular Biology
- 2008

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)

- Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern
- BMC Bioinformatics
- 2004

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)

- Michael A. Bekos, Michael Kaufmann, Antonios Symvonis, Alexander Wolff
- Graph Drawing
- 2004

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)

- Ulrich Fößmeier, Michael Kaufmann
- Graph Drawing
- 1995

We consider the problem of drawing plane graphs with an arbitrarily high vertex degree orthogonally into the plane such that the number of bends on the edges should be minimized. It has been known how to achieve the bend minimum without any respect to the size of the vertices. Naturally, the vertices should be represented by uniformly small squares. In… (More)

- Henning Fernau, Michael Kaufmann, Mathias Poths
- FSTTCS
- 2005

Two trees with the same number of leaves have to be embedded in two layers in the plane such that the leaves are aligned in two adjacent layers. Additional matching edges between the leaves give a one-to-one correspondence between pairs of leaves of the different trees. Do there exist two planar embeddings of the two trees that minimize the crossings of the… (More)

- Andreas Keller, Christina Backes, +5 authors Hans-Peter Lenhof
- BMC Bioinformatics
- 2008

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)

- Michael Kaufmann, Jop F. Sibeyn, Torsten Suel
- SODA
- 1994

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)

- Therese C. Biedl, Goos Kant, Michael Kaufmann
- Algorithmica
- 1994

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)

- Jop F. Sibeyn, Michael Kaufmann
- CIAC
- 1997

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)