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- Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern
- BMC Bioinformatics
- 2005

BACKGROUND
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… (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)

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

- 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

BACKGROUND
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… (More)

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

BACKGROUND
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… (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)

- Markus Eiglsperger, Martin Siebenhaller, Michael Kaufmann
- J. Graph Algorithms Appl.
- 2004

Sugiyama's algorithm for layered graph drawing is very popular and commonly used in practical software. The extensive use of dummy vertices to break long edges between non-adjacent layers often leads to unsatis-fying performance. The worst-case running-time of Sugiyama's approach is O(|V ||E| log |E|) requiring O(|V ||E|) memory, which makes it unusable for… (More)

A major factor affecting the readability of an illustration that contains textual labels is the degree to which the labels obscure graphi-cal features of the illustration as a result of spatial overlaps. Boundary labeling addresses this problem by attaching the labels to the boundary of a rectangle that contains all features. Then, each feature should be… (More)

- Michael A. Bekos, Michael Kaufmann, Katerina Potika, Antonios Symvonis
- Graph Drawing
- 2007

We consider the problem of drawing a set of simple paths along the edges of an embedded underlying graph G = (V, E), so that the total number of crossings among pairs of paths is minimized. This problem arises when drawing metro maps, where the embedding of G depicts the structure of the underlying network, the nodes of G correspond to train stations, an… (More)