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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)

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)

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)

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)

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)

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)

We introduce the concept of subdivision drawings of hyper-graphs. In a subdivision drawing each vertex corresponds uniquely to a face of a planar subdivision and, for each hyperedge, the union of the faces corresponding to the vertices incident to that hyperedge is connected. Vertex-based Venn diagrams and concrete Euler diagrams are both subdivision… (More)

In this paper, we present algorithms to produce orthogonal drawings of arbitrary graphs. As opposed to most known algorithms, we do not restrict ourselves to graphs with maximum degree 4. The best previous result gave an (m ? 1) (m 2 + 1)-grid for graphs with n nodes and m edges. We present algorithms for two scenarios. In the static scenario, the graph is… (More)