32 research outputs found
eXamine: a Cytoscape app for exploring annotated modules in networks
Background. Biological networks have growing importance for the
interpretation of high-throughput "omics" data. Statistical and combinatorial
methods allow to obtain mechanistic insights through the extraction of smaller
subnetwork modules. Further enrichment analyses provide set-based annotations
of these modules.
Results. We present eXamine, a set-oriented visual analysis approach for
annotated modules that displays set membership as contours on top of a
node-link layout. Our approach extends upon Self Organizing Maps to
simultaneously lay out nodes, links, and set contours.
Conclusions. We implemented eXamine as a freely available Cytoscape app.
Using eXamine we study a module that is activated by the virally-encoded
G-protein coupled receptor US28 and formulate a novel hypothesis about its
functioning
Colored Non-Crossing Euclidean Steiner Forest
Given a set of -colored points in the plane, we consider the problem of
finding trees such that each tree connects all points of one color class,
no two trees cross, and the total edge length of the trees is minimized. For
, this is the well-known Euclidean Steiner tree problem. For general ,
a -approximation algorithm is known, where is the
Steiner ratio.
We present a PTAS for , a -approximation algorithm
for , and two approximation algorithms for general~, with ratios
and
On Embeddability of Buses in Point Sets
Set membership of points in the plane can be visualized by connecting
corresponding points via graphical features, like paths, trees, polygons,
ellipses. In this paper we study the \emph{bus embeddability problem} (BEP):
given a set of colored points we ask whether there exists a planar realization
with one horizontal straight-line segment per color, called bus, such that all
points with the same color are connected with vertical line segments to their
bus. We present an ILP and an FPT algorithm for the general problem. For
restricted versions of this problem, such as when the relative order of buses
is predefined, or when a bus must be placed above all its points, we provide
efficient algorithms. We show that another restricted version of the problem
can be solved using 2-stack pushall sorting. On the negative side we prove the
NP-completeness of a special case of BEP.Comment: 19 pages, 9 figures, conference version at GD 201