Andreas Gerasch

University of Tuebingen | EKU Tübingen · Department of Computer Science

Motivation: Gene set analysis has revolutionized the interpretation of high-throughput transcriptomic data. Nowadays, with comprehensive studies that measure multiple -omics from the same sample, powerful tools for the integrative analysis of multi-omics datasets are required. Results: Here we present GeneTrail2, a web service allowing the integ...

Cancer is a large class of diseases that are characterized by a common set of features, known as the Hallmarks of Cancer. One of these hallmarks is the acquisition of genome instability and mutations. This, combined with high proliferation rates and failure of repair mechanisms, leads to clonal evolution as well as a high genotypic and phenotypic d...

Over the last decade, advances in high-throughput technologies have resulted in a flood of new biological data. Here, individual samples can extend up into terabyte size. While potential applications are broad, ranging from biotechnology to medical applications, the analysis of these datasets poses massive challenges. In order to make use of the pr...

The display of data related to graphical objects on a map is a well studied problem in cartography and several approaches have been published. Adapting the idea of boundary labeling using a focus region, we face the problem of emphasizing additional information and labels for objects within a focus region even when the region might be moving. We pr...

Static drawings of biological pathways are still an important research tool for biologists. Gerhard Michal created his seminal drawings of metabolic networks in the 1960s and thus defined canonical representations of some key pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides the most popular static drawings of biological network...

Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily...

Unlabelled: The deregulation of biochemical pathways plays a central role in many diseases like cancer or Parkinsons's disease. In silico tools for calculating these deregulated pathways may help to gain new insights into pathogenic mechanisms and may open novel avenues for therapy stratification in the sense of personalized medicine. Here, we pre...

Expression profiling provides new insights into regulatory and metabolic processes and in particular into pathogenic mechanisms associated with diseases. Besides genes, non-coding transcripts as microRNAs (miRNAs) gained increasing relevance in the last decade. To understand the regulatory processes of miRNAs on genes, integrative computer-aided ap...

Deregulation of cell signaling pathways plays a crucial role in the development of tumors. The identification of such pathways requires effective analysis tools that facilitate the interpretation of expression differences. Here, we present a novel and highly efficient method for identifying deregulated subnetworks in a regulatory network. Given a s...

In a proportional contact representation of a planar graph, each vertex is represented by a simple polygon with area proportional to a given weight, and edges are represented by adjacencies between the corresponding pairs of polygons. In this paper we first study proportional contact representations that use rectilinear polygons without wasted area...

Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis. Thus, a computational tool flexible enough to realize a wide variety of FBA algorithms and able to handle batch series of flux-balance optimizations...

Deregulated signaling cascades are known to play a crucial role in many pathogenic processes, among them are tumor initiation and progression. In the recent past, modern experimental techniques that allow for measuring the amount of mRNA transcripts of almost all known human genes in a tissue or even in a single cell have opened new avenues for stu...

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...

DDL Diagram of BNDB. The general structure of the database schema.

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying...

Recent years have seen an explosive growth in the amount of biochemical data available. Numerous databases have been established and are being used as an essential resource by biologists around the world. The sheer amount and heterogeneity of these data poses a major challenge: data integration and, based thereupon, the integrative analysis of thes...

Recent years have seen an explosive growth in the amount of biochemical data available. Numerous databases have been established and are being used as an essential resource by biologists around the world. The sheer amount and heterogeneity of these data poses a major challenge: data integration and, based thereupon, the integrative analysis of thes...

In most practical applications a certain aspect ratio for the layout of a graph is required or at least should be obeyed. This problem has been attacked for certain graph classes, especially for binary trees and also for directed graphs. Here, we introduce three generalized hv-layouts for ordered trees with arbitrary degree that keep the easy reada...