:: Bioinformatics ::

Modern molecular biology requires mathematical models and efficient algorithms to interprete the mass of observations generated by current experimental techniques. This necessity has given birth to the new discipline of bioinformatics. No one can say today how far away we are from fully understanding even the most fundamental mechanisms of life, but it is clear that the quality of our bioinformatics resources determines the rate of progress along this road.

Bioinformatics can roughly be split in two branches:
Algorithmic Bioinformatics is concerned with new methods of data analysis, resulting in new or better models, algorithms and tools. This branch needs input from biology, but is mainly a computer science acticity with its typical cycle of algorithm development, implementation and evaluation.

Applied Bioinformatics is the actual interpretation of biological data with the tools developed in the algorithmic branch of the field. This requires close cooperation between biologists and bioinformaticians, in particular when novel experimental techniques or novel tools are involved.

Our group is engaged in both kinds of activities.

current projects

Arabidopsis miRNA targets 
Prediction and experimental validation of Arabidopsis microRNA targets

Bielefeld University BioInformatics Service 
The Bielefeld University Bioinformatics Server (BiBiServ) supports internet-based collaborative research and education in bioinformatics. It was established in 1996 and currently provides over 20 software tools, together with a repository of educational material.

BioDOM - the bioinformatics XML solution 
BioDOM is a JAVA library for converting native non-XML output from various bioinformatics tools to XML formats that can be validated against XML schemas.

Comparative PRE/TRE analysis 
Comparative analysis of Drosophila Polycomb/Trithorax Response Elements

EST Clustering 
Suffix array based clustering of EST and cDNA data

A system for interactive high throughput sequence analysis and (differential) comparative genomics.

Human miRNA targets 
Prediction and experimental validation of human microRNA targets

Consensus structure prediction for multiple RNA sequences

RNA secondary structure prediction based on abstract shapes

past projects

Large Scale Repeat Analysis requires extensive algorithmic support. The program GenAlyzer was designed to serve as a fundamental tool for repetitive DNA studies on a genomic as well as inter-genomic scale.

Helmholtz Open Bioinformatics Technology 
The HOBIT initiative is dedicated to form the core of a network linking bioinformatic centres together. It shall be understood as an initial organisational and technological platform for interconnection of bioinformatics activities. The aim of the network is to concatenate applications and resources in a uniform way so providing an efficient communication tier between for bioinformatics resource access.

Hypa - A system for the declarative description and efficient search of hybrid patterns in large genomic data sets.

Genome-wide prediction of Polycomb/Trithorax Response Elements in Drosophila melanogaster

Fast and effective prediction of microRNA/target duplexes

Prediction of Alternating RNA Secondary Structures

Prediction of RNA Secondary Structures including Pseudoknots

Fri Dec 19 10:54:56 CET 2014