Fabian Horn
Personal Data:
Country of Origin: Germany
Start of PhD: September 2009
Institution: HKI
PhD Project:
Prediction of Gene Regulatory Networks Involved in the Differentiation, Secondary Metabolism and
Cross Talk of Aspergillus nidulans
Supervisor(s):
R. Guthke (HKI)
Abstract:
Biological data is collected in many hundreds of different experiments where each consists of
thousands of data points. They are published and stored in several databases and scientific
jounals in different data formats and abstraction layers. The challenge for bioinformatics
is to gather, preprocess and model these data consistently. By the integration of the information
from several experiments, new scientific findings can be obtained with the help of methods
from systems biology and comparative analysis.
Aspergillus nidulans is a filamentous fungus which is able to form sexual spores through meiosis.
It is therefore used to research the eukaryotic cell biology. A.nidulans has been completely sequenced
and there has been great progress in elucidaton of the molecular regulation of the biosynthesis of secondary metabolites.
In this project there are two main methods which are to be applied to A.nidulans:
1. A new microarray probe design has already been developed and is currently applied
to investigated the transriptome under different environmental conditions.
To improve the quality of the data, published microarray data for A.nidulans can be
integrated and methods which mine gene expression across different experiments are to be developed and employed.
2. We are looking for the connection of transcriptome data with metabolome data.
Until now such relationships have only be analyzed for the primary metabolism, e.g.
in Escherichia coli. The project aims to adapt these existing methods for the specific
characteristics of secondary metabolite pathways. The methods should be applicable for
organisms like A.nidulans, where less prior knowledge is available.
Publications:
, Nutzmann HW, Schroeckh V, Guthke R, Hummert C (2011)
Optimization of a Microarray Probe Design Focusing on the
Minimization of Cross-Hybridization. Proc. International
Conference on Bioinformatics and Computational Biology
BIOCOMP'11, USA
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