Alexander Schleiffer /Computational Biologist () Maria Novatchkova /Computational Biologist () Wolfgang Lugmayr /Scientific Software Architect ()
In case of general requests please contact the group via .
The Bioinformatics unit assists research groups in molecular biology-related fields, by providing sequence analysis services, scientific data mining, hardware and software infrastructure, and training in bioinformatics. For more information please also visit the Mendel Site.
Sequence Analysis
The IMP-IMBA Bioinformatics unit has its main expertise in the field of sequence analysis. Typical tasks include the functional and structural characterisation of proteins and genomic regions using methods such as pattern matching, complexity analysis and homology searches. As bioinformatics conclusions are a synthesis of results from multiple algorithms, we maintain and develop a set of specialised software tools to support this type of meta-analysis.
Large Scale Data Analysis
Figure 1 (Click to view legend)
Additional demands arise from the investigation of large functional genomics or high-throughput biological datasets. We engage in custom software and database development, and design computational and mathematical solutions that can cope with the higher load and memory requirements. To perform complex sequence analysis tasks we also maintain the IMP ANNOTATOR, a user-friendly web application and high-throughput protein annotation system. For heterogeneous computational tasks, we manage a computing cluster with a state-of-the-art processing system using batch and parallel computing environments.
Training
We provide hands-on training courses on the ANNOTATOR, where participants learn the basis and limitations of sequence analysis and data integration.
Selected Publications
2009
Agrelo, R., Souabni, A., Novatchkova, M., Haslinger, C., Leeb, M., Komnenovic, V., Kishimoto, H., Gresh, L., Kohwi-Shigematsu, T., Kenner, L., Wutz, A. (2009). SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells.
Dev Cell. 16(4):507-16
(abstract)
Cipak, L., Spirek, M., Novatchkova, M., Chen, Z., Rumpf, C., Lugmayr, W., Mechtler, K., Ammerer, G., Csaszar, E., Gregan, J. (2009). An improved strategy for tandem affinity purification-tagging of Schizosaccharomyces pombe genes.
Proteomics. 9(20):4825-8
(abstract)
Mummery-Widmer, JL., Yamazaki, M., Stoeger, T., Novatchkova, M., Bhalerao, S., Chen, D., Dietzl, G., Dickson, BJ., Knoblich, JA. (2009). Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi.
Nature. 458(7241):987-92
(abstract)
Ooi, HS., Kwo, CY., Wildpaner, M., Sirota, FL., Eisenhaber, B., Maurer-Stroh, S., Wong, WC., Schleiffer, A., Eisenhaber, F., Schneider, G. (2009). ANNIE: integrated de novo protein sequence annotation.
Nucleic Acids Res. 37(Web Server issue):W435-40
(abstract)
2008
Tomasi, T., Hakeda-Suzuki, S., Ohler, S., Schleiffer, A., Suzuki, T. (2008). The transmembrane protein Golden goal regulates R8 photoreceptor axon-axon and axon-target interactions.
Neuron. 57(5):691-704
(abstract)
