Research Focus
We are a computational biology group that is interested in the prediction of function and the understanding of molecular evolution. In this context, the identification and functional characterisation of alternative splicing is an important key to the understanding of functional complexity.
We study a number of topics around alternative splicing since the end of the 90s. For example, using comparative genome analysis, we were among the first to identify support for the notion of a considerable number of human alternative splice variants. We also try to trace the evolution of alternative splicing using several evidence types.
Finally, we study functional consequences of alternative splicing in proteins and protein networks as well as at the level of tissue expression. We have applied literature mining to capture knowledge on alternative splicing and have developed visualisation tools to represent and compare complex splice events in different organisms.
Publications
- Soldà, G., Suyama, M., Pelucchi, P., Boi, S., Guffanti, A., Rizzi, E., Bork, P., Tenchini, M.L., Ciccarelli, F.D. (2008). Non-random retention of protein-coding overlapping genes in Metazoa. BMC Genomics 9, 174.
- Harrington, E.D., Jensen, L.J., Bork, P. (2008). Predicting biological networks from genomic data. FEBS Letters 582(8), 1251-8. PMID: 18294967. [PubMed - in process]
- Kuhn, M., Campillos, M., González, P., Jensen, L.J., Bork, P. (2008). Large-scale prediction of drug-target relationships. FEBS Letters 582(8), 1283-90. PMID: 18291108. [PubMed - in process]
- Letunic, I., Yamada, T., Kanehisa, M., Bork, P. (2008). iPath: interactive exploration of biochemical pathways and networks. Trends in Biochemical Sciences 33(3), 101-3. PMID: 18276143. [PubMed - in process]
- Harrington, E.D., Boue, S., Valcarcel, J., Reich, J.G., and Bork, P. (2004). Estimating rates of alternative splicing in mammals and invertebrates. Nature Genetics 36, 916-917.
- Kriventseva, E.V., Koch, I., Apweiler, R., Vingron, M., Bork, P., Gelfand, M.S. and Sunyaev, S (2003). Increase of functional diversity by alternative splicing. Trends in Genetics 19, 124-128.
- Brett, D., Popisil, H., Valcarcel, J., Reich, J. and Bork, P. (2002). Alternative splicing and genome complexity. Nature Genetics 30, 29-30.
- Brett, D., Hanke, J. Lehmann, G., Haase, S., Delbruck, S., Krueger, S, Reich, J.-G. and Bork, P., (2000). EST comparison indicates 38% of human mRNAs contain alternative splice forms. FEBS Letters 474, 83-86.
- Hanke, J., Zastrow, I., Aydin, A., Lehmann, G., Luft, S, Reich, J.G. and Bork, P. (1999). Alternative splicing in human genes: More the rule than the exception? Trends in Genetics 15, 389-390.
Key lab techniques: Computational Biology tools
Lab contact: Eoghan Harrington: harringt@embl.de
Lab website: www.bork.embl.de
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