Rolf Apweiler

Education

Research Focus

Rolf Apweiler is an EMBL Senior Scientist and Head of the EBI's Sequence Database group. This group, around 100 life and computer scientists, develops and maintains main public high-quality data resources and bioinformatics services like the EMBL nucleotide sequence database, the UniProt protein sequence database and the InterPro database of protein families, domains and functional sites. Medium scale projects comprise Gene Ontology (GO) annotation, IntEnz (enzyme nomenclature database), ChEBI (small molecules database), and Integr8 (genomes and proteomes web portal). The manually annotated data resources are complemented by well-evaluated automated systems to provide optimum coverage of knowledge space. Also, locally installable database and analysis systems for complex data types are developed, like UniProt-DAS, PRIDE and IntAct. The group is also actively involved in many international collaborations and initiatives like the HUPO Proteomics Standards Initiative (PSI). In addition, the group has been involved in research and development activities on alternative splicing. A computational pipeline has been developed that delineates alternative splice events and alternate splice patterns as well as generates automated annotation for various biological properties. A comprehensive database on alternative splicing (ASD) has been made available (which combines computationally predicted data and manually curated data), along with user-friendly interfaces, and a workbench of RNA splice analysis tools. Different resources on alternative splicing are being integrated and synchronized.

Publications

Patient, S., Wieser, D., Kleen, M., Kretschmann, E., Jesus Martin, M., Apweiler, R. (2008). UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics 24(10), 1321-2.
Côté, R.G., Jones, P., Martens, L., Apweiler, R., Hermjakob, H. (2008). The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Research 2008 May 8. [epub ahead of print]
Zhang, J., Li, X., Mueller, M., Wang, Y., Zong, C., Deng, N., Vondriska, T.M., Liem, D.A., Yang, J.I., Korge, P., Honda, H., Weiss, J.N., Apweiler, R., Ping, P. (2008). Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics 8(8), 1564-75.
Wu, C.H., Apweiler, R., Bairoch, A., Natale, D.A, Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Mazumder, R., O'Donovan, C., Redaschi, N., and Suzek, B. (2006). The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research 34, D187-D91.
Cochrane, G., Aldebert, P., Althorpe, N., Andersson, M., Baker, W., Baldwin, A., Bates, K., Bhattacharyya, S., Browne, P., Van Den Broek, A., Castro, M., Duggan, K., Eberhardt, R., Faruque, N., Gamble, J., Kanz, C., Kulikova, T., Lee, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., McHale, M., McWilliam, H., Mukherjee, G., Nardone, F., Pastor, M.P., Sobhany, S., Stoehr, P., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W., and Apweiler R. (2005). EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Research 34, D10-D15.
Orchard, S., Hermjakob, H., and Apweiler, R. (2005). Annotating the human proteome. Molecular and Cellular Proteomics 4, 435-440.
Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R. H., Apweiler, R., Cheung, K., Costello, C. E., Hermjakob, H., Huang, S., Julian, R. K., Kapp, E., McComb, M. E., Oliver, S. G., Omenn, G., Paton, N. W., Simpson, R., Smith, R., Taylor, C.F., Zhu, W., Aebersold, R. (2004). A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnology 22, 1459-1466.
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.