Description of organisation
Center for Biological Sequence Analysis (CBS, www.cbs.dtu.dk) headed by professor Søren Brunak, is part of the Dept. of Systems Biology at DTU. CBS is one of the largest academic bioinformatics and systems biology centers in Europe with more than 110 employees. CBS has strong expertise in network biology and in data integration, including human variation data as well as data on drugs, environmental chemicals and nutrients. The center has created many original approaches, including a powerful phenome interactome approach combining protein protein interaction data and text mining of clinical disease phenotype descriptions such as electronic patient records possible.
Previous experience
CBS has gained a reputation in the field of bioinformatics and systems biology as a highly dynamic and collaborative group, establishing itself among the internationally leading groups. Within the last 5 years the center has participated in more than 30 projects funded by the EU and the NIH, and many more over its 20 years of existence. Thus the level of international collaboration is very high. In addition to collaborative projects financed by joint grants, many other collaboration projects have been established with groups in Europe, North and South America, Africa, Australia and Asia.
Profile of staff members
Prof. Brunak is the founding Director of the Center for Biological Sequence Analysis, which was formed in 1993 as a multi disciplinary research group of molecular biologists, biochemists, medical doctors, physicists, and computer scientists. Søren Brunak has been highly active within biological data integration, where machine learning techniques often have been used to integrate predicted or experimentally established functional genome and proteome annotation. His current research does combine molecular level systems biology and healthcare sector data such as electronic patient records and biobank questionnaires. The aim is to group and stratify patients not only from their genotype, but also phenotypically based on the clinical descriptions in the medical records. An additional focus area is now adverse drug reactions.
Prof. Søren Brunak, Dr. Phil, PhD has published 185+ peer reviewed papers, and has around 23,500 ISI citations, h factor 61. Brunak is a leading expert in bioinformatics and systems biology through invention and introduction of new computational strategies for analysis of biological data for use in molecular biology, medicine and biotechnology. Brunak has served on a large number of scientific advisory boards and funding bodies, including; the Bioinformatics Advisory Committee at the European Bioinformatics Institute; the "Molecules, Genes and Cells Funding Committee" at the Wellcome Trust, and the Scientific Council at the Institut Pasteur, Paris. Prof Brunak has been EMBO member since 2009.
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Five recent publications relevant to the project
Mining electronic health records: towards better research applications and clinical care. Jensen PB, Jensen LJ, Brunak S. Nat Rev Genet. 13, 395 405, 2012.
SignalP 4.0: discriminating signal peptides from transmembrane regions, Petersen TN, Brunak S, von Heijne G, Nielsen H. Nature Methods, 8, 785 6, 2011.
Meta analysis of heterogeneous data sources for genome scale identification of risk genes in complex phenotypes. Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S. Genet Epidemiol. 2011 Apr 11.
A large scale analysis of tissue specific pathology and gene expression of human disease genes and complexes. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S. Proc Natl Acad Sci U S A. 105, 20870 5, 2008.
A human phneome interactome network of protein complexes implicated in genetic disorders, K. Lage, E.O. Karlberg, Z.M. Størling, P.I. Olason, A.G. Pedersen, O. Rigina, Z. Tümer, Y. Moreau, F. Pociot, N. Tommerup, and S. Brunak. Nature Biotech., 25, 309 16, 2007.
