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2003 News Archive


Interview in The Times with CBS researchers on the development of a Sars vaccine (December 2003)
In collaboration with Institute of Medical Microbiology and Immunology (IMMI), University of Copenhagen, researchers at CBS have developed a sophisticated computer program that tries to mimic the human body?s immune system when a pathogen - like Sars - invades. Through the examination of the Sars virus and the computer program's prediction of how the immune system and the virus interact, the researchers at CBS and IMMI have pinpointed certain portions of the Sars genome that might make a good vaccine target.
Read more in Anjana Ahuja excellent article:  The hunt is on for a Sars vaccine

For more information, please contact  Søren Brunak
or visit the homepage of the  CBS Immunological Bioinformatics research group


Two new CBS courses in Spring 2004 (November 2003)
In the Spring semester 2004, CBS offers two new courses: The courses will be taught in English, and is targeted for students on their 5th semester or above as well as PhD-students.

For more information about these and other CBS courses, visit the CBS courses page


Steen Knudsen appointed full professor at CBS (November, 2003)
Cand.polyt, Ph.D. Steen Knudsen took up the appointment as professor of Bioinformatics in October 2003 at the Center for Biological Sequence Analysis, Tehnical University of Denmark.

Steen Knudsen has been employed at CBS since 1996. Aside from being the deputy director of CBS, Steen Knudsen leads CBS's Gene Finding and Expression research group conducting research into DNA microarray design, probe selection, data normalization, statistical analysis and functional annotation.
The professorship will focus on developing methods within DNA microarray analysis, DNA array experiments, reconstruction af regulatory networks and interpretation of diverse data domains including gene-databases, publication databases and gene-ekspressions data.

Steen Knudsen has an M.Sc. in Engineering from Technical University of Denmark, 1987 and a Ph.D. in Microbiology from University of Copenhagen 1990. After his Ph.D. he worked as a post.doc at Biostatistics Dept., Harvard University, Boston, MA, USA, 1990-1992 and as assistant professor at University of West Florida, USA, 1992-1996.

Steen Knudsen has published articles in many international peer-review journals and is also author of the book, A Biologist's Guide to analysis of DNA microarray Data, (Wiley 2002).
He is actively involved in DTU's collaboration with external research groups, both national and international.
Steen Knudsen is 42 years old, lives in Birker?d with his wife Tarja and her two children.

For more information about Steen Knudsen, call +45 45 25 24 80 or visit his Homepage


BioSapiens - First steps towards a European Virtual Institute for Genome Annotation (August, 2003)
CBS is partner in the BioSapiens proposal where the co-ordinating institution European Bioinformatics Institute (EBI), following a successful grant review, has been invited to enter contract negotiations with the Commission of the European Union to discuss funding for a new pan-European bioinformatics initiative.
If negotiations are successful, up to 12,000,000 Euro could be made available for a network that will address the current fragmentation of European bioinformatics by creating a virtual institute that will organize a European school for bioinformatics.

21 institutes and organisations in 14 countries put together the BioSapiens proposal for an NoE in bioinformatics in response to the EU's first call for proposals for NoEs in the priority area of 'life sciences, genomics and biotechnology for health'. Having received a favourable evaluation by the review panel, BioSapiens is one of the first NoE selected to enter into contract negotiations with the EU, and is the first within its thematic priority area. This invitation does not in any way represent a formal commitment from the EU to fund BioSapiens and, if successful, the proposal is likely to evolve on its way through contract negotiations. Nevertheless, this is an important step en route to the coordination of bioinformatics research in Europe.

'BioSapiens has leapt the first hurdle because the proposal captures the most important objectives of an NoE', explains Janet Thornton, Director of EBI and coordinator the BioSapiens proposal along with a steering committee comprising S?ren Brunak (CBS), Kerstin Nyberg (EBI), Anna Tramontano (University of Rome "La Sapienza") and Alfonso Valencia (Consejo Superior de Investigaciones Cient?ficas, Madrid). 'Firstly, it will coordinate and focus excellent research in bioinformatics, by creating a Virtual Institute for Genome Annotation. (Annotation is the process by which features of the genes or proteins stored in a database are extracted from other sources, defined and interpreted.) Secondly, The Institute will establish a permanent European School of Bioinformatics, to train bioinformaticians and to encourage best practice in the exploitation of genome annotation data for biologists. Thirdly, it will facilitate the exploitation of biological information to address important social objectives, including improved health-care, better drugs, new vaccines, personalized medicine, and improved understanding of diet and health. By understanding how the normal human organism functions and develops we can improve diet, behaviour and environment to optimize quality of life for all,' she adds.

CBS is involved in other FP6 consortia entering into contract negotiations with the EU.

For more information, please contact  Søren Brunak


CBS Researchers part of team behind the development of potential SARS vaccine (June, 2003)
A new method for rapidly identifying and validating antigens has been developed in a collaboration between the American biotech company SIGA Technologies, Center for Biological Sequence Analysis (CBS), Technical University of Denmark and Institute of Medical Microbiology and Immunology (IMMI), University of Copenhagen. The research is coordinated by CBS researchers Ole Lund and Morten Nielsen with the participation of research teams headed by Søren Brunak, CBS and Søren Buus, IMMI. The partners have developed computational and experimental methods that incorporate knowledge of various aspects of the human immune system response, to predict and confirm which antigens will be effective for a range of human population variants, particularly for organisms with a high mutation rate.

From the moment the Corona-virus was identified, the groups needed 36 hours to identify a number of potential SARS-epitopes using the computer methods. The predictions have now been tested experimentally, and a validated set has been identified which is likely to be effective for a range of human populations.

A patent application covering the new proprietary method and parts of the SARS vaccine has already been filed in Denmark, and the experimental work on the design of a SARS vaccine is currently underway.
Susan Burgess, president of SIGA Technologies, says the company potentially might be ready to study the vaccine in a so-called safety test in about six months. It is however too early for speculations on when a SARS vaccine can be marketed.

Reference:
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations, M. Nielsen, C. Lundegaard, P. Worning, S.L. Lauemøller, K. Lamberth, S. Buus, S. Brunak, O. Lund, Protein Science, 12, 1007-17, 2003.
PMID: 12717023 (full text version available)

For more information, please contact  Søren Brunak
or visit the homepage of the  CBS Immunological Bioinformatics research group




2-year Master of Science programme in Bioinformatics opens in September 2003
The Master of Science programme in Bionformatics is open to international as well as Danish students. All courses are in english and tuition is free. The aim is to educate skilled graduates to a high level in this multidisciplinary field. Applicants should hold a B.Sc., M.Sc. or Masters degree.

Deadline for applications was:   March 17, 2003

More information and detailed outline of programme


CBS co-authored publications number 2 and 3 on most cited list from December 2002
In December 2002, the Danish, weekly journal Mandag Morgen published a list of the 50 most cited articles (citations from 2000 and 2001) for papers published in the period 1994-2001 in international, peer-reviewed journals, where one or more authors came from a Danish research organisation.
Three articles from CBS were on that list, two of them in the top 3.
  • #2 with 634 citations:
    Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites,
    H. Nielsen, J. Engelbrecht, S. Brunak and G. von Heijne, Protein Eng., 10, 1-6, 1997.
  • #3 with 507 citations:
    Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence,
    S.T. Cole et al (A. Krogh), Nature, 393, 537-544, 1998.
  • #30 with 123 citations:
    Predicting subcellular localization of proteins based on their N-terminal amino acid sequence,
    O. Emmanuelsson, H. Nielsen, S. Brunak and G. von Heijne, J. Mol. Biol., 300, 1005-1016, 2000.
Full list of CBS publications from 1993 to today


Center director, professor Søren Brunak appointed doctor philosophiae honoris causa at Stockholm University
At a ceremony held at the town hall in Stockholm, Sweden, in September 2002 center director, professor Søren Brunak was appointed doctor philosophiae honoris causa at the Natural Science Faculty, Stockholm University.