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2004 News Archive

First bioinformaticians in space?   (December 20, 2004)
Even though Hanne Jarmer, Martin Miller and Anders Fausbøll are content with their work, they are nevertheless trying to get as far away from CBS as possible. The three CBS researchers are among the 266 applicants aspirering to be one of the first Danish astronauts. Graduate engineer, PhD Hanne Jarmer is one out of only 37 women candidates.

Read more (in Danish)
Link to live feature in the Danish TV News, Sunday, December 19

CBS receives 5 year grant from the National Institute of Health (NIH)   (December 16, 2004)
Press release (in Danish)
Together with research groups at MAI and IMMI, University of Copenhagen, associate professor Ole Lund (PI), professor Søren Brunak and the rest of the CBS immunological bioinformatics group have received a US$3,751,185 grant (DKK 22 millions) over 5 years under the Large Scale Antibody and T Cell Epitope Discovery Program (RFP- NIH-NIAID-DAIT-04-39) The goal of the programme is:
To establish and support several highly interactive, multi-disciplinary teams focused on large-scale discovery of novel antibody (B cell) and/or T cell epitopes, including potential Category A-C agents of bioterrorism. Also to develop novel or improved high-throughput screening methods for antibody and/or T cell epitope identification.
Infected cells are recognized and killed by the immune system when they display fragments of the infecting agent, called epitopes, on the surface of the cell. Knowledge of epitopes can be used to design vaccines that protect against infection. In the project, improved methods for prediction of cytotoxic T cell (CTL) epitopes will be developed. The methods will then be used to scan 15 different microorganisms from the NIAID A-C list for epitopes. Many of these microorganisms cause major health problems in the world, as for example Mycobacterium tuberculosis which WHO estimates killed 1.5 million people in 2002 or Influenza which killed 20 million people during the 1918-1919 pandemic. Others are emerging vira such as Ebola, Marburg or West Nile Virus which may become major health threats.

For each of the 15 pathogens we will predict the top 15 CTL epitopes for each of 14 different HLA alleles. These 3150 peptides will be produced synthetically and their binding affinity to the relevant HLA molecules will be tested. For 3 selected pathogens: Influenza, Smallpox vaccine and tuberculosis vaccine (BCG) we will test which of these peptides cytotoxic T cells from blood donors can react to.

The project is a collaboration between the groups of Ole Lund (PI) and S?ren Brunak from CBS at the Technical University of Denmark who will do the bioinformatics part of the project, and the groups of S?ren Buus, IMMI and Mogens Claesson, MAI, both from the University of Copenhagen which will test peptide binding and CTL response, respectively.

List of pathogens studied in the project
PathogenHLA bindingCTL
Variola major (smallpox) vaccine strainXX
Yersinia pestisX
Francisella tularensis (tularemia)X
Lymphocytic choriomeningitis virus (LCM)X
Lassa FeverX
Hantaan virus (Korean hemorrhagic fever virus)X
Rift Valley FeverX
Multi-drug resistant TB (BCG vaccine)XX
Yellow feverX
Typhys fever (Rickettsia prowazekii)X
West Nile VirusX

Press release (in Danish)
More information about NIH/NIAID's Biodefense initiative
More information about the CBS immunological bioinformatics group
More information about NIAID

Chemoinformatics at CBS (December 15, 2004)
Associate professor Svava Ósk Jónsdottir starts chemoinformatics research group at CBS. The group will be funded by grants from the Danish Technical Research Council (STVF) and the NABIIT initiative (Programme committee for nano science and technology, biotechnology and IT).
The chemoinformatics group at CBS will have extensive collaboration with professor Flemming Steen Jørgensen, the Danish Pharmaceutical University, Copenhagen, professor, MD Tudor Oprea, Division of Biocomputing, University of New Mexico School of Medicine, and several biotech- and medico companies in the Medicon Valley region.

Read more

CBS partner in EU FP6 Network of Excellence on Biosimulation - BIOSIM (December 2004)
BIOSIM - A new Tool in Drug Development, coordinated by professor Erik Mosekilde, Department of Physics, Technical University of Denmark, brings together the scientific excellence of 25 leading European research institutions, nine SME companies, Novo Nordisk, and the public Medicines Agencies in Denmark, Spain, the Netherlands, and Sweden. The project will be funded with a total of 10.7 Million Euros for five years within the 6th Framework Programme of the European Commission.
Biosimulation is a rather new discipline that apply many of the advanced methods within chaos research to describe and explore biological systems. The BIOSIM network will strenghten and further the development of new and better drugs in Europe. In many cases, the use of experimental animals and experiments on human beings that are usually part of drug development, can be reduced or simply avoided, as still more advanced computermodels for simulation of biological systems are developed.

Read more (in Danish)

CBS website rated Excellent by Genetic Engineering News   -   Strong points: Useful Analysis   Weak points: None    (December 2004)
In a recent volume of Genetic Engineering News (vol 24 (20), 2004), the CBS website was reviewed and received the following assessment from Kevin Ahern, editor of GEN's On the Web column:
...a very attractively designed collection of pages to show off the work and data of (CBS's) 45 scientists....The analyses are the best, spanning whole genome analysis, gene finding, splice site analysis, promotor identification, microarray analyses, protein sorting (subsequence identification), and post-translational modification sites, among others. This is a very useful collection, folks! Indeed, if I were working with anything from new gene sequences to new genomic sequences, I'd check this site out...

CBS to host Danish Hightechnology Network within Bioinformatics (November, 2004)
Together with five academic partners and 15 biotech- and medico companies, CBS has received a DKK 4 million grant from the Danish Ministry for Science, Technology and Innovation for a hightechnology network within bioinformatics. The purpose of the network is to further the collaboration between academia and industry in a more formal setting.
The bioinformatics network will create an environment, actual as well as virtual, where the network partners can meet, develop and exchange knowledge and ideas.
The network will focus on research and methods for interpretation of biotechnological data as well as development of techniques for simulation and modelling.

Read more (in Danish)

Lord Sainsbury visits CBS and DTU (October 2004)
On October 6, the British Minister for Science and Innovation, Lord Sainsbury of Turville, visited DTU. At a meeting held at CBS, the minister met with research group leaders and PhD students from BioCentrum-DTU with the purpose of initiating a dialogue between the UK and Denmark about innovative collaborations within biotechnology.

Read more (in Danish)
More Information about Lord Sainsbury

CBS researcher part of biomedical research team to receive funding from the National Institute of Health (NIH), USA (April 2004)
Together with a research group headed by professor, Søren Buus at Institute of Medical Microbiology and Immunology (IMMI), University of Copenhagen, CBS' Immunological Bioinformatics group has won an international invitation for tenders for a biomedical research project. The researchers at DTU and University of Copenhagen will use their expertise within immunology and bioinformatics to compile a database of vaccine candidates that will be able to combat pathogens like SARS and other life threatening vira.

Read more (in Danish)

CBS partner in the Integrated Project INTERACTION PROTEOME - the largest EU-funded project in the field of proteomics to date (March, 2004)
Interaction Proteome, coordinated by the Max Planck Institute for Biochemisty in Martinsried, Germany, brings together the scientific excellence of eleven leading European research institutions and companies. The project will be funded with a total of 12 Million Euros for five years within the 6th Framework Programme of the European Commission to develop novel technologies for proteomics research.

More information about Interaction Proteome
Interaction Proteome Homepage

CBS first in the world to acquire a geniom?one 'time machine' from Febit AG (February 24, 2004)
geniom?one from the German biotech company Febit AG is fully automatic, single benchtop instrument for producing DNA chips. Previously, producing a new DNA chip took between 3 and 6 months. With geniom?one a new chip can be made over night, which have given rise to the nick name 'time machine'. DNA chips are widely used within biological and medical research to locate gene mutations and for measuring the level of activity of all genes at a given time within a human cell.

"The geniom?one technique opens a whole range of new perspectives within bio-medical research", says professor Steen Knudsen, CBS, "We will now be able to develop new, much faster tests for cancer diagnostics and other related diseases."
One of the areas that will benefit from the new chip technology is an already existing project on improving the methods for treatment of childhood leukemia done in collaboration with Rigshospitalet, Copenhagen.
"With DNA chips we will be able to see what is going on in the sick cells in the bone marrow of the individual patients. This will enable us to tailor the treatment to the individual patient", says Steen Knudsen.

The geniom?one is funded by grants from the Danish Research Counsils for the Natural and for the Technical Sciences. CBS are already offering a course in DNA Microarray Chip Analysis and will shortly be offering courses in using the equipment within biological and medical research activities.

For more information, contact professor Steen Knudsen

BioSapiens - European Virtual Institute for Genome Annotation receives 12 million Euro (January 2004)
CBS is one of 24 bioinformatics groups based in 14 countries throughout Europe that has been awarded a total of 12,000,000 Euro by the Commission of the European Union to create a pan-European BioSapiens Network of Excellence in Bioinformatics. The network aims to address the current fragmentation of European bioinformatics by creating a virtual research institute and by organizing a European school for training in bioinformatics.

BioSapiens is coordinated by a steering committee comprising Janet Thornton (chair), S?ren Brunak (Technical University of Denmark), Anna Tramontano (University of Rome "La Sapienza") and Alfonso Valencia (Consejo Superior de Investigaciones Cientificas, Madrid), and a project manager, Kerstin Nyberg (EBI).

Full length article about BioSapiens
BioSapiens Homepage

EU press release about BioSapiens
Link to interview (in Danish) in BiotechDenmark with Søren Brunak
Previous news item about BioSapiens

Former CBS PhD student Lars Juhl Jensen receives the Lundbeck Foundation Talent Prize, 2003 (January 2004)
At a reception at the Lundbeck Foundation in Hellerup, Denmark on January 14, 2004 graduate engineer, PhD Lars Juhl Jensen received the Lundbeck Foundation Talent Prize 2003. The prize is awarded annually to three younger researcher who have shown outstan ding research results within medicin or the natural sciences.
Lars Juhl Jensen was nominated by his former supervisor, professor Søren Brunak, CBS.

Lars Juhl Jensen is currently employed as a postdoctoral fellow at EMBL - European Molecular Biology Laboratory in Heidelberg, Germany.

More information about the Lundbeck Foundation