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News
For download: THE CBS MAP - electronic version of the new CBS folder. Center Director, professor Søren Brunak new EMBO member (October 19, 2009) The European Molecular Biology Organization (EMBO) announced on October 19, 2009 the election of 66 leading life scientists to its membership. The latest scientists to join the group - including professor Søren Brunak - come from 16 different countries and represent a broad cross-section of researchers from all fields of molecular biology, ranging from evolutionary to computational biology, neuroscience and plant science. For more information, contact professor Søren Brunak Press Release Center Director, professor Søren Brunak awarded The Grundfos Prize 2009 (September 29, 2009) At an award ceremony at Grundfos, Monday, September 29, Søren Brunak was awarded The Grundfos Prize 2009 in the amount of DKK 1 million. Søren Brunak receives the award for his important and ground breaking research within systems biology and bioinformatics which forms the basis of treating serious diseases such as cancer, Alzheimer's and HIV. The Grundfos Prize was established by the Poul Due Jensen Foundation in 2001. Its purpose is to promote, acknowledge and support national and international research in innovative and foresighted solutions useful to the community within the engineering and scientific area. The jury consists of Niels Due Jensen, Grundfos Group Chairman, Lars Kolind, Director, Chairman of the Board of Directors, Sven Caspersen, Vice-chancellor at Aalborg University, Vice Rector, Ms. Nina Smith, Aarhus University, and Preben Terndrup Pedersen, Professor at the Technical University of Denmark. For more information, contact professor Søren Brunak Press Release (in Danish) DTU News (in Danish) CBS researchers winner of machine learning in immunology (MLI) competition (September 17, 2009) On Thursday, September 17, 2009, the Immunological Bioinformatics group from Center for Biological Sequence Analysis at DTU Systems Biology won the machine learning in immunology (MLI) competion. The competition was run as an open international contest which was concluded at a special workshop as a part of the ICANN 2009 conference on Cyprus on "Combining machine learning, instrumentation, and immunology to enhance vaccine development". The aim of the competition was to identify machine learning methods that will improve upon currently available tools for prediction of peptide binding to MHC molecules. The target of the competion was to predict 9- and 10-mer peptide binding to a subset of 3 HLA class I molecules. The group participated with 4 prediction systems which have been developed in a concerted effort within the group. Three of these predictors were awarded as being best for one or more alleles, submitted by Associate professor Morten Nielsen, Associate professor Claus Lundegaard, and Professor Ole Lund, respectively, and the consensus method of the three systems was taking the prize as the overall best performing method. The prize of EUR 1,000 was received by Claus Lundegaard, who represented the group at the workshop as an invited speaker. The proceedings of the competition will be published in a special issue of the international "Journal of Immunological Methods". For more information, contact Claus Lundegaard Read more about the ICANN 2009 Workshop It's good to be chimp-like (July 11, 2008) 
Foto: Malene Thyssen A research collaboration between the Center for Biological Sequence Analysis, Department of Systems Biology, DTU and the Department of Theoretical Biology, Utrecht University, has shown that humans with chimpanzee alike immune system molecules tend to progress to AIDS more slowly. In humans, the immunodeficiency virus HIV-1 causes the development of AIDS. How long a patient can fight the virus and postpone the onset of AIDS depends on many factors, among those the so-called major histocompatibility complex (MHC) molecules. These molecules are present on the surface of most cells, where they display fractions of the proteins that are produced inside the cell. In this way, they allow the immune system to get a glimpse of what is going on in the cell and detect if a cell is infected and has to be killed. The diversity of these molecules is extremely high and differs between individuals. Different molecules have different binding specificities, which means they present different protein fractions on the cell surface. In humans, the MHC molecules are called human leukocyte antigen (HLA). Certain HLA molecules (e.g. HLA-B*5703) have been associated with a slow progression to AIDS. Other HLAs (e.g. HLA-B*1801) have been associated with faster progression to AIDS. In this way, we can say that some HLA molecules are protective during HIV-1 infection, while other HLA molecules are unfavorable. A close relative of us humans, the chimpanzee, is also susceptible to infection by HIV-1 and SIVcpz, the chimpanzee-equivalent of HIV-1. Chimpanzees, however, even though they can be infected, are resistant to the development of AIDS. It has been detected that chimpanzees show a lower diversity of MHC molecules than expected. This has been assumed to have been caused by a widespread viral infection, wiping out all those chimpanzees that did not carry the right MHC molecules to cope with the viral infection. The virus that caused this bottleneck for the chimpanzee population was suggested to be a common ancestor of the modern viruses SIVcpz and HIV-1. This would imply that all or at least the most common MHC molecules of chimpanzee are protective during immunodeficiency virus infection. The natural question to ask is therefore if these chimpanzee molecules share common features with those HLA molecules that are protective in humans? In our work, we used a computational, neural-network based method to predict the binding specificity of all available human and chimpanzee MHC molecules. Based on the predicted binding specificities, we then calculated the similarity between all HLA molecules and chimpanzee molecules and compared the different groups of HLA molecules with respect to their similarity to chimpanzee. It turned out that protective HLA molecules are significantly more similar to chimpanzees than unfavorable HLA molecules, meaning that protective HLA molecules and chimpanzee molecules present similar fractions of HIV-1 proteins on the cell surface of infected cells, which allows the immune system to recognize and kill these cells. In other words, this suggests that the closer the binding specificities of an HIV infected person's MHC molecules resemble those of chimpanzee, the better the chances of this person of having a slow progression to AIDS. The results of this work also show that pathogens may have an influence on the evolution of their host. In the case of chimpanzees, this resulted in the selection of the most protective MHC molecules. First signs of a similar development in humans have been observed in Southern African populations with a high incidence of HIV-1 infection, where protective HLA molecules show tendencies to become more prevalent in future generations. The work was recently published in the international journal AIDS (AIDS. 2008 Jul 11;22(11):1299-303.). "Official Journal of the International AIDS Society" (AIDS) PhD student at CBS receives Chinese Government Award (June 11, 2008) At a ceremony in the Chinese Embassy ambassador Xie Hangsheng awarded PhD Student Long Zhang with the 2007 Chinese Government Award for Outstanding Self-financed Students Abroad and $5000. In his PhD study, which is mainly funded by the Technical University of Denmark, Long Zhang researches the Enzymatic Production of Ceramide from Sphingomyelin. Ceramide plays a major role in maintaining the water-retaining properties of the epidermis. Ceramide can be used in hair and skin care products. Many ceramide-containing products have already been introduced to the cosmetic market, as well as treatments for patients with skin diseases such as atopic dermatitis. These products have excellent effects, thus there is large commercial potential in ceramides for the cosmetic and pharmaceutical industries. However, chemical synthesis of specific ceramide structures is a costly and time consuming process; therefore, the development of alternative cost-efficient, high yield production methods is of great interest. Together with his supervisors Lars I. Hellgren and Xuebing Xu, Long Zhang attempts to perform a systematic study on the production of ceramide through enzymatic hydrolysis of sphingomyelin. I am very happy and excited to receive this award. The significant influence of lipids on human health and the high potential of lipids in many applications attracted me in the research area of lipid technology. I believe that modern biotechnology can be applied to improve the production process of ceramide, thus decreasing its price in the long run, which will be to the benefit of consumers and patients in the future, Long Zhang says. Long Zhang holds a Master's degree in Biotechnology from the Department of Systems Biology at the Technical University of Denmark with the thesis Optimization of Enzymatic Modification of Sphingomyelin, and he expects to complete his PhD project at the Center for Biological Sequence Analysis at the Technical University of Denmark in August 2008. For more information, contact PhD student Long Zhang Article in Nature Biotechnology (May 10, 2007) New research is published in this week's issue of Nature Biotechnology, which describes a method of increasing coverage of the Drosophila melanogaster proteome by iteration between experiments and bioinformatical analysis. Read more here: Article in Nature Biotechnology Pubmed For more information, contact Professor Søren Brunak Article in Nature Biotechnology (March 13, 2007) New research, published in this week's issue of Nature Biotechnology, shows that genes involved in the development of inherited diseases, such as Alzheimer's disease, work together in protein complexes. This knowledge has been used to predict new genes involved in hundreds of diseases such as sclerosis and type 2-diabetes. Read more here: Danish Press release Article in Nature Biotechnology Pubmed For more information, contact Professor Søren Brunak New Center for Disease Systems Biology (March 13, 2007) The VILLUM KANN RASMUSSEN FOUNDATION supports the establishment of a new Center for Disease Systems Biology. Participants in this center are Professor Søren Brunak from Center for Biological Sequence Analysis at BioCentrum-DTU and Professor Anders Juul from the Juliane Marie Center at Rigshospitalet (Copenhagen University Hospital). The center was founded on March 1, 2007 with a grant of DKK 24,200,000 over 4 years, and Professor Søren Brunak is the center director. The center is a VILLUM KANN RASMUSSEN Centre of Excellence, and its overall purpose is to create an interdisciplinary platform for system biological analysis of genetic networks behind diseases focusing on fertility, growth and reproduction. For more information, contact Professor Søren Brunak Read more about the VILLUM KANN RASMUSSEN FOUNDATION CBS researcher awarded the Danish Independent Research Council's Young Researcher's Award (25 January, 2007) On 25 January 2007, postdoc researcher and doctor in chemical engineering Irene Kouskoumvekaki from Center for Biological Sequence Analysis at BioCentrum-DTU receives the Danish Independent Research Council's Young Researcher's Award. The award is given as a supplement to the granted project by the Danish Research Council for Technology and Production Sciences on reintegration of natural drugs in the search for novel drugs by chemoinformatics and chemogenomics tools. The award is of DKK 200,000 and is presented by Helge Sander, the Minister for Science, Technology and Innovation. Irene Kouskoumvekaki is awarded the prize, because her research activities so far have contributed to the development and application of chemical modeling, and because her proposed project is expected to provide new insight into natural product chemistry and assist the pharmaceutical companies in the search for new drugs. The award will give Irene Kouskoumvekaki the opportunity to arrange a short external stay at a research group of a university outside Denmark in order to participate as a guest researcher in their curriculum. Furthermore, it will offer her extra flexibility in selecting international conferences and workshops, which are ideal meeting points for exchanging and evaluating novel ideas with top researchers within her field. For more information, contact Irene Kouskoumvekaki Read more about the Danish Independent Research Council's Young Researcher's Award CBS has, together with TIGR and NCL, mapped the genes of the parasite that causes trichomoniasis, the world's most common non-viral sexually transmitted infections (January 12, 2007 issue of Science) Full of surprises, Trichomonas vaginalis has 10 times the genetic material of its closest microbial peers and more confirmed genes (26.000) than its human host. With the potential for up to 34,000 yet-to-be confirmed genes, the eukaryote has the biggest genome of any single-celled organism yet sequenced. Its genome is also the most repetitive ever sequenced, more than 65 percent of the genetic information is a repeat, and those copies are very close. More than 800 genes code for surface proteins that likely enable Trichomonas vaginalis to adhere to cells in the urinary and genital tracts and cause infection. Over 150 instances, where bacterial genes may have transferred into the parasite's genome, suggest that bacteria may have influenced the development of the parasite's metabolism. It is not entirely clear why the genome is so large and repetitive, the current theory is that the parasite evolved over time, previously inhabiting the intestine and later moving to the urogenital tract, which resulted in increased cell size and, subsequently, a considerably expanded genome. For more information, contact Thomas Sicheritz-Pont?n, PhD Read more about the Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis Joint CBS/EMBL article in Nature selected as the Scientific Breakthrough of 2006 (December 22, 2006) The Weekly News Magazine Ingeni?ren - Denmark?s leading publication in the fields of science and technology ? has selected the joint CBS/EMBL Nature article Co-evolution of transcriptional and post-translational cell-cycle regulation (Nature, 443, 594-597, 2006) as the Scientific Breaktrough of 2006. All in all 5 scientific discoveries by Danish researchers have been selected with the CBS/EMBL work as # 1. The article describes a surprising mechanism behind the cell division and reveals that despite the fact that many of the core cell cycle protein complexes are conserved during evolution, their regulation has evolved considerably. For more information, contact Professor Søren Brunak Read more about the Danish Scientific Breakthroughs 2006 Related news items New chemoinformatics related grant to encourage and support collaboration between academia and industry (December 4, 2006) For the second time within a year, CBS' chemoinformatics group has received a grant from the Danish Strategic Research Council's for the SME (Small to Medium sized Enterprises) pilot project Information Technologies for Chemoinformatics. The target of this program is to encourage and support collaboration between academic research and industries of small to medium size, and to promote the active involvement of the industry in the research work. The focus is especially put on establishing new research partners and motivating collaboration with industries with up to now limited (or even non-existing) contact with the research world, in order to built an initial collaboration. As part of this new program, the chemoinformatics group is seeking SME industry partners within pharmacology and/or biotechnology for projects that can be initiated in the Spring 2007. The collaboration will involve the development and implementation of chemoinformatics methods taking the actual needs and wishes of the SME partners as starting point. Application Deadline: February 1, 2007 For more information, contact Groupleader, Associate professor Svava Jonsdottir Read more about the initiative CBS researcher awarded the Danish Biotechnological Society's Annual Award 2006 (November 20, 2006) On November 30, 2006 CBS researcher Ulrik de Lichtenberg receives the DBS Annual Award for his work within the area of systems biology with focus on the cell cycle. This work, which have been done in close collaboration with the European Molecular Biology Laboratory (EMBL), has so far led to two high profile publications in Science and Nature, respectively. For more information, contact Professor Søren Brunak Programme for the Annual DBS lecture and Annual DBS awards 2006 More information about DBS CBS groupleader, associate professor Ole Lund receives the Torkil Holm Foundation's Research Award 2006 (November 20, 2006) At an award ceremony at DTU, Monday, November 20, CBS groupleader Ole Lund is awarded the Torkil Holm Foundation's Research Award 2006 for his extra-ordinary research achievements within the area of immunology and systems biology. For more information, contact Ole Lund How nature tinkers with the cellular clock (October 5, 2006) This week, the Journal Nature publishes exciting new results from the Brunak and Bork groups which reveals that despite the fact that many of the core cell cycle protein complexes are conserved during evolution, their regulation has evolved considerably. The results are in perfect agreement with the just-in-time assembly principle that we proposed last year for yeast and even demonstrate co-evolution of different layers of regulation. Read more here: Danish Press release Article in Nature Commentary in Nature Pubmed Supplementary Information For more information, contact Professor Søren Brunak The Lundbeck Foundation awards grant for the CBS Galathea3 project 'The DNA of the Polar seas' (May, 2006) The LUNDBECK FOUNDATION has granted DKK 600.000 to the project "The DNA of the Polar seas", which has been selected for participation in the Galathea3 expedition. Thanks to the Lundbeck Foundation and another grant from the Villum Kann Rasmussen Foundation, all of the funding for the project is now secured, and CBS employee, associate professor Nikolaj Blom and his team can now concentrate on the last preparations before sailing of in August from Thorshavn on the Faroe Islands to Nuuk in Greenland. For more information, contact associate professor Nikolaj Blom More information about Galathea3 More information about the Lundbeck Foundation CBS employee receives grant for project on 'The DNA of the Polar seas' (March 15, 2006) The VILLUM KANN RASMUSSEN FOUNDATION has granted DKK 1 million to the project "The DNA of the Polar seas", which has been selected for participation in the Galathea3 expedition. CBS employee, associate professor Nikolaj Blom, is now preparing for cold weather and long working hours. In a few months, Nikolaj Blom and his team will board the Galathea3 vessel, sailing from Thorshavn on the Faroe Islands to Nuuk in Greenland, collecting samples from the polar seas. A few months later - on the other side of the globe - Nikolaj and his team will again join the Galathea3 expedition, this time boarding in Hobart, Tasmania. This time, they will spend four weeks collecting DNA samples close to Antarctica. Together with his team, Nikolaj Blom will study the yet unexplored microbiological diversity in the environments of the Polar seas and how these new discoveries at the DNA-level can be applied in practice. Thanks to the VILLUM KANN RASMUSSEN FOUNDATION, most of the funding for the project is now secured. For more information, contact associate professor Nikolaj Blom DTU Press Release (in Danish) More information about Galathea3 More information about the Villum Kann Rasmussen Foundation Center Director, professor Søren Brunak awarded Denmark's largest, scientific prize (January 23, 2006) At an award ceremony at DTU, Monday, January 23, Søren Brunak is awarded the Villum Kann Rasmussen Research Award 2006 in the amount of DKK 2,5 millions. Søren Brunak receives the award for his important and ground breaking role in the introduction of bioinformatics in Denmark and Scandinavia, and for being one of the key figures in Denmark's leading, international position within bioinformatics and systems biology. The Villum Kann Rasmussen Research Award is the largest scientific prize in Denmark. It is given out by the Villum Kann Rasmussen Foundation founded in 1987 by dr.techn. h.c. Villum Kann Rasmussen, who is known for his innovative and creative mind which, among other things, led him to the invention of the VELUX skylight windows. For more information, contact Søren Brunak Press Release (in Danish) Article in Jyllandsposten, January 23 (in Danish) More information about the Villum Kann Rasmussen Foundation New course in Protein Structure and Computational Biology (January 2006) In Spring 2006 CBS is offering a new, exciting course in Protein Structure and Computational Biology. The three-dimensional structure and flexibility of proteins determine their function in biological processes. Knowledge about protein structure is used in structure-based drug design and optimization of biocatalysts. The goal of the recent years "structural genomics" projects is to map the fold space, to make it possible to generate a useful homology model of any protein of interest in the future. In this course, the students will analyze the proteins from avian influenza, where they will investigate the molecular mechanisms underlying the different phases of the virus cycle. This will give the students a deeper understanding of protein structure analysis and knowledge about the newest techniques in homology modeling, protein engineering and directed evolution. Course Home Page Course Organizer: Anne Mølgaard CBS receives new chemoinformatics related grant to encourage and support collaboration between academia and industry (January 2006) CBS has recently received a grant from the Danish Strategic Research Council's for the SME (Small to Medium sized Enterprises) pilot project Information Technologies for Chemoinformatics. The target of this program is to encourage and support collaboration between academic research and industries of small to medium size, and to promote the active involvement of the industry in the research work. The focus is especially put on establishing new research partners and motivating collaboration with industries with up to now limited (or even non-existing) contact with the research world, in order to built an initial collaboration. As part of this new program, the chemoinformatics group is seeking SME industry partners within pharmacology and/or biotechnology for projects that can be initiated in the Spring 2006. The collaboration will involve the development and implementation of Chemoinformatics methods taking the actual needs and wishes of the SME partners as starting point. Project coordinator: Olivier Taboureau Read more about the initiative |
