Søren Brunak

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Søren Brunak
Søren Brunak ISMB 2010.jpg
Søren Brunak speaking at the Intelligent Systems for Molecular Biology conference in 2010
Born 1958 (age 58–59)[1]
Residence Copenhagen, Denmark
Nationality Danish
Fields Bioinformatics and systems biology
Institutions University of Copenhagen Technical University of Denmark
Alma mater University of Copenhagen
Technical University of Denmark
Known for Development of computational tools for data integration across molecular and phenotypic levels
Notable awards Senior Scientist Award, International Society for Computational Biology. Dir. Ib Henriksens Price for Outstanding Science Achievement, Villum Kann Rasmussen Price for Research within the Natural and Technical Sciences.
Website
www.cpr.ku.dk
www.cbs.dtu.dk

Søren Brunak, Ph.D. (born 1958) is a Danish biological and physical scientist working in bioinformatics, systems biology and medical informatics. He is professor of Disease Systems Biology at the University of Copenhagen and professor of Bioinformatics at the Technical University of Denmark. As Research Director at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen Medical School he leads a research effort where molecular level systems biology data are combined with phenotypic data from the healthcare sector, such as electronic patient records, registry information and biobank questionnaires. A major aim is to understand the network biology basis for time-ordered comorbidities and discriminate between treatment related disease correlations and other comorbidities in disease trajectories. Søren Brunak also holds a position as Medical Informatics Officer at Rigshospitalet, Capital Region of Denmark.

Education[edit]

Søren Brunak obtained his Master of Science degree in Physics, in 1987 at the Niels Bohr Institute, University of Copenhagen (thesis title: The Physics of Computation), in 1991 his Ph.D. in Computational Biology at the Department of Structural Properties of Materials, Technical University of Denmark (thesis title: System in Genes), and in 2002 a Dr.phil. (Honoris causa) from the Natural Science Faculty of the Stockholm University.

Career[edit]

Søren Brunak was in 1993 the founding director of the Center for Biological Sequence Analysis at the Department of Systems Biology of the Technical University of Denmark.[2][3][4] a major, early center in bioinformatics that has existed for more than 20 years. In 2007 Søren Brunak was with Matthias Mann the founding research directors of the Novo Nordisk Foundation Center for Protein Research at the Faculty for Health and Medical Sciences of the University of Copenhagen, a leading center for the study of human proteins of therapeutic value.

He has been a member of the Danish Academy for the Natural Sciences since 1997, member of the Board of directors of the International Society for Computational Biology 2001-2004, of the Danish Academy of Technical Sciences (da) since 2002, the Danish Royal Society of Sciences and Letters since 2004, and of the Royal Swedish Academy of Sciences from 2016. He is a fellow of the International Society for Computational Biology (2009), and a Member of European Molecular Biology Organization (2009).

He has been participating in scientific advisory committees of several scientific organizations, such as EMBL (Heidelberg), Ensembl at the European Bioinformatics Institute/Sanger Centre (chairman), the Bioinformatics Advisory Committee at the European Bioinformatics Institute (chairman), Institut Pasteur, the Max Planck Institute for Molecular Genetics (Berlin), the Science for Life Laboratory (Stockholm) and the Swiss Institute of Bioinformatics.

Søren Brunak has received the Senior Scientist Award from the International Society for Computational Biology (2016). Julius Thomsen’s Gold Medal (2013). Dir. Ib Henriksens Price for Outstanding Science Achievement (2002). Villum Kann Rasmussen Price for Research within the Natural and Technical Sciences (2006).

Research[edit]

Brunak's main research is in Bioinformatics and systems biology. In particular, machine learning based prediction and the general area of integrative systems biology where heterogeneous data from the molecular level are combined with phenotypic data from the healthcare sector. A general aim is to understand disease mechanisms at the level of protein network biology. An additional focus area is human proteome variation and percision medicine, where patient-specific adverse drug reaction profiles and the discrimination between treatment related disease correlations and other comorbidities are investigated. The group engages in non-hypothesis driven research, where massive amounts of data from widely different experimental technologies are combined and analysed with the objective of making discoveries that emerge from the data rather than being the result of specific experiments designed to confirm or disprove given hypotheses. The Brunak group has also over the years been highly within machine learning and have produced numerous, highly used prediction methods, including SignalP, TargetP, NetGene, NetPhos, NetOglyc, NetNES, distanceP and many others.[5][6][7][8]

Selected book publications[edit]

  • Brunak S, Lautrup B (1990). Neural Networks - Computers with Intuition. World Scientific Publishing. ISBN 9971-5-0939-3.  (also published in Danish and German)
  • Baldi P, Brunak S (1998). Bioinformatics: The Machine Learning Approach. MIT Press. ISBN 0-262-02442-X. 
  • Baldi P, Brunak S (2001). Bioinformatics: The Machine Learning Approach (2nd ed.). MIT Press. 
  • Baldi P, Brunak S (2003). Bioinformatics: The Machine Learning Approach. Citec Publishing House, Translated Chinese edition. 
  • Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S (2005). Immunological Bioinformatics. MIT Press. 

References[edit]

  1. ^ http://viaf.org/viaf/200207241/
  2. ^ Soren Brunak page at the Technical University of Denmark
  3. ^ Soren Brunak Biography
  4. ^ Søren Brunak's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  5. ^ Nielsen, H.; Engelbrecht, J.; Brunak, S.; Von Heijne, G. (1997). "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites". Protein Engineering Design and Selection. 10: 1–6. doi:10.1093/protein/10.1.1. PMID 9051728. 
  6. ^ Dyrløv Bendtsen, J.; Nielsen, H.; Von Heijne, G.; Brunak, S. (2004). "Improved Prediction of Signal Peptides: SignalP 3.0". Journal of Molecular Biology. 340 (4): 783–795. doi:10.1016/j.jmb.2004.05.028. PMID 15223320. 
  7. ^ Brunak, S.; Engelbrecht, J.; Knudsen, S. (1990). "Neural network detects errors in the assignment of mRNA splice sites". Nucleic Acids Research. 18 (16): 4797–4801. doi:10.1093/nar/18.16.4797. PMC 331948Freely accessible. PMID 2395643. 
  8. ^ Brunak, S.; Engelbrecht, J.; Knudsen, S. (1990). "Cleaning up gene databases". Nature. 343 (6254): 123–123. doi:10.1038/343123a0. PMID 2296305.