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Click on a theme or a project in the table below for more information.
Project leader:
Dr. Leen Stougie (CWI/TU/e)
Consortium:
CWI, TU/e
Industrial partners (non-exhaustive):
Perrot Enterpr., Philips, Unilever
Total FTE: 6.63 (heads: 19, PD:1 , PhD: 3)
Key BRICKS publications:
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Van den Berg and Brouwer: "Self-organized forest-fires near the critical time" In: Comm. Math. Phys. 67, 2006, 265-277
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Cilibrasi, Vitanyi: "Clustering by compression" In: IEEE Trans. Info. Inform. Th. 51:4, 2005, 1523- 1545)
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Huisman, Pham Thi, Karl, Sommeijer: "Reduced mixing generates oscillations and chaos in the oceanic deep chlorophyll maximum" In: Nature 439, 2006, 322-325
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V. Iersel, Keijsper, Kelk, Stougie, Hagen, Boekhout: "Constructing level-2 phylogenetic networks from rooted triplets" In: Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Singapore, LNCS 4955, pages 450-462, 2008.
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Li, Chen, Li, Ma, Vitanyi: "The similarity metric" In: IEEE Trans. Inform. Th., 50:12, 2004, 3250- 3264
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Project AFM2: Algorithms and Processes in Life Sciences
Spectacular developments in future industry and technology, hence
in economy and society, are expected to come from biology: novel
foods and production methods, novel medical drugs and diagnostic
tools, etc. In recent years, particularly since the unravelling of
the genetic code, biological sciences have seen a rapid
development. Both on the molecular and on the cellular level
detailed knowledge of the building stones of life becomes rapidly
available. Areas on the interface of computer science and applied
mathematics have played a prominent role here and this role will
become more and more important in the future. This interface is
particularly relevant for processing wet-lab results in order to
synthesize an over-all picture of a particular molecule, a
biochemical process in a cell, and in the future even a whole
organism. The great diversity of problems from biology and medicine
requires an equivalent diversity of computer science and
mathematical expertise. Such expertise will be concentrated and
further developed in the new and wide interdisciplinary field of
bio-informatics. Bio-informatics encompasses for example database
research, virtual reality, combinatorics, algorithmic statistics
and numerical analysis.
In this project we focus on three subprojects:
Industrial cooperation
The nature of the theme and the state of the art of research in
biology and medicine is conducive to cooperation with researchers
from other disciplines rather than with industrial partners.
Cooperation on various problems has been established with several
departments within the Swammerdam Institute for Life Sciences of
the University of Amsterdam, the Institute of Molecular Cell
Biology of the Free University Amsterdam, and AMOLF, partly
formalised in the Netherlands Institute for Systems Biology.
Phylogeny problems are studied with the KNAW Centraal Bureau voor
Schimmelcultures. Various problems are studied with the Netherlands
Cancer Institute. Industrial contacts are limited to Perrot
Enterprises Netherlands, Unilever and the above mentioned
contacts with Phiilps.
International cooperation
NRIA Rhone-Alpes, Lyon, France; Univ. of Rome La Sapienza; Univ. of
Bielefeld; Ioffe Inst. & Polytechnical Inst. St. Petersburg; Univ.
of Waterloo; UC Riverside and UC Berkeley; Moscow State Univ.; ENS
Paris, Rutgers Univ.; IMPA (Rio de Janeiro); Chalmers Univ.
Gothenburg.
Highlights 2004-2006
Research highlights
Cooperation of Sommeijer with non-BRICKS partners resulted in a
publication in Nature. Long term research into complexity theory of
Vitanyi and Cilibrasi generated much publicity after they published
their results on similarity metrics based on compression and Google
co-occurrence. Van Iersel et al. found new algorithms for finding
phylogenetic networks, supporting hybridization events in biological
evolution. Van den Berg et al. presented new results on formal
modeling of forest fires.
Economic & societal impact
CWI started a Life Sciences group led by Arjen Doelman hired computational
biologist Gunnar Klau as tenure track project leader, having another such
position vacant, and biologist Frank Bruggeman as PostDoc for three
years. The group also hosts core modelling group of Roeland Merks of
the Netherlands Consortium for Systems Biology (NCSB). Including
parttimers the Life Sciences group contains more than 20 researchers.
The Netherlands Institute for Systems Biology (NISB) has been founded and
resides at CWI. Frank Bruggeman and Leen Stougie obtained a NWO
Computational Life Sciences grant for research on metabolic networks.
All these initiatives are inspired by this BRICKS theme.
Future work 2009
Finishing some of the projects, among others the PhD of Wouter Koolen-Wijkstra.
Organising a final meeting. Acquiring further projects, researchers and
PhD-students to enhance computational biology over the end of the BRICKS
project. Giving bioinformatics/biomathematics a place in university education.
For more information, please refer to the publications and posters of this project.
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