2000-2004 Special Focus on Computational Molecular Biology: Overview

Starting in September 2000, the planned special focus is motivated by major developments at the interface between biology and information science:

  • First, because of new technologies, we are receiving massive amounts of data and, moreover, the data are arriving in diverse forms and are often unstructured and non-homogeneous. This requires the intervention of experts at handling databases and processing massive amounts of information. Moreover, data are now available at much higher levels of organization than heretofore (for example at the whole genome level rather than at the gene level), which makes possible dramatic new biological understanding if we can find ways to handle the complex algorithmic questions that arise.

  • Second, new biotechnologies such as gene expression arrays are powerful new experimental tools, but these tools and the development of new ones need to be integrated with fundamental research concerning algorithms. Thus, close collaborations between biological scientists and computer scientists need to be developed and/or strengthened.

  • Third, new mathematical and computational tools have made it possible to understand biological processes at a much more complex level than before, for example at the level of cellular communities, the immune system, protein structure and design, and processes of learning and memory. This comes at a time when biologists are finding tools to explore how parts of a biological system (e.g., genes or molecules) interact, something that has long been understood to be just as important as understanding the parts themselves but which has been largely inaccessible to experimental or analytical techniques. These new tools make it possible to formulate powerful new mathematical models of biological systems, grounded in the communication and information transmission fundamental to those systems. This calls out for the expertise of mathematical modelers and information scientists who are best able to take advantage of the powerful new mathematical methods while at the same time keeping their models realistic through interactions with biological scientists.

    The DIMACS Special Year on Mathematical Support for Molecular Biology commenced in 1994-95 with a very intense level of activity and has continued at a significantly lower level since then. Through that special year, we have focused the interests of a large number of computer scientists and mathematicians on the field of molecular biology, created real partnerships between mathematical and biological scientists, and trained outstanding young people to work in computational biology. We feel that the time is right for another highly visible special year thrust, like the one in 1994-95. At the time of our first special year, there was a need to address, review, and coordinate a variety of topics and methods, as well as to introduce many people to the field. Computational biology prior to the first special year was largely focused on a few problems such as alignments, physical mapping, and reconstructing phylogenies. Now, many of the topics emphasized in the first special year have become ``standard'' topics of research in computational biology and the field has become much broader in its focus. Other topics have begun to be investigated in a much more far-reaching way using methods of computer science, for example problems involving gene finding and motif recognition, protein and RNA folding, protein structure prediction, and linkage analysis. New biotechnologies such as SBH (sequencing by hybridization), optical mapping, and EST (expressed sequence tags) have been brought to the attention of a much larger number of computer scientists so that they can formulate and research the right questions concerning new technologies. But a whole host of new problems that lie at the interface between the computational/mathematical sciences and the biological sciences have arisen, stimulated, as we have noted, by the availability of massive amounts of new data, the integration of new experimental methods with algorithmic methods, and the development of powerful new mathematical tools for modeling ever-more-complex biological systems.

    The title of the special focus, ``Computational Molecular Biology,'' is certainly too broad to define its focus. We will concentrate on those areas where discrete mathematics (DM) and theoretical computer science (TCS) seem likely to have a major impact. A fundamental premise of the special focus is that some of the most central problems in modern molecular biology are essentially problems involving the combinatorial and algorithmic questions of DM and TCS and it is a basic objective of the focus to create partnerships between biological and mathematical/computer scientists so that some of these central biological questions can be precisely formulated and analyzed. It is our expectation that by bringing together some of the world's leading mathematicians/computer scientists with leading biological scientists, major progress can be made. Moreover, it is our expectation that we can establish and nurture lines of communication and collaboration so that the new methods of information science that arise from the special focus can be quickly adapted to biological applications, and can be readily communicated to the biological community.

    Opportunities to Participate: The Special Focus will include:

    If you would like to receive updates on the special focus and event announcements by email please contact the DIMACS
    Publicity Coordinator and ask to be placed on the Computational Molecular Biology mailing list.

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    Document last modified on April 21, 2003.