Computational Biology & Bioinformatics

PHD in Computational Biology & Bioinformatics

Program Principles & Goals

The PhD Program in Computational Biology & Bioinformatics (CBB) is an integrative, multi-disciplinary training program that encompasses the study of biology using computational and quantitative methods. In and out of the classroom, students learn to apply the tools of statistics, mathematics, computer science and informatics to biological problems. The vibrant and innovative Duke research in these fields provides exciting interactions between biological and computational scientists. Because the Program in Computational Biology and Bioinformatics is based in the Duke Center for Genomic and Computational Biology, it offers a unique opportunity for students to become one of tomorrow's leaders in the genome sciences.

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Meet A Faculty Member

  • Professor of Mathematics

    Professor Reed is engaged in a large number of research projects that involve the application of mathematics to questions in physiology and medicine. He also works on questions in analysis that are stimulated by biological questions. For a general discussion of the applications of mathematics to problems in biology, see his article, ``Why is Mathematical Biology so Hard?'' in the March, 2004, Notices of the American Mathematical Society, pp. 338-342.

    Since 2003, Professor Reed has worked with Professor Fred Nijhout (Duke Biology) to use mathematical methods to understand regulatory mechanisms in cell metabolism. Most of the questions studied are directly related to public health questions. A list of publications in this area and the corresponding pdfs are available at the website metabolism.math.duke.edu (no www).

    A primary topic of interest has been liver cell metabolism where Reed and Nijhout have created mathematical models for the methionine cycle, the folate cycle, and glutathione metabolism. The goal is to understand the system behavior of these parts of cell metabolism. The models have enabled them to answer biological questions in the literature and to give insight into a variety of disease processes and syndromes including: neural tube defects, Down’s syndrome, autism, vitamin B6 deficiency, acetaminophen toxicity, and arsenic poisoning.

    A second major topic has been the investigation of dopamine and serotonin metabolism in the brain. The biochemistry of these neurotransmitters affects the electrophysiology of the brain and the electrophysiology affects the biochemistry. Both affect gene expression and behavior. In this complicated situation, especially because of the difficulty of experimentation, mathematical models are an essential investigative tool that can shed like on questions that are difficult to get at experimentally or clinically. This work has been done by Reed and Nijhout jointly with Janet Best, a mathematician at Ohio State. The models have shed new light on the mode of action of selective serotonin reuptake inhibitors (used for depression) and the interactions between the serotonin and dopamine systems in Parkinson’s disease.

    Professor Reed is engaged in a large number of research projects that involve the application of mathematics to questions in physiology and medicine. He also works on questions in analysis that are stimulated by biological questions. For a general discussion of
    the applications of mathematics to problems in biology, see
    his
    article,
    ``Why is Mathematical Biology so Hard?'' in the March, 2004,
    Notices of the American Mathematical Society, pp. 338-342.
    <p>

    Since 2003, Professor Reed has worked with Professor Fred Nijhout (Duke Biology) to use mathematical methods to understand regulatory mechanisms in cell metabolism. Most of the questions studied are directly related to public health questions. A list of publications in this area and the corresponding pdfs are available at the website metabolism.math.duke.edu (no www).

    <p>

    A primary topic of interest has been liver cell metabolism where Reed and Nijhout have created mathematical models for the methionine cycle, the folate cycle, and glutathione metabolism. The goal is to understand the system behavior of these parts of cell metabolism. The models have enabled them to answer biological questions in the literature and to give insight into a variety of disease processes and syndromes including: neural tube defects, Down’s syndrome, autism, vitamin B6 deficiency, acetaminophen toxicity, and arsenic poisoning.

    <p>

    A second major topic has been the investigation of dopamine and serotonin metabolism in the brain. The biochemistry of these neurotransmitters affects the electrophysiology
    of the brain and the electrophysiology affects the biochemistry. Both affect gene expression and behavior. In this complicated situation, especially because of the difficulty of experimentation, mathematical models are an essential investigative tool that can shed like on questions that are difficult to get at experimentally or clinically.
    This work has been done by Reed and Nijhout jointly with Janet Best, a mathematician at Ohio State. The models have shed new light on the mode of action of selective serotonin reuptake inhibitors (used for depression) and the interactions between the serotonin and dopamine systems in Parkinson’s disease.

    <p>

    Other areas in which Reed uses mathematical models to understand physiological questions include: models of pituitary cells that make luteinizing hormone and follicle stimulating hormone, models of the mammalian auditory brainstem, models of maternal-fetal competition, models of the owl’s optic tectum, and models of insect
    metabolism.

    <p>
    Often, problems in biology give rise to new questions in pure mathematics. Examples of work with collaborators on such questions follow:

    <p>
    Laurent, T, Rider, B., and M. Reed (2006) Parabolic Behavior of a Hyberbolic Delay Equation, SIAM J. Analysis, 38, 1-15.

    <p>

    Mitchell, C., and M. Reed (2007) Neural Timing in Highly Convergent Systems, SIAM J. Appl. Math. 68, 720-737.

    <p>

    Anderson,D., Mattingly, J., Nijhout, F., and M. Reed (2007) Propagation of Fluctuations in Biochemical Systems, I: Linear SSC Networks, Bull. Math. Biol. 69, 1791-1813.

    <p>

    McKinley S, Popovic L, and M. Reed M. (2011) A Stochastic compartmental model for fast axonal transport, SIAM J. Appl. Math. 71, 1531-1556.

    Research Interests
    • Analysis
    • Applications of Mathematics to Physiology and Medicine

Kai Fan

3rd year CBB Student Katherine Heller Lab