Computational Biology & Bioinformatics

PHD in Computational Biology & Bioinformatics

Program Principles & Goals

The Ph.D. Program in Computational Biology & Bioinformatics (CBB) is an integrative, multi-disciplinary training program that encompasses 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. Vibrant and innovative research in these fields provides exciting interactions between biological and computational scientists. Because CBB is based in the Duke Center for Genomic and Computational Biology (GCB), it offers a unique opportunity for students to become tomorrow's leaders in genome sciences.

Group photo of CBB students and faculty



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Meet A Faculty Member

  • Mike Reed
    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 recent work on cell metabolism and public health, go to sites@duke.edu/metabolism.

    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 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; this is collaborative work with Professor Nijhiout and with Janet Best, a mathematician at The Ohio State University.  The biochemistry of these neurotransmitters affects the electrophysiology of the brain and the electrophysiology affects the biochemistry. Both affect gene expression, the endocrine system, 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. The models have shed new light on the mode of action of selective serotonin reuptake inhibitors (used for depression), the interactions between the serotonin and dopamine systems in Parkinson’s disease and levodopa therapy, and the interactions between histamine and serotonin. 

    Recent work on homeostatic mechanisms in cell biochemistry in health and disease have shown how difficult the task of precision medicine is. A gene polymorphism may make a protein such as an enzyme less effective but often the system compensates through a variety of homeostatic mechanisms. So even though an individual's genotype is different, his or her phenotype may not be different. The individuals with common polymorphisms tend tend to live on homeostatic plateaus and only those individuals near the edges of the plateau are at risk for disease processes. Interventions should try to enlarge the homeostatic plateau around the individual's genotype. 

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

    For general discussions of the connections between mathematics and biology, see his articles: ``Why is Mathematical Biology so Hard?,'' 2004, Notices of the AMS, 51,  pp. 338-342, and ``Mathematical Biology is Good for Mathematics,'' 2015, Notices of the AMS, 62, pp., 1172-1176.

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

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

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

    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.

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

    Lawley, S. Reed, M., Mattingly, S. (2014), Sensitivity to switching rates in stochastically switched ODEs,'' Comm. Math. Sci. 12, 1343-1352.

    Lawley, S., Mattingly, J, Reed, M. (2015), Stochastic switching in infinite dimensions with applications to parabolic PDE, SIAM J. Math. Anal. 47, 3035-3063.


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

Mengqi Zhang

3rd year CBB Student Andrew Allen Lab
Jan 23
Tomas Gedeon, PhD, Montana State University, Department of Mathematical Sciences
CBB Seminar Series

Dynamics of gene regulatory networks with unknown parameters

Jan 30
Amy Schmid, PhD, Duke University, Department of Biology
CBB Seminar Series

"Calm under stress: how regulatory networks control cellular decision-making in archaeal extremophiles."

Feb 13
Geoffrey Ginsburg, MD, PhD, Duke University, Applied Genomics and Precision Medicine
CBB Seminar Series

Novel genomic paradigms for early detection and diagnosis of acute infectious disease