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Michael A. Gilchrist

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Research Interests

As an evolutionary biologist my research covers a wide array of topics, from intra-cellular processes to development to life-history evolution.
All of this work is motivated by an interest in understanding the origin and resolution of trade-offs organisms face in various aspects of their lifecycle.  In order to understand these trade offs, I generally employ a modeling approach that involves the nesting of mathematical models at different biological scales.

For example, since the 1980's evolutionary biologists have generally understood that the evolution of a pathogen's virulence is dependent on the functional relationship between virulence and transmission rates.  In various studies (e.g. Gilchrist and Sasaki, 2002, Gilchrist and Coombs 2006, Coombs, Gilchrist, and Ball 2007) I have nested a within host models of viral dynamics inside of a between host model of disease dynamics to understand what the relationship between virulence and transmission might look like under certain assumptions.

Another example using nested models in my research is in the study of codon usage bias.  Genes that are highly expressed tend to use certain codons preferentially over others (e.g.~the CAC codon for histidine is generally preferred over the CAT codon).  Various hypotheses have been proposed to explain such preferences, but in order to understand such preferences better I have nested an intra-cellular model of ribosome movement (Gilchrist and Wagner 2006) within a population genetics model of gene fixation.  Doing so results in some important insights and better methods for predicting protein production rates from codon usage bias patterns (Gilchrist 2007).

In addition to my work in evolutionary biology, I am also interested in the developing new methods for improving our ability to interpret data.  As with my other work, these methods have a nested quality to them.  For example, in order to better interpret protein complex composition using high-throughput immunocoprecipitation datasets (e.g.~Gavin et al. 2002), I developed a model of the purification step of the experimental processes (Gilchrist, Salter, and Wagner 2004).  More recently, I have worked with my colleague here at UTK, Dr. Russell Zaretzki, showing that SAGE datasets are inherently biased in their composition and how such bias can be adjusted for (Gilchrist, Qin, and Zaretzki, 2007).  This work has convinced me of the fact that we are in a very exciting time in which we can begin to bridge the gap between models and data in molecular and evolutionary biology.

Education

  • 2001 - Ph.D., Duke University

Selected Publications

  • M.A. Gilchrist, Qin, H., and R. Zaretzki. 2007. Model for SAGE Data Analysis Accounting for Cleavage and Sampling Errors.  BMC Bioinformatics. 8: 403-411.
  • Coombs, D., M.A. Gilchrist, and C.L. Ball. 2007. Evaluating the Importance of Within- and Between-Host Selection Pressures in the Evolution of Chronic Pathogens. Theoretical Population Biology.  72: 576-591
  • White, E.P. and M.A. Gilchrist. 2007. Effects of Temporal Structure of Individuals on the Species-Time Relationship in Two Desert Communities.  Evolutionary Ecology Research.: 1329–1347
  • Gilchrist, M.A. 2007. Combining Models of Protein Translation and Population Genetics to Predict Protein Production Rates from Codon Usage Patterns. Molecular Biology & Evolution. 24: 2362-2373
  • Rong, L., M.A. Gilchrist, Z. Feng. and A. Perelson. 2007. Modeling within-host HIV-dynamics and the evolution of drug resistance: Trade-offs in viral enzyme function and drug susceptibility. Journal of Theoretical Biology. 247: 804-818
  • Ball, C. L.*, M.A. Gilchrist, and D. Coombs.  2007. Modeling Within-Host Evolution of HIV: Mutation, Competition and Strain Replacement.  Bulletin of Mathematical Biology. 69: 2361-2385.
  • Gilchrist, M.A. and D. Coombs. 2006. Evolution of Virulence: Interdependence, Constraints, and
  • Gilchrist, M.A. and A. Wagner. 2006. A Model of Protein Translation Including Codon Usage Bias, Nonsense Errors, and Ribosome Recycling.  Journal of Theoretical Biology. 239: 417-434
  • christ, M.A., D. L. Sulsky, and A. Pringle. 2006. Identifying Fitness and Optimal Life-History Strategies for an Asexual Filamentous Fungus.  Evolution. 60: 970-979
Michael A. Gilchrist

Contact Information

Michael A. Gilchrist
Assistant Professor
Evolutionary Bioinformatics
569 Dabney Hall
University of Tennessee
Knoxville, TN 37996-1610

Phone: (865) 974-2925
Lab: (865)974-6453
Fax: (865) 974-3067
Email: mikeg@utk.edu