Publications

Google Scholar Page

  1. Gilchrist, M.A., and H.F. Nijhout. 2001. Nonlinear Developmental Processes as Sources of Dominance. Genetics 159: 423-432.
  2. Gilchrist, M.A. and A. Sasaki. 2002. Modeling host-parasite coevolution: a nested approach based on mechanistic models. Journal of Theoretical Biology 218: 289-308.
  3. Hickerson, M.J., M.A. Gilchrist, and N. Takebayashi. 2003. Calculating a Molecular Clock from Phylogeographic Data: Moments and Likelihood Estimators. Evolution 57: 2216 -2225.
  4. Coombs, D., M.A. Gilchrist, J. Percus, and A.S. Perelson. 2003. Optimal Viral Production. Bulletin of Mathematical Biology 65: 1003-1023.
  5. Gilchrist, M.A., L.A. Salter, and A. Wagner. 2004. A Statistical Framework for Combining and Interpreting Proteomic Datasets. Bioinformatics 20: 689-700.
  6. Gilchrist, M.A., D. Coombs, and A.S. Perelson. 2004. Optimizing Within-host Viral fitness: Infected Cell Lifespan and Virion Production Rate. Journal of Theoretical Biology 229: 281-288.
  7. Nelson, P.W., M.A. Gilchrist, D. Coombs, J.M. Hyman, and A.S. Perelson. 2004. An age-structured model of HIV infection that allows for variations in the production rate of viral particles and the death rate of productively infected cells.Mathematical Biosciences & Engineering 1: 267-288.
  8. Gilchrist, M.A. and D. Coombs. 2006. Evolution of Virulence: Interdependence, Constraints, and Selection using Nested Models. Theoretical Population Biology 63: 145-153.
  9. 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.
  10. Gilchrist, 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.
  11. 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.
  12. Rong, L., M.A. Gilchrist, Z. Feng. and A.S. 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.
  13. 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.
  14. 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 9: 1329-1347.
  15. 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.
  16. Gilchrist, M.A., H. Qin and R. Zaretzki. 2007. Model for SAGE Data Analysis Accounting for Cleavage and Sampling Errors. BMC Bioinformatics 8: 403-411.
  17. Gilchrist, M.A., P. Shah, and R. Zaretzki. 2009. Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation. Genetics 183:1493-1505.
  18. Zaretzki, R., M.A. Gilchrist, W.M. Briggs, and A. Armagan 2010. Bias Correction and Bayesian Analysis of Aggregate Counts in SAGE Libraries. BMC Bioinformatics 11: 72.
  19. Roy, B., J.N. Vaughn, B-H Kim, F. Zhou, M.A. Gilchrist, and A.G. Von Arnim. 2010. The h Subunit of eIF3 Helps to Maintain Reinitiation Competence during Translation of mRNAs Harboring Upstream Open Reading Frames.RNA 16: 748-761.
  20. Shah, P. and M.A. Gilchrist. 2010. Thermosensing Property of RNA Thermometers Is Not Unique. PLoS One 5:e11308.
  21. Shah, P. and M.A. Gilchrist. 2010. Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias. PLoS Genetics 6:e1001128.
  22. Harp, J.R., M.A. Gilchrist, and T.M. Onami. 2010. Memory T cells are enriched in lymph nodes of selectin-ligand deficient mice. Journal of Immunology 185: 5751-5761.
  23. Shah, P. and M.A. Gilchrist. 2011. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proceedings of the National Academy of Sciences U.S.A. 108: 10231-10236.

* Lab members are marked in bolt.