Daniel Coombs

Summary

Affiliation: University of British Columbia
Country: Canada

Publications

  1. pmc A role for rebinding in rapid and reliable T cell responses to antigen
    Omer Dushek
    Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 5:e1000578. 2009
  2. doi request reprint Assessing the optimal virulence of malaria-targeting mosquito pathogens: a mathematical study of engineered Metarhiziumanisopliae
    Bernhard P Konrad
    Institute of Applied Mathematics and Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada
    Malar J 13:11. 2014
  3. pmc Vaccination against 2009 pandemic H1N1 in a population dynamical model of Vancouver, Canada: timing is everything
    Jessica M Conway
    Division of Mathematical Modeling, University of British Columbia Centre for Disease Control, 655 West 12th Avenue, V5Z 4R4 Vancouver, British Columbia, Canada
    BMC Public Health 11:932. 2011
  4. pmc Equilibrium thermodynamics of cell-cell adhesion mediated by multiple ligand-receptor pairs
    Daniel Coombs
    Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
    Biophys J 86:1408-23. 2004
  5. pmc Effects of the geometry of the immunological synapse on the delivery of effector molecules
    Daniel Coombs
    Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
    Biophys J 87:2215-20. 2004
  6. pmc A stochastic model of latently infected cell reactivation and viral blip generation in treated HIV patients
    Jessica M Conway
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 7:e1002033. 2011
  7. ncbi request reprint Evaluating the importance of within- and between-host selection pressures on the evolution of chronic pathogens
    Daniel Coombs
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada V6T 1Z2
    Theor Popul Biol 72:576-91. 2007
  8. doi request reprint Analysis of membrane-localized binding kinetics with FRAP
    Omer Dushek
    Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
    Eur Biophys J 37:627-38. 2008
  9. ncbi request reprint Modeling within-host evolution of HIV: mutation, competition and strain replacement
    Colleen L Ball
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada
    Bull Math Biol 69:2361-85. 2007
  10. pmc A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton
    Raibatak Das
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 5:e1000556. 2009

Collaborators

Detail Information

Publications22

  1. pmc A role for rebinding in rapid and reliable T cell responses to antigen
    Omer Dushek
    Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 5:e1000578. 2009
    ..We discuss our results in the context of existing models and recent experimental work and propose new experiments to test our findings...
  2. doi request reprint Assessing the optimal virulence of malaria-targeting mosquito pathogens: a mathematical study of engineered Metarhiziumanisopliae
    Bernhard P Konrad
    Institute of Applied Mathematics and Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada
    Malar J 13:11. 2014
    ..It has been proposed that efforts should be made to minimize the virulence of the fungal pathogen, in order to slow the development of resistant mosquitoes following an actual deployment...
  3. pmc Vaccination against 2009 pandemic H1N1 in a population dynamical model of Vancouver, Canada: timing is everything
    Jessica M Conway
    Division of Mathematical Modeling, University of British Columbia Centre for Disease Control, 655 West 12th Avenue, V5Z 4R4 Vancouver, British Columbia, Canada
    BMC Public Health 11:932. 2011
    ..We adapted a city-level contact network model to study different campaigns on influenza morbidity and mortality...
  4. pmc Equilibrium thermodynamics of cell-cell adhesion mediated by multiple ligand-receptor pairs
    Daniel Coombs
    Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
    Biophys J 86:1408-23. 2004
    ..We demonstrate our model by application to the T cell/antigen-presenting-cell system and outline applications to natural killer cell adhesion...
  5. pmc Effects of the geometry of the immunological synapse on the delivery of effector molecules
    Daniel Coombs
    Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
    Biophys J 87:2215-20. 2004
    ..We apply our model to the stimulation of B cells by secreted interleukin-4 (IL-4), and find that very few molecules of IL-4 need be released to essentially saturate the IL-4 receptors on the B-cell surface...
  6. pmc A stochastic model of latently infected cell reactivation and viral blip generation in treated HIV patients
    Jessica M Conway
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 7:e1002033. 2011
    ..Stochastic models of this type provide insight into treatment-outcome variability that cannot be found from deterministic models...
  7. ncbi request reprint Evaluating the importance of within- and between-host selection pressures on the evolution of chronic pathogens
    Daniel Coombs
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada V6T 1Z2
    Theor Popul Biol 72:576-91. 2007
    ..Although we emphasize the application to human viral diseases, we expect this methodology to be applicable to be many host-parasite systems...
  8. doi request reprint Analysis of membrane-localized binding kinetics with FRAP
    Omer Dushek
    Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
    Eur Biophys J 37:627-38. 2008
    ..We present simulated experiments illustrating our protocol and lay down guidelines for parameter estimation...
  9. ncbi request reprint Modeling within-host evolution of HIV: mutation, competition and strain replacement
    Colleen L Ball
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada
    Bull Math Biol 69:2361-85. 2007
    ..Our model lays the groundwork for more detailed models of HIV selection and mutation. We outline future directions and application of related models to other biological situations...
  10. pmc A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton
    Raibatak Das
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 5:e1000556. 2009
    ..Our analysis reveals that the diffusion of LFA-1 is indeed approximately two-state, and is characterized by large changes in cytoskeletal interactions upon cellular activation...
  11. pmc Effects of intracellular calcium and actin cytoskeleton on TCR mobility measured by fluorescence recovery
    Omer Dushek
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 3:e3913. 2008
    ....
  12. doi request reprint Mechanical force regulates integrin turnover in Drosophila in vivo
    Mary Pines
    Department of Cellular and Physiological Sciences, University of British Columbia, Life Science Institute, Vancouver, British Columbia V6T 1Z3, Canada
    Nat Cell Biol 14:935-43. 2012
    ..We propose that integrin-ECM adhesive stability is continuously controlled by force in vivo through integrin-dependent auto-regulatory feedback mechanisms so that tissues can quickly adapt to and withstand mechanical stresses...
  13. ncbi request reprint Improving parameter estimation for cell surface FRAP data
    Omer Dushek
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2
    J Biochem Biophys Methods 70:1224-31. 2008
    ..We propose that the use of a small bleach region along with a two dimensional diffusion model is the ideal protocol for cell surface FRAP...
  14. pmc Analysis of serial engagement and peptide-MHC transport in T cell receptor microclusters
    Omer Dushek
    Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, Canada
    Biophys J 94:3447-60. 2008
    ..Finally, we analyze the effects of multiple TCR microclusters, showing that the size of individual clusters only weakly affects our prediction of TCR serial engagement by pMHC. Throughout, we draw parameter estimates from published data...
  15. doi request reprint Modeling effect of a γ-secretase inhibitor on amyloid-β dynamics reveals significant role of an amyloid clearance mechanism
    Raibatak Das
    Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC V6T 1Z2, Canada
    Bull Math Biol 73:230-47. 2011
    ..These results point to the need for a more detailed investigation of soluble Aβ clearance mechanisms and their interaction with Aβ-reducing drugs...
  16. ncbi request reprint Quantification and modeling of tripartite CD2-, CD58FC chimera (alefacept)-, and CD16-mediated cell adhesion
    Michael L Dustin
    Department of Pathology, New York University School of Medicine and Helen L and Martin S Kimmel Center for Biology and Medicine of Skirball Institute of Biomolecular Medicine, New York, New York 10016, USA
    J Biol Chem 282:34748-57. 2007
    ..These results suggest that additional information is needed to correctly predict Alefacept-mediated bridge formation...
  17. ncbi request reprint Analysis of peptide/MHC-induced TCR downregulation: deciphering the triggering kinetics
    Clemens Utzny
    INSERM U563, Institut Claude de Preval, CHU Purpan, 31059 Toulouse Cedex 3, France
    Cell Biochem Biophys 46:101-11. 2006
    ..We provide a unified picture of productive TCR engagement and downregulation in which TCR triggering characteristics evolve from an initial cooperative phase to a sustained phase of signal accumulation...
  18. ncbi request reprint A theoretical and experimental study of competition between solution and surface receptors for ligand in a Biacore flow cell
    Xiaoyi He
    Computational Modeling Center, Air Products and Chemicals, Inc, 7201 Hamilton Boulevard, Allentown, PA 18195, USA
    Bull Math Biol 68:1125-50. 2006
    ..In developing our method to analyze these experiments we obtain an expression for the transport limited rate constant for a Biacore experiment when soluble receptor is present during dissociation...
  19. pmc T cell receptor binding kinetics required for T cell activation depend on the density of cognate ligand on the antigen-presenting cell
    Pablo A González
    Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago 8331010, Chile
    Proc Natl Acad Sci U S A 102:4824-9. 2005
    ..According to these results, effective T cell activation depends on a complex interplay between inherent TCR-pMHC binding kinetics and the epitope density on the APC...
  20. ncbi request reprint Activated TCRs remain marked for internalization after dissociation from pMHC
    Daniel Coombs
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Nat Immunol 3:926-31. 2002
    ..We show here that kinetic proofreading provides an explanation for the different requirements for activation observed in naïve and memory T cells...
  21. ncbi request reprint Optimizing within-host viral fitness: infected cell lifespan and virion production rate
    Michael A Gilchrist
    Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Theor Biol 229:281-8. 2004
    ..Our findings suggest that HIV replication rates should vary between cells with different life spans, as has been suggested by recent observation...
  22. ncbi request reprint Optimal viral production
    Daniel Coombs
    Theoretical Biology and Biophysics Group, Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bull Math Biol 65:1003-23. 2003
    ..We present a general mathematical framework for studying problems of this type, which may be adapted to many host-parasite systems, and use it to examine the optimal virus production scheduling problem from the perspective of the virus...