Research Topics
Species  Daniel CoombsSummaryAffiliation: University of British Columbia Country: Canada Publications
 Collaborators

Detail Information
Publications
 A role for rebinding in rapid and reliable T cell responses to antigenOmer 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...  Assessing the optimal virulence of malariatargeting mosquito pathogens: a mathematical study of engineered MetarhiziumanisopliaeBernhard 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...  Vaccination against 2009 pandemic H1N1 in a population dynamical model of Vancouver, Canada: timing is everythingJessica 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 citylevel contact network model to study different campaigns on influenza morbidity and mortality...  Equilibrium thermodynamics of cellcell adhesion mediated by multiple ligandreceptor pairsDaniel Coombs
Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
Biophys J 86:140823. 2004..We demonstrate our model by application to the T cell/antigenpresentingcell system and outline applications to natural killer cell adhesion...  Effects of the geometry of the immunological synapse on the delivery of effector moleculesDaniel Coombs
Department of Mathematics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
Biophys J 87:221520. 2004..We apply our model to the stimulation of B cells by secreted interleukin4 (IL4), and find that very few molecules of IL4 need be released to essentially saturate the IL4 receptors on the Bcell surface...  A stochastic model of latently infected cell reactivation and viral blip generation in treated HIV patientsJessica 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 treatmentoutcome variability that cannot be found from deterministic models...  Evaluating the importance of within and betweenhost selection pressures on the evolution of chronic pathogensDaniel Coombs
Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada V6T 1Z2
Theor Popul Biol 72:57691. 2007..Although we emphasize the application to human viral diseases, we expect this methodology to be applicable to be many hostparasite systems...  Analysis of membranelocalized binding kinetics with FRAPOmer Dushek
Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
Eur Biophys J 37:62738. 2008..We present simulated experiments illustrating our protocol and lay down guidelines for parameter estimation...  Modeling withinhost evolution of HIV: mutation, competition and strain replacementColleen 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 69:236185. 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...  A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA1 and the actin cytoskeletonRaibatak 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 LFA1 is indeed approximately twostate, and is characterized by large changes in cytoskeletal interactions upon cellular activation...  Effects of intracellular calcium and actin cytoskeleton on TCR mobility measured by fluorescence recoveryOmer Dushek
Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
PLoS ONE 3:e3913. 2008....  Mechanical force regulates integrin turnover in Drosophila in vivoMary Pines
Department of Cellular and Physiological Sciences, University of British Columbia, Life Science Institute, Vancouver, British Columbia V6T 1Z3, Canada
Nat Cell Biol 14:93543. 2012..We propose that integrinECM adhesive stability is continuously controlled by force in vivo through integrindependent autoregulatory feedback mechanisms so that tissues can quickly adapt to and withstand mechanical stresses...  Improving parameter estimation for cell surface FRAP dataOmer Dushek
Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2
J Biochem Biophys Methods 70:122431. 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...  Analysis of serial engagement and peptideMHC transport in T cell receptor microclustersOmer Dushek
Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, Canada
Biophys J 94:344760. 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...  Modeling effect of a γsecretase inhibitor on amyloidβ dynamics reveals significant role of an amyloid clearance mechanismRaibatak Das
Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC V6T 1Z2, Canada
Bull Math Biol 73:23047. 2011..These results point to the need for a more detailed investigation of soluble Aβ clearance mechanisms and their interaction with Aβreducing drugs...  Quantification and modeling of tripartite CD2, CD58FC chimera (alefacept), and CD16mediated cell adhesionMichael 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 282:3474857. 2007..These results suggest that additional information is needed to correctly predict Alefaceptmediated bridge formation...  Analysis of peptide/MHCinduced TCR downregulation: deciphering the triggering kineticsClemens Utzny
INSERM U563, Institut Claude de Preval, CHU Purpan, 31059 Toulouse Cedex 3, France
Cell Biochem Biophys 46:10111. 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...  A theoretical and experimental study of competition between solution and surface receptors for ligand in a Biacore flow cellXiaoyi He
Computational Modeling Center, Air Products and Chemicals, Inc, 7201 Hamilton Boulevard, Allentown, PA 18195, USA
Bull Math Biol 68:112550. 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...  T cell receptor binding kinetics required for T cell activation depend on the density of cognate ligand on the antigenpresenting cellPablo 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 102:48249. 2005..According to these results, effective T cell activation depends on a complex interplay between inherent TCRpMHC binding kinetics and the epitope density on the APC...  Activated TCRs remain marked for internalization after dissociation from pMHCDaniel Coombs
Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Nat Immunol 3:92631. 2002..We show here that kinetic proofreading provides an explanation for the different requirements for activation observed in naïve and memory T cells...  Optimizing withinhost viral fitness: infected cell lifespan and virion production rateMichael A Gilchrist
Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
J Theor Biol 229:2818. 2004..Our findings suggest that HIV replication rates should vary between cells with different life spans, as has been suggested by recent observation...  Optimal viral productionDaniel Coombs
Theoretical Biology and Biophysics Group, Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Bull Math Biol 65:100323. 2003..We present a general mathematical framework for studying problems of this type, which may be adapted to many hostparasite systems, and use it to examine the optimal virus production scheduling problem from the perspective of the virus...