Daniel Coombs
Professor
Research Classification
Cell Signaling and Infectious and Immune Diseases
Mathematics
Epidemiology
Research Interests
Mathematical biology
Cell biophysics
Immune cell signalling
Disease models
Relevant Degree Programs
Research Methodology
Super-resolution microscopy
Mathematical modelling of cell processes
Recruitment
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Master's students
Doctoral students
Any time / year round
Postdoctoral Fellows
-
Michael Irvine (Community Health / Public Health, Modelization and Simulation)
Graduate Student Supervision
Doctoral Student Supervision (2008-2018)
Master's Student Supervision (2010-2017)
Publications
- A novel Bayesian approach to predicting reductions in HIV incidence following increased testing interventions among gay, bisexual and other men who have sex with men in Vancouver, Canada. (2018)
Irvine MA and Konrad BP and Michelow W and Balshaw R and Gilbert M and Coombs D
Journal of the Royal Society, Interface - Limitations of Qdot labelling compared to directly-conjugated probes for single particle tracking of B cell receptor mobility. (2017)
Abraham L and Lu HY and Falcão RC and Scurll J and Jou T and Irwin B and Tafteh R and Gold MR and Coombs D
Scientific reports - On the duration of the period between exposure to HIV and detectable infection. (2017)
Konrad BP and Taylor D and Conway JM and Ogilvie GS and Coombs D
Epidemics - Sustained Reduction in Sexual Behavior that May Pose a Risk of HIV Transmission Following Diagnosis During Early HIV Infection Among Gay Men in Vancouver, British Columbia. (2017)
Gilbert M and Taylor D and Michelow W and Grace D and Balshaw R and Kwag M and Lim E and Fischer B and Patrick D and Ogilvie G and Coombs D and Steinberg M and Rekart M
AIDS and behavior - Applied stretch initiates directional invasion through the action of Rap1 GTPase as a tension sensor (2016)
Spencer A. Freeman and Sonja Christian and Pamela Austin and Irene Iu and Marcia L. Graves and Lin Huang and Shuo Tang and Daniel Coombs and Michael R. Gold and Calvin D. Roskelley
Journal of Cell Science 130 (1) 152--163 - Conditions for eradicating hepatitis C in people who inject drugs: A fibrosis aware model of hepatitis C virus transmission (2016)
Rozada, I. and Coombs, D. and Lima, V.D.
Journal of Theoretical Biology 395 31-39 - In vivo regulation of integrin turnover by outside-in activation (2016)
Lopez-Ceballos, P. and DonajiHerrera-Reyes, A. and Coombs, D. and Tanentzapf, G.
Journal of Cell Science 129 (15) 2912-2924 - Conditional mean first passage times to small traps in a 3-D domain with a sticky boundary: Applications to T cell searching behavior in lymph nodes (2015)
Delgado, M.I. and Ward, M.J. and Coombs, D.
Multiscale Modeling and Simulation 13 (4) 1224-1258 - Design Parameters for Granzyme-Mediated Cytotoxic Lymphocyte Target-Cell Killing and Specificity (2015)
Woodsworth, D.J. and Dunsing, V. and Coombs, D.
Biophysical Journal 109 (3) 477-488 - Erratum: Correction: The Impact of Implementing a Test, Treat and Retain HIV Prevention Strategy in Atlanta among Black Men Who Have Sex with Men with a History of Incarceration: A Mathematical Model (PLoS ONE (2015) 10:5 (e0128734) doi:10.1371/journal.po (2015)
Lima, V.D. and Graf, I. and Beckwith, C.G. and Springer, S. and Altice, F.L. and Coombs, D. and Kim, B. and Messina, L. and Montaner, J.S.G. and Spaulding, A.
PLoS ONE 10 (5) - Erratum: Toll-like receptor ligands sensitize B-cell receptor signalling by reducing actin-dependent spatial confinement of the receptor (2015)
Freeman, S.A. and Jaumouille, V. and Choi, K. and Hsu, B.E. and Wong, H.S. and Abraham, L. and Graves, M.L. and Coombs, D. and Roskelley, C.D. and Das, R. and Grinstein, S. and Gold, M.R.
Nature Communications 6 - In vivo quantitative analysis of Talin turnover in response to force (2015)
Hakonardottir, G.K. and Lopez-Ceballos, P. and Herrera-Reyes, A.D. and Das, R. and Coombs, D. and Tanentzapf, G.
Molecular Biology of the Cell 26 (22) 4149-4162 - Probability of a false-negative HIV antibody test result during the window period: a tool for pre- and post-test counselling (2015)
Taylor, D. and Durigon, M. and Davis, H. and Archibald, C. and Konrad, B. and Coombs, D. and Gilbert, M. and Cook, D. and Krajden, M. and Wong, T. and Ogilvie, G.
International Journal of STD and AIDS 26 (4) 215-224 - Sir-network model and its application to dengue fever (2015)
Stolerman, L.M. and Coombs, D. and Boatto, S.
SIAM Journal on Applied Mathematics 75 (6) 2581-2609 - The impact of implementing a test, treat and retain HIV prevention strategy in Atlanta among black men who have sex with men with a history of incarceration:A mathematical model (2015)
Lima, V.D. and Graf, I. and Beckwith, C.G. and Springer, S. and Altice, F.L. and Coombs, D. and Kim, B. and Messina, L. and Montaner, J.S.G. and Spaulding, A.
PLoS ONE 10 (4) - Toll-like receptor ligands sensitize B-cell receptor signalling by reducing actin-dependent spatial confinement of the receptor (2015)
Freeman, S.A. and Jaumouille, V. and Choi, K. and Hsu, B.E. and Wong, H.S. and Abraham, L. and Graves, M.L. and Coombs, D. and Roskelley, C.D. and Das, R. and Grinstein, S. and Gold, M.R.
Nature Communications 6 - Assessing the optimal virulence of malaria-targeting mosquito pathogens: A mathematical study of engineered Metarhizium anisopliae (2014)
Konrad, B.P. and Lindstrom, M. and Gumpinger, A. and Zhu, J. and Coombs, D.
Malaria Journal 13 (1) - Asymptotic Analysis of First Passage Time Problems Inspired by Ecology (2014)
Kurella, V. and Tzou, J.C. and Coombs, D. and Ward, M.J.
Bulletin of Mathematical Biology 77 (1) 83-125 - Regulatory vs. helper CD4+ T-cell ratios and the progression of HIV/AIDS disease (2014)
Wilfred Ndifon and Jonathan Dushoff and Daniel Coombs - Stochastic analysis of pre-and postexposure prophylaxis against hiv infection (2013)
Conway, J.M. and Konrad, B.P. and Coombs, D.
SIAM Journal on Applied Mathematics 73 (2) 904-928 - Mechanical force regulates integrin turnover in Drosophila in vivo (2012)
Pines, M. and Das, R. and Ellis, S.J. and Morin, A. and Czerniecki, S. and Yuan, L. and Klose, M. and Coombs, D. and Tanentzapf, G.
Nature Cell Biology 14 (9) 935-943 - Mechanical modulation of receptor-ligand interactions at cell-cell interfaces (2012)
Allard, J.F. and Dushek, O. and Coombs, D. and Anton Van Der Merwe, P.
Biophysical Journal 102 (6) 1265-1273 - A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies (2011)
Gutenkunst, R.N. and Coombs, D. and Starr, T. and Dustin, M.L. and Goldstein, B.
PLoS ONE 6 (5) - A stochastic model of latently infected cell reactivation and viral blip generation in treated HIV patients (2011)
Conway, J.M. and Coombs, D.
PLoS Computational Biology 7 (4) - Antigen potency and maximal efficacy reveal a mechanism of efficient T cell activation (2011)
Dushek, O. and Aleksic, M. and Wheeler, R.J. and Zhang, H. and Cordoba, S.-P. and Peng, Y.-C. and Chen, J.-L. and Cerundolo, V. and Dong, T. and Coombs, D. and Van Der Merwe, P.A.
Science Signaling 4 (176) - Modeling effect of a γ-secretase inhibitor on amyloid-β dynamics reveals significant role of an amyloid clearance mechanism (2011)
Das, R. and Nachbar, R.B. and Edelstein-Keshet, L. and Saltzman, J.S. and Wiener, M.C. and Bagchi, A. and Bailey, J. and Coombs, D. and Simon, A.J. and Hargreaves, R.J. and Cook, J.J.
Bulletin of Mathematical Biology 73 (1) 230-247 - Modeling Membrane Domains (2011)
Coombs, D. and Das, R. and Morrison, J.S.
Cellular Domains 71-84 - Reverse engineering an amyloid aggregation pathway with dimensional analysis and scaling (2011)
Bailey, J. and Potter, K.J. and Verchere, C.B. and Edelstein-Keshet, L. and Coombs, D.
Physical Biology 8 (6) - Vaccination against 2009 pandemic H1N1 in a population dynamical model of Vancouver, Canada: Timing is everything (2011)
Conway, J.M. and Tuite, A.R. and Fisman, D.N. and Hupert, N. and Meza, R. and Davoudi, B. and English, K. and Van Den Driessche, P. and Brauer, F. and Ma, J. and Meyers, L.A. and Smieja, M. and Greer, A. and Skowronski, D.M. and Buckeridge, D.L. and Kwong, J.C. and Wu, J. and Moghadas, S.M. and Coombs, D. and Brunham, R.C. and Pourbohloul, B.
BMC Public Health 11 - Dependence of T Cell Antigen Recognition on T Cell Receptor-Peptide MHC Confinement Time (2010)
Aleksic, M. and Dushek, O. and Zhang, H. and Shenderov, E. and Chen, J.-L. and Cerundolo, V. and Coombs, D. and van der Merwe, P.A.
Immunity 32 (2) 163-174 - Dynamic regulation of CD45 lateral mobility by the spectrin-ankyrin cytoskeleton of T Cells (2010)
Cairo, C.W. and Das, R. and Albohy, A. and Baca, Q.J. and Pradhan, D. and Morrow, J.S. and Coombs, D. and Golan, D.E.
Journal of Biological Chemistry 285 (15) 11392-11401 - Microelastohydrodynamics of swimming organisms near solid boundaries in complex fluids (2010)
Balmforth, N.J. and Coombs, D. and Pachmann, S.
Quarterly Journal of Mechanics and Applied Mathematics 63 (3) 267-294 - The space and time frames of T cell activation at the immunological synapse (2010)
Valitutti, S. and Coombs, D. and Dupre, L.
FEBS Letters 584 (24) 4851-4857 - A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton (2009)
Das, R. and Cairo, C.W. and Coombs, D.
PLoS Computational Biology 5 (11) - A role for rebinding in rapid and reliable T cell responses to antigen (2009)
Dushek, O. and Das, R. and Coombs, D.
PLoS Computational Biology 5 (11) - Analysis of membrane-localized binding kinetics with FRAP (2008)
Dushek, O. and Das, R. and Coombs, D.
European Biophysics Journal 37 (5) 627-638 - Analysis of serial engagement and peptide-MHC transport in T cell receptor microclusters (2008)
Dushek, O. and Coombs, D.
Biophysical Journal 94 (9) 3447-3460 - Effects of intracellular calcium and actin cytoskeleton on TCR mobility measured by fluorescence recovery (2008)
Dushek, O. and Mueller, S. and Soubies, S. and Depoil, D. and Caramalho, I. and Coombs, D. and Valitutti, S.
PLoS ONE 3 (12) - Improving parameter estimation for cell surface FRAP data. (2008)
Dushek, O. and Coombs, D.
Journal of biochemical and biophysical methods 70 (6) 1224-1231 - Kinetic proofreading model (2008)
Goldstein, B. and Coombs, D. and Faeder, J.R. and Hlavacek, W.S.
Advances in Experimental Medicine and Biology 640 82-94 - Evaluating the importance of within- and between-host selection pressures on the evolution of chronic pathogens (2007)
Coombs, D. and Gilchrist, M.A. and Ball, C.L.
Theoretical Population Biology 72 (4) 576-591 - Modeling within-host evolution of HIV: Mutation, competition and strain replacement (2007)
Ball, C.L. and Gilchrist, M.A. and Coombs, D.
Bulletin of Mathematical Biology 69 (7) 2361-2385 - Quantification and modeling of tripartite CD2-, CD58FC chimera (Alefacept)-, and CD16-mediated cell adhesion (2007)
Dustin, M.L. and Starr, T. and Coombs, D. and Majeau, G.R. and Meier, W. and Hochman, P.S. and Douglass, A. and Vale, R. and Goldstein, B. and Whitty, A.
Journal of Biological Chemistry 282 (48) 34748-34757 - A theoretical and experimental study of competition between solution and surface receptors for ligand in a biacore flow cell (2006)
He, X. and Coombs, D. and Myszka, D.G. and Goldstein, B.
Bulletin of Mathematical Biology 68 (5) 1125-1150 - Analysis of peptide/MHC-induced TCR downregulation: Deciphering the triggering kinetics (2006)
Utzny, C. and Coombs, D. and Muller, S. and Valitutti, S.
Cell Biochemistry and Biophysics 46 (2) 101-111 - Evolution of virulence: Interdependence, constraints, and selection using nested models (2006)
Gilchrist, M.A. and Coombs, D.
Theoretical Population Biology 69 (2) 145-153 - T cell activation: Kinetic proofreading, serial engagement and cell adhesion (2005)
Coombs, D. and Goldstein, B.
Journal of Computational and Applied Mathematics 184 (1) 121-139 - T cell receptor binding kinetics required for T cell activation depend on the density of cognate ligand on the antigen-presenting cell (2005)
Gonzalez, P.A. and Carreno, L.J. and Coombs, D. and Mora, J.E. and Palmieri, E. and Goldstein, B. and Nathenson, S.G. and Kalergis, A.M.
Proceedings of the National Academy of Sciences of the United States of America 102 (13) 4824-4829 - 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. (2004)
Nelson PW and Gilchrist MA and Coombs D and Hyman JM and Perelson AS
Mathematical biosciences and engineering : MBE - Effects of the geometry of the immunological synapse on the delivery of effector molecules (2004)
Coombs, D. and Goldstein, B.
Biophysical Journal 87 (4) 2215-2220 - Equilibrium Thermodynamics of Cell-Cell Adhesion Mediated by Multiple Ligand-Receptor Pairs (2004)
Coombs, D. and Dembo, M. and Wofsy, C. and Goldstein, B.
Biophysical Journal 86 (3) 1408-1423 - Equilibrium thermodynamics of cell-cell adhesion mediated by multiple ligand-receptor pairs. (2004)
Coombs D and Dembo M and Wofsy C and Goldstein B
Biophysical journal - Optimizing within-host viral fitness: Infected cell lifespan and virion production rate (2004)
Gilchrist, M.A. and Coombs, D. and Perelson, A.S.
Journal of Theoretical Biology 229 (2) 281-288 - Optimal Viral Production (2003)
Coombs, D. and Gilchrist, M.A. and Percus, J. and Perelson, A.S.
Bulletin of Mathematical Biology 65 (6) 1003-1023 - Activated TCRs remain marked for internalization after dissociation from pMHC (2002)
Coombs, D. and Kalergis, A.M. and Nathenson, S.G. and Wofsy, C. and Goldstein, B.
Nature Immunology 3 (10) 926-931 - Erratum: Activated TCRs remain marked for internalization after dissociation from pMHC (Nature Immunology (2002) vol. 3 (926-931)) (2002)
Coombs, D. and Kalergis, A.M. and Nathenson, S.G. and Wofsy, C. and Goldstein, B.
Nature Immunology 3 (11) - Periodic chirality transformations propagating on bacterial flagella (2002)
Coombs, D. and Huber, G. and Kessler, J.O. and Goldstein, R.E.
Physical Review Letters 89 (11) - Periodic chirality transformations propagating on bacterial flagella. (2002)
Coombs D and Huber G and Kessler JO and Goldstein RE
Physical review letters - Calculations Show Substantial Serial Engagement of T Cell Receptors (2001)
Carla Wofsy and Daniel Coombs and Byron Goldstein
Biophysical Journal 80 (2) 606--612 - Calculations show substantial serial engagement of T cell receptors (2001)
Wofsy, C. and Coombs, D. and Goldstein, B.
Biophysical Journal 80 (2) 606-612 - The influence of transport on the kinetics of binding to surface receptors: Application to cells and BIAcore (1999)
Goldstein, B. and Coombs, D. and He, X. and Pineda, A.R. and Wofsy, C.
Journal of Molecular Recognition 12 (5) 293-299
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