Publications - Dan Coombs

[ My UBC home page | UBC Math dept ]

  1. L. Abraham, H.Y. Lu, R.C. Falcao, J. Scurll, T. Jou, B. Irwin, R. Tafteh, M.R. Gold and D. Coombs. Limitations of Qdot labelling compared to directly-conjugated probes for single particle tracking of B cell receptor mobility. Scientific Reports 7:11379 (2017). DOI: 10.1038/s41598-017-11563-9.

  2. D. Coombs and B. Goldstein. Spatial Kinetics in Immunological Modeling. To appear in: Systems Immunology: An Introduction to Modeling Methods for Scientists, a book edited by J. Das and C. Jayaprakash (CRC Press).

  3. B.P. Konrad, D. Taylor, J.M. Conway, G. Ogilvie and D. Coombs. On the duration of the period between exposure to HIV and detectable infection. Epidemics 20:73-83 (2017). DOI: 10.1016/j.epidem.2017.03.002.

  4. M. Gilbert, D. Taylor, W. Michelow, D. Grace, R. Balshaw, M. Kwag, E. Lim, B. Fischer, D. Patrick, G. Ogilvie, D. Coombs, M. Steinberg and M. Rekart. 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. AIDS and Behavior (2017). DOI:10.1007/s10461-017-1702-0.

  5. S.A. Freeman, I. Lu, P. Austin, M.L. Graves, S. Christian, L. Huang, S. Tang, D. Coombs, M.R. Gold and C. Roskelley. Applied stretch regulates directional invasion via the action of Rap1 GTPase as a tension sensor. Journal of Cell Science, 130:152-163 (2017). DOI:10.1242/jcs.180612.

  6. P. Lopez-Ceballos, A.D. Herrera-Reyes, D. Coombs and G. Tanentzapf. In vivo regulation of integrin turnover by outside-in activation. Journal of Cell Science, 129:2912-2924 (2016). DOI:10.1242/jcs.190256.

  7. I. Rozada, D. Coombs and V.D. Lima. Conditions for eradicating Hepatitis C in people who inject drugs: a fibrosis aware model of Hepatitis C virus transmission. Journal of Theoretical Biology, 395:31-39 (2016). DOI:10.1016/j.jtbi.2016.01.030.

  8. G.K. Hakonardottir, P. Lopez-Ceballos, A.D. Herrera-Reyes, R. Das, D. Coombs and G. Tanentzapf. In Vivo Quantitative Analysis of Talin turnover in response to force. Molecular Biology of the Cell, mbc.E15-05-0304 (2015). DOI:10.1091/mbc.E15-05-0304.

  9. L.M. Stolerman, D. Coombs and S. Boatto. SIR-Network model and its application to Dengue fever. SIAM Journal of Applied Mathematics 75:2581-2609 (2015) DOI:10.1137/140996148. This paper was highlighted as a SIAM Nugget, Dec 23, 2015. Also a piece from the Brazilian Society for Tropical Medicine (in Portugese): link here.

  10. M.I. Delgado, M.J. Ward and D. Coombs. Conditional mean first passage times to small traps in a 3-D domain with a sticky boundary: Applications to T cell searching behaviour in lymph nodes. SIAM Multiscale Modeling and Simulation 13:1224-1258 (2015) DOI:10.1137/140978314.

  11. D.J. Woodsworth, V. Dunsing and D. Coombs. Design parameters for granzyme-mediated cytotoxic lymphocyte target-cell killing and specificity. Biophysical Journal 109:477-488 (2015). DOI:10.1016/j.bpj.2015.06.045.

  12. V.D. Lima, I. Graf, C.G. Beckwith, S. Springer, D. Coombs, F. Altice, B. Kim, L. Messina, J. Montaner and A. Spaulding. 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 10(4): e0123482 (2015). DOI:10.1371/journal.pone.0123482.

  13. V. Kurella, J. Tzou, D. Coombs and M.J. Ward. Asymptotic Analysis of First Passage Time Problems Inspired by Ecology. Bulletin of Mathematical Biology 77:83-125 (2014). DOI:10.1007/s11538-014-0053-5.

  14. S.A. Freeman, V. Jamouille, K. Choi, B.E. Hsu, H.S. Wong, L. Abraham, M.L. Graves, D. Coombs, C.D. Roskelley, R. Das, S. Grinstein and M.R. Gold. Toll-like receptor ligands sensitize B-cell receptor signalling by reducing actin-dependent spatial confinement of the receptor. Nature Communications, 6, 6168 (2015). DOI:10.1038/ncomms7168.

  15. D. Taylor, M. Durigon, H. Davis, C. Archibald, B. Konrad, D. Coombs, M. Gilbert, D. Cook, M. Krajden, T. Wong and G. Ogilvie. Probability of a false negative HIV antibody test result during the window period: a tool for pre- and post-test counselling. International Journal of STD and AIDS. DOI:10.1177/0956462414542987.

  16. B.P. Konrad, M. Lindstrom, A. Gumpinger, J. Zhu and D. Coombs. Assessing the optimal virulence of malaria-targeting mosquito pathogens: a mathematical study of engineered Metarhizium anisopliae. Malaria Journal, 13(1), 11 (2014). DOI:10.1186/1475-2875-13-11. As part of the course SCIE300, Communicating Science, UBC students made a blog post and short video on Malaria, which includes some description of this paper. Link to their work.

  17. J.M. Conway, B.P. Konrad and D. Coombs. Stochastic analysis of pre- and post-exposure prophylaxis against HIV infection. SIAM Journal of Applied Mathematics, 73(2):904-928 (2013). DOI:10.1137/120876800. This paper was highlighted as a SIAM Nugget, May 31, 2013.

  18. M. Pines, R. Das, S.J. Ellis, A. Morin, S. Czerniecki, L. Yuan, M. Klose, D. Coombs and G. Tanentzapf. Mechanical force regulates integrin turnover in Drosophila in vivo. Nature Cell Biology 14:935-943 (2012) DOI:10.1038/ncb2555. News and views by He and Montell in the same issue.

  19. J.F. Allard, O. Dushek, D. Coombs and P.A. van der Merwe. Mechanical modulation of receptor-ligand interactions at cell-cell interfaces. Biophysical Journal, 102:1265-1273 (2012) DOI:10.1016/j.bpj.2012.02.006.

  20. J.M. Conway, A.R. Tuite, D.N. Fisman, N. Hupert, R. Meza, B. Davoudi, K. English, P. van den Driessche, F. Brauer, J. Ma, L. Ancel Meyers, M. Smieja, A. Greer, D.M. Skowronski, D.L. Buckeridge, J.C. Kwong, J. Wu, S.M. Moghadas, D. Coombs, R.C. Brunham and B. Pourbohloul. Vaccination against 2009 pandemic H1N1 in a population dynamical model of Vancouver, Canada: timing is everything. BMC Public Health 11:932 (2011) DOI:10.1186/1471-2458-11-932.

  21. J. Bailey, K.J. Potter, B. Verchere, L. Edelstein-Keshet and D. Coombs. Reverse engineering an amyloid aggregation pathway with dimensional analysis and scaling. Physical Biology 8:066009 (2011) DOI:10.1088/1478-3975/8/6/066009.

  22. O. Dushek, M. Aleksic, R. J. Wheeler, H. Zhang, S.-P. Cordoba, Y.-C. Peng, J.-L. Chen, V. Cerundolo, T. Dong, D. Coombs, P. A. van der Merwe, Antigen potency and maximal efficacy reveal a mechanism of efficient T cell activation. Science Signaling, 4: ra39 (2011) DOI:10.1126/scisignal.2001430.
  23. R.N. Gutenkunst, D. Coombs, T. Starr, M.L. Dustin and B. Goldstein. A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies. PLoS ONE 6(5): e19701 (2011) DOI:10.1371/journal.pone.0019701.

  24. J.M. Conway and D. Coombs. A stochastic model of latently infected cell reactivation and viral blip generation in treated HIV patients. PLoS Computational Biology, 7(4):e1002033 (2011) DOI:10.1371/journal.pcbi.1002033. Aspects of HIV infection, including some parts of this paper, were described in a blog post and short video made by UBC students Stefania Gorgopa, Nahal Haghbin, and Garkin Lo in the SCIE300 Communicating Science class. Link to their work. Note to self: tidy office before filming starts.

  25. D. Coombs, R. Das and J.S. Morrison. Modeling membrane domains. In Cellular Domains, Wiley 2011 (Ed. I.R. Nabi).

  26. D. Coombs, O. Dushek and P.A. van der Merwe. A review of mathematical models for T cell receptor triggering and antigen discrimination. In Mathematical Models and Immune Cell Biology, Springer 2011 (Ed. C. Molina-Paris and G. Lythe).
  27. S. Valitutti, D. Coombs and L. Dupre. The space and time frames of T cell activation at the immunological synapse. FEBS Letters, 584:4851-4857 (2010) DOI:10.1016/j.febslet.2010.10.010
  28. N.J. Balmforth, D. Coombs and S. Pachmann. Microelastohydrodynamics of swimming organisms near solid boundaries in complex fluids. Quarterly Journal of Mechanics and Applied Mathematics, 63:267-294 (2010) DOI:10.1093/qjmam/hbq011

  29. C.W. Cairo, R. Das, A. Albohy, Q.J. Baca, D. Pradhan, J.S. Morrow, D. Coombs and D.E. Golan. Dynamic regulation of CD45 lateral mobility by the spectrin-ankyrin cytoskeleton of T cells. Journal of Biological Chemistry, 285:11392-11401 (2010). DOI:10.1074/jbc.M109.075648
  30. R. Das, R.B. Nachbar, J.S. Saltzman, A. Bagchi, J. Bailey, L. Edelstein-Keshet, D. Coombs, L. Cook, R. Hargreaves and A. Simon. Modeling effect of a gamma-secretase inhibitor on amyloid-beta dynamics reveals significant role of an amyloid clearance mechanism. Bulletin of Mathematical Biology, 73:230-247 (2011) DOI:10.1007/s11538-010-9540-5

  31. O. Dushek, R. Das and D. Coombs. A role for rebinding in rapid and reliable T cell responses to antigen. PLoS Computational Biology, 5(11):e1000578 DOI:10.1371/journal.pcbi.1000578
  32. M. Aleksic, O. Dushek, H. Zhang, E. Shenderov, J.-L. Chen, V. Cerundolo, D. Coombs and P.A. van der Merwe. Dependence of T cell antigen recognition on TCR/pMHC confinement time. Immunity, 32(2):163-174 (2010). DOI:10.1016/j.immuni.2009.11.013
    Preview by Govern and Chakraborty DOI:10.1016/j.immuni.2010.02.005
  33. R. Das, C.W. Cairo and D. Coombs. A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton. PLoS Computational Biology, 5(11):e1000556 DOI:10.1371/journal.pcbi.1000556
  34. D. Coombs, R. Straube and M. Ward. Diffusion on a sphere with localized traps: Mean first passage time, eigenvalue asymptotics, and Fekete points. SIAM Journal of Applied Mathematics, 70:302-332 DOI:10.1137/080733280
  35. O. Dushek, S. Muller, S. Soubies, D. Depoil, I. Caramalho, D. Coombs and S. Valitutti, Effects of intracellular calcium and actin cytoskeleton on TCR mobility PLoS One, 3(12): e3913. DOI:10.1371/journal.pone.0003913
  36. O. Dushek, R. Das and D. Coombs. Analysis of membrane-localized binding kinetics with FRAP. European Biophysical Journal, DOI:10.1007/s00249-008-0286-z
  37. B. Goldstein, D. Coombs, J. R. Faeder and W. S. Hlavacek (2008) Kinetic proofreading model. Adv. Exp. Med. Biol. 640, 82-94. In Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease (A.B. Sigalov, Editor), Ch. 8. Landes Bioscience, Austin, TX. ISBN: 978-0-387-09788-6 Landes Bioscience
  38. O. Dushek and D. Coombs. Analysis of serial engagement and peptide-MHC transport in T cell receptor microclusters. Biophysical Journal, DOI:10.1529/biophysj.107.116897
  39. D. Coombs, C.L. Ball and M.A. Gilchrist. Competition among viruses at the within- and between-host scales. (Conference proceedings, Nonlinear Theory and Applications, Vancouver 2007). PDF
  40. O. Dushek and D. Coombs. Improving parameter estimation for cell surface FRAP data. Journal of Biochemical and Biophysical Methods 70:1224-1231 (2008). DOI:10.1016/j.jbbm.2007.07.002
  41. D. Coombs, M.A. Gilchrist and C.L. Ball. Evaluating the importance of within- and between-host selection pressures on the evolution of chronic pathogens. Theoretical Population Biology 72:576-591 (2007). DOI:10.1016/j.tpb.2007.08.005
  42. M.L. Dustin, T. Starr, D. Coombs, G.R. Majeau, W. Meier, P.S. Hochman, A. Douglass, R. Vale, B. Goldstein and A. Whitty. Quantification and modeling of tripartite CD2, CD58FC chimera (ALEFACEPT) and CD16 mediated cell adhesion. Journal of Biological Chemistry 282:34748-34757 (2007). DOI:10.1074/jbc.M705616200
  43. C.L. Ball, M.A. Gilchrist and D. Coombs. Modeling within-host evolution of HIV: mutation, competition and strain replacement. Bulletin of Mathematical Biology 69:2361-2385 (2007). DOI:10.1007/s11538-007-9223-z
  44. C. Utzny*, D. Coombs*, S. Muller and S. Valitutti. Analysis of peptide/MHC induced TCR downregulation: deciphering the triggering kinetics. *Joint first author. Cell Biochemistry and Biophysics, 46:101-112 (2006).
  45. X. He, D. Coombs, D.G. Myzska and B. Goldstein. Competition between solution and surface receptors for ligand: blocking rebinding during dissociation in a Biacore flow cell. Bulletin of Mathematical Biology 68:1125-1150 (2006).
  46. M.A. Gilchrist and D. Coombs, The evolution of virulence: interdependence, constraints and selection using nested models. Theoretical Population Biology 69:145-153 (2006). [PDF]
  47. P.A. Gonzalez, L.J. Carreno, D. Coombs, J.E. Mora, E. Palmieri, B. Goldstein, S.G. Nathenson, and A.M. Kalergis. Effects of pMHC density and TCR dwell time on T cell activation. Proceedings of the National Academy of Sciences USA 102:4824-4829 (2005). [PDF]

  48. D. Coombs and B. Goldstein, T Cell Activation: Kinetic Proofreading, Serial Engagement and Cell Adhesion. Journal of Computational and Applied Mathematics 184:121-139 (2005). [Preprint PDF]
  49. D. Coombs and B. Goldstein, Effects of the geometry of the immunological synapse on the delivery of effector molecules. Biophysical Journal 87:2215-2220 (2004) . [PDF]
  50. P.W. Nelson, M.A. Gilchrist, D. Coombs, J.M. Hyman & A.S. Perelson. 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 and Engineering 1:267-288 (2004). [PDF]
  51. M.A. Gilchrist, D. Coombs and A.S. Perelson, Optimizing within host viral fitness: Infected cell lifespan and virion production rate. Journal of Theoretical Biology 229: 281-288 (2004). [PDF]
  52. D. Coombs, M. Dembo, C. Wofsy and B. Goldstein, Equilibrium thermodynamics of cell-cell adhesion mediated by multiple ligand-receptor pairs. Biophysical Journal 86:1408-1423 (2004). [PDF]
  53. D. Coombs, M.A. Gilchrist, J. Percus and A.S. Perelson, Optimal viral production. Bulletin of Mathematical Biology 65:1003-1023 (2003). [PDF]
  54. D. Coombs, A.M. Kalergis, S.G. Nathenson, C. Wofsy and B. Goldstein, Activated TCR remain marked for internalization after dissociation from peptide-MHC. Nature Immunology 3:926- 931 (2002). [PDF] Supplementary material [PDF] [Commentary, News and Views, pp. 895-896.][PDF]
  55. D. Coombs, G. Huber, J.O. Kessler and R.E. Goldstein, Periodic chirality transformations propagating on bacterial flagella. Physical Review Letters 89:118102 (2002).[PDF]
  56. D. Coombs, C. Wofsy and B. Goldstein, The roles of serial engagement and kinetic proofreading in peptide-induced TCR down-regulation. (Conference proceedings, Mathematical Theory of Networks and Systems, Notre Dame 2002). [PDF]
  57. C. Wofsy, D. Coombs and B. Goldstein, Calculations show substantial serial engagement of T cell receptors. Biophysical Journal 80:606-612 (2001) [PDF]
  58. B. Goldstein, D. Coombs, X. He, A.R. Pineda and C. Wofsy, The influence of transport on the kinetics of binding to surface receptors: application to cells and BIAcore. Journal of Molecular Recognition 12:293-299 (1999) [PDF]