Publications

31. Drawert, B., Jacob, B., Li, Z., Yi, T.-M. & Petzold, L. A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems. J. Comput. Phys. 378, 1–17 (2019). [PDF]


31b. Drawert, B., Jacob, B., Li, Z., Yi, T.-M. & Petzold, L. Validation data for a hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) method. Data Brief 22, 11–15 (2019). [PDF]


30. Trogdon, M. et al. The effect of cell geometry on polarization in budding yeast. PLoS Computational Biology 14, e1006241 (2018). [PDF]


29. Renardy, M., Yi, T.-M., Xiu, D. & Chou, C.-S. Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization. PLoS Computational Biology 14, e1006181.  (2018).


28. Banavar, S. P. et al. Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis PLOS Computational Biology 14, e1005940 (2018). [PDF]


27. Drawert, B., Hellander, S., Trogdon, M., Yi, T.-M. & Petzold, L. A framework for discrete stochastic simulation on 3D moving boundary domains. J Chem Phys 145, 184113 (2016).


26. Chen, W., Nie, Q., Yi, T.-M. & Chou, C.-S. Modelling of yeast mating reveals robustness strategies for cell-cell interactions. PLoS Computational Biology 12, e1004988 (2016). [PDF]


25. Chou, C.-S., Moore, T. I., Nie, Q. & Yi, T.-M. Alternative cell polarity behaviours arise from changes in G-protein spatial dynamics. IET Systems Biology, doi:10.1049/iet-syb.2013.0018 (2014). [PDF]


24. Lawson, M. J., Drawert, B., Khammash, M., Petzold, L. & Yi, T.-M. Spatial stochastic dynamics enable robust cell polarization. PLoS Computational Biology 9, e1003139 (2013). [PDF]


23. Moore, T. I., Tanaka, H., Kim, H. J., Jeon, N. L. & Yi, T.-M. Yeast G-proteins mediate directional sensing and polarization behaviors in response to changes in pheromone gradient direction. Mol. Biol. Cell 24, 521-534 (2013). [PDF]


22. Chou, C.-S., Moore, T. I., Chang, S., Nie, Q. & Yi, T.-M. Signaling Regulated Endocytosis and Exocytosis Lead to Mating Pheromone Concentration Dependent Morphologies in Yeast. FEBS Letters 586, 4208-4214 (2012). [PDF]

21. Chou, C.-S., Bardwell, L., Nie, Q. & Yi, T.-M. Noise filtering tradeoffs in spatial gradient sensing and cell polarization response. BMC Systems Biology 5, 196 (2011). [PDF]

20. Zheng, Z., Chou, C.-S., Yi, T.-M. & Nie, Q. Mathematical analysis of steady-state solutions in compartment and continuum models of cell polarization. Mathematical Biosciences and Engineering 8, 1135-1168 (2011). [PDF]

19. Tanaka, H. & Yi, T.-M. The effects of replacing Sst2 with the heterologous RGS4 on polarization and mating in yeast. Biophys. J. 99, 1007-1017 (2010). [PDF]

18. Tanaka, H. & Yi, T.-M. Reverse engineering a signaling network using alternative inputs. PLoS ONE 4, e7622 (2009). [PDF]

17. Tanaka, H. & Yi, T.-M. Synthetic morphology using alternative inputs. PLoS ONE 4, e6946 (2009). [PDF]

16. Moore, T. I., Chou, C.-S., Nie, Q., Jeon, N. L. & Yi, T.-M. Robust spatial sensing of mating pheromone gradients by yeast cells. PLoS ONE 3, e3865 (2008). [PDF]

15. Chou, C.-S., Nie, Q. & Yi, T.-M. Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients. PLoS ONE , e3103 (2008). [PDF]

14. Yi, T.-M., Chen, S., Chou, C.-S. & Nie, Q. Modeling yeast cell polarization induced by pheromone gradients. J. Stat. Phys. 128 , 193 - 207 (2007). [PDF]

13. Yi, T.-M., Andrews, B. W. & Iglesias, P. A. Control analysis of bacterial chemotaxis signaling. Methods in Enzymology 422 , 123 - 140 (2007).

12. Ingalls, B. P., Yi, T.-M. & Iglesias, P. A. in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts (eds. Szallasi, Z., Stelling, J. & Periwal, V.) (The MIT Press, Cambridge, MA, 2006).

11. Andrews, B. W., Yi, T.-M. & Iglesias, P. A. Optimal noise filtering in the chemotactic response of E. coli PLoS Comp. Biol. , 1407 - 1418 (2006). [PDF]

10. Tanaka, R., Yi, T.-M. & Doyle, J. Some protein interaction data do not exhibit power law statistics.FEBS Lett. 579 , 5140 - 5144 (2005). [PDF]

9. Yi, T.-M., Kitano, H. & Simon, M. I. A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci U S A 100 , 10764-9 (2003). [PDF] [Supplemental Data]

8. Yi, T.-M. in Foundations of Systems Biology (ed. Kitano, H.) (MIT Press, Boston, 2001).

7. Yi, T.-M., Huang, Y., Simon, M. I. & Doyle, J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl. Acad. Sci. USA 97 , 4649-4653 (2000). [PDF] [Supplemental Data] [Commentary]