Journal Papers

• Xiaole Li, Yulong Xing and Ching-Shan Chou. (2020).  Optimal energy conserving and energy dissipative local discontinuous Galerkin methods for the Benjamin-Bona-Mahony equation, Journal of Scientific Computing, 83:17.
• Xiaole Li, Weizhou Sun, Yulong Xing and Ching-Shan Chou. (2020).  Energy conserving local discontinuous Galerkin methods for the improved Boussinesq equation, Journal of Computational Physics, 401.
• Yanli Wang, Wing-Cheong Lo, and Ching-Shan Chou. (2020). Modeling stem cell aging: a multi-compartment continuum approach, Royal Society Open Science, 7(3):191848.
• Subhashis Hazarika, Ching-Shan Chou and Han-Wei Shen. (2020). NNVA: Neural network assisted visual analysis of yeast cell polarization simulation, IEEE Transaction on Visualization and Computer Graphics, 26(1), pp. 34-44. (Best paper honorable mention of IEEE VIS 2019)
• Kristi Miller, Wing-Cheong Lo, Ching-Shan Chou and Hay-Oak Park. (2019). Temporal regulation of cell polarity via the interaction of the Ras GTPase Rsr1 and the scaffold protein Bem1, Molecular Biology of the Cell, 30(20), pp. 2543-2557.
• Brenton Hall, Ching-Shan Chou and Jen-Ping Chen. (2019).  Using the non-uniform dynamic mode Decomposition to reduce the storage required for PDE simulations, International Journal of Aerospace Engineering, Volume 2019, Article ID 8291616, 15 pages.
• Ching-Shan Chou, Yukun Li and Dongbin Xiu. (2019).  Energy conserving Galerkin approximation of two dimensional wave equations with random coefficients, Journal of Computational Physics, 381, pp. 52-66.
• Muhammed Emin Ozturk, Marissa Renardy, Yukun Li, Gagan Agrawal and Ching-Shan Chou. (2018).  A novel approach for handling soft error in conjugate gradients, Proceedings of the 25th International Conference on High Performance Computing (HiPC), IEEE.
• Marissa Renardy, Dongbin Xiu, Tau-Mu Yi and Ching-Shan Chou. (2018).  Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization, PLoS Computational Biology, 14(5):e1006181.
• Betul Senay, Yongcheng Zhou, Adriana Dawes, and Ching-Shan Chou. (2018).  The importance of mechanical constraints for proper polarization and pseudo-cleavage furrow generation in early Caenorhabditis elegans embryo, PLoS Computational Biology, 14(7):e1006294.
• Marissa Renardy, Leili Shahriyari, Alexandra Jilkine and Ching-Shan Chou. (2018).  Control of cell fraction and population recovery during tissue regeneration in stem cell lineages, Journal of Theoretical Biology, 445, pp. 33-50.
• Yanli Wang, Wing-Cheong Lo and Ching-Shan Chou. (2017).  A modeling study of budding yeast colony formation and its relationship to budding pattern and aging, PLoS Computational Biology 13(11): e1005843.
• Ching-Shan Chou, Weizhou Sun, Yulong Xing and He Yang. (2017). Local discontinuous Galerkin methods for the Khokhlov-Zabolotskaya-Kuznetzov equation, Journal of Scientific Computing, 73, pp. 593-616.
• Yingda Cheng, Ching-Shan Chou Fengyan Li and Yulong Xing. (2017). L^2-stable discontinuous Galerkin methods for one-dimensional two-way wave equations, Mathematics of Computation, 86(303), pp. 121-155.
• Weitao Chen, Qing Nie, Tau-Mu Yi and Ching-Shan Chou. (2016). Modelling of yeast mating reveals robustness strategies for cell-cell interactions, PLoS Computational Biology, 12(7):e1004988.
• Weitao Chen, Ching-Shan Chou and Chiu-Yen Kao. (2016). Minimizing eigenvalues for inhomogeneous rods and plates, Journal of Scientific Computing, 69(3), pp. 983-1013.
• Mid Eum Lee, Wing-Cheong Lo, Kristi E. Miller, Ching-Shan Chou and Hay-Oak Park. (2015). Regulation of Cdc42 polarization by the Rsr1 GTPase and Rga1, a Cdc42 GTPase activating protein, in budding yeast, Journal of Cell Science 128, pp. 2106-2117.
• Weitao Chen, Ching-Shan Chou and Chiu-Yen Kao. (2015). Lax-Friedrichs multigrid fast sweeping methods for steady state problems for hyperbolic conservation laws, Journal of Scientific Computing, 64(3), pp. 591-618.
• Ching-Shan Chou, Travis Moore, Qing Nie and Tau-Mu Yi. (2015). Alternative cell polarity behaviours arise from changes in G-protein spatial dynamics, IET Systems Biology, 9(2), pp. 52-63.
• Wing-Cheong Lo, Hay-Oak Park and Ching-Shan Chou, (2014). Mathematical analysis of spontaneous emergence of cell polarity, Bulletin of Mathematical Biology, 76(8), pp. 1835-1865.
• Ching-Shan Chou, Chi-Wang Shu and Yulong Xing. (2014). Optimal energy conserving local discontinuous Galerkin methods for second-order wave equation in heterogeneous media, Journal of Computational Physics, 272(1), pp. 88-107.
• Yulong Xing, Ching-Shan Chou, Chi-Wang Shu. (2013). Energy conserving local discontinuous Galerkin methods for wave propagation problems, Inverse Problem and Imaging, 7(3), pp. 967-986.
• Wing-Cheong Lo, Mid Eum Lee, Monisha Narayan, Ching-Shan Chou and Hay-Oak Park. (2013). Polarization of diploid daughter cells directed by spatial cues and GTP hydrolysis of Cdc42 in budding yeast, PLoS ONE, 8(2): e56665.
• Weitao Chen, Ching-Shan Chou and Chiu-Yen Kao. (2013). Lax-Friedrichs fast sweeping methods for steady state problems for hyperbolic conservation laws, Journal of Computational Physics, 234, pp. 452-471.
• Ching-Shan Chou, Travis Moore, Qing Nie and Tau-Mu Yi. (2012). Signaling regulated endocytosis and exocytosis lead to mating pheromone concentration dependent morphologies in yeast, FEBS Letters, 586(23), pp. 4208-4214.
• *Chuan Xue, *Ching-Shan Chou, Chiu-Yen Kao, Chandan K. Sen and Avner Friedman. (2012). Propagation of cutaneous thermal injury: a mathematical model,Wound Repair and Regeneration, 20(1), pp. 114-122. (* equal contribution)
• Ching-Shan Chou, Qing Nie and Tau-Mu Yi. (2011). Noise filtering tradeoffs in spatial gradient sensing and cell polarization responses, BMC Systems Biology, 5(1):196.
• *Zhenzhen Zheng, *Ching-Shan Chou, Tau-Mu Yi and Qing Nie. (2011) Mathematical analysis of steady-state solutions in compartment and continuum models of cell polarization, Mathematical Biosciences and Engineering, 8(4), pp 1135-1168. (* equal contribution)
• Ching-Shan Chou, Wing-Cheong Lo, Kimberly K. Gokoffski, Yong-Tao Zhang, Frederic Y.M. Wan, Arthur D. Lander, Anne L. Calof and Qing Nie. (2010). Spatial dynamics of multistage cell lineages in tissue stratification, Biophysical Journal, 99(10), pp 3145-3154.
• Wing-Cheong Lo, Ching-Shan Chou, Kimberly K. Gokoffski, Frederic Y.M. Wan, Arthur D. Lander, Anne L. Calof and Qing Nie. (2009). Feedback regulation in multistage cell lineages, Mathematical Biosciences and Engineering, 6(1), pp 59-82.
• Travis I. Moore, Ching-Shan Chou, Qing Nie, Noo Li Joen and Tau-Mu Yi. (2008). Robust spatial sensing of mating pheromone gradients by yeast cells, PLoS ONE, 3(12):e3865.
• Ching-Shan Chou, Qing Nie and Tau-Mu Yi. (2008). Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients, PLoS ONE, 3(9):e3103.
• Tau-Mu Yi, Shanqin Chen, Ching-Shan Chou and Qing Nie. (2007). Modeling yeast cell polarization induced by pheromone gradients, Journal of Statistical Physics, 128(1), pp. 193-207.
• Ching-Shan Chou, Yong-Tao Zhang, Rui Zhao and Qing Nie. (2007). Numerical methods for stiff reaction-diffusion systems, Discrete and Continuous Dynamical Systems - Series B, 7(3), pp. 515-525.
• Ching-Shan Chou and Chi-Wang Shu. (2007). High order residual distribution conservative finite difference WENO schemes for convection-diffusion steady state problems on non-smooth meshes, Journal of Computational Physics, 224, pp. 992-1020.
• Ching-Shan Chou and Chi-Wang Shu. (2006). High order residual distribution conservative finite difference WENO schemes for steady state problems on non-smooth meshes, Journal of Computational Physics, 214, pp. 698-724.

Book

Introduction to Mathematical Biology (Modeling, Analysis, and Simulations), by Ching-Shan Chou and Avner Friedman, Springer International Publishing, 2016. (eBook ISBN: 978-3-319-29638-8; Hardcover ISBN: 978-3-319-29636-4)

MATLAB m-files are available for the numerical sections in this book.