| Yang, Y.-J., & Qian, H. Bivectorial Nonequilibrium Thermodynamics: Cycle Affinity, Vorticity Potential, and Onsager’s Principle. J Stat. Phys. 182, 46 (2021). |
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Biophysics, Dynamical Systems, Mathematical Biology, Mathematical Physics, Probability, Stochastic Modeling |
| Maass, K., Kim, M., & Aravkin, A. (2020). A nonconvex optimization approach to IMRT planning with dose-volume constraints. arXiv preprint arXiv:1907.10712. |
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Applied Mathematics, Cancer Modeling, Inverse Problems, Optimization and Variational Analysis |
| Phillips, Austin and Kot, Mark. (2015). Persistence in a two-dimensional moving-habitat model. Bulletin of Mathematical Biology, 77, 2125-2159. |
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Climate Modeling, Mathematical Biology |
| Barker, Blake, Rose Nguyen, Bjorn Sandstede, Nathaniel Ventura, and Colin Wahl. "Computing Evans functions numerically via boundary-value problems." Physica D: Nonlinear Phenomena. Accepted Dec 2017. |
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Computational Methods, Dynamical Systems, Mathematical Methods, Nonlinear Waves and Coherent Structures, Partial Differential Equations |
| Liu, Y.H., Smith, S.J., Mihalas S., Shea-Brown E., Sumbul U., “A solution to temporal credit assignment using cell-type-specific modulatory signals”, bioRxiv, 2020. |
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Machine Learning, Mathematical Neuroscience |
| Liu, Y.H., Smith, S.J., Mihalas S., Shea-Brown E., Sumbul U., “Cell-type–specific neuromodulation guides synaptic credit assignment in a spiking neural network”, Proceedings of the National Academy of Sciences, 2021. |
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Computer Science, Machine Learning, Mathematical Neuroscience |
| Ahlstrom, Austin, "Computational Regiospecific Analysis of Brain Lipidomic Profiles" (2019). Undergraduate Honors Theses. 70. https://scholarsarchive.byu.edu/studentpub_uht/70 |
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Applied Mathematics, Biochemistry, Machine Learning, Mathematical Biology |
| Angelini E, Wang Y, Zhou JX, Qian H, Huang S (2022) A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness. PLoS Comput Biol 18(7): e1010319. https://doi.org/10.1371/journal.pcbi.1010319 |
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Applied Mathematics, Cancer Modeling, Dynamical Systems, Mathematical Biology |
| Anne Greenbaum and Timothy P. Chartier. (2012) Numerical Methods: Design, Analysis, and Computer Implementation of Algorithms. Princeton University Press. |
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Computational Methods, Numerical Analysis |
| Anne Greenbaum. (1987) Iterative Methods for Solving Linear Systems. SIAM. |
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Applied Mathematics |
| Bradley C. Naylor, Christian N. K. Anderson, Marcus Hadfield, David H. Parkinson, Austin Ahlstrom, Austin Hannemann, Chad R. Quilling, Kyle J. Cutler, Russell L. Denton, Robert Adamson, Thomas E. Angel, Rebecca S. Burlett, Paul S. Hafen, John. C. Dallon, Mark K. Transtrum, Robert D. Hyldahl, and John C. Price.
"Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans" (Sep 2022).
Journal of Proteome Research 2022 21 (11), 2703-2714.
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Applied Mathematics, Biochemistry |
| Chen, X. and K. K. Tung: "Global surface warming enhanced by weak Atlantic overturning circulation", Nature, 559, 387-391, July 2018. |
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Atmospheric Sciences, Climate Modeling, Geophysics |
| Chen, X. and K. K. Tung: "Varying planetary heat sink led to global-warming slowdown and acceleration", Science, 345, 897 (2014) |
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Atmospheric Sciences, Climate Modeling, Geophysics |
| D. Rim, S. Moe, and R. J. LeVeque, Transport Reversal for Model Reduction of Hyperbolic Partial Differential Equations, SIAM/ASA Journal on Uncertainty Quantification 6(2018), pp. 118-150. doi:10.1137/17M1113679 |
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Applied Mathematics, Computational Methods, Numerical Analysis, Reduced-Order Models, Scientific Computing |
| Hong Qian and Daniel Beard. (2008) Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge University Press. |
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Biophysics |
| Hong Qian. (2017) Mathematical Kinetic Models: Applications in Biophysics and Biochemistry. Peking University Press. |
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Biochemistry, Biophysics |
| J. Nathan Kutz, Steven L. Brunton, Bingni W. Brunton, and Joshua Proctor (2016). Dynamic Mode Decomposition: Data-Driven Modeling of Complex Systems. SIAM. |
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Dynamical Systems |
| J. Nathan Kutz. (2013) Data-Driven Modeling & Scientific Computation: Methods for Complex Systems & Big Data. Oxford University Press. |
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Data Science |
| John B. Guerard, Jr., Introduction to financial forecasting in investment analysis, Springer, 2013. |
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Financial Mathematics |
| Ka-Kit Tung. (2007) Topics in Mathematical Modeling. Princeton University Press |
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Applied Mathematics |
| Le, V., Nagpal, C., & Dubrawski, A. (2023). Identification of patients with stable coronary artery disease who benefit from ACE inhibitors using Cox mixture model for heterogeneous treatment effects. Journal of Critical Care, 74, 154208. |
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Machine Learning |
| Liu, Benjamin R., and Elizabeth M. Cherry. "Image-based structural modeling of the cardiac Purkinje network." BioMed research international 2015 (2015). |
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Mathematical Biology, Mathematical Methods |
| Liu, Hexuan, Jimin Kim, and Eli Shlizerman. "Functional connectomics from neural dynamics: probabilistic graphical models for neuronal network of Caenorhabditis elegans." Philosophical Transactions of the Royal Society B: Biological Sciences 373.1758 (2018): 20170377. |
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Mathematical Neuroscience |
| Liu, Y.H., Baratin A., Cornford J., Mihalas S., Shea-Brown E., Lajoie G., “How connectivity structure shapes rich and lazy learning in neural circuits”, International Conference on Learning Representations (ICLR), 2024 (accepted). |
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Applied Mathematics, Computer Science, Machine Learning, Mathematical Neuroscience |
| Liu, Y.H., Ghosh A., Richards B. A., Shea-Brown E., Lajoie G., “Beyond accuracy: generalization properties of bio-plausible temporal credit assignment rules”, Advances in Neural Information Processing Systems, 2022. |
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Applied Linear Algebra, Applied Mathematics, Computer Science, Dynamical Systems, Machine Learning, Mathematical Neuroscience |
