Publications

1. Wong T, Böttcher L, Chou T, D'Orsogna MR. Alcohol-induced deaths in the United States across age, race, gender, geography, and the COVID-19 pandemic.. PLOS global public health, 2025.
2. Zhang J, Li X, Guo X, You Z, Böttcher L, Mogilner A, Hoffmann A, Chou T, Xia M. Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations.. PLoS computational biology, 2025.
3. Böttcher L, D'Orsogna MR, Chou T. Correction: Aggregating multiple test results to improve medical decision-making.. PLoS computational biology, 2025.
4. Böttcher L, D'Orsogna MR, Chou T. Aggregating multiple test results to improve medical decision-making.. PLoS computational biology, 2025.
5. Xia M, Chou T. Kinetic theories of state- and generation-dependent cell populations.. Physical review. E, 2024.
6. Li X, Chou T. Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies.. PLoS computational biology, 2024.
7. Mao S, Chou T, D'Orsogna MR. A probabilistic model of relapse in drug addiction.. Mathematical biosciences, 2024.
8. Xia M, Li X, Chou T. Overcompensation of transient and permanent death rate increases in age-structured models with cannibalistic interactions.. ArXiv, 2024.
9. Wang Y, Shtylla B, Chou T. Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm.. Bulletin of mathematical biology, 2024.
10. Böttcher L, Chou T, D'Orsogna MR. Forecasting drug-overdose mortality by age in the United States at the national and county levels.. PNAS nexus, 2024.
11. Li X, Chou T. Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.. The Journal of chemical physics, 2023.
12. Li X, Habibipour S, Chou T, Yang OO. The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus.. Virus evolution, 2023.
13. Böttcher L, Wald S, Chou T. Mathematical Characterization of Private and Public Immune Receptor Sequences.. Bulletin of mathematical biology, 2023.
14. Li X, Chou T. Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.. ArXiv, 2023.
15. Wang Y, Shtylla B, Chou T. Order-of-mutation effects on cancer progression: models for myeloproliferative neoplasm.. medRxiv : the preprint server for health sciences, 2023.
16. Wang Y, Shtylla B, Chou T. Order-of-mutation effects on cancer progression: models for myeloproliferative neoplasm.. ArXiv, 2023.
17. Li X, Habibipour S, Chou T, Yang OO. The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus.. ArXiv, 2023.
18. Böttcher L, Chou T, D'Orsogna MR. Modeling and forecasting age-specific drug overdose mortality in the United States.. The European physical journal. Special topics, 2023.
19. Böttcher L, Chou T, D'Orsogna MR. Modeling and forecasting age-specific drug overdose mortality in the United States.. ArXiv, 2023.
20. D'Orsogna MR, Böttcher L, Chou T. Fentanyl-driven acceleration of racial, gender and geographical disparities in drug overdose deaths in the United States.. PLOS global public health, 2023.
21. Masoomy H, Chou T, Böttcher L. Impact of random and targeted disruptions on information diffusion during outbreaks.. Chaos (Woodbury, N.Y.), 2023.
22. Pan Y, D'Orsogna MR, Tang M, Stiehl T, Chou T. Clonal abundance patterns in hematopoiesis: Mathematical modeling and parameter estimation.. Frontiers in systems biology, 2023.
23. Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling.. Biophysical journal, 2022.
24. Wang Y, Mistry BA, Chou T. Discrete stochastic models of SELEX: Aptamer capture probabilities and protocol optimization.. The Journal of chemical physics, 2022.
25. Wang Y, Dessalles R, Chou T. Modelling the impact of birth control policies on China's population and age: effects of delayed births and minimum birth age constraints.. Royal Society open science, 2022.
26. Dessalles R, Pan Y, Xia M, Maestrini D, D'Orsogna MR, Chou T. How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation.. Frontiers in immunology, 2022.
27. Chou T, D'Orsogna MR. A mathematical model of reward-mediated learning in drug addiction.. Chaos (Woodbury, N.Y.), 2022.
28. Zuo X, Chou T. Density- and elongation speed-dependent error correction in RNA polymerization.. Physical biology, 2022.
29. Markaki Y, Chong JG, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Sch?neberg J, Heard E, Guttman M, Chou T, Plath K. Xist nucleates local protein gradients to propagate silencing across the X chromosome.. Cell, 2021.
30. Böttcher L, D'Orsogna MR, Chou T. A statistical model of COVID-19 testing in populations: effects of sampling bias andtesting errors.. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 2021.
31. Markaki Y, Gan Chong J, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, Guttman M, Chou T, Plath K. Xist nucleates local protein gradients to propagate silencing across the X chromosome.. Cell, 2021.
32. Pardridge WM, Chou T. Mathematical Models of Blood-Brain Barrier Transport of Monoclonal Antibodies Targeting the Transferrin Receptor and the Insulin Receptor.. Pharmaceuticals (Basel, Switzerland), 2021.
33. Böttcher L, D'Orsogna MR, Chou T. A statistical model of COVID-19 testing in populations: effects of sampling bias and testing errors.. medRxiv : the preprint server for health sciences, 2021.
34. Böttcher L, D'Orsogna MR, Chou T. Using excess deaths and testing statistics to determine COVID-19 mortalities.. European journal of epidemiology, 2021.
35. Wylie J, Chou T. Uniformly accurate nonlinear transmission rate models arising from disease spread through pair contacts.. Physical review. E, 2021.
36. Böttcher L, D'Orsogna MR, Chou T. Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities.. medRxiv : the preprint server for health sciences, 2021.
37. Böttcher L, D'Orsogna MR, Chou T. Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities.. ArXiv, 2021.
38. Yang Z, Olszewski D, He C, Pintea G, Lian J, Chou T, Chen RC, Shtylla B. Machine learning and statistical prediction of patient quality-of-life after prostate radiation therapy.. Computers in biology and medicine, 2020.
39. Cheng X, D'Orsogna MR, Chou T. Mathematical modeling of depressive disorders: Circadian driving, bistability and dynamical transitions.. Computational and structural biotechnology journal, 2020.
40. Böttcher L, Xia M, Chou T. Why case fatality ratios can be misleading: individual- and population-based mortality estimates and factors influencing them.. Physical biology, 2020.
41. Böttcher L, Xia M, Chou T. Why estimating population-based case fatality rates during epidemics may be misleading.. medRxiv : the preprint server for health sciences, 2020.
42. Xu S, Böttcher L, Chou T. Diversity in biology: definitions, quantification and models.. Physical biology, 2020.
43. Xia M, Greenman CD, Chou T. PDE MODELS OF ADDER MECHANISMS IN CELLULAR PROLIFERATION.. SIAM journal on applied mathematics, 2020.
44. Lewkiewicz SM, Chuang YL, Chou T. Dynamics of T cell receptor distributions following acute thymic atrophy and resumption.. Mathematical biosciences and engineering : MBE, 2019.
45. Lewkiewicz S, Chuang YL, Chou T. A Mathematical Model of the Effects of Aging on Naive T Cell Populations and Diversity.. Bulletin of mathematical biology, 2019.
46. Mistry BA, Chou T. Nonspecific probe binding and automatic gating in flow cytometry and fluorescence activated cell sorting (FACS).. Mathematical biosciences and engineering : MBE, 2019.
47. Manuchehrfar F, Tian W, Chou T, Liang J. Evolution of Coagulation-Fragmentation Stochastic Processes Using Accurate Chemical Master Equation Approach.. Communications in information and systems, 2019.
48. Chang SS, Chou T. A Dynamical Bifurcation Model of Bipolar Disorder Based on Learned Expectation and Asymmetry in Mood Sensitivity.. Computational psychiatry (Cambridge, Mass.), 2018.
49. Xu S, Kim S, Chen ISY, Chou T. Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque.. PLoS computational biology, 2018.
50. Mistry BA, D'Orsogna MR, Chou T. The Effects of Statistical Multiplicity of Infection on Virus Quantification and Infectivity Assays.. Biophysical journal, 2018.
51. Kim LU, D'Orsogna MR, Chou T. Perturbing the Hypothalamic-Pituitary-Adrenal Axis: A Mathematical Model for Interpreting PTSD Assessment Tests.. Computational psychiatry (Cambridge, Mass.), 2018.
52. Chang JC, Liu Y, Chou T. Reconstruction of Cell Focal Adhesions using Physical Constraints and Compressive Regularization.. Biophysical journal, 2017.
53. de Anda J, Lee EY, Lee CK, Bennett RR, Ji X, Soltani S, Harrison MC, Baker AE, Luo Y, Chou T, O'Toole GA, Armani AM, Golestanian R, Wong GCL. High-Speed "4D" Computational Microscopy of Bacterial Surface Motility.. ACS nano, 2017.
54. Suryawanshi GW, Xu S, Xie Y, Chou T, Kim N, Chen ISY, Kim S. Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow.. Journal of visualized experiments : JoVE, 2017.
55. Mistry B, D'Orsogna MR, Webb NE, Lee B, Chou T. Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor Expression.. The journal of physical chemistry. B, 2016.
56. Chou T, Greenman CD. A Hierarchical Kinetic Theory of Birth, Death and Fission in Age-Structured Interacting Populations.. Journal of statistical physics, 2016.
57. Chuang YL, Chou T, D'Orsogna MR. Swarming in viscous fluids: Three-dimensional patterns in swimmer- and force-induced flows.. Physical review. E, 2016.
58. Kim LU, D'Orsogna MR, Chou T. Onset, timing, and exposure therapy of stress disorders: mechanistic insight from a mathematical model of oscillating neuroendocrine dynamics.. Biology direct, 2016.
59. Greenman CD, Chou T. Kinetic theory of age-structured stochastic birth-death processes.. Physical review. E, 2016.
60. Goyal S, Kim S, Chen IS, Chou T. Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques.. BMC biology, 2015.
61. Chang JC, Fok PW, Chou T. Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis.. Biophysical journal, 2015.
62. D'Orsogna MR, Lei Q, Chou T. First assembly times and equilibration in stochastic coagulation-fragmentation.. The Journal of chemical physics, 2015.
63. Chou T, Wang Y. Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases.. Journal of theoretical biology, 2015.
64. Amini N, Nowroozizadeh S, Cirineo N, Henry S, Chang T, Chou T, Coleman AL, Caprioli J, Nouri-Mahdavi K. Influence of the disc-fovea angle on limits of RNFL variability and glaucoma discrimination.. Investigative ophthalmology & visual science, 2014.
65. Chikere K, Webb NE, Chou T, Borm K, Sterjovski J, Gorry PR, Lee B. Distinct HIV-1 entry phenotypes are associated with transmission, subtype specificity, and resistance to broadly neutralizing antibodies.. Retrovirology, 2014.
66. Nowroozizadeh S, Cirineo N, Amini N, Knipping S, Chang T, Chou T, Caprioli J, Nouri-Mahdavi K. Influence of correction of ocular magnification on spectral-domain OCT retinal nerve fiber layer measurement variability and performance.. Investigative ophthalmology & visual science, 2014.
67. Chang JC, Chou T. Iterative graph cuts for image segmentation with a nonlinear statistical shape prior.. Journal of mathematical imaging and vision, 2014.
68. Berenji B, Chou T, D'Orsogna MR. Recidivism and rehabilitation of criminal offenders: a carrot and stick evolutionary game.. PloS one, 2014.
69. D'Orsogna MR, Zhao B, Berenji B, Chou T. Combinatoric analysis of heterogeneous stochastic self-assembly.. The Journal of chemical physics, 2013.
70. Hosseini H, Nassiri N, Azarbod P, Giaconi J, Chou T, Caprioli J, Nouri-Mahdavi K. Measurement of the optic disc vertical tilt angle with spectral-domain optical coherence tomography and influencing factors.. American journal of ophthalmology, 2013.
71. Chikere K, Chou T, Gorry PR, Lee B. Affinofile profiling: how efficiency of CD4/CCR5 usage impacts the biological and pathogenic phenotype of HIV.. Virology, 2013.
72. Yvinec R, D'Orsogna MR, Chou T. First passage times in homogeneous nucleation and self-assembly.. The Journal of chemical physics, 2012.
73. Chou T, Siegel M. A mechanical model of retinal detachment.. Physical biology, 2012.
74. Chang JC, Brennan KC, Chou T. Tracking monotonically advancing boundaries in image sequences using graph cuts and recursive kernel shape priors.. IEEE transactions on medical imaging, 2011.
75. Chou T, D'Orsogna MR. Coarsening and accelerated equilibration in mass-conserving heterogeneous nucleation.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2011.
76. Gibbons MM, Chou T, D'Orsogna MR. Diffusion-dependent mechanisms of receptor engagement and viral entry.. The journal of physical chemistry. B, 2010.
77. Posta F, Chou T. A mathematical model of intercellular signaling during epithelial wound healing.. Journal of theoretical biology, 2010.
78. Nowak SA, Chakrabarti B, Chou T, Gopinathan A. Frequency-dependent chemolocation and chemotactic target selection.. Physical biology, 2010.
79. Nowak SA, Chou T. Models of dynamic extraction of lipid tethers from cell membranes.. Physical biology, 2010.
80. D'Orsogna MR, Chou T. Optimal cytoplasmic transport in viral infections.. PloS one, 2009.
81. Johnston SH, Lobritz MA, Nguyen S, Lassen K, Delair S, Posta F, Bryson YJ, Arts EJ, Chou T, Lee B. A quantitative affinity-profiling system that reveals distinct CD4/CCR5 usage patterns among human immunodeficiency virus type 1 and simian immunodeficiency virus strains.. Journal of virology, 2009.
82. Chou T. Enhancement of charged macromolecule capture by nanopores in a salt gradient.. The Journal of chemical physics, 2009.
83. Fok PW, Chou T. Accelerated search kinetics mediated by redox reactions of DNA repair enzymes.. Biophysical journal, 2009.
84. Posta F, D'Orsogna MR, Chou T. Enhancement of cargo processivity by cooperating molecular motors.. Physical chemistry chemical physics : PCCP, 2009.
85. Nowak SA, Chou T. Mechanisms of receptor/coreceptor-mediated entry of enveloped viruses.. Biophysical journal, 2009.
86. Fok PW, Guo CL, Chou T. Charge-transport-mediated recruitment of DNA repair enzymes.. The Journal of chemical physics, 2008.
87. Nowak SA, Chou T. Membrane lipid segregation in endocytosis.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2008.
88. Kim KS, Chou T, Rudnick J. Degenerate ground-state lattices of membrane inclusions.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2008.
89. Lakhanpal A, Chou T. Brownian ratchets driven by asymmetric nucleation of hydrolysis waves.. Physical review letters, 2007.
90. Nowak SA, Fok PW, Chou T. Dynamic boundaries in asymmetric exclusion processes.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2007.
91. Chou T, D'Orsogna MR. Multistage adsorption of diffusing macromolecules and viruses.. The Journal of chemical physics, 2007.
92. Chou T. Peeling and sliding in nucleosome repositioning.. Physical review letters, 2007.
93. D'Orsogna MR, Chou T, Antal T. Exact steady-state velocity of ratchets driven by random sequential adsorption.. Journal of physics A: Mathematical and general, 2007.
94. Chou T. Stochastic entry of enveloped viruses: fusion versus endocytosis.. Biophysical journal, 2007.
95. Chou T. Band gaps and the Kelvin-Helmholtz instability.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2007.
96. D'Orsogna MR, Chou T. First passage and cooperativity of queuing kinetics.. Physical review letters, 2005.
97. Lakatos G, Chou T, Bergersen B, Patey GN. First passage times of driven DNA hairpin unzipping.. Physical biology, 2005.
98. Lakatos G, Chou T, Kolomeisky A. Steady-state properties of a totally asymmetric exclusion process with periodic structure.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2005.
99. Chou T, Lakatos G. Clustered bottlenecks in mRNA translation and protein synthesis.. Physical review letters, 2004.
100. Blower SM, Chou T. Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance.. Nature medicine, 2004.
101. Klapstein K, Chou T, Bruinsma R. Physics of RecA-mediated homologous recognition.. Biophysical journal, 2004.
102. Foster WJ, Chou T. Physical mechanisms of gas and perfluoron retinopexy and sub-retinal fluid displacement.. Physics in medicine and biology, 2004.
103. Chou T. Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport.. Biophysical journal, 2004.
104. D'Orsogna MR, Chou T. Chiral molecule adsorption on helical polymers.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2004.
105. D'Orsogna MR, Suchard MA, Chou T. Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2003.
106. Chou T. Ribosome recycling, diffusion, and mRNA loop formation in translational regulation.. Biophysical journal, 2003.
107. Chou T. Geometry-dependent electrostatics near contact lines.. Physical review letters, 2001.
108. Chou T, Kim KS, Oster G. Statistical thermodynamics of membrane bending-mediated protein-protein attractions.. Biophysical journal, 2001.