Tom Chou

Title(s)Professor, Computational Medicine
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    Tracking clonal dynamics during hematopoiesis: mechanistic insight via modeling and data analysis
    NIH R01HL146552Apr 15, 2019 - Feb 28, 2023
    Role: Principal Investigator
    Mouse and mathematical models for HIV-1 suppression through HSPC
    NIH R56HL126544Sep 6, 2014 - Aug 31, 2016
    Role: Co-Principal Investigator
    Multiscale studies of HIV infection and treatment
    NIH K25AI058672Mar 1, 2004 - Nov 28, 2010
    Role: Principal Investigator
    Systems in Integrative Biology
    NIH T32GM008185Jul 1, 1987 - Jun 30, 2023
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Fentanyl-driven acceleration of racial, gender and geographical disparities in drug overdose deaths in the United States. PLOS Glob Public Health. 2023; 3(3):e0000769. D'Orsogna MR, B?ttcher L, Chou T. PMID: 36962959; PMCID: PMC10032521.
      View in: PubMed   Mentions:
    2. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J. 2023 01 03; 122(1):254-266. Li X, Chou T. PMID: 36199250; PMCID: PMC9822797.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. Discrete stochastic models of SELEX: Aptamer capture probabilities and protocol optimization. J Chem Phys. 2022 Jun 28; 156(24):244103. Wang Y, Mistry BA, Chou T. PMID: 35778075.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    4. Modelling the impact of birth control policies on China's population and age: effects of delayed births and minimum birth age constraints. R Soc Open Sci. 2022 Jun; 9(6):211619. Wang Y, Dessalles R, Chou T. PMID: 35706677; PMCID: PMC9174737.
      View in: PubMed   Mentions: 1  
    5. How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation. Front Immunol. 2021; 12:735135. Dessalles R, Pan Y, Xia M, Maestrini D, D'Orsogna MR, Chou T. PMID: 35250963; PMCID: PMC8891377.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    6. A mathematical model of reward-mediated learning in drug addiction. Chaos. 2022 Feb; 32(2):021102. Chou T, D'Orsogna MR. PMID: 35232044; PMCID: PMC8816520.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    7. Density- and elongation speed-dependent error correction in RNA polymerization. Phys Biol. 2022 01 25; 19(2). Zuo X, Chou T. PMID: 34937012.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    8. A statistical model of COVID-19 testing in populations: effects of sampling bias andtesting errors. Philos Trans A Math Phys Eng Sci. 2022 Jan 10; 380(2214):20210121. Böttcher L, D'Orsogna MR, Chou T. PMID: 34802274; PMCID: PMC8607147.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    9. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell. 2021 12 09; 184(25):6174-6192.e32. 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. PMID: 34813726; PMCID: PMC8671326.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    10. Mathematical Models of Blood-Brain Barrier Transport of Monoclonal Antibodies Targeting the Transferrin Receptor and the Insulin Receptor. Pharmaceuticals (Basel). 2021 Jun 03; 14(6). Pardridge WM, Chou T. PMID: 34205013; PMCID: PMC8226686.
      View in: PubMed   Mentions: 11  
    11. A statistical model of COVID-19 testing in populations: effects of sampling bias and testing errors. medRxiv. 2021 May 26. Böttcher L, D'Orsogna MR, Chou T. PMID: 34075386; PMCID: PMC8168390.
      View in: PubMed   Mentions:
    12. Using excess deaths and testing statistics to determine COVID-19 mortalities. Eur J Epidemiol. 2021 May; 36(5):545-558. Böttcher L, D'Orsogna MR, Chou T. PMID: 34002294; PMCID: PMC8127858.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    13. Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities. medRxiv. 2021 Jan 12. Böttcher L, D'Orsogna MR, Chou T. PMID: 33469606; PMCID: PMC7814852.
      View in: PubMed   Mentions:
    14. Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities. ArXiv. 2021 Jan 10. Böttcher L, D'Orsogna MR, Chou T. PMID: 33442558; PMCID: PMC7805454.
      View in: PubMed   Mentions:
    15. Why case fatality ratios can be misleading: individual- and population-based mortality estimates and factors influencing them. Phys Biol. 2020 09 23; 17(6):065003. Böttcher L, Xia M, Chou T. PMID: 32554901; PMCID: PMC8849595.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCellsPHPublic Health
    16. Why estimating population-based case fatality rates during epidemics may be misleading. medRxiv. 2020 Mar 30. Böttcher L, Xia M, Chou T. PMID: 32511575; PMCID: PMC7276002.
      View in: PubMed   Mentions:
    17. Diversity in biology: definitions, quantification and models. Phys Biol. 2020 03 19; 17(3):031001. Xu S, Böttcher L, Chou T. PMID: 31899899; PMCID: PMC8788892.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    18. PDE MODELS OF ADDER MECHANISMS IN CELLULAR PROLIFERATION. SIAM J Appl Math. 2020; 80(3):1307-1335. Xia M, Greenman CD, Chou T. PMID: 35221385; PMCID: PMC8871769.
      View in: PubMed   Mentions: 1  
    19. Dynamics of T cell receptor distributions following acute thymic atrophy and resumption. Math Biosci Eng. 2019 09 23; 17(1):28-55. Lewkiewicz SM, Chuang YL, Chou T. PMID: 31731338; PMCID: PMC8788929.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    20. A Mathematical Model of the Effects of Aging on Naive T Cell Populations and Diversity. Bull Math Biol. 2019 07; 81(7):2783-2817. Lewkiewicz S, Chuang YL, Chou T. PMID: 31201663.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    21. Nonspecific probe binding and automatic gating in flow cytometry and fluorescence activated cell sorting (FACS). Math Biosci Eng. 2019 05 21; 16(5):4477-4490. Mistry BA, Chou T. PMID: 31499672.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    22. A Dynamical Bifurcation Model of Bipolar Disorder Based on Learned Expectation and Asymmetry in Mood Sensitivity. Comput Psychiatr. 2018 Dec; 2:205-222. Chang SS, Chou T. PMID: 30627671; PMCID: PMC6317753.
      View in: PubMed   Mentions: 6  
    23. The Effects of Statistical Multiplicity of Infection on Virus Quantification and Infectivity Assays. Biophys J. 2018 06 19; 114(12):2974-2985. Mistry BA, D'Orsogna MR, Chou T. PMID: 29925033; PMCID: PMC6026352.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    24. Perturbing the Hypothalamic-Pituitary-Adrenal Axis: A Mathematical Model for Interpreting PTSD Assessment Tests. Comput Psychiatr. 2018 Feb; 2:28-49. Kim LU, D'Orsogna MR, Chou T. PMID: 30090861; PMCID: PMC6067831.
      View in: PubMed   Mentions: 3  
    25. Reconstruction of Cell Focal Adhesions using Physical Constraints and Compressive Regularization. Biophys J. 2017 Dec 05; 113(11):2530-2539. Chang JC, Liu Y, Chou T. PMID: 29212006; PMCID: PMC5738527.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    26. Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow. J Vis Exp. 2017 06 14; (124). Suryawanshi GW, Xu S, Xie Y, Chou T, Kim N, Chen ISY, Kim S. PMID: 28654067; PMCID: PMC5608418.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    27. Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor Expression. J Phys Chem B. 2016 07 07; 120(26):6189-99. Mistry B, D'Orsogna MR, Webb NE, Lee B, Chou T. PMID: 27137677.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    28. A Hierarchical Kinetic Theory of Birth, Death and Fission in Age-Structured Interacting Populations. J Stat Phys. 2016; 164:49-76. Chou T, Greenman CD. PMID: 27335505; PMCID: PMC4894939.
      View in: PubMed   Mentions: 9  
    29. Swarming in viscous fluids: Three-dimensional patterns in swimmer- and force-induced flows. Phys Rev E. 2016 04; 93:043112. Chuang YL, Chou T, D'Orsogna MR. PMID: 27176395.
      View in: PubMed   Mentions: 5     Fields:    
    30. Onset, timing, and exposure therapy of stress disorders: mechanistic insight from a mathematical model of oscillating neuroendocrine dynamics. Biol Direct. 2016 Mar 25; 11(1):13. Kim LU, D'Orsogna MR, Chou T. PMID: 27013324; PMCID: PMC4807591.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    31. Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis. Biophys J. 2015 Sep 01; 109(5):966-74. Chang JC, Fok PW, Chou T. PMID: 26331254; PMCID: PMC4564684.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    32. First assembly times and equilibration in stochastic coagulation-fragmentation. J Chem Phys. 2015 Jul 07; 143(1):014112. D'Orsogna MR, Lei Q, Chou T. PMID: 26156470.
      View in: PubMed   Mentions: 4     Fields:    
    33. Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases. J Theor Biol. 2015 May 07; 372:65-73. Chou T, Wang Y. PMID: 25744205; PMCID: PMC4390531.
      View in: PubMed   Mentions: 2     Fields:    
    34. Recidivism and rehabilitation of criminal offenders: a carrot and stick evolutionary game. PLoS One. 2014; 9(1):e85531. Berenji B, Chou T, D'Orsogna MR. PMID: 24454884; PMCID: PMC3894186.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    35. Combinatoric analysis of heterogeneous stochastic self-assembly. J Chem Phys. 2013 Sep 28; 139(12):121918. D'Orsogna MR, Zhao B, Berenji B, Chou T. PMID: 24089730.
      View in: PubMed   Mentions: 4     Fields:    
    36. First passage times in homogeneous nucleation and self-assembly. J Chem Phys. 2012 Dec 28; 137(24):244107. Yvinec R, D'Orsogna MR, Chou T. PMID: 23277928.
      View in: PubMed   Mentions: 8     Fields:    
    37. A mechanical model of retinal detachment. Phys Biol. 2012 Aug; 9(4):046001. Chou T, Siegel M. PMID: 22733081.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    38. Tracking monotonically advancing boundaries in image sequences using graph cuts and recursive kernel shape priors. IEEE Trans Med Imaging. 2012 May; 31(5):1008-20. Chang JC, Brennan KC, Chou T. PMID: 22156978; PMCID: PMC5510452.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    39. Coarsening and accelerated equilibration in mass-conserving heterogeneous nucleation. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul; 84(1 Pt 1):011608. Chou T, D'Orsogna MR. PMID: 21867184.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    40. Diffusion-dependent mechanisms of receptor engagement and viral entry. J Phys Chem B. 2010 Nov 25; 114(46):15403-12. Gibbons MM, Chou T, D'Orsogna MR. PMID: 21038861.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    41. A mathematical model of intercellular signaling during epithelial wound healing. J Theor Biol. 2010 Sep 07; 266(1):70-8. Posta F, Chou T. PMID: 20685318; PMCID: PMC4403800.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    42. Models of dynamic extraction of lipid tethers from cell membranes. Phys Biol. 2010 May 07; 7(2):026002. Nowak SA, Chou T. PMID: 20453295.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    43. Frequency-dependent chemolocation and chemotactic target selection. Phys Biol. 2010 May 07; 7(2):026003. Nowak SA, Chakrabarti B, Chou T, Gopinathan A. PMID: 20453297.
      View in: PubMed   Mentions:    Fields:    
    44. Optimal cytoplasmic transport in viral infections. PLoS One. 2009 Dec 30; 4(12):e8165. D'Orsogna MR, Chou T. PMID: 20046829; PMCID: PMC2797302.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    45. A quantitative affinity-profiling system that reveals distinct CD4/CCR5 usage patterns among human immunodeficiency virus type 1 and simian immunodeficiency virus strains. J Virol. 2009 Nov; 83(21):11016-26. Johnston SH, Lobritz MA, Nguyen S, Lassen K, Delair S, Posta F, Bryson YJ, Arts EJ, Chou T, Lee B. PMID: 19692480; PMCID: PMC2772777.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    46. Enhancement of charged macromolecule capture by nanopores in a salt gradient. J Chem Phys. 2009 Jul 21; 131(3):034703. Chou T. PMID: 19624217; PMCID: PMC2723907.
      View in: PubMed   Mentions: 9     Fields:    
    47. Accelerated search kinetics mediated by redox reactions of DNA repair enzymes. Biophys J. 2009 May 20; 96(10):3949-58. Fok PW, Chou T. PMID: 19450467; PMCID: PMC2712205.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    48. Enhancement of cargo processivity by cooperating molecular motors. Phys Chem Chem Phys. 2009 Jun 28; 11(24):4851-60. Posta F, D'Orsogna MR, Chou T. PMID: 19506760.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    49. Mechanisms of receptor/coreceptor-mediated entry of enveloped viruses. Biophys J. 2009 Apr 08; 96(7):2624-36. Nowak SA, Chou T. PMID: 19348746; PMCID: PMC2711287.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    50. Charge-transport-mediated recruitment of DNA repair enzymes. J Chem Phys. 2008 Dec 21; 129(23):235101. Fok PW, Guo CL, Chou T. PMID: 19102557; PMCID: PMC2671188.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    51. Membrane lipid segregation in endocytosis. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Aug; 78(2 Pt 1):021908. Nowak SA, Chou T. PMID: 18850866.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    52. Degenerate ground-state lattices of membrane inclusions. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jul; 78(1 Pt 1):011401. Kim KS, Chou T, Rudnick J. PMID: 18763950.
      View in: PubMed   Mentions: 3     Fields:    
    53. Brownian ratchets driven by asymmetric nucleation of hydrolysis waves. Phys Rev Lett. 2007 Dec 14; 99(24):248302. Lakhanpal A, Chou T. PMID: 18233496.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    54. Dynamic boundaries in asymmetric exclusion processes. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Sep; 76(3 Pt 1):031135. Nowak SA, Fok PW, Chou T. PMID: 17930227.
      View in: PubMed   Mentions: 5     Fields:    
    55. Multistage adsorption of diffusing macromolecules and viruses. J Chem Phys. 2007 Sep 14; 127(10):105101. Chou T, D'Orsogna MR. PMID: 17867780.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    56. Peeling and sliding in nucleosome repositioning. Phys Rev Lett. 2007 Aug 03; 99(5):058105. Chou T. PMID: 17930799.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    57. Exact steady-state velocity of ratchets driven by random sequential adsorption. J Phys A Math Gen. 2007 May 25; 40(21):5575-5584. D'Orsogna MR, Chou T, Antal T. PMID: 19081764; PMCID: PMC2600482.
      View in: PubMed   Mentions: 2  
    58. Stochastic entry of enveloped viruses: fusion versus endocytosis. Biophys J. 2007 Aug 15; 93(4):1116-23. Chou T. PMID: 17513379; PMCID: PMC1929032.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    59. Band gaps and the Kelvin-Helmholtz instability. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jan; 75(1 Pt 2):016315. Chou T. PMID: 17358261.
      View in: PubMed   Mentions:    Fields:    
    60. First passage and cooperativity of queuing kinetics. Phys Rev Lett. 2005 Oct 21; 95(17):170603. D'Orsogna MR, Chou T. PMID: 16383812.
      View in: PubMed   Mentions: 5     Fields:    
    61. First passage times of driven DNA hairpin unzipping. Phys Biol. 2005 Sep 12; 2(3):166-74. Lakatos G, Chou T, Bergersen B, Patey GN. PMID: 16224122.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    62. Steady-state properties of a totally asymmetric exclusion process with periodic structure. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jan; 71(1 Pt 1):011103. Lakatos G, Chou T, Kolomeisky A. PMID: 15697576.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    63. Clustered bottlenecks in mRNA translation and protein synthesis. Phys Rev Lett. 2004 Nov 05; 93(19):198101. Chou T, Lakatos G. PMID: 15600884.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    64. Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance. Nat Med. 2004 Oct; 10(10):1111-6. Blower SM, Chou T. PMID: 15378053.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCellsPHPublic Health
    65. Physics of RecA-mediated homologous recognition. Biophys J. 2004 Sep; 87(3):1466-77. Klapstein K, Chou T, Bruinsma R. PMID: 15345529; PMCID: PMC1304555.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    66. Physical mechanisms of gas and perfluoron retinopexy and sub-retinal fluid displacement. Phys Med Biol. 2004 Jul 07; 49(13):2989-97. Foster WJ, Chou T. PMID: 15285260.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    67. Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport. Biophys J. 2004 May; 86(5):2827-36. Chou T. PMID: 15111400; PMCID: PMC1304152.
      View in: PubMed   Mentions: 6     Fields:    
    68. Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Aug; 68(2 Pt 1):021925. D'Orsogna MR, Suchard MA, Chou T. PMID: 14525024.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    69. Ribosome recycling, diffusion, and mRNA loop formation in translational regulation. Biophys J. 2003 Aug; 85(2):755-73. Chou T. PMID: 12885626; PMCID: PMC1303200.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    70. Statistical thermodynamics of membrane bending-mediated protein-protein attractions. Biophys J. 2001 Mar; 80(3):1075-87. Chou T, Kim KS, Oster G. PMID: 11222274; PMCID: PMC1301305.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
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