Publications

Tajadura-Ortega V, Garg R, Allen R, Owczarek C, Bright MD, Kean S, Mohd-Noor A, Grigoriadis A, Elston TC, Hahn KM, Ridley AJ. An RNAi screen of Rho signalling networks identifies RhoH as a regulator of Rac1 in prostate cancer cell migration. BMC Biol. 2018 Mar 6;16(1):29. doi: 10.1186/s12915-018-0489-4.

Tunc-Ozdemir M, Liao KL, Ross-Elliott TJ, Elston TC, Jones AM. Long-distance communication in Arabidopsis involving a self-activating G protein. Plant Direct. 2018 Feb 26;2(2):e00037. doi: 10.1002/pld3.37. eCollection 2018 Feb.
Free PMC Article

Liao KL, Melvin CE, Sozzani R, Jones RD, Elston TC, Jones AM. Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling.  PLoS One. 2017 Dec 29;12(12):e0190000. doi: 10.1371/journal.pone.0190000. eCollection 2017.
Free PMC Article

Sandefur CI, Boucher RC, Elston TC.  Mathematical model reveals role of nucleotide signaling in airway surface liquid homeostasis and its dysregulation in cystic fibrosis. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7272-E7281. doi: 10.1073/pnas.1617383114. Epub 2017 Aug 14.
Free Article

Mohan K, Nosbisch JL, Elston TC, Bear JE, Haugh JM. A Reaction-Diffusion Model Explains Amplification of the PLC/PKC Pathway in Fibroblast Chemotaxis. Biophys J. 2017 Jul 11;113(1):185-194. doi: 10.1016/j.bpj.2017.05.035.

Lakhani V, Elston TC. Testing the limits of gradient sensing. PLoS Comput Biol. 2017 Feb 16;13(2):e1005386. doi: 10.1371/journal.pcbi.1005386. eCollection 2017 Feb.
Free PMC Article

Liao KL, Jones RD, McCarter P, Tunc-Ozdemir M, Draper JA, Elston TC, Kramer D, Jones AM. A shadow detector for photosynthesis efficiency. J Theor Biol. 2017 Feb 7;414:231-244. doi: 10.1016/j.jtbi.2016.11.027. Epub 2016 Dec 3.

Chu PH, Tsygankov D, Berginski ME, Dagliyan O, Gomez SM, Elston TC, Karginov AV, Hahn KM. Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms. Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12420-5. doi: 10.1073/pnas.1404487111. Epub 2014 Aug 12.
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Tsygankov D, Chu PH, Chen H, Elston TC, Hahn KM. User-friendly tools for quantifying the dynamics of cellular morphology and intracellular protein clusters. Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12-420138-5.00022-7.
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Karginov AV, Tsygankov D, Berginski M, Chu P-H, Trudeau ED, Yi JJ, Gomez G, Elston TC, Hahn KM.Dissecting motility signaling through activation of specific Src-effector complexes. Nature Chem Biol.2014 Apr;10(4):286-90. doi: 10.1038/nchembio.1477. Epub 2014 Mar 9.
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Tsygankov D, Bilancia CG, Vitriol EA, Hahn KM, Peifer M, Elston TC. CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries. J Cell Biol. 2014 Feb 3;204(3):443-60
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Bilancia CG, Winkelman JD, Tsygankov D, Nowotarski SH, Sees JA, Comber K, Evans I, Lakhani V, Wood W, Elston TC, Kovar DR, Peifer M. Enabled negatively regulates diaphanous-driven actin dynamics in vitro and in vivo. Dev Cell. 2014 Feb 24;28(4):394-408
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Allen RJ, Tsygankov D, Zawistowski JS, Elston TC, Hahn KM. Automated line scan analysis to quantify biosensor activity at the cell edge. Methods. 2014 Mar 15;66(2):162-7. doi: 10.1016/j.ymeth.2013.08.025. Epub 2013 Aug 30.
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Garcia GJ, Boucher RC, Elston TC. Biophysical model of ion transport across human respiratory epithelia allows quantification of ion permeabilities. Biophys J. 2013 Feb 5; 104(3):716-26.
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Herschlag G, Garcia GJ, Button B, Tarran R, Lindley B, Reinhardt B, Elston TC, Forest MG. A mechanochemical model for auto-regulation of lung airway surface layer volume. J Theor Biol. 2013 May 21; 325:42-51.
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Kapustina M, Elston TC, Jacobson K. Compression and dilation of the membrane-cortex layer generates rapid changes in cell shape. J Cell Biol. 2013 Jan 7; 200(1):95-108.
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Kesseler KJ, Blinov ML, Elston TC, Kaufmann WK, Simpson DA. A predictive mathematical model of the DNA damage G2 checkpoint. J Theor Biol. 2013 Mar 7; 320:159-69.
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Dyer JM, Savage NS, Jin M, Zyla TR, Elston TC, Lew DJ. Tracking shallow chemical gradients by actin-driven wandering of the polarization site. Curr Biol. 2013 Jan 7; 23(1):32-41.
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Houser JR, Ford E, Chatterjea SM, Maleri S, Elston TC, Errede B. An improved short-lived fluorescent protein transcriptional reporter for Saccharomyces cerevisiae. Yeast. 2012 Dec; 29(12):519-30.
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Hao N, Yildirim N, Nagiec MJ, Parnell SC, Errede B, Dohlman HG, Elston TC. Combined computational and experimental analysis reveals mitogen-activated protein kinase-mediated feedback phosphorylation as a mechanism for signaling specificity. Mol Biol Cell. 2012 Oct; 23(19):3899-910.
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Houser JR, Ford E, Nagiec MJ, Errede B, Elston TC. Positive roles for negative regulators in the mating response of yeast. Mol Syst Biol. 2012 Jun 5; 8:e586.
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Howell AS, Jin M, Wu CF, Zyla TR, Elston TC, Lew DJ. Negative feedback enhances robustness in the yeast polarity establishment circuit. Cell. 2012 Apr 13; 149(2):322-33.
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Xu K, Morgan KT, Todd Gehris A, Elston TC, Gomez SM. A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasis. PLoS Comput Biol.2011 Dec 1; 7(12):e1002272.
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Jin M, Errede B, Behar M, Mather W, Nayak S, Hasty J, Dohlman HG, Elston TC. Yeast dynamically modify their environment to achieve better mating efficiency. Sci Signal. 2011 Aug 16;4(186):ra54
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Tsygankov D, Serohijos AW, Dokholyan NV, Elston TC. A physical model reveals the mechanochemistry responsible for dynein’s processive motion. Biophys J. 2011 Jul 6; 101(1):144-50.
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Garcia GJ, Picher M, Zuo P, Okada SF, Lazarowski ER, Button B, Boucher RC, Elston TC. Computational model for the regulation of extracellular ATP and adenosine in airway epithelia. Subcell Biochem. 2011; 55:51-74.
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Strychalski W, Adalsteinsson D, Elston TC. Simulating biochemical networks in complex moving geometries. SIAM Journal on Scientific Computing. 2010 Oct 12; 32(5):3039–3070.
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Costigliola N, Kapustina MT, Weinreb GE, Monteith A, Rajfur Z, Elston TC, Jacobson K. RhoA regulates calcium-independent periodic contractions of the cell cortex. Biophys J. 2010 Aug 9; 99(4):1053-63.
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Kapustina M, Vitriol E, Elston TC, Loew LM, Jacobson K. Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics. Cytoskeleton (Hoboken). 2010 Aug; 67(8):519-34.
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Strychalski W, Adalsteinsson D, Elston TC. A cut-cell method for simulating spatial models of biochemical reactions in arbitrary geometries. Comm. in Appl. Math. and Comp. Sci. 2010; 5(1): 31-53.
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Haugh JM, Elston TC, Cirit M, Wang C-C, Hao N, Yildirim N. Data-driven, mechanistic modeling of biochemical reaction networks. In Methods in Bioengineering: Systems Analysis of Biological Networks. A. Jayaraman and J. Hahn, eds., 2009 (Artech House), 57-74.
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Tsygankov D, Liu Y, Sanoff HK, Sharpless NE, Elston TC. A quantitative model for age-dependent expression of the p16INK4a tumor suppressor. Proc Natl Acad Sci U S A. 2009 Sep 29; 106(39): 16562-16567.
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Serohijos AWR, Tsygankov D, Liu S, Elston TC, Dokholyan NV. Multiscale approaches for studying energy transduction in dynein. Phys Chem Chem Phys. 2009 Jun 28; 11(24): 4840-50.
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Weinreb GE, Kapustina MT, Jacobson K, Elston TC. In Silico Generationof Alternative Hyposthesis Using Causal Mapping (CMAP). PLoS One. 2009 epub Apr 29; 4(4): e5378.
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Fricks J, Yao L, Elston TC, Forest G. Time-Domain Methods for Diffusive Transport in Soft Matter. SIAM Journal on Applied Mathematics. 2009 Feb 19; 69(5): 1277-1308.
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Tsygankov D, Serohijos AW, Dokholyan NV, Elston TC. Kinetic models for the coordinated stepping of cytoplasmic dynein. J Chem Phys. 2009 Jan 14;130(2):025101
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Hao N, Zeng Y, Elston TC, Dohlman HG. Control of MAPK specificity by feedback phosphorylation of shared adaptor protein Ste50. J. Biol. Chem. 2008 Dec 5; 283(49):33798-802.
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Lan Y, Elston TC, Papoian GA. Elimination of fast variables in chemical Langevin equations. J. Chem. Phys.2008 Dec 7; 129(21):214115.
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Elston TC. Probing Pathways Periodically. Sci Signal. 2008 Oct 21;1(42):pe47.
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Behar M, Hao N, Dohlman HG, Elston TC. Dose-to-duration encoding and signaling beyond saturation in intracellular signaling networks. PLoS Comput Biol. 2008 Oct;4(10):e1000197. Epub 2008 Oct 10.
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Zuo P, Picher M, Okada SF, Lazarowski ER, Button B, Boucher RC, Elston TC. Mathematical model of nucleotide regulation on airway epithelia: Implications for airway homeostasis. J Biol Chem. 2008 Sept 26; 283(39):26805-26819
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Hao N, Nayak S, Behar M, Shanks RH, Nagiec MJ, Errede B, Hasty J, Elston TC, Dohlman HG. Regulation of cell signaling dynamics by the protein kinase-scaffold Ste5. Mol Cell. 2008 Jun 6; 30(5):649-56
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Kapustina M, Weinreb GE, Costigliola N, Rajfur Z, Jacobson K, Elston TC. Mechanical and biochemical modeling of cortical oscillations in spreading cells. Biophys J. 2008 Jun; 94(12):4605-20
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Wang X, Errede B, Elston TC. Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters. Biophys J. 2008 Mar 15; 94(6):2017-26.
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Violin JD, DiPilato LM, Yildirim N, Elston TC, Zhang J, Lefkowitz RJ. β2-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real time cAMP dynamics. J Biol Chem. 2008 Feb 1; 283(5):2949-61
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Guido NJ, Lee P, Wang X, Elston TC, Collins JJ. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophys J. 2007 Dec 1; 93(11):L55-7
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Kesseler KJ, Kaufmann WK, Reardon JT, Elston TC, Sancar A. A mathematical model for human nucleotide excision repair. J Theor Biol. 2007 Nov 21; 249(2):361-75.
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Behar M, Dohlman HG, Elston TC. Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks. Proc Natl Acad Sci U S A. 2007 Oct 9; 104(41):16146-51. Epub 2007 Oct 3.
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Behar M, Hao N, Dohlman HG, Elston TC. Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophys J. 2007 Aug 1; 93(3):806-21
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Hao N, Behar M, Elston TC, Dohlman HG. Systems biology analysis of G protein and MAP kinase signaling in yeast. Oncogene. 2007 May 14; 26(22):3254-66
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Hao N, Behar M, Parnell SC, Torres MP, Borchers CH, Elston TC, Dohlman HG. A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway. Curr Biol. 2007 Apr 17; 17(8):659-67
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Erban R, Frewen TA, Wang X, Elston TC, Coifman R, Nadler B, Kevrekidis IG. Variable-free exploration of stochastic models: a gene regulatory network example. J Chem Phys. 2007 Apr 21; 126(15):155103
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Serohijos AW, Chen Y, Ding F, Elston TC, Dokholyan NV. A structural model reveals energy transduction in dynein. Proc Natl Acad Sci U S A. 2006 Dec 5; 103(49):18540-5
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Wang X, Hao N, Dohlman HG, Elston TC. Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade. Biophys J. 2006 Mar 15; 90(6):1961-78
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Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ. A bottom-up approach to gene regulation. Nature. 2006 Feb 16; 439(7078):856-60
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Fricks J, Wang H, Elston TC. A numerical algorithm for investigating the role of the motor-cargo linkage in molecular motor-driven transport. J Theor Biol. 2006 Mar 7; 239(1):33-48
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Weinreb GE, Elston TC, Jacobson K. Causal mapping as a tool to mechanistically interpret phenomena in cell motility: application to cortical oscillations in spreading cells. Cell Motil Cytoskeleton. 2006 Sep; 63(9):523-32
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Erban R, Kevrekidis IG, Adalsteinsson D, Elston TC. Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation. J Chem Phys. 2006 Feb 28; 124(8):084106
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Morgan KT, Jayyosi Z, Hower MA, Pino MV, Connolly TM, Kotlenga K, Lin J, Wang M, Schmidts HL, Bonnefoi MS, Elston TC, Boorman GA. The hepatic transcriptome as a window on whole-body physiology and pathophysiology. Toxicol Pathol. 2005; 33(1): 136-45. Review.
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Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes.Nat Rev Genet. 2005 Jun; 6(6):451-64.
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Goedecke DM, Elston TC. A model for the oscillatory motion of single dynein molecules. J Theor Biol. 2005 Jan 7; 232(1):27-39
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Pirone JR, Elston TC. Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression. J Theor Biol. 2004 Jan 7; 226(1):111-21
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Morgan KT, Pino M, Crosby LM, Wang M, Elston TC, Jayyosi Z, Bonnefoi M, Boorman G. Complimentary roles for toxicologic pathology and mathematics in toxicogenomics, with special reference to data interpretation and oscillatory dynamics. Toxicol Pathol. 2004 Mar-Apr; 32 Suppl 1:13-25. Review.
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Adalsteinsson D, McMillen D, Elston TC. Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics. 2004 Mar 8; 5:24
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Yildirim N, Hao N, Dohlman HG, Elston TC. Mathematical modeling of RGS and G-protein regulation in yeast. Methods Enzymol. 2004; 389:383-98
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Hao N, Yildirim N, Wang Y, Elston TC, Dohlman HG. Regulators of G protein signaling and transient activation of signaling: experimental and computational analysis reveals negative and positive feedback controls on G protein activity. J Biol Chem. 2003 Nov 21; 278(47):46506-15
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Morgan KT, Casey W, Easton M, Creech D, Ni H, Yoon L, Anderson S, Qualls CW Jr, Crosby LM, MacPherson A, Bloomfield P, Elston TC. Frequent sampling reveals dynamic responses by the transcriptome to routine media replacement in HepG2 cells. Toxicol Pathol. 2003 Jul-Aug; 31(4):448-61
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Wang H, Peskin CS, Elston TC. A robust numerical algorithm for studying biomolecular transport processes. J Theor Biol. 2003 Apr 21; 221(4):491-511
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Elston TC. The brownian ratchet and power stroke models for posttranslational protein translocation into the endoplasmic reticulum. Biophys J. 2002 Mar; 82(3):1239-53
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Mogilner, A. T. Elston, H. Wang, and G. Oster. Molecular Motors: Theory. In Computational Cell Biology,C.Fall,E. Marland, J. Tyson, and J. Wagner, Eds. 2002. (Springer, NY), 321-355.
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Mogilner, A. T. Elston, H. Wang, and G. Oster. Molecular Motors: Examples. In Computational Cell Biology,C.Fall,E. Marland, J. Tyson, and J. Wagner, Eds. 2002. (Springer, NY), 356-380.
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Elston, T. and T. Kepler. A linear two-State model with complex dynamics. PLA 2001 280:204-208
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Kepler TB, Elston TC. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys J. 2001 Dec; 81(6): 3116-36.
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Charles S. Peskin and Timothy C. Elston. The Role of Protein Flexibility in Molecular Motor Function: Coupled Diffusion in a Tilted Periodic Potential. SIAP (2000); 60 (3):842-867
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Charles S. Peskin, Dwight You., and Timothy C. Elston. Protein Flexibility and the Correlation Ratchet. SIAP(2000); 61 (3):776-791
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Elston TC. Models of post-translational protein translocation. Biophys J. 2000 Nov; 79(5):2235-51.
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Elston TC. A macroscopic description of biomolecular transport. J Math Biol. 2000 Sep; 41(3): 189-206.
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Wang HY, Elston T, Mogilner A, Oster G. Force generation in RNA polymerase. Biophys J. 1998 Mar; 74(3): 1186-202.
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Elston T, Wang H, Oster G. Energy transduction in ATP synthase. Nature. 1998 Jan 29; 391(6666):510-3.
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Glick BS, Elston T, Oster G. A cisternal maturation mechanism can explain the asymmetry of the golgi stack. FEBS Lett. 1997 Sep 8; 414(2):177-81. Review.
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Elston TC, Oster G. Protein turbines I: The bacterial flagellar motor. Biophys J. 1997 Aug; 73(2): 703-21.
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Elston TC, Bulsara AR. First passage statistics of periodically driven models for neural dynamics.Biosystems. 1997; 40(1-2): 37-43.
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Reimann P, Elston TC. Kramers’ rate for thermal plus dichotomous noise applied to ratchets. Phys Rev Lett. 1996 Dec 30; 77(27): 5328-5331.
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Bulsara AR, Elston TC, Doering CR, Lowen SB, Lindenberg K. Cooperative behavior in periodically driven noisy integrate-fire models of neuronal dynamics. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Apr; 53(4): 3958-3969.
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Elston TC and Doering C. Numerical and analytic studies of nonequilibrium fluctuation induced transport processes. J. Stat. Phys. 1996 83: 359-383.
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Doering C. and Elston TC. Random walks, resonance, and ratchets. In Nonequilibrium Statistical Mechanics in One Dimension, ed. V. Privman. 1996 (Cambridge University Press), 359-370.
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Elston TC. Numerical studies of escape problems. CNLS Newsletter 117 (Los Alamos National Laboratory LALP-95-012). 1996.

Fox RF, Elston TC. Chaos and a quantum-classical correspondence in the kicked top. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1994 Oct; 50(4): 2553-2563.
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Fox RF, Elston TC. Chaos and quantum-classical correspondence in the kicked pendulum. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1994 May; 49(5): 3683-3696.
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Elston TC, Fox RF. Enhanced quantum fluctuations in a chaotic single mode ammonia laser. Chaos. 1994 Mar; 4(1): 1-13.
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Fox RF, Elston TC. Amplification of intrinsic fluctuations by the Lorenz equations. Chaos. 1993 Jul; 3(3): 313-323.
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Elston TC, Fox RF. Stochastic effects in Rayleigh-Bénard pattern formation. Phys Rev A. 1991 Dec 15; 44(12): 8403-8405.
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