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Parameter sensitivity analysis for biochemical reaction networks.

Minas G, Rand DA.

Math Biosci Eng. 2019 May 6;16(5):3965-3987. doi: 10.3934/mbe.2019196.


Disentangling juxtacrine from paracrine signalling in dynamic tissue.

Momiji H, Hassall KL, Featherstone K, McNamara AV, Patist AL, Spiller DG, Christian HC, White MRH, Davis JRE, Finkenstädt BF, Rand DA.

PLoS Comput Biol. 2019 Jun 13;15(6):e1007030. doi: 10.1371/journal.pcbi.1007030. eCollection 2019 Jun.


Temperature regulates NF-κB dynamics and function through timing of A20 transcription.

Harper CV, Woodcock DJ, Lam C, Garcia-Albornoz M, Adamson A, Ashall L, Rowe W, Downton P, Schmidt L, West S, Spiller DG, Rand DA, White MRH.

Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5243-E5249. doi: 10.1073/pnas.1803609115. Epub 2018 May 14.


Asymmetry between Activation and Deactivation during a Transcriptional Pulse.

Dunham LSS, Momiji H, Harper CV, Downton PJ, Hey K, McNamara A, Featherstone K, Spiller DG, Rand DA, Finkenstädt B, White MRH, Davis JRE.

Cell Syst. 2017 Dec 27;5(6):646-653.e5. doi: 10.1016/j.cels.2017.10.013. Epub 2017 Nov 15.


Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference.

Minas G, Rand DA.

PLoS Comput Biol. 2017 Jul 24;13(7):e1005676. doi: 10.1371/journal.pcbi.1005676. eCollection 2017 Jul.


Inferring transcriptional logic from multiple dynamic experiments.

Minas G, Jenkins DJ, Rand DA, Finkenstädt B.

Bioinformatics. 2017 Nov 1;33(21):3437-3444. doi: 10.1093/bioinformatics/btx407.


ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

Minas G, Momiji H, Jenkins DJ, Costa MJ, Rand DA, Finkenstädt B.

BMC Bioinformatics. 2017 Jun 26;18(1):316. doi: 10.1186/s12859-017-1695-8.


Systems Chronotherapeutics.

Ballesta A, Innominato PF, Dallmann R, Rand DA, Lévi FA.

Pharmacol Rev. 2017 Apr;69(2):161-199. doi: 10.1124/pr.116.013441. Review.


Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states.

Adamson A, Boddington C, Downton P, Rowe W, Bagnall J, Lam C, Maya-Mendoza A, Schmidt L, Harper CV, Spiller DG, Rand DA, Jackson DA, White MR, Paszek P.

Nat Commun. 2016 Jul 6;7:12057. doi: 10.1038/ncomms12057.


Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells.

Atia J, McCloskey C, Shmygol AS, Rand DA, van den Berg HA, Blanks AM.

PLoS Comput Biol. 2016 Apr 22;12(4):e1004828. doi: 10.1371/journal.pcbi.1004828. eCollection 2016 Apr.


PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

Domijan M, Brown PE, Shulgin BV, Rand DA.

BMC Bioinformatics. 2016 Mar 10;17:124. doi: 10.1186/s12859-016-0972-2.


Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis.

Bechtold U, Penfold CA, Jenkins DJ, Legaie R, Moore JD, Lawson T, Matthews JS, Vialet-Chabrand SR, Baxter L, Subramaniam S, Hickman R, Florance H, Sambles C, Salmon DL, Feil R, Bowden L, Hill C, Baker NR, Lunn JE, Finkenstädt B, Mead A, Buchanan-Wollaston V, Beynon J, Rand DA, Wild DL, Denby KJ, Ott S, Smirnoff N, Mullineaux PM.

Plant Cell. 2016 Feb;28(2):345-66. doi: 10.1105/tpc.15.00910. Epub 2016 Feb 3.


Spatially coordinated dynamic gene transcription in living pituitary tissue.

Featherstone K, Hey K, Momiji H, McNamara AV, Patist AL, Woodburn J, Spiller DG, Christian HC, McNeilly AS, Mullins JJ, Finkenstädt BF, Rand DA, White MR, Davis JR.

Elife. 2016 Feb 1;5:e08494. doi: 10.7554/eLife.08494.


Frequency modulated translocational oscillations of Nrf2, a transcription factor functioning like a wireless sensor.

Xue M, Momiji H, Rabbani N, Bretschneider T, Rand DA, Thornalley PJ.

Biochem Soc Trans. 2015 Aug;43(4):669-73. doi: 10.1042/BST20150060. Epub 2015 Aug 3.


Coupling between the Circadian Clock and Cell Cycle Oscillators: Implication for Healthy Cells and Malignant Growth.

Feillet C, van der Horst GT, Levi F, Rand DA, Delaunay F.

Front Neurol. 2015 May 11;6:96. doi: 10.3389/fneur.2015.00096. eCollection 2015. Review.


A stochastic transcriptional switch model for single cell imaging data.

Hey KL, Momiji H, Featherstone K, Davis JR, White MR, Rand DA, Finkenstädt B.

Biostatistics. 2015 Oct;16(4):655-69. doi: 10.1093/biostatistics/kxv010. Epub 2015 Mar 26.


Using constraints and their value for optimization of large ODE systems.

Domijan M, Rand DA.

J R Soc Interface. 2015 Mar 6;12(104):20141303. doi: 10.1098/rsif.2014.1303.


Frequency Modulated Translocational Oscillations of Nrf2 Mediate the Antioxidant Response Element Cytoprotective Transcriptional Response.

Xue M, Momiji H, Rabbani N, Barker G, Bretschneider T, Shmygol A, Rand DA, Thornalley PJ.

Antioxid Redox Signal. 2015 Sep 1;23(7):613-29. doi: 10.1089/ars.2014.5962. Epub 2014 Oct 3.


The inwardly rectifying K+ channel KIR7.1 controls uterine excitability throughout pregnancy.

McCloskey C, Rada C, Bailey E, McCavera S, van den Berg HA, Atia J, Rand DA, Shmygol A, Chan YW, Quenby S, Brosens JJ, Vatish M, Zhang J, Denton JS, Taggart MJ, Kettleborough C, Tickle D, Jerman J, Wright P, Dale T, Kanumilli S, Trezise DJ, Thornton S, Brown P, Catalano R, Lin N, England SK, Blanks AM.

EMBO Mol Med. 2014 Sep;6(9):1161-74. doi: 10.15252/emmm.201403944.


Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle.

Feillet C, Krusche P, Tamanini F, Janssens RC, Downey MJ, Martin P, Teboul M, Saito S, Lévi FA, Bretschneider T, van der Horst GT, Delaunay F, Rand DA.

Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9828-33. doi: 10.1073/pnas.1320474111. Epub 2014 Jun 23.


Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response.

Sidaway-Lee K, Costa MJ, Rand DA, Finkenstadt B, Penfield S.

Genome Biol. 2014 Mar 3;15(3):R45. doi: 10.1186/gb-2014-15-3-r45.


Inference on periodicity of circadian time series.

Costa MJ, Finkenstädt B, Roche V, Lévi F, Gould PD, Foreman J, Halliday K, Hall A, Rand DA.

Biostatistics. 2013 Sep;14(4):792-806. doi: 10.1093/biostatistics/kxt020. Epub 2013 Jun 6.


A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number.

Woodcock DJ, Vance KW, Komorowski M, Koentges G, Finkenstädt B, Rand DA.

Bioinformatics. 2013 Jun 15;29(12):1519-25. doi: 10.1093/bioinformatics/btt201. Epub 2013 May 14.


Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.

Gould PD, Ugarte N, Domijan M, Costa M, Foreman J, Macgregor D, Rose K, Griffiths J, Millar AJ, Finkenstädt B, Penfield S, Rand DA, Halliday KJ, Hall AJ.

Mol Syst Biol. 2013;9:650. doi: 10.1038/msb.2013.7.


A temporal switch model for estimating transcriptional activity in gene expression.

Jenkins DJ, Finkenstädt B, Rand DA.

Bioinformatics. 2013 May 1;29(9):1158-65. doi: 10.1093/bioinformatics/btt111. Epub 2013 Mar 11.


Balance equations can buffer noisy and sustained environmental perturbations of circadian clocks.

Domijan M, Rand DA.

Interface Focus. 2011 Feb 6;1(1):177-86. doi: 10.1098/rsfs.2010.0007. Epub 2010 Dec 1.


Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.

Komorowski M, Costa MJ, Rand DA, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8645-50. doi: 10.1073/pnas.1015814108. Epub 2011 May 6.


Dynamic analysis of stochastic transcription cycles.

Harper CV, Finkenstädt B, Woodcock DJ, Friedrichsen S, Semprini S, Ashall L, Spiller DG, Mullins JJ, Rand DA, Davis JR, White MR.

PLoS Biol. 2011 Apr;9(4):e1000607. doi: 10.1371/journal.pbio.1000607. Epub 2011 Apr 12.


Picosecond pulses from a cryogenically cooled, composite amplifier using Yb:YAG and Yb:GSAG.

Rand DA, Shaw SE, Ochoa JR, Ripin DJ, Taylor A, Fan TY, Martin H, Hawes S, Zhang J, Sarkisyan S, Wilson E, Lundquist P.

Opt Lett. 2011 Feb 1;36(3):340-2. doi: 10.1364/OL.36.000340.


Quantitative analysis of regulatory flexibility under changing environmental conditions.

Edwards KD, Akman OE, Knox K, Lumsden PJ, Thomson AW, Brown PE, Pokhilko A, Kozma-Bognar L, Nagy F, Rand DA, Millar AJ.

Mol Syst Biol. 2010 Nov 2;6:424. doi: 10.1038/msb.2010.81.


Physiological levels of TNFalpha stimulation induce stochastic dynamics of NF-kappaB responses in single living cells.

Turner DA, Paszek P, Woodcock DJ, Nelson DE, Horton CA, Wang Y, Spiller DG, Rand DA, White MR, Harper CV.

J Cell Sci. 2010 Aug 15;123(Pt 16):2834-43. doi: 10.1242/jcs.069641. Epub 2010 Jul 27.


Robustness from flexibility in the fungal circadian clock.

Akman OE, Rand DA, Brown PE, Millar AJ.

BMC Syst Biol. 2010 Jun 24;4:88. doi: 10.1186/1752-0509-4-88.


Measurement of single-cell dynamics.

Spiller DG, Wood CD, Rand DA, White MR.

Nature. 2010 Jun 10;465(7299):736-45. doi: 10.1038/nature09232. Review.


Population robustness arising from cellular heterogeneity.

Paszek P, Ryan S, Ashall L, Sillitoe K, Harper CV, Spiller DG, Rand DA, White MR.

Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11644-9. doi: 10.1073/pnas.0913798107. Epub 2010 Jun 7.


The dynamic architecture of the metabolic switch in Streptomyces coelicolor.

Nieselt K, Battke F, Herbig A, Bruheim P, Wentzel A, Jakobsen ØM, Sletta H, Alam MT, Merlo ME, Moore J, Omara WA, Morrissey ER, Juarez-Hermosillo MA, Rodríguez-García A, Nentwich M, Thomas L, Iqbal M, Legaie R, Gaze WH, Challis GL, Jansen RC, Dijkhuizen L, Rand DA, Wild DL, Bonin M, Reuther J, Wohlleben W, Smith MC, Burroughs NJ, Martín JF, Hodgson DA, Takano E, Breitling R, Ellingsen TE, Wellington EM.

BMC Genomics. 2010 Jan 6;11:10. doi: 10.1186/1471-2164-11-10.


Prediction of photoperiodic regulators from quantitative gene circuit models.

Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ.

Cell. 2009 Dec 11;139(6):1170-9. doi: 10.1016/j.cell.2009.11.029.


Bayesian inference of biochemical kinetic parameters using the linear noise approximation.

Komorowski M, Finkenstädt B, Harper CV, Rand DA.

BMC Bioinformatics. 2009 Oct 19;10:343. doi: 10.1186/1471-2105-10-343.


Pulsatile stimulation determines timing and specificity of NF-kappaB-dependent transcription.

Ashall L, Horton CA, Nelson DE, Paszek P, Harper CV, Sillitoe K, Ryan S, Spiller DG, Unitt JF, Broomhead DS, Kell DB, Rand DA, Sée V, White MR.

Science. 2009 Apr 10;324(5924):242-6. doi: 10.1126/science.1164860.


Reconstruction of transcriptional dynamics from gene reporter data using differential equations.

Finkenstädt B, Heron EA, Komorowski M, Edwards K, Tang S, Harper CV, Davis JR, White MR, Millar AJ, Rand DA.

Bioinformatics. 2008 Dec 15;24(24):2901-7. doi: 10.1093/bioinformatics/btn562. Epub 2008 Oct 30.


Mapping global sensitivity of cellular network dynamics: sensitivity heat maps and a global summation law.

Rand DA.

J R Soc Interface. 2008 Aug 6;5 Suppl 1:S59-69. doi: 10.1098/rsif.2008.0084.focus.


Isoform switching facilitates period control in the Neurospora crassa circadian clock.

Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA.

Mol Syst Biol. 2008;4:164. doi: 10.1038/msb.2008.5. Epub 2008 Feb 12. Erratum in: Mol Syst Biol. 2008;4:186.


Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study.

Heron EA, Finkenstädt B, Rand DA.

Bioinformatics. 2007 Oct 1;23(19):2596-603. Epub 2007 Jul 28.


Quantitative theories of T-cell responsiveness.

van den Berg HA, Rand DA.

Immunol Rev. 2007 Apr;216:81-92. Review.


Design principles underlying circadian clocks.

Rand DA, Shulgin BV, Salazar D, Millar AJ.

J R Soc Interface. 2004 Nov 22;1(1):119-30.


The effect of an 18-hour electrical power outage on an urban emergency medical services system.

Rand DA, Mener DJ, Lerner EB, DeRobertis N.

Prehosp Emerg Care. 2005 Oct-Dec;9(4):391-7.


Modelling antigenic drift in weekly flu incidence.

Finkenstädt BF, Morton A, Rand DA.

Stat Med. 2005 Nov 30;24(22):3447-61.


Uncovering the design principles of circadian clocks: mathematical analysis of flexibility and evolutionary goals.

Rand DA, Shulgin BV, Salazar JD, Millar AJ.

J Theor Biol. 2006 Feb 7;238(3):616-35. Epub 2005 Aug 18.


Foreignness as a matter of degree: the relative immunogenicity of peptide/MHC ligands.

van den Berg HA, Rand DA.

J Theor Biol. 2004 Dec 21;231(4):535-48.


Dynamics of T cell activation threshold tuning.

van den Berg HA, Rand DA.

J Theor Biol. 2004 Jun 7;228(3):397-416.


Antigen presentation on MHC molecules as a diversity filter that enhances immune efficacy.

van den Berg HA, Rand DA.

J Theor Biol. 2003 Sep 21;224(2):249-67.


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