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Models in biology: lessons from modeling regulation of the eukaryotic cell cycle.

Tyson JJ, Novák B.

BMC Biol. 2015 Jul 1;13(1):46. doi: 10.1186/s12915-015-0158-9.


A Mathematical Framework for Understanding Four-Dimensional Heterogeneous Differentiation of [Formula: see text] T Cells.

Hong T, Oguz C, Tyson JJ.

Bull Math Biol. 2015 Jun;77(6):1046-64. doi: 10.1007/s11538-015-0076-6. Epub 2015 Mar 17.


Cell cycle control by a minimal Cdk network.

Gérard C, Tyson JJ, Coudreuse D, Novák B.

PLoS Comput Biol. 2015 Feb 6;11(2):e1004056. doi: 10.1371/journal.pcbi.1004056. eCollection 2015 Feb.


Bistability, oscillations, and traveling waves in frog egg extracts.

Tyson JJ, Novak B.

Bull Math Biol. 2015 May;77(5):796-816. doi: 10.1007/s11538-014-0009-9. Epub 2014 Sep 4.


Control of cell growth, division and death: information processing in living cells.

Tyson JJ, Novak B.

Interface Focus. 2014 Jun 6;4(3):20130070. doi: 10.1098/rsfs.2013.0070. Review.


A stochastic model correctly predicts changes in budding yeast cell cycle dynamics upon periodic expression of CLN2.

Oguz C, Palmisano A, Laomettachit T, Watson LT, Baumann WT, Tyson JJ.

PLoS One. 2014 May 9;9(5):e96726. doi: 10.1371/journal.pone.0096726. eCollection 2014.


Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer.

Chen C, Baumann WT, Xing J, Xu L, Clarke R, Tyson JJ.

J R Soc Interface. 2014 May 7;11(96):20140206. doi: 10.1098/rsif.2014.0206. Print 2014 Jul 6.


Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.

Palmisano A, Hoops S, Watson LT, Jones TC Jr, Tyson JJ, Shaffer CA.

BMC Syst Biol. 2014 Apr 4;8:42. doi: 10.1186/1752-0509-8-42.


Modelling the effect of GRP78 on anti-oestrogen sensitivity and resistance in breast cancer.

Parmar JH, Cook KL, Shajahan-Haq AN, Clarke PA, Tavassoly I, Clarke R, Tyson JJ, Baumann WT.

Interface Focus. 2013 Aug 6;3(4):20130012. doi: 10.1098/rsfs.2013.0012.


Role for regulated phosphatase activity in generating mitotic oscillations in Xenopus cell-free extracts.

Zhang T, Tyson JJ, Novák B.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20539-44. doi: 10.1073/pnas.1318065110. Epub 2013 Dec 2.


Potential role of a bistable histidine kinase switch in the asymmetric division cycle of Caulobacter crescentus.

Subramanian K, Paul MR, Tyson JJ.

PLoS Comput Biol. 2013;9(9):e1003221. doi: 10.1371/journal.pcbi.1003221. Epub 2013 Sep 12.


Measurement and modeling of transcriptional noise in the cell cycle regulatory network.

Ball DA, Adames NR, Reischmann N, Barik D, Franck CT, Tyson JJ, Peccoud J.

Cell Cycle. 2013 Oct 1;12(19):3203-18. doi: 10.4161/cc.26257. Epub 2013 Sep 4.


Modeling the estrogen receptor to growth factor receptor signaling switch in human breast cancer cells.

Chen C, Baumann WT, Clarke R, Tyson JJ.

FEBS Lett. 2013 Oct 11;587(20):3327-34. doi: 10.1016/j.febslet.2013.08.022. Epub 2013 Aug 28.


Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model.

Oguz C, Laomettachit T, Chen KC, Watson LT, Baumann WT, Tyson JJ.

BMC Syst Biol. 2013 Jun 28;7:53. doi: 10.1186/1752-0509-7-53.


Top-down network analysis to drive bottom-up modeling of physiological processes.

Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM.

J Comput Biol. 2013 May;20(5):409-18. doi: 10.1089/cmb.2012.0274.


Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates.

Gérard C, Tyson JJ, Novák B.

Biophys J. 2013 Mar 19;104(6):1367-79. doi: 10.1016/j.bpj.2013.02.012. Epub 2013 Mar 19.


Molecular mechanisms creating bistable switches at cell cycle transitions.

Verdugo A, Vinod PK, Tyson JJ, Novak B.

Open Biol. 2013 Mar 13;3(3):120179. doi: 10.1098/rsob.120179.


A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells.

Hong T, Xing J, Li L, Tyson JJ.

BMC Syst Biol. 2012 Jun 14;6:66. doi: 10.1186/1752-0509-6-66.


Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells.

Fu Y, Glaros T, Zhu M, Wang P, Wu Z, Tyson JJ, Li L, Xing J.

PLoS Comput Biol. 2012;8(5):e1002526. doi: 10.1371/journal.pcbi.1002526. Epub 2012 May 17.


Endoplasmic reticulum stress, the unfolded protein response, autophagy, and the integrated regulation of breast cancer cell fate.

Clarke R, Cook KL, Hu R, Facey CO, Tavassoly I, Schwartz JL, Baumann WT, Tyson JJ, Xuan J, Wang Y, Wärri A, Shajahan AN.

Cancer Res. 2012 Mar 15;72(6):1321-31. doi: 10.1158/0008-5472.CAN-11-3213. Review.

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