Computational Biology Publications:

P. Krupinski, V. Chickarmane, C. Peterson, ”Simulating the mammalian blastocyst-molecular and mechanical interactions pattern the embryo”, PLoS Comput Biol. 2011 May;7(5):e1001128.

[abs]

A.H.K. Roeder, P.T. Tarr, C. Tobin, X. Zhang, V. Chickarmane, A. Cunha, E.M. Meyerowitz, "Computational morphodynamics of plants: integrating development over space and time.", Nat Rev Mol Cell Biol. 2011, 12(4):265-73.

[abs]

V. Chickarmane, A.H.K. Roeder, P.T. Tarr, A. Cunha, C. Tobin, E.M. Meyerowitz, “Computational Morphodynamics: A modeling framework to understand plant growth”, Annu Rev Plant Biol. 2010, 61:65-87

[abs]

A.H.K Roeder, V. Chickarmane, A. Cunha, B. Obara, B.S. Manjunath, E.M Meyerowitz, “Variability in the control of cell division underlies sepal epidermal patterning in Arabidopsis thaliana.”, PLoS Biol. 2010, 8(5):e1000367.

[abs] [faculty of 1000]

S.P. Gordon, V. Chickarmane, C. Ohno, E.M. Meyerowitz, “Multiple feedback loops control stem cell number within the Arabidopsis shoot meristem.” Proc Natl Acad Sci U S A. 2009, 106(38):16529-34.

[abs][faculty of 1000]

V. Chickarmane, T. Enver, C. Peterson, “Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into co-operativity, priming and irreversibility” PLoS Computational Biology, 2009, 5(1):e1000268

[abs]

V. Chickarmane, C. Peterson, “A computational model for understanding stem cell, trophectoderm and endoderm lineage determination” PLoS ONE. 2008, 3(10), e3478

[abs]

V. Chickarmane, A. Ray, H.M. Sauro, A. Nadim, “A model for p53 Dynamics Triggered by DNA Damage,” SIAM J Appl. Dyn. Sys, 2007, 6(1), 61-78.

[abs]

V. Chickarmane, B.N. Kholodenko, H.M. Sauro, “Oscillatory Dynamics arising from Competitive Inhibition and Multisite Phosphorylation in MAPK cascades,” J Theor Biol, 2007, 244(1):68-76.

[abs]

V. Chickarmane, C. Troein, U. Nuber, H.M. Sauro, C. Peterson, “Transcriptional Dynamics of the Embryonic Stem Cell Switch,” PLoS Computational Biology, 2006, 2(9):e123

[abs]

R.R. Vallabhajosyula, V. Chickarmane, H.M. Sauro, “Conservation analysis of large biochemical networks,” Bioinformatics, 2006, 22(3):346-53.

[abs]

S. Paladugu, V. Chickarmane, A. Deckard, J. Frumkin, M. McCormack, H.M. Sauro, “In-Silico Evolution of Functional Modules in Biochemical Networks,” IEE Proc Sys Bio, 2006, 153( 4), 223-235.

[abs]

V. Chickarmane, A. Nadim, A. Ray, H.M. Sauro, “A p53 Oscillator Model of DNA Break Repair Control,” Quantitative Biology. Oct 2005, q-bio.MN/0510002.

[abs]

V. Chickarmane, S. Paladugu, F. Bergman, H.M. Sauro, “Bifurcation Discovery Tool,” Bioinformatics, 2005, 21(18):3688-3690.

[abs]

C. Wellock, V. Chickarmane, H.M. Sauro, “The SBW-MATLAB Interface,” Bioinformatics, 2005, 21(6):824-825.

[abs]