Publications in Systems Biology

 

 

1.      V. Chickarmane and C. Peterson, “Effects of Stochasticity in Incoherent Type I Feed-Forward  Genetic Networks” in preparation.

 

2.      V. Chickarmane, T. Enver and C. Peterson, “How does the hematopoietic erythroid-myeloid switch  live up to its commitment?” in preparation.

 

3.      V. Chickarmane and C. Peterson, “Signaling networks can put the brakes on developmental switches.” in preparation.

 

4.      V. Chickarmane, C. Troein, U. Nuber, H.M. Sauro and C. Peterson, (2006) “Transcriptional Dynamics of the Embryonic Stem Cell Switch,”  PLoS Computational Biology, 2(9), / 10.1371/journal.pcbi.0020123.eor [published ahead of print]

 

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

 

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

 

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

 

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

 

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

 

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

 

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