Now showing items 1-3 of 3

    • ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra 

      Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard (2011-07-20)
      Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The ...
    • Modeling stochasticity and variability in gene regulatory networks 

      Murrugarra, David; Veliz-Cuba, Alan; Aguilar, Boris; Arat, Seda; Laubenbacher, Reinhard (2012-06-06)
      Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used ...
    • The effect of negative feedback loops on the dynamics of Boolean networks 

      Sontag, Eduardo; Veliz-Cuba, Alan; Laubenbacher, Reinhard; Jarrah, Abdul Salam (CELL PRESS, 2008-07)
      Feedback loops play an important role in determining the dynamics of biological networks. To study the role of negative feedback loops, this article introduces the notion of distance-to-positive-feedback which, in essence, ...