Now showing items 1-5 of 5

    • A Network Biology Approach to Denitrification in Pseudomonas aeruginosa 

      Arat, Seda; Bullerjahn, George S.; Laubenbacher, Reinhard (2015-02-23)
      Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of ...
    • 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 ...
    • The Genome-Wide Early Temporal Response of Saccharomyces cerevisiae to Oxidative Stress Induced by Cumene Hydroperoxide 

      Sha, Wei; Martins, Ana M.; Laubenbacher, Reinhard; Mendes, Pedro; Shulaev, Vladimir (PLOS, 2013-09-20)
      Oxidative stress is a well-known biological process that occurs in all respiring cells and is involved in pathophysiological processes such as aging and apoptosis. Oxidative stress agents include peroxides such as hydrogen ...
    • 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 ...
    • A virtual look at Epstein-Barr virus infection: Biological interpretations 

      Duca, Karen A.; Shapiro, Michael; Delgado-Eckert, Edgar; Hadinoto, Vey; Jarrah, Abdul S.; Laubenbacher, Reinhard; Lee, Kichol; Luzuriaga, Katherine; Polys, Nicholas F.; Thorley-Lawson, David A. (PLOS, 2007-10-19)
      The possibility of using computer simulation and mathematical modeling to gain insight into biological and other complex systems is receiving increased attention. However, it is as yet unclear to what extent these techniques ...