Parameter estimation for Boolean models of biological networks (2009)
Dimitrova, Elena, Garcia-Puente, Luis David, Hinkelmann, Franziska, Jarrah, Abdul S., Laubenbacher, Reinhard, Stigler, Brandilyn, ...
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web...
On the algebraic geometry of polynomial dynamical systems (2008)
Jarrah, Abdul S., Laubenbacher, Reinhard
This paper focuses on polynomial dynamical systems over finite fields. These systems appear in a variety of contexts, in computer science, engineering, and computational biology, for instance as...
Oosawa, Chikoo, Savageau, Michael A., Jarrah, Abdul S., Laubenbacher, Reinhard C., Sontag, Eduardo D.
We demonstrate the effects of embedding subgraphs using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical...
A mathematical formalism for agent-based modeling (2007)
Laubenbacher, Reinhard, Jarrah, Abdul S., Mortveit, Henning, Ravi, S. S.
Many complex systems can be modeled as multiagent systems in which the constituent entities (agents) interact with each other. The global dynamics of such a system is determined by the nature of the...
A Virtual Look at Epstein–Barr Virus Infection: Biological Interpretations (2007)
Karen A. Duca, Michael Shapiro, Edgar Delgado-Eckert, Vey Hadinoto, Abdul S. Jarrah, Reinhard Laubenbacher, ...
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...
A Foundation of Combinatorial Time Series Analysis, preprint (2000)
Michael Coombs, Abdul S. Jarrah, C. Laubenbacher
Abstract. The results in this paper pertain to the analysis of the dynamical properties of autonomous agent systems, with special emphasis on emergent structure resulting from the flow of...
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, ...
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...