99 citations · 492 across the 22 of their papers we have counts for
10 papers · 1 filter
Canalization reduces the nonlinearity of regulation in biological networks
Claus Kadelka, David Murrugarra
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structu…
Modular control of Boolean network models
David Murrugarra, Alan Veliz-Cuba, Elena Dimitrova +3
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation,…
Quantifying the Total Effect of Edge Interventions in Discrete Multistate Networks
David Murrugarra, Elena Dimitrova
Developing efficient computational methods to assess the impact of external interventions on the dynamics of a network model is an important problem in systems biology. This paper…
Estimating Propensity Parameters using Google PageRank and Genetic Algorithms
David Murrugarra, Jacob Miller, Alex Mueller
Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity s…
Identification of control targets in Boolean molecular network models via computational algebra
David Murrugarra, Alan Veliz-Cuba, Boris Aguilar +1
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or o…
Molecular Network Control Through Boolean Canalization
David Murrugarra, Elena S. Dimitrova
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boole…
Stabilizing Gene Regulatory Networks Through Feedforward Loops
Claus Kadelka, David Murrugarra, Reinhard Laubenbacher
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes…
Modeling Stochasticity and Variability in Gene Regulatory Networks
David Murrugarra, Alan Veliz-Cuba, Boris Aguilar +2
Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such…
Structure and Dynamics of Polynomial Dynamical Systems
Reinhard Laubenbacher, David Murrugarra, Alan Veliz-Cuba
Discrete models have a long tradition in engineering, including finite state machines, Boolean networks, Petri nets, and agent-based models. Of particular importance is the questio…
Regulatory patterns in molecular interaction networks
David Murrugarra, Reinhard Laubenbacher
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network t…