249 citations · 529 across the 6 of their papers we have counts for
6 papers
An unbiased metric of antiproliferative drug effect in vitro
Leonard A. Harris, Peter L. Frick, Shawn P. Garbett +5
In vitro cell proliferation assays are widely used in pharmacology, molecular biology, and drug discovery. Using theoretical modeling and experimentation, we show that current anti…
BioNetGen 2.2: Advances in Rule-Based Modeling
Leonard A. Harris, Justin S. Hogg, Jose-Juan Tapia +7
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model spe…
Exact hybrid particle/population simulation of rule-based models of biochemical systems
Justin S. Hogg, Leonard A. Harris, Lori J. Stover +2
Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad…
Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm
Krishna A. Iyengar, Leonard A. Harris, Paulette Clancy
There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial i…
Quantifying Stochastic Effects in Biochemical Reaction Networks using Partitioned Leaping
Leonard A. Harris, Aaron M. Piccirilli, Emily R. Majusiak +1
"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping…
A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics
Leonard A. Harris, Paulette Clancy
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" method…