4 citations · 10 across the 9 of their papers we have counts for
9 papers
DigiPhen: a new paradigm for building predictive models of biological systems
H. Steven Wiley, Angela Cintolesi, Niaz Bahar Chowdhury +7
Reengineered biological systems have the potential to revolutionize chemical and material production, enhance critical mineral recovery, serve as threat sensors and improve human h…
From FAIR to CURE: Guidelines for Computational Models of Biological Systems
Herbert M. Sauro, Eran Agmon, Michael L. Blinov +48
Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific…
SBbadger: Biochemical Reaction Networks with Definable Degree Distributions
Michael A. Kochen, H. Steven Wiley, Song Feng +1
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against…
Dynamics and Sensitivity of Signaling Pathways
Michael A. Kochen, Steven S. Andrews, H. Steven Wiley +2
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic m…
Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response
Song Feng, Emily Heath, Brett Jefferson +25
Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular d…
Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks
Yen Ting Lin, Song Feng, William S. Hlavacek
Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit ti…
Prediction of Optimal Drug Schedules for Controlling Autophagy
Afroza Shirin, Isaac Klickstein, Song Feng +3
The effects of molecularly targeted drug perturbations on cellular activities and fates are difficult to predict using intuition alone because of the complex behaviors of cellular…
In silico evolution of signaling networks using rule-based models: bistable response dynamics
Song Feng, Orkun S. Soyer
One of the ultimate goals in biology is to understand the design principles of biological systems. Such principles, if they exist, can help us better understand complex, natural bi…
Generalizing Gillespie's direct method to enable network-free simulations
Ryan Suderman, Eshan D. Mitra, Yen Ting Lin +3
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration…