194 citations · 678 across the 20 of their papers we have counts for
5 papers · 1 filter
Convenient Interface to Inverse Ising (ConIII): A Python 3 Package for Solving Ising-Type Maximum Entropy Models
Edward D. Lee, Bryan C Daniels
ConIII (pronounced CON-ee) is an open-source Python project providing a simple interface to solving the pairwise and higher order Ising model and a base for extension to other maxi…
Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression
Bryan C. Daniels, Ilya Nemenman
The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these…
Automated adaptive inference of coarse-grained dynamical models in systems biology
Bryan C. Daniels, Ilya Nemenman
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experi…
Statistical properties of multistep enzyme-mediated reactions
Wiet H. de Ronde, Bryan C. Daniels, Andrew Mugler +2
Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermedia…
Sloppiness, robustness, and evolvability in systems biology
Bryan C. Daniels, Yan-Jiun Chen, James P. Sethna +2
The functioning of many biochemical networks is often robust -- remarkably stable under changes in external conditions and internal reaction parameters. Much recent work on robustn…