Torkel E. Loman

Mixed positive and negative feedback loops drive diverse single-cell gene expression dynamics

The paper uses stochastic modeling and experiments to show mixed feedback loops in bacteria generate diverse gene expression dynamics.

PEtab.jl: Advancing the Efficiency and Utility of Dynamic Modelling

PEtab.jl improves dynamic modelling efficiency by comparing ODE solvers and parameter estimation methods, showing faster performance than pyPESTO for medium-sized models.

A BRC1-modulated switch in auxin transport accounts for the competition between Arabidopsis axillary buds

This paper develops a mathematical model of bud-bud competition in Arabidopsis, showing that BRC1 modulates auxin efflux to influence bud competitiveness.

Catalyst: Fast and flexible modeling of reaction networks

Catalyst introduces a Julia library for modeling and simulating chemical reaction networks with high performance and flexibility.

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit

The paper shows that the σV circuit in B. subtilis generates tunable phenotypic variability in response to stress, memory of previous stress, and genetic perturbations.