491 citations · 4.4k across the 45 of their papers we have counts for
6 papers · 1 filter
Lower glycolysis carries a higher flux than any biochemically possible alternative
Steven J. Court, Bartlomiej Waclaw, Rosalind J. Allen
The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a l…
Non-Stationary Forward Flux Sampling
Nils B. Becker, Rosalind J. Allen, Pieter Rein ten Wolde
We present a new method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method…
DNA looping provides stability and robustness to the bacteriophage lambda switch
Marco J. Morelli, Pieter Rein ten Wolde, Rosalind J. Allen
The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensiv…
Exact solution of a model DNA-inversion genetic switch with orientational control
Paolo Visco, Rosalind J. Allen, Martin R. Evans
DNA inversion is an important mechanism by which bacteria and bacteriophage switch reversibly between phenotypic states. In such switches, the orientation of a short DNA element is…
Reaction coordinates for the flipping of genetic switches
M. J. Morelli, S. Tanase-Nicola, R. J. Allen +1
We present a detailed analysis, based on the Forward Flux Sampling (FFS) simulation method, of the switching dynamics and stability of two models of genetic toggle switches, consis…
Sampling rare switching events in biochemical networks
Rosalind J. Allen, Patrick B. Warren, Pieter Rein ten Wolde
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in exp…