Tools and Models

PEPSDI (Particles Engine for Population Stochastic DynamIcs) framework
Bayesian inference framework for dynamic state space mixed effects models (SSMEM).

yMSA (Multi-Scale Model of Yeast Replicative Ageing)
The model consists of three interconnected modules: a Boolean signalling network model, an enzyme-constrained flux balance model of the central carbon metabolism, and a dynamic model of growth and protein damage accumulation with discrete cell divisions.

Single-cell and whole population model of damage accumulation in yeast
A dynamic model based on ordinary differential equations (ODE) capable of simulating and mapping replicative ageing on single-cell and population level. The model includes novel features on the population level, such as the health span and the rejuvenation index, in addition to previously known metrics, such as the replicative life span, growth per cell cycle and cumulative growth,  characterising the precise large-scale impact of single-cell properties on the lineage.

Yeast Hybrid Model
A hybrid model, combining a Boolean module, describing the main pathways of glucose and nitrogen signalling, and an enzyme-constrained model accounting for the central carbon metabolism of Saccharomyces cerevisiae, using a regulatory network as a link.

Automated heuristic detection of upstream Open Reading Frames in yeast
A series of Perl scripts for large-scale analysis of yeast 5’UTR.