Marija Cvijović

PEtab Select: specification standard and supporting software for automated model selection

PEtab Select provides a standardized format and software for automated model selection in systems biology, supporting diverse modeling frameworks and enabling efficient evaluation of large model spaces.

The origin of septin ring size control in budding yeast

This study investigates how septin ring size scales with cell size in budding yeast by combining computational modeling, live-cell imaging, and genetic experiments.

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.

The choice of the objective function in flux balance analysis is crucial for predicting replicative lifespans in yeast

This study shows that choosing the right objective function in flux balance analysis improves predictions of replicative lifespan in yeast.

Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing

The paper develops a multi-scale model of yeast replicative ageing, identifying metabolic phases and interventions that influence lifespan by linking protein damage and ATP demand.

PEPSDI: Scalable and flexible inference framework for stochastic dynamic single-cell models

PEPSDI infers model parameters from time-lapse data to identify extrinsic noise sources in yeast nutrient sensing pathways.

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

The paper develops a hybrid modeling framework integrating Boolean and enzyme-constrained networks to study the interplay between nutrient signaling and metabolism in yeast, revealing new insights into their regulatory effects.

Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability

This study develops and validates a 3D bulk-surface model of Cdc42 dynamics, showing that cell polarisation can result from both classic and non-classic Turing instabilities.

The Synergy of Damage Repair and Retention Promotes Rejuvenation and Prolongs Healthy Lifespans in Cell Lineages

The paper shows that damage retention and early repair in yeast promote rejuvenation and longer healthy lifespans by reducing damage variability and stress susceptibility.

Symmetry structures in dynamic models of biochemical systems

The paper explores symmetry structures in biochemical models, showing improved model selection using symmetry-based methods over residual-based approaches.

Repair, resilience and asymmetric segregation of damage in the context of replicative ageing: it is a balancing act

The paper develops a dynamic model of damage accumulation in yeast cells to understand how damage retention and asymmetric division affect replicative ageing.