Ruth E. Baker

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

The paper shows RecA* structure dynamics predict spontaneous cell death in E. coli by linking SOS response magnitude to DNA repair kinetics.

This paper introduces a deep attention network model to infer cell-cell interaction dynamics from trajectory data, providing interpretable insights into how interactions affect cell movement.

The paper investigates organ-specific fibroblast dynamics in cardiac and pulmonary fibrosis using experimental and computational methods, revealing differences in collagen matrix organization and motility behavior.

This paper develops a mathematical model of heart-tumour interactions under immune checkpoint inhibitor therapy and uses optimal control to design dosing schedules that balance therapeutic and toxic effects.

The paper uses an agent-based model to simulate how Trail, Colec12, and Dan confine cranial neural crest cells to stereotypical migration pathways in vivo.

The paper develops two new mechanochemical vertex models of apical constriction during neural tube closure, incorporating Ca2+ signalling and mechanical interactions to better align with experimental observations.

This study uses a continuum mechanics framework to show that epithelial tissues regulate energy expenditure to maintain efficient migration, and demonstrates this through electrotaxis experiments.

The paper identifies critical genes for neural crest and cancer cell invasion using high-throughput screening and deep learning analysis.

This study develops a continuum model to explain spatial velocity heterogeneity in collective electrotaxis and applies it to design electric field protocols for controlled tissue migration.

The paper investigates whether the segmentation clock and PSM morphogenesis exhibit developmental modularity in zebrafish, finding the clock is robust to morphogenetic variations.

This paper introduces a mathematical framework to determine winner/loser status in cell competition using quantitative criteria and applies it to cell-based models to identify key factors.

The paper introduces a minibatch Bayesian inference method to efficiently analyze high-throughput imaging data, revealing density-dependent interactions in wound healing.

This paper analyzes identifiability in stochastic differential equation models using case studies and synthetic data, showing they can extract more parameter information than deterministic models.

The paper investigates the role of Aquaporin-1 in neural crest cell migration, finding it affects speed, direction, and filopodia stability through interactions with MMPs and pFAK.

The paper models mRNA localization in Drosophila egg chambers and finds that transport saturation contributes to robustness against mRNA synthesis variation.

The paper investigates dynamic feedback between tissue growth and neural crest cell migration during chick head morphogenesis using time-lapse imaging, modeling, and perturbations, revealing its role in robust craniofacial development.

The paper demonstrates that process noise can distinguish between indistinguishable stochastic population dynamics models using Bayesian methods and summary statistics.

The paper develops a free boundary model to describe epithelial dynamics by deriving a continuum-limit PDE that accurately predicts cell-based model behavior with a mass-conserving boundary condition.

This study uses approximate Bayesian computation to show that repeated measurements are essential for reliably parameterizing cell-based models of tissue growth.

The paper shows how cell populations can appear heterogeneous in migration despite identical individual behavior, highlighting statistical pitfalls in analyzing heterogeneity.

The paper examines how implementation choices in vertex models affect quantitative predictions of tissue dynamics, finding sensitivity to parameters like time step size and cell rearrangement thresholds.

This study shows that domain growth mechanisms affect species dominance and spatial density variation in multispecies agent populations.

This paper develops a computational model to study size control in Drosophila embryonic tissues, showing that passive mechanical forces can explain size regulation but require patterning for asymmetries in cell death.

The paper models bacterial reorientation in Rhodobacter sphaeroides using tracking data and three models, finding evidence for active reorientation rather than Brownian rotation.