Dongya Jia

This paper develops a computational model of cancer metabolism integrating catabolic and anabolic pathways, identifying four metabolic phenotypes and their association with patient survival.

The paper studies chaotic dynamics in hematopoiesis using mouse data, showing leukocyte fluctuations are chaotic and can transition to oscillations with B cell accumulation.

The paper identifies a drug-tolerant metabolic state in melanoma cells that reduces both glycolysis and oxidative phosphorylation, supporting survival but limiting growth.

The paper uses computational methods to classify gene expression profiles into epithelial, hybrid E/M, and mesenchymal categories based on EMT dynamics and scoring metrics.

The paper models the coupling of gene regulation and metabolic pathways in cancer, showing AMPK and HIF-1 activity correlates with metabolic pathway activities in tumor samples.

RACIPE is a computational tool that models gene regulatory circuits by randomizing parameters to identify robust dynamical features without requiring detailed kinetic data.

The paper introduces RACIPE, a computational method to assess the robustness of gene regulatory circuits by analyzing their dynamical behavior under parameter perturbations, showing topology dominates over kinetic parameters.