Author Archives: dingqy

Final Project: Qingyang Ding – How dynamics of transcription factor control gene expression

   Inspired by the idea that signaling dynamics can encode cellular information, I built a set of toy models of gene transcription controlled by different dynamics of transcription factor (that is oscillatory or sustained) to investigate how different promoter response to those dynamic inputs. Many software I learned from the course are involved in the implement and analysis of the models, including XPP, Copasi, and CRNT. I tried to understand the feature of promoter with the help of bifurcation diagram, and also optimize a designed variable of the model to qualitatively fit the experimental results. While plain promoter (with only mass action rules) didn’t discriminate oscillatory and sustained input much, promoters with feed forward loop and positive self-feed-forward loop shows that the average level of oscillatory response is much lower than that of sustained response. What’s more, the feed forward loops also contribute to a significant delay in terms of gene expression. The methods and workflow can be used in building and analyze more transcription models with diverse regulatory mechanisms.


Project Idea: Dynamics and Transcription – Qingyang Ding [Harris]

I plan to work on a toy model extracted from p53 signaling pathway.

This model consists of two parts: 1. An oscillator module with a negative feedback loop, the transcription factor level (p53) can therefore be oscillatory; 2. Gene transcription process with probably feed forward loop or phosphorylation cascade. What I’m interested in is how gene expression level/pattern is controlled by dynamic inputs.

I think I’ll first use Vcell and BioNetGen to implement the model, and explore the feature of the model with XPP as much as I can. Hopefully, this toy model can capture the interesting experimental phenomena in this paper.


Qingyang (Iris), University of Pittsburgh

Qingyang (Iris), University of Pittsburgh