Developing New Algorithms for Modeling Gene Regulatory Circuits

Tuesday, September 12, 2017 | 12:30 p.m. - 1:30 p.m. Add to Calendar

The Center for Theoretical Biological Physics

Seminar Speaker
Mingyang Lu
Assistant Professor
The Jackson Laboratory

“Developing New Algorithms for Modeling
Gene Regulatory Circuits”

Tuesday, September 12, 2017
12:30 – 1:30 PM
BRC, 10th Floor, Room 1060 A/B

Abstract: Traditional systems biology approaches have simulated the dynamics of a gene regulatory network, but often suffer from two key issues. (1) There is no rational rule to choose an appropriate set of genes to model. (2) Modeling results are usually based on a set of guessed kinetic parameters, limiting the application of mathematical modeling to large systems and the prediction power of systems biology. To address these issues, we are developing an integrated computational framework to identify the core gene regulatory circuit from a large network and reliably predict its dynamics and its regulatory functions. The cornerstone of this framework is our recently developed algorithm named random circuit perturbation (RACIPE), which simulates circuit dynamics without the need for detailed kinetic parameters. I will talk about our recent progress in developing enhanced RACIPE algorithms, the application of RACIPE to a cell cycle circuit and our first attempt to integrate genomics data.

Bio: Mingyang received his B.S. degree in physics at Fudan University. Afterwards, he obtained his Ph.D. degree in Biochemistry and Molecular Biology at Baylor College of Medicine in the laboratory of Dr. Jianpeng Ma. During that time, he worked on computational methodology development for coarse-grained modeling of bimolecular structures and their applications to x-ray crystallographic refinement of flexible supramolecular complexes. He then worked as a postdoctoral fellow in the Center for Theoretical Biological Physics (CTBP) at Rice University with Dr. José Onuchic on computational systems biology. He is currently an Assistant Professor at The Jackson Laboratory and University of Maine.

An Official Seminar of the Ph.D. Program in Systems, Synthetic and Physical Biology at Rice University

Learn more


BioScience Research Collaborative (BRC), 10th Floor, Room 1060 A/B

6500 Main Street


Lisa Bennett