Research Highlights

Computer model to study gene expression

Published online 31 July 2013

Biplab Das

Gene circuits are clusters of genes that can influence each other's expression by proteins known as transcription factors. The large number of unknown reaction parameters involved during protein synthesis from genes that make up such gene circuits makes it difficult for available computer-based models to simulate this process.

A team of researchers from King Abdullah University of Science and Technology (KAUST) in Thuwal, Saudi Arabia, and Texas A&M University in the United States came up with a new model to estimate these reaction parameters in order to help map gene circuits, publishing their results in Bioinformatics1.

The model, dubbed Parameter Estimation by Decomposition and Integration (PEDI), is designed specifically for gene circuits as opposed to most other parameter estimation models which produce more generic results.

To test the model, the team fed computer-generated mRNA data from three gene circuits that are common to many species into PEDI and other already existing parameter estimation models to compare the outputs. PEDI outperformed other similar existing methods in accuracy, with an error at least 30% lower than the best parameter solution produced by the other models.

To test the model against experimental data, they used mRNA data from yeast. The results from PEDI closely resembled the experimental results.

"This new model can speed up reverse-engineering of gene regulatory systems, integrating computational models and experimental studies for better understanding of biological systems," says Xin Gao, the principal investigator of the study.


  1. Kuwahara, H. et al. A framework for scalable parameter estimation of gene circuit models using structural information. Bioinformatics 29, 98-107 (2013) | Article |