Combining tree-based and dynamical systems for the inference of gene regulatory networks.

ABSTRACT:

Motivation

Reconstructing the topology of gene regulatory networks (GRNs) from time series of gene expression data remains an important open problem in computational systems biology. Existing GRN inference algorithms face one of two limitations: model-free methods are scalable but suffer from a lack of interpretability and cannot in general be used for out of sample predictions. On the other hand, model-based methods focus on identifying a dynamical model of the system. These are clearly interpretable and can be used for predictions; however, they rely on strong assumptions and are typically very demanding computationally.

Results

Here, we propose a new hybrid approach for GRN inference, called Jump3, exploiting time series of expression data. Jump3 is based on a formal on/o

SUBMITTER: Huynh-Thu VA 

PROVIDER: S-EPMC4426834 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature