An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells.

ABSTRACT:

Motivation

Primary purpose of modeling gene regulatory networks for developmental process is to reveal pathways governing the cellular differentiation to specific phenotypes. Knowledge of differentiation network will enable generation of desired cell fates by careful alteration of the governing network by adequate manipulation of cellular environment.

Results

We have developed a novel integer programming-based approach to reconstruct the underlying regulatory architecture of differentiating embryonic stem cells from discrete temporal gene expression data. The network reconstruction problem is formulated using inherent features of biological networks: (i) that of cascade architecture which enables treatment of the entire complex network as a set of interconnected modules and

SUBMITTER: Banerjee I 

PROVIDER: S-EPMC2865861 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature