Selected publications in 2012

A systems biology approach to identifying the signaling network regulated by Rho-GDI-γ during neural stem cell differentiation.
Wang J, Hu F, Cheng H, Zhao XM, Wen T.
Molecular BioSystems (2012)

Therefore, a novel systems biology approach is presented here to identify putative signalling pathways regulated by Rho-GDI-γ during NSC differentiation, and these pathways can provide insights into the NSC differentiation mechanisms.

FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model.
Wang M, Zhao XM, Takemoto K, Xu H, Li Y, Akutsu T, Song J.
PLoS ONE (2012)

We built a two-stage random forest (RF) model, termed as FunSAV, to predict the functional effect of SAVs by combining sequence, structure and residue-contact network features with other additional features that were not explored in previous studies.

Identifying dysregulated pathways in cancers from pathway interaction networks.
Liu KQ, Liu ZP, Hao JK, Chen L, Zhao XM.
BMC Bioinformatics (2012)

In this paper, we propose a novel approach to identify dysregulated pathways in cancer based on a pathway interaction network.

Identifying disease genes and module biomarkers by differential interactions.
Liu X, Liu ZP, Zhao XM, Chen L.
Journal of the American Medical Informatics Association : JAMIA (2012)

In this paper, we present a novel approach to predict disease genes and identify dysfunctional networks or modules, based on the analysis of differential interactions between disease and control samples, in contrast to the analysis of differential gene or protein expressions widely adopted in existing methods.

Predicting drug targets based on protein domains.
Wang YY, Nacher JC, Zhao XM.
Molecular BioSystems (2012)

Here, we present a novel statistical approach, namely PDTD (Predicting Drug Targets with Domains), to predict potential target proteins of new drugs based on derived interactions between drugs and protein domains.

Exploring drug combinations in genetic interaction network.
Wang YY, Xu KJ, Song J, Zhao XM.
BMC Bioinformatics (2012)

In this work, we present a network biology approach to investigate drug combinations and their target proteins in the context of genetic interaction networks and the related human pathways, in order to better understand the underlying rules of effective drug combinations.

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information.
Zhang X, Zhao XM, He K, Lu L, Cao Y, Liu J, Hao JK, Liu ZP, Chen L.
Bioinformatics (2012)

In this work, we present a novel method, namely NARROMI, to improve the accuracy of GRN inference by combining ordinary differential equation-based recursive optimization (RO) and information theory-based mutual information (MI).