Selected publications in 2008

Uncovering signal transduction networks from high-throughput data by integer linear programming.
Zhao XM, Wang RS, Chen L, Aihara K.
Nucleic Acids Research (2008)

In this article, we propose a novel method for uncovering signal transduction networks (STNs) by integrating protein interaction with gene expression data.

Gene function prediction using labeled and unlabeled data.
Zhao XM, Wang Y, Chen L, Aihara K.
BMC Bioinformatics (2008)

In this paper, we present a new technique, namely Annotating Genes with Positive Samples (AGPS), for defining negative samples in gene function prediction.

Protein classification with imbalanced data.
Zhao XM, Li X, Chen L, Aihara K.
Proteins (2008)

This article presents a new technique for protein classification with imbalanced data.

Protein domain annotation with integration of heterogeneous information sources.
Zhao XM, Wang Y, Chen L, Aihara K.
Proteins (2008)

In this article, two new methods, that is, the threshold-based classification method and the support vector machines method, are proposed for protein domain function prediction by integrating heterogeneous information sources, including protein–domain mapping features, domain–domain interactions, and domain coexisting features.

Protein function prediction with high-throughput data.
Zhao XM, Chen L, Aihara K.
Amino Acids (2008)

In this review, we provide a comprehensive description of the computational methods that are currently applicable to protein function prediction, especially from the perspective of machine learning.