A systems-level understanding of biological processes and information flow requires the mapping of cellular component interactions, among which protein-protein interactions are particularly important. Fission yeast (Schizosaccharomyces pombe) is a valuable model organism for which no systematic protein-interaction data are available. We exploited gene and protein properties, global genome regul...

One of major goals of functional genomics is to elucidate protein interaction networks for whole organisms. Determining protein interactions provides not only detailed functional insights on characterized proteins, but also an information base for identifying biological complexes and metabolic or signal transduction pathways [1]. The recent emergence of high-throughput proteomics techniques has...

We investigate a very simple model describing the evolution of protein-protein interaction networks via duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the probability to retain a duplicated link during divergence. When this parameter is large, the network growth is not self-averaging and an average node degree increases algebraically. ...

6 The increasing growth of data on protein-protein interaction (PPI) networks has boosted research 7 on their comparative analysis. In particular, recent studies proposed models and algorithms for 8 performing network alignment, that is, the comparison of networks across species for discovering 9 conserved functional complexes. In this paper, we present an algorithm for dividing PPI networks, 1...

background: numerous studies used microarray gene expression data to extract metastasis-driving gene signatures for the prediction of breast cancer relapse. however, the accuracy and generality of the previously introduced biomarkers are not acceptable for reliable usage in independent datasets. this inadequacy is attributed to ignoring gene interactions by simple feature selection methods, due...

High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with...

Physical interactions between proteins mediate a variety of biological functions, including signal transduction, physical structuring of the cell and regulation. While extensive catalogs of such interactions are known from model organisms, their evolutionary histories are difficult to study given the lack of interaction data from phylogenetic outgroups. Using phylogenomic approaches, we infer a...

Identifying candidate genes related to complex diseases or traits and mapping their relationships require a system-level analysis at a cellular scale. The objective of the present study is to systematically analyze the complex effects of interrelated genes and provide a framework for revealing their relationships in association with a specific disease (asthma in this case). We observed that pro...

Studying protein interaction networks of all proteins in an organism ("interactomes") remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map inter...

I, Haogang ZHU, confirm that this dissertation and the work presented in it are my own achievement.