Protein structural models provide essential information for the research on proteinprotein interactions. In this dissertation, we describe two projects on the analysis of protein interactions using structural information. The focus of the first is to characterize and classify different types of interactions. We discriminate between biological obligate and biological non-obligate interactions, a...

Several bioinformatics data sets are naturally represented as graphs, for instance gene regulation, metabolic pathways, and proteinprotein interactions. The graphs are often large and complex, and their straightforward visualizations are incomprehensible. We have recently developed a new method called local multidimensional scaling for visualizing high-dimensional data sets. In this paper we ad...

A substantial amount of knowledge about biomolecular interactions resides in the biomedical literature and has been increasingly made available as structured, curated database entries. Although recent research in biological assertion extraction has mostly focused on automatically detecting interacting entities, automated generation of provenance for interacting pairs remains of equal importance...

We propose here a multi-label semi-supervised learning algorithm, PfunBG, to predict protein functions, employing a bi-relational graph (BG) of proteins and function annotations. Different from most, if not all, existing methods that only consider the partially labeled proteinprotein interaction (PPI) network, the BG comprises three components, a PPI network, a function class graph induced from...

Random walk methods have been successfully applied to prioritizing disease causal genes. In this paper, we propose a bi-random walk algorithm (BiRW) based on a regularization framework for graph matching to globally prioritize disease genes for all phenotypes simultaneously. While previous methods perform random walk either on the proteinprotein interaction network or the complete phenome-genom...

Comparison of the protein interaction networks from different species is of paramount importance for understanding physical and functional interactions between biological functions and processes within a cell. In this paper, we introduce a novel algorithm for a global alignment of multiple proteinprotein interaction (PPI) networks called MAPPIN. The latter combines information available for the...

Motivations In recent years, the role of alternative splicing in protein function regulation has been widely investigated. Examples have been reported in which alternative splicing modulates the interaction between two proteins by removing interacting regions. However, despite the large amount of data available about alternative splicing isoforms and protein-protein interactions, only a few sys...

To clarify the underlying mechanism of radioresistance nasopharyngeal carcinoma, we identified correlated gene modules and key genes through analyzing expression omnibus dataset with weighted co-expression network analysis. GSE32389 were obtained from omnibus. The analysis was introduced to establish a mine important genes. Gene ontology enrichment performed in which related carcinoma. Then, es...

© Translational Andrology and Urology. All rights reserved. Transl Androl Urol, 2015;4(S1) www.amepc.org/tau pVHL, HIF-2a and Glut-1 was obviously lower than constant cell line; the half-time of missense mutant pVHL was shorter than the wild-type one(t1/2 mut =1.5 h vs. t1/2 wt =4 h). After treated with celastrol, the half-time of mutant pVHL increased to 3 h. Co-IP indicated that celastrol inc...

After the publication of this work [1], we became aware of the fact that the Saccharomyces cerevisiae physical interaction table from the MIPS database that was used to count the number of protein-protein interactions per S. cerevisiae protein contains numerous redundant entries http:// mips.gsf.de/proj/yeast/tables/interaction/ physical_interact.html. These redundancies were not removed initia...