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Compared to the available protein sequences of different organisms, the number of revealed protein-protein interactions (PPIs) is still very limited. So many computational methods have been developed to facilitate the identification of novel PPIs. However, the methods only using the information of protein sequences are more universal than those that depend(More)
OBJECTIVE MicroRNA have recently been identified as regulators that modulate target gene expression and are involved in shaping the immune response. This study was undertaken to investigate the contribution of microRNA-146a (miR-146a), which was identified in the pilot expression profiling step, to the pathogenesis of systemic lupus erythematosus (SLE). (More)
INTRODUCTION Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with a heterogeneous course and varying degrees of severity and organ damage; thus, there is increasing interest in identifying biomarkers for SLE. In this study we correlated the combined expression level of multiple interferon-inducible chemokines with disease activity,(More)
Protein-protein interactions (PPIs) are crucial for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. Given the importance of PPIs, several methods have been developed to detect them. Since the experimental methods are time-consuming and expensive, developing computational methods for(More)
Determining G-protein coupled receptors (GPCRs) coupling specificity is very important for further understanding the functions of receptors. A successful method in this area will benefit both basic research and drug discovery practice. Previously published methods rely on the transmembrane topology prediction at training step, even at prediction step.(More)
INTRODUCTION Dysregulated cytokine action on immune cells plays an important role in the initiation and progress of systemic lupus erythematosus (SLE), a complex autoimmune disease. Comprehensively quantifying basal STATs phosphorylation and their signaling response to cytokines should help us to better understand the etiology of SLE. METHODS(More)
In proteins, the number of interacting pairs is usually much smaller than the number of non-interacting ones. So the imbalanced data problem will arise in the field of protein-protein interactions (PPIs) prediction. In this article, we introduce two ensemble methods to solve the imbalanced data problem. These ensemble methods combine the based-cluster(More)
In the structural models determined by X-ray crystallography, contacts between molecules can be divided into two categories: biologically relevant contacts and crystal packing contacts. With the growth in the number and quality of available large crystal packing contacts structures, distinguishing crystal packing contacts from biologically relevant contacts(More)
Flavin mono-nucleotide (FMN) closely evolves in many biological processes. In this study, a computational method was proposed to identify FMN binding sites based on amino acid sequences of proteins only. A modified Position Specific Score Matrix was used to characterize the local environmental sequence information, and a visible improvement of performance(More)
In this study, we focus on different types of Gram-negative bacterial secreted proteins, and try to analyze the relationships and differences among them. Through an extensive literature search, 1612 secreted proteins have been collected as a standard data set from three data sources, including Swiss-Prot, TrEMBL and RefSeq. To explore the relationships(More)