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DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the(More)
Extensive studies have shown that mining microarray data sets is important in bioinformatics research and biomedical applications. In this paper, we explore a novel type of gene-sample-time microarray data sets, which records the expression levels of various genes under a set of samples during a series of time points. In particular, we propose the mining of(More)
Kinetic data on a number of protein-protein associations have provided evidence for the initial formation of a pre-equilibrium encounter complex that subsequently relaxes to the final stereospecific complex. Site-directed mutagenesis and brownian dynamics simulations have suggested that the rate of association can be modulated by perturbations in charge(More)
Microarray technologies are capable of simultaneously measuring the signals for thousands of messenger RNAs and large numbers of proteins from single samples. Arrays are now widely used in basic biomedical research for mRNA expression profiling and are increasingly being used to explore patterns of gene expression in clinical research. Most research has(More)
Mining microarray gene expression data is an important research topic in bioinformatics with broad applications. While most of the previous studies focus on clustering either genes or samples, it is interesting to ask whether we can partition the complete set of samples into exclusive groups (called <i>phenotypes)</i> and find a set of <i>informative(More)
GOALS We aim to characterize the fungal microbiota in the intestinal mucosa and feces in patients with Crohn's disease (CD). BACKGROUND Fungi represent a diverse microbial community in the human intestine and might play a role in the pathogenesis of CD; however, little is known about the structure and composition of the fungal microbiota especially(More)
BACKGROUND The dysbiosis of intestinal microbiota has been established in Crohn's disease (CD), but the molecular characterization of this dysbiosis in Chinese subjects with CD remains unclear. This study aims to investigate the predominant bacterial composition of the faecal and mucosal-associated microbiota in Chinese CD patients using culture-independent(More)
Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in(More)
Recent advances in the use of paramagnetic relaxation enhancement (PRE) in structure refinement and in the analysis of transient dynamic processes involved in macromolecular complex formation are presented. In the slow exchange regime, we show, using the SRY/DNA complex as an example, that the PRE provides a powerful tool that can lead to significant(More)