Yangyang Deng

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It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although several methods have been suggested, their performances are not satisfactory for datasets with high missing percentages. The paper explores the feasibility(More)
Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring(More)
ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated. In this paper, we have developed a computational method to generate the first(More)
Recently, a number of high-resolution genome-wide maps of nucleosome locations in S. cerevisiae have been derived experimentally. However, nucleosome positions are determined in vivo by the combined effects of numerous factors. Consequently, nucleosomes are not simple static units, which may explain the discrepancies in reported nucleosome positions as(More)
Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo. Motivated by our observation that transcriptional interaction is discriminative information for nucleosome occupancy, we(More)
Eukaryotic genomes are packaged into chromatin by histone proteins whose chemical modification can profoundly influence gene expression. The histone modifications often act in combinations, which exert different effects on gene expression. Although a number of experimental techniques and data analysis methods have been developed to study histone(More)
BACKGROUND A 47-year-old male presented with retrosternal chest pain, which had started 4 days previously and had become excruciating for the past 6 h. He had undergone mechanical aortic valve replacement surgery 4 months previously. INVESTIGATION Electrocardiography, echocardiography, computed tomography-angiography of the aorta. DIAGNOSIS Rupture of(More)
The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning plays a central role in diverse cellular processes that rely on access to genomic DNA. Experimental evidence suggests that the genomic DNA sequence is one important determinant of nucleosome positioning. Yet it is less clear whether the role of the underlying DNA sequence in(More)
The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown. We found that transcription factor binding sites (TFBSs) with particular(More)