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Molecular dynamics is an important method for protein structure research, which is called the holy grail of bioinformatics. It is also a popular application in large super-computers. GROMACS is a widely used software package for molecular dynamics simulation. Almost all current attempts are only focus on the most costly part (consuming less than 70% of the time), while other parts are still running...
Histone modification is an important epigenetic event which plays essential roles in cell differentiation and tissue development. Recent studies show that a unique dimethylation of lysine 4 residue on histone 3 (H3K4me2) distribution pattern around transcription starting sites (TSS) of genes marks tissue specific genes in human CD4 + T cells and mouse nervous tissue cells. However, existence of this...
We propose a signal processing approach for detecting enrichment regions from ChIP-seq datasets. A wavelet transform of the ChIP-seq data offers a direct visualization for both short- and long-range patterns of the genome-wide mapping profile for protein binding site on DNA. To investigate the location of transcription factor binding site (TFBS) from ChIP-seq data, a wavelet-based peak detection algorithm...
We are developing a new framework for discovery of genes involved in the breast carcinogenesis process. Among families that have a predisposition to breast cancer, approximately 25% have inherited mutations in either breast cancer associated (ldquoBRCArdquo) genes BRCA1 or BRCA2, but the predisposing mutated genes in the majority of the families are unknown. BRCA1 and BRCA2 gene products both regulate...
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