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As the fundamental unit of eukaryotic chromatin structure, nucleosome plays critical roles in gene expression and regulation by controlling physical access to transcription factors. In this paper, based on the geometrically transformed Tsallis entropy and two index-vectors, a valid nucleosome positioning information model is developed to describe the(More)
Determination of sequence similarity is one of the major steps in computational phylogenetic studies. As we know, during evolutionary history, not only DNA mutations for individual nucleotide but also subsequent rearrangements occurred. It has been one of major tasks of computational biologists to develop novel mathematical descriptors for similarity(More)
The purpose of the present study was designed to develop a new mathematical model for comparison of DNA sequences. Instead of the classical distances, a new distance based on dinucleotide absolute frequency in large DNA sequences is introduced. The proposed distance that requires neither homologous sequences nor prior sequence alignments is used to search(More)
Instead of leading eigenvalue of the matrix associated with a DNA sequence, we propose a new invariant base on the 2DD-Curves of DNA sequences which is simple for calculation and is proved to be highly effective for comparison of DNA sequences and construction of phylogenetic tree. The utility of the new invariant is illustrated on the primate mitochondrial(More)
Apoptosis proteins play a crucial role in the development and home-ostasis of an organism. Obtaining information about subcellular location of these proteins is very important to understand the mechanism of programmed cell death. In this paper, based on the hydropathy characteristics, we introduce the frequency of 2-blocks and pK value of the α-NH + 3 group(More)
Gene selection is important for cancer classification based on gene expression data, because of high dimensionality and small sample size. In this paper, we present a new gene selection method based on clustering, in which dissimilarity measures are obtained through kernel functions. It searches for best weights of genes iteratively at the same time to(More)
  • Li Yang, Changyou Xing, Yusen Zhang, Jinshuang Wang
  • 2010
To improve the resource location efficiency and guarantee resource download quality of nodes in P2P systems, we propose a node Interest bias based P2P Interest domain partition mechanism, give the concept of Interest similarity as well as its computation method, and then present an adaptive P2P topology evolvement model ISPT based on interest similarity(More)