Osamu Maruyama

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MOTIVATION The prediction of localization sites of various proteins is an important and challenging problem in the field of molecular biology. TargetP, by Emanuelsson et al. (J. Mol. Biol., 300, 1005-1016, 2000) is a neural network based system which is currently the best predictor in the literature for N-terminal sorting signals. One drawback of neural(More)
A hot research topic in Genome Science is to analyze the interactions between genes by systematic gene disruptions and gene overexpressions. This paper analyzes the problem of identifying a gene regulatory network from data obtained by multiple gene disruptions and overexpressions in regard to the number of experiments and the complexity of experiments. An(More)
Analysis of the interactions between genes by systematic gene disruptions and gene overexpressions is an important topic in molecular biology. This paper analyses the problem of identifying a genetic network from the data obtained by multiple gene disruptions and overexpressions in regard to the number of experiments and the complexity of experiments. An(More)
A hot research topic in Genome Science is to analyze the interactions between genes by systematic gene disruptions and gene overexpressions. This paper analyzes the problem of identifying a gene regulatory network from data obtained by multiple gene disruptions and overexpressions in regard to the number of experiments and the complexity of experiments. An(More)
To identify molecules to serve as diagnostic markers for renal cell carcinoma (RCC) and as targets for novel therapeutic drugs, we investigated genome-wide expression profiles of RCCs using a cDNA microarray. We subsequently confirmed that hypoxia-inducible protein-2 (HIG2) was expressed exclusively in RCCs and fetal kidney. Induction of HIG2 cDNA into COS7(More)
The DNA methylation status of human X chromosomes from male and female neutrophils was identified by high-throughput sequencing of HpaII and MspI digested fragments. In the intergenic and intragenic regions on the X chromosome, the sites outside CpG islands were heavily hypermethylated to the same degree in both genders. Nearly half of X chromosome(More)
BACKGROUND Transforming growth factor beta (TGF-beta) facilitates metastasis during the advanced stages of cancer. Smad6, Smad7, and c-Ski block signaling by the TGF-beta superfamily proteins through different modes of action. We used adenovirus-mediated gene transfer of these natural inhibitors in a mouse model of breast cancer to examine the roles of(More)
A hot research topic in genomics is to analyze the interactions between genes by systematic gene disruptions and gene overexpressions. Based on a boolean network model without time delay, we have been investigating efficient strategies for identifying a genetic network by multiple gene disruptions and overexpressions. This paper first shows the relationship(More)
In this paper we propose a Markov chain Monte Carlo sampling method for predicting protein complexes from protein-protein interactions (PPIs). Many of the existing tools for this problem are designed more or less based on a density measure of a subgraph of the PPI network. This kind of measures is less effective for smaller complexes. On the other hand, it(More)
MOTIVATION The problem of finding transcription factor binding sites in the upstream regions of given genes is algorithmically an interesting and challenging problem in computational biology. A degenerate pattern over a finite alphabet Sigma is a sequence of subsets of Sigma. A string over IUPAC nucleic acid codes is also a degenerate pattern over Sigma =(More)