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Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their(More)
BACKGROUND Peritoneal relapse is the most common pattern of tumor progression in advanced gastric cancer. Clinicopathological findings are sometimes inadequate for predicting peritoneal relapse. The aim of this study was to identify patients at high risk of peritoneal relapse in a prospective study based on molecular prediction. METHODS RNA samples from(More)
MOTIVATION The DNA Data Bank of Japan (DDBJ) has developed a new DNA database system with a new schema design to accommodate rapid change and growth of requirements on the system. RESULTS The new schema and systems were created using an object-oriented design approach. The design was accomplished in accordance with ANSI/SPARC three-level schema(More)
Introduction of biologics, such as infliximab, to the therapy of rheumatoid arthritis (RA) patients has revolutionized the treatment of this disease. However, biomarkers for predicting the efficacy of the drug at an early phase of treatment for selecting real responders have not been found. We here present predictive markers based on a thorough(More)
In reconstruction of phylogenetic trees from molecular data, it has been pointed out that multifurcate phylogenetic trees are difficult to be correctly reconstructed by the conventional methods like maximum likelihood method(ML). In order to resolve this problem, we have been engaged in developing a new phylogenetic tree reconstruction method, based on the(More)
In this study, starting with a newly introduced concept of data complexity ("empirical data complexity"), we specify the concept of complexity more concretely in relation to mathematical modeling and introduce "model-based complexity (MBC)". Inductive inference based on the minimum model-based complexity method is then applied to the reconstruction of(More)
As the molecular biology has made a rapid progress these years, there has bee n a g r eat number of changes required of the methodology for maintaining and utilizing DNA sequence data. For example, annotation to sequences has become complex and extensive. DDBJ which recognized the impending requirements decided to develop a new DNA sequence database system(More)
In this study, a new method based on the concept of complexity in inductive inference is proposed for reconstructing molecular phylogenetic tree. This method describes the complexity of molecular phylogenetic tree by three terms, which are related to tree topology, the branch lengths and fitness between the model and data measured by likelihood function.(More)
As a novel application of MDL, the concept of model-based c omplexity is proposed in this study. This method have good asymptotic property and compensates the bias of maximum likelihood method. The eciency of this method for reconstructing the correct phylogenetic tree is studied b y c omputer simulation, and results suggest that it is superior to the(More)