Masanori Arita

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MOTIVATION The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused on the estimation of only network structures, and they were ineffective in inferring a network structure with feedback loops. We previously proposed a method to(More)
MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry (EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MS(n) data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10,286(More)
To elucidate the organizational and evolutionary principles of the metabolism of living organisms, recent studies have addressed the graph-theoretic analysis of large biochemical networks responsible for the synthesis and degradation of cellular building blocks [Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabási, A. L. (2000) Nature 407, 651-654;(More)
Plant metabolism is a complex set of processes that produce a wide diversity of foods, woods, and medicines. With the genome sequences of Arabidopsis and rice in hands, postgenomics studies integrating all "omics" sciences can depict precise pictures of a whole-cellular process. Here, we present, to our knowledge, the first report of investigation for(More)
We present a software system that computationally reproduces biochemical radioisotope-tracer experiments. It consists of three main components: A mapping database of substrate-product atomic correspondents derived from known reaction formulas, a tracing engine that can compute all pathways between two given compounds by using the mapping database, and a(More)
A simple, practical method to watermark short trademarks or signatures into genomic DNA is introduced. Since the marking method is biologically innocuous, it can be applied to all commercialized bacteria to help establish brand names for the engineered strains and to resolve legal disputes regarding gene-related patents. The first such strain of Bacillus(More)
This paper introduces a graph-oriented representation of metabolism, and shows how to apply the shortest path algorithm to reconstruct metabolic pathways. Our metabolic model is constructed from molecular structures of compounds and reaction formulas of enzymes, and its output is all the logically possible pathways consisting of input reactions. We also(More)
A {formula is a Boolean formula in which each variable occurs at most once. The paper treats its molecular representation including its queries using techniques in molecular biology. The novelty is that this method can evaluate a Boolean formula in a single tube within a short time. The preliminary experimental result suggests the possibility of parallel(More)
Sequence design is a crucial problem in information-based biotechnology such as DNA-based computation. We introduce a simple strategy namedtemplate method that systematically generates a set of sequences of lengthl such that any of its member will have approximatelyl/3 mismatches with other sequences, their complements, and the overlaps of their(More)
The genome-wide detection of alternative splicing and transcriptional initiation (ASTI) was conducted in six eukaryotes (human, mouse, fruit fly, nematode, cress and rice) whose genome sequencing has been completed or nearly completed. Transcriptional isoforms were collected by mapping a batch of full-length cDNA sequences onto the respective cognate(More)