FLOW MODEL OF THE PROTEIN-PROTEIN INTERACTION NETWORK FOR FINDING CREDIBLE INTERACTIONS (2009)
Kinya Okada, Kiyoshi Asai, Masanori Arita
Large-scale protein-protein interactions (PPIs) detected by yeast-two-hybrid (Y2H) systems are known to contain many false positives. The separation of credible interactions from background noise is...
GEISHA SYSTEM: An Environment for Simulating Protein Interaction (2009)
Masanori Arita, Masami Hagiya, Tomoki Shiratori
Abstract Biological analysis of Drosophila embryogenesis has provided a model of protein interaction in segment formation. In this paper we introduce GEISHA system, which verifies and revises the...
Heterogeneous distribution of metabolites across plant species (2009)
Takemoto, Kazuhiro, Arita, Masanori
We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as...
A pitfall of wiki solution for biological databases (2009)
Not a few biologists tend to consider wiki as a solution to manage and reorganize data by a community. However, in its basic functionality, wiki lacks a measure to check data consistency and is not...
DETECTION OF MONOSACCHARIDE TYPES FROM COORDINATES (2008)
Masanori Arita, Toshiaki Tokimatsu
Almost half of biological molecules (proteins and metabolites) are extrapolated as glycosylated within cells. Detection of glycosylation patterns and of attached sugar types is therefore an important...
Arita, Masanori, Suwa, Kazuhiro
Abstract Background In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers...
Time-resolved metabolomics reveals metabolic modulation in rice foliage (2008)
Sato, Shigeru, Arita, Masanori, Soga, Tomoyoshi, Nishioka, Takaaki, Tomita, Masaru
Abstract Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent...
PRIME: Platform for RIKEN Metabolomics (2008)
Atsushi Fukushima, Miyako Kusano, Kenji Akiyama, Takeshi Obayashi, Shigehiko Kanaya, ...
Although Arabidopsis thaliana is the most widely studied model plant, functions of those genes and the structure of gene-to-metabolite networks are largely unknown. As an approach complementary to...
GEISHA SYSTEM: An Environment for Simulating Protein Interaction (2008)
Masanori Arita, Masami Hagiya, Tomoki Shiratori
Abstract Biological analysis of Drosophila embryogenesis has provided a model of protein interaction in segment formation. In this paper we introduce GEISHA system, which verifies and revises the...
SVD-based Anatomy of Gene Expressions for Correlation Analysis in Arabidopsis thaliana (2008)
Fukushima, Atsushi, Wada, Masayoshi, Kanaya, Shigehiko, Arita, Masanori
Gene co-expression analysis has been widely used in recent years for predicting unknown gene function and its regulatory mechanisms. The predictive accuracy depends on the quality and the diversity...
No. 84 Arita et al. 169 Graph Modeling of Metabolism (2007)
Masanori Arita, Kiyoshi Asai, Takaaki Nishioka
Metabolism is a network of chemical reactions catalyzed by enzymes. In a cell, ingested sugars and proteins are metabolized to basic compounds such as amino or fatty acids, and they are used to...
Kusano, Miyako, Fukushima, Atsushi, Arita, Masanori, Jonsson, Pär, Moritz, Thomas, Kobayashi, Makoto, ...
Abstract Background Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular...
Automated Metabolic Reconstruction at the Molecular Level (2007)
The analysis of metabolism in bacteria facilitates a new application area such as drug synthesis or toxin degradation, using genetically engineered bacteria. However, the understanding of bacterial...
Automated Metabolic Reconstruction at the Molecular Level (2007)
The analysis of metabolism in bacteria facilitates a new application area such as drug synthesis or toxin degradation, using genetically engineered bacteria. However, the understanding of bacterial...
One major player in the post-sequencing biology is the metabolome, i.e. comprehensive study on metabolism. Although there are established on-line pathway databases [4], they are not designed to be...
Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh
Motivation: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step toward detailed studies of the functional implication and...
Nagasaki, Hideki, Arita, Masanori, Nishizawa, Tatsuya, Suwa, Makiko, Gotoh, Osamu
Motivation: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and...
Scale-Freeness and Biological Networks (2005)
The notion of scale-freeness and its prevalence in both natural and artificial networks have recently attracted much attention. The concept of scale-freeness is enthusiastically applied to almost any...
Computational resources for metabolomics (2004)
Metabolomics, a comprehensive extension of traditional targeted metabolite analysis, has recently attracted much attention as the biological jigsaw puzzle's missing piece that can complement...
Processing Sequence Annotation Data Using the Lua Programming Language (2003)
Yutaka Ueno, Masanori Arita, Toshitaka Kumagai, Kiyoshi Asai
The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research....
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...
Dynamic modeling of genetic networks using genetic algorithm and S-system (2003)
Kikuchi, Shinichi, Tominaga, Daisuke, Arita, Masanori, Takahashi, Katsutoshi, Tomita, Masaru
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...
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...
Pages S27–S34 Modeling splicing sites with pairwise correlations (2002)
Masanori Arita, Koji Tsuda, Kiyoshi Asai
Motivation: A new method for finding subtle patterns in sequences is introduced. It approximates the multiple correlations among residuals with pair-wise correlations, with the learning cost O(m 2 n)...
DNA Sequence Design Using Templates (2002)
Sequencedesig is a crucial problem in information-based biotechnolog such as DNA-based computation. We introduce a simple strateg named template method that systematicallygystemat a set of sequences...
Modeling splicing sites with pairwise correlations (2002)
Arita, Masanori, Tsuda, Koji, Asai, Kiyoshi
Motivation: A new method for finding subtle patterns in sequences is introduced. It approximates the multiple correlations among residuals with pair-wise correlations, with the learning cost O(m2n)...
Improving sequence design for DNA computing (2000)
Masanori Arita, Akio Nishikawa, Masami Hagiya, Ken Komiya, Hidetaka Gouzu, Kensaku Sakamoto
Good design of sequences is a necessity for successful DNA computing, but how to achieve this `goodness ' is unknown. We point out the importance of adjusting the composition of sequences to t...
Finding precursor compounds in secondary metabolism (1999)
Masanori Arita, Kiyoshi Asai, Takaaki Nishioka
A precursor is a compound which is transformed to a class of functional molecules within short steps. It is an important process in the production of natural drugs to decide whether a given compound...
A heuristic approach for Hamiltonian Path Problem with molecules (1997)
Masanori Arita, Akira Suyama, Masami Hagiya
A new molecular solution of Hamiltonian Path Problem (HPP) is introduced. In this method, longer paths are generated by combining shorter paths and by eliminating paths containing duplicate vertices....
Towards parallel evaluation and learning of boolean µ-formulas with molecules (1997)
Masami Hagiya, Masanori Arita, Daisuke Kiga, Kensaku Sakamoto, Shigeyuki Yokoyama
Abstract. 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...
A Heuristic Approach for Hamiltonian Path Problem with Molecules (1997)
Masanori Arita, Akira Suyama, Masami Hagiya
A molecular solution of Hamiltonian Path Problem (HPP) is introduced. In this method, longer paths are generated by combining shorter paths and by eliminating paths containing duplicate vertices. For...
Towards Parallel Evaluation and Learning of Boolean ...-Formulas with Molecules (1997)
Masami Hagiya, Masanori Arita, Daisuke Kiga, Kensaku Sakamoto, Shigeyuki Yokoyama
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...
Joining and Rotating Data with Molecules (1997)
Masanori Arita, Masami Hagiya, Akira Suyama
DNA--based computing is an attempt to solve computational problems with a large number of DNA molecules. Many theoretical results have been reported so far, but their conclusions are seldom supported...
Solid Phase DNA Solution to the Hamiltonian Path Problem (1997)
Nobuhiko Morimoto, Masanori Arita, Akira Suyamay
. A solid-phase method for solving the Hamiltonian path problem (HPP) is described. The method employs only fast and simple DNA operations amenable to full automation. Single-stranded DNA molecules...
Biosynthesis of Camptothecin. In Silico and in Vivo Tracer Study from [1-13C]Glucose1
Yamazaki, Yasuyo, Kitajima, Mariko, Arita, Masanori, Takayama, Hiromitsu, Sudo, Hiroshi, Yamazaki, Mami, ...
Camptothecin derivatives are clinically used antitumor alkaloids that belong to monoterpenoid indole alkaloids. In this study, we investigated the biosynthetic pathway of camptothecin from...
The metabolic world of Escherichia coli is not small
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...
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...
Hirai, Masami Yokota, Yano, Mitsuru, Goodenowe, Dayan B., Kanaya, Shigehiko, Kimura, Tomoko, Awazuhara, Motoko, ...
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...
Biosynthesis of Camptothecin. In Silico and in Vivo Tracer Study from [1-13C]Glucose1
Yamazaki, Yasuyo, Kitajima, Mariko, Arita, Masanori, Takayama, Hiromitsu, Sudo, Hiroshi, Yamazaki, Mami, ...
Camptothecin derivatives are clinically used antitumor alkaloids that belong to monoterpenoid indole alkaloids. In this study, we investigated the biosynthetic pathway of camptothecin from...
The metabolic world of Escherichia coli is not small
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...
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...
Hirai, Masami Yokota, Yano, Mitsuru, Goodenowe, Dayan B., Kanaya, Shigehiko, Kimura, Tomoko, Awazuhara, Motoko, ...
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...
Kusano, Miyako, Fukushima, Atsushi, Arita, Masanori, Jonsson, Pär, Moritz, Thomas, Kobayashi, Makoto, ...
Time-resolved metabolomics reveals metabolic modulation in rice foliage
Sato, Shigeru, Arita, Masanori, Soga, Tomoyoshi, Nishioka, Takaaki, Tomita, Masaru
SVD-based Anatomy of Gene Expressions for Correlation Analysis in Arabidopsis thaliana
Fukushima, Atsushi, Wada, Masayoshi, Kanaya, Shigehiko, Arita, Masanori
Gene co-expression analysis has been widely used in recent years for predicting unknown gene function and its regulatory mechanisms. The predictive accuracy depends on the quality and the diversity...