Knowledge-Based Simulation of Regulatory Action in lambda phage. - Tomoaki Shimada; Masami Hagiya; Masanori Arita; Shin-ya Nishizaki; Chew Lim Tan (Int. J. Artif. Intell. Tools, 1995)

Stepwise Generation of Hamiltonian Path with Molecules. - Nobuhiko Morimoto; Masanori Arita; Akira Suyama (BCEC, 1997)

Towards parallel evaluation and learning of Boolean μ-formulas with molecules. - Masami Hagiya; Masanori Arita; Daisuke Kiga; Kensaku Sakamoto; Shigeyuki Yokoyama (DNA Based Computers, 1997)

Solid phase DNA solution to the Hamiltonian path problem. - Nobuhiko Morimoto; Masanori Arita; Akira Suyama (DNA Based Computers, 1997)

Joining and rotating data with molecules. - Masanori Arita; Masami Hagiya; Akira Suyama (ICEC, 1997)

Successive State Transitions with I/O Interface by Molecules. - Ken Komiya; Kensaku Sakamoto; Hidetaka Gouzu; Shigeyuki Yokoyama; Masanori Arita; Akio Nishikawa; Masami Hagiya (DNA Computing, 2000)

Reconstructing Metabolic Pathways with New Enzyme Classification. - Masanori Arita; Kiyoshi Asai; Takaaki Nishioka (German Conference on Bioinformatics, 2000)

Improving Sequence Design for DNA Computing. - Masanori Arita; Akio Nishikawa; Masami Hagiya; Ken Komiya; Hidetaka Gouzu; Kensaku Sakamoto (GECCO, 2000)

Metabolic reconstruction using shortest paths. - Masanori Arita (Simul. Pract. Theory, 2000)

On Template Method for DNA Sequence Design. - Satoshi Kobayashi; Tomohiro Kondo; Masanori Arita (DNA, 2002)

Modeling splicing sites with pairwise correlations. - Masanori Arita; Koji Tsuda; Kiyoshi Asai (ECCB, 2002)

DNA Sequence Design Using Templates. - Masanori Arita; Satoshi Kobayashi (New Gener. Comput., 2002)

Dynamic modeling of genetic networks using genetic algorithm and S-system. - Shinichi Kikuchi; Daisuke Tominaga; Masanori Arita; Katsutoshi Takahashi; Masaru Tomita (Bioinform., 2003)

Writing Information into DNA. - Masanori Arita (Aspects of Molecular Computing, 2004)

Comma-free design for DNA words. - Masanori Arita (Commun. ACM, 2004)

Searching Similar Modules in Protein Interaction Netwo. - Hiroyuki Oka; Masanori Arita (ICDE Workshops, 2005)

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. - Hideki Nagasaki; Masanori Arita; Tatsuya Nishizawa; Makiko Suwa; Osamu Gotoh (Bioinform., 2006)

Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions. - Kinya Okada; Kiyoshi Asai; Masanori Arita (APBC, 2007)

Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. - Miyako Kusano; Atsushi Fukushima; Masanori Arita; Pär Jonsson; Thomas Moritz; Makoto Kobayashi; Naomi Hayashi; Takayuki Tohge; Kazuki Saito (BMC Syst. Biol., 2007)

Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms. - Hisashi Tuji; Md. Altaf-Ul-Amin; Masanori Arita; Hirokazu Nishio; Yoko Shinbo; Ken Kurokawa; Shigehiko Kanaya (Inf. Media Technol., 2007)

Comparison of ESI-MS Spectra in MassBank Database. - Hisayuki Horai; Masanori Arita; Takaaki Nishioka (BMEI (2), 2008)

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database. - Masanori Arita; Kazuhiro Suwa (BioData Min., 2008)

Time-resolved metabolomics reveals metabolic modulation in rice foliage. - Shigeru Sato; Masanori Arita; Tomoyoshi Soga; Takaaki Nishioka; Masaru Tomita (BMC Syst. Biol., 2008)

Ontology Checking and Integration of Crude-Drug and Kampo Information. - Masanori Arita; Kazuhiro Suwa; Miwa Yoshimoto; Aki Hirai; Shigehiko Kanaya (BMEI, 2009)

Traceable Analysis of Multiple-Stage Mass Spectra through Precursor-Product Annotations. - Hisayuki Horai; Masanori Arita; Yuya Ojima; Yoshito Nihei; Shigehiko Kanaya; Takeshi Nishioka (GCB, 2009)

A pitfall of wiki solution for biological databases. - Masanori Arita (Briefings Bioinform., 2009)

Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. - Henning Redestig; Miyako Kusano; Atsushi Fukushima; Fumio Matsuda; Kazuki Saito; Masanori Arita (BMC Bioinform., 2010)

Reconstructing phylogeny from metabolic substrate-product relationships. - Che-Wei Chang; Ping-Chiang Lyu; Masanori Arita (BMC Bioinform., 2011)

GC/MS Based Metabolomics: Development of a Data Mining System for Metabolite Identification by using Soft Independent Modeling of Class Analogy (SIMCA). - Hiroshi Tsugawa; Yuki Tsujimot; Masanori Arita; Takeshi Bamba; Eiichiro Fukusaki (BMC Bioinform., 2011)

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. - Atsushi Fukushima; Miyako Kusano; Henning Redestig; Masanori Arita; Kazuki Saito (BMC Syst. Biol., 2011)

Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics. - Henning Redestig; Miyako Kusano; Kaworu Ebana; Makoto Kobayashi; Akira Oikawa; Yozo Okazaki; Fumio Matsuda; Masanori Arita; Naoko Fujita; Kazuki Saito (BMC Syst. Biol., 2011)

DNA Memory. - Masanori Arita; Masami Hagiya; Masahiro Takinoue; Fumiaki Tanaka (Handbook of Natural Computing, 2012)

MRMPROBS suite for metabolomics using large-scale MRM assays. - Hiroshi Tsugawa; Mitsuhiro Kanazawa; Atsushi Ogiwara; Masanori Arita (Bioinform., 2014)

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems. - Kansuporn Sriyudthsak; Ramon Francisco Pacquiao Mejia; Masanori Arita; Masami Y. Hirai (Nucleic Acids Res., 2016)

Visualization of consensus genome structure without using a reference genome. - Ipputa Tada; Yasuhiro Tanizawa; Masanori Arita (BMC Genom., 2017)

Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. - Hiroshi Tsugawa; Kazutaka Ikeda; Wataru Tanaka; Yuya Senoo; Makoto Arita; Masanori Arita (J. Cheminformatics, 2017)

Computational Metabolomics (NII Shonan Meeting 2017-3). - Masanori Arita; Sebastian Böcker; Steffen Neumann (NII Shonan Meet. Rep., 2017)

Comparative analysis of probiotic bacteria based on a new definition of core genome. - Maria Satti; Yasuhiro Tanizawa; Akihito Endo; Masanori Arita (J. Bioinform. Comput. Biol., 2018)

Rearrangement analysis of multiple bacterial genomes. - Mehwish Noureen; Ipputa Tada; Takeshi Kawashima; Masanori Arita (BMC Bioinform., 2019)

Development of the portal site of COVID-19 data in Japan: poster abstract. - Jun-ichi Onami; Koji Sakaguchi; Masanori Arita; Kazutsuna Yamaji (SenSys, 2020)

The international nucleotide sequence database collaboration. - Masanori Arita; Ilene Karsch-Mizrachi; Guy Cochrane (Nucleic Acids Res., 2021)

InChI isotopologue and isotopomer specifications. - Hunter N. B. Moseley; Philippe Rocca-Serra; Reza M. Salek; Masanori Arita; Emma Schymanski (J. Cheminformatics, 2024)

Data Sovereignty and Open Sharing: Reconceiving Benefit-Sharing and Governance of Digital Sequence Information. - Masanori Arita (Data Sci. J., 2025)