RIKEN Center for Sustainable Resource Science Metabolome Informatics Research Team

Team Leader: Masanori Arita (D.Sc.)

Japanese Page

Research Summary

Our team develops software platforms necessary for metabolomic analyses, network analyses and computer simulations. We also design databases that help more efficient identification of metabolites. The developed software will be applied to integrated analysis of metabolomic and transcriptomic data collated by other teams to enable systematic understanding of plants.

Main Research Fields

Complex Systems

Related Research Fields

Biological Sciences

Keywords

Genome
Database
Metabolome
Algorithm

Selected Publications

1.Tsugawa H, Ikeda K, Tanaka W, Senoo Y, Arita M, Arita M
"Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library"
Journal of Cheminformatics 9:19, 2017
2.Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O
"SPLASH, a hashed identifier for mass spectra"
Nature Biotechnology 34(11):1099-1101, 2016
3.Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, Cajka T, Saito K, Fiehn O, Arita M.
"Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software"
Analytical Chemistry 88(16):7946-7958, 2016
4.Fukushima A, Nakamura M, Suzuki H, Yamazaki M, Knoch E, Mori T, Umemoto N, Morita M, Hirai G, Sodeoka M, Saito K
"Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling"
Frontiers in Plant Science 7:1883, 2016
5.Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M:
"MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis"
Nature Methods 12(6), 523-526, 2015
6.Fukushima A, Nakamura M, Suzuki H, Saito K, Yamazaki M:
"High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome"
PLOS One 10(6), e0129154, 2015
7.Hasegawa Y, Arita M:
"Optimal implementations for reliable circadian clocks"
Physical Review Letters 113(10), 108101, 2014
8.Fukushima A, Kusano M.:
"Recent progress in the development of metabolome databases for plant systems biology"
Frontiers in Plant Science, 4(73), 2013
9.Fukushima A.:
"DiffCorr: an R package to analyze and visualize differential correlations in biological networks"
Gene, 518(1), 209-214, 2013
10.Tsugawa H, Arita M, Kanazawa M, Ogiwara A, Bamba T, Fukusaki E.:
"MRMPROBS: a data assessment and metabolite identification tool for large-scale multiple reaction monitoring based widely targeted metabolomics"
Anal Chem, 85(10), 5191-5199, 2013