Recent Publications


Li, D., Ono, N., Sato, T., Sugiura, T., Altaf-Ul-Amin, M., Ohta, D., … Kanaya, S. (2015). Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species. Plant and Cell Physiology, pcv008.

Nakao, M., Takemoto, S., Sugiura, T., Sawada, K., Kawakami, R., Nemoto, T., & Matsuda, T. (2014). Interactive visual exploration of overlapping similar structures for three-dimensional microscope images. BMC Bioinformatics, 15(1), 415.

Huang, M., Tamura, T., Chen, W., & Kanaya, S. (2015). Evaluation of structural and thermophysical effects on the measurement accuracy of deep body thermometers based on dual-heat-flux method. Journal of Thermal Biology, 47, 26–31.


Fukushima, A., Kanaya, S., & Nishida, K. (2014). Integrated network analysis and effective tools in plant systems biology. Plant Systems Biology, 5, 598.

Bai, Y., Iwasaki, Y., Kanaya, S., Zhao, Y., & Ikemura, T. (2014). A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data. BioMed Research International, 2014, e765648.

Huang, M., Tamura, T., Chen, W., Kitamura, K.-I., Nemoto, T., & Kanaya, S. (2014). Characterization of ultradian and circadian rhythms of core body temperature based on wavelet analysis. In 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) (pp. 4220–4223).

Nakamura, Y., Mochamad Afendi, F., Kawsar Parvin, A., Ono, N., Tanaka, K., Hirai Morita, A., … Kanaya, S. (2014). KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities. Plant and Cell Physiology, 55(1), e7–e7.

Ogawa, T., Furuhashi, T., Okazawa, A., Nakai, R., Nakazawa, M., Kind, T., … Ohta, D. (2014). Exploration of polar lipid accumulation profiles in Euglena gracilis using LipidBlast, an MS/MS spectral library constructed in silico. Bioscience, Biotechnology, and Biochemistry, 78(1), 14–18.

Ohtana, Y., Abdullah, A. A., Altaf-Ul-Amin, M., Huang, M., Ono, N., Sato, T., … Kanaya, S. (2014). Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities. Molecular Informatics, 33(11-12), 790–801.

Sriyudthsak, K., Sawada, Y., Chiba, Y., Yamashita, Y., Kanaya, S., Onouchi, H., … Hirai, M. Y. (2014). A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. BMC Systems Biology, 8(Suppl 5), S4.

Wijaya, S. H., Husnawati, H., Afendi, F. M., Batubara, I., Darusman, L. K., Altaf-Ul-Amin, M., … Kanaya, S. (2014). Supervised Clustering Based on DPClusO: Prediction of Plant-Disease Relations Using Jamu Formulas of KNApSAcK Database. BioMed Research International, 2014, e831751.

Altaf-Ul-Amin, M., Afendi, F. M., Kiboi, S. K., & Kanaya, S. (2014). Systems Biology in the Context of Big Data and Networks. BioMed Research International, 2014, e428570.

Altaf-Ul-Amin, M., Katsuragi, T., Sato, T., Ono, N., & Kanaya, S. (2014). An Unsupervised Approach to Predict Functional Relations between Genes Based on Expression Data. BioMed Research International, 2014, e154594.

Kanaya, S., Altaf-Ul-Amin, M., Kiboi, S. K., & Mochamad Afendi, F. (2014). Big Data and Network Biology. BioMed Research International, 2014.

Nishida, K., Ono, K., Kanaya, S., & Takahashi, K. (2014). KEGGscape: a Cytoscape app for pathway data integration. F1000Research, 3.


(1) Genome

Abe, T., Kanaya, S., Kinouchi, M., Ichiba, Y., Kozuki, T., & Ikemura, T. (2003). Informatics for Unveiling Hidden Genome Signatures. Genome Research, 13(4), 693–702.

Genka H., Baba T., Tsuda M., Kanaya S., Mori H., Yoshida T., Noguchi M. T., Tsuchiya K., Sawada H., Comparative analysis of argK-tox clusters and their flanking regions in phaseolotoxin-producing Pseudomonas syringae pathovars, J. Mol. Evol. 63, 401–414 (2006)
Kobayashi H, Akitomi J, Fujii N, Kobayashi K, Altaf-Ul-Amin M, Kurokawa K, Ogasawara N, Kanaya S., The entire organization of transcription units on the Bacillus subtilis genome, BMC Genomics, 8, 197.1-11 (2007)
Abe T, Kanaya S, Uehara H, Ikemura T., A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses, DNA Res. 16, 287-97 (2009)
Abe T, Ikemura T, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H., tRNADB-CE: tRNA gene database curated manually by experts, Nucleic Acids Res. 37(Database issue):D163-8, (2009)
Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H., tRNADB-CE 2011: tRNA gene database curated manually by experts, Nucleic Acids Res. 39(Database issue):D210-3, (2011)

(2) Plant Transcriptomics & Metabolomics

Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K, Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana, Proc Natl Acad Sci USA., 101, 10205-10 (2004)
Hirai M.Y., Klein M., Fujikawa Y., Yano M., Goodenowe D.B., Yamazaki Y., Kanaya S., Nakamura Y., Kitayama M., Suzuki H., Sakurai N, Shibata D., Tokuhisa J., Reichelt M., Gershenzon J., Papenbrock J., Saito K., Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics, J Biol Chem. 280, 25590-5 (2005)
Oikawa A, Nakamura Y, Ogura T, Kimura A, Suzuki H, Sakurai N, Shinbo Y, Shibata D, Kanaya S, Ohta D., Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiol. 142, 398-413 (2006),
Morioka R, Kanaya S, Hirai, MY, Yano M., Ogasawara N., Saito, K., Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model, BMC Bioinformatics 8, 343.1-10, (2007)
Nakamura Y, Kimura A, Saga H, Oikawa A, Shinbo Y, Kai K, Sakurai N, Suzuki H, Kitayama M, Shibata D, Kanaya S, Ohta D., Differential metabolomics unraveling light/dark regulation of metabolic activities in Arabidopsis cell culture, Planta. 227, 57-66, (2007)
Ohta D., Shibata, D., Kanaya, S., Metabolic profiling using Fourier-transform ion-cyclotron-resonance mass spectrometry, Anal Bioanal Chem 389, 1469–1475 (2007)
Fukushima A, Wada M, Kanaya S, Arita M., SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana, DNA Res. 15, 367-74 (2008)
Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki T, Suzuki H, Okazaki K, Kitayama M, Kanaya S, Aoki K, Shibata D., Metabolite annotations based on the integration of mass spectral information, Plant J., 949-62 (2008)
Nakamura, Y., Kanaya, S., Sakurai, N., Iijima, Y., Aoki, K.,Okazaki, K., Suzuki, H., Kitayama, M., Shibata, D., A tool for high-throughput prediction of molecular formulas and identification of isotopic peaks from large-scale mass spectrometry data, Plant Biotechnol. 25, 377–380 (2008)
Suzuki H, Sasaki R, Ogata Y, Nakamura Y, Sakurai N, Kitajima M, Takayama H, Kanaya S, Aoki K, Shibata D, Saito K., Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry, Phytochemistry. 69, 99-111 (2008)
Matsuda F, Shinbo Y, Oikawa A, Hirai MY, Fiehn O, Kanaya S, Saito K , Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches., PLoS One. 16, e7490, (2009)
Fukushima, A., Kanaya, S., Arita, M., Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach, Plant Biotechnol., 26, 485–493 (2009)
Hirai MY, Sawada Y, Kanaya S, Kuromori T, Kobayashi M, Klausnitzer R, Hanada K, Akiyama K, Sakurai T, Saito K, Shinozaki K., Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources, J Plant Res. 123, 291-8, (2010)
Matsuura H, Ishibashi Y, Shinmyo A, Kanaya S, Kato K., Genome-wide analyses of early translational responses to elevated temperature and high salinity in Arabidopsis thaliana, Plant Cell Physiol., 51, 448-62 (2010)
Ohta D, Kanaya S, Suzuki H., Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification, Curr Opin Biotechnol. 21, 35-44 (2010)
Matsuda F, Nakabayashi R, Sawada Y, Suzuki M, Hirai MY, Kanaya S, Saito K., Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity, Front Plant Sci. 2, 40, (2011)
Kai, K., Takahashi, H., Saga, H., Ogawa, T., Kanaya, S., Ohta, D., Metabolomic characterization of the possible involvement of a Cytochrome P450, CYP81F4, in the biosynthesis of indolic glucosinolate in Arabidopsis, Plant Biotechnol., 28, 379–385 (2011)
Wada M, Takahashi H, Altaf-Ul-Amin M, Nakamura K, Hirai MY, Ohta D, Kanaya S., Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes, Gene, 503, 56-64 (2012)
Chiba Y, Mineta K, Hirai MY, Suzuki Y, Kanaya S, Takahashi H, Onouchi H, Yamaguchi J, Naito S., Changes in mRNA stability associated with cold stress in Arabidopsis cells, Plant Cell Physiol. 54, 180-94, (2013).
Matsuura H, Takenami S, Kubo Y, Ueda K, Ueda A, Yamaguchi M, Hirata K, Demura T, Kanaya S, Kato K, A computational and experimental approach reveals that the 5′-proximal region of the 5′-UTR has a Cis-regulatory signature responsible for heat stress-regulated mRNA translation in Arabidopsis, Plant Cell Physiol. 54, 474-83, (2013)

(3) Bacteria Transcriptomics & metabolomics

Takahashi H, Kai K, Shinbo Y, Tanaka K, Ohta D, Oshima T, Altaf-Ul-Amin M, Kurokawa K, Ogasawara N, Kanaya S, Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry, Anal Bioanal Chem., 391, 2769-82 (2008)
Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Kanaya S, Ara K, Ozaki K, Ogasawara N., Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis, DNA Res. 30, 15, 73-81, (2008)
Strassburg K, Walther D, Takahashi H, Kanaya S, Kopka J, Dynamic transcriptional and metabolic responses in yeast adapting to temperature stress, OMICS. 14, 249-59 (2010)
Chumsakul O, Takahashi H, Oshima T, Hishimoto T, Kanaya S, Ogasawara N, Ishikawa S., G enome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation, Nucleic Acids Res. 39, 414-28, (2011)
Takahashi H, Morioka R, Ito R, Oshima T, Altaf-Ul-Amin M, Ogasawara N, Kanaya S., Dynamics of time-lagged gene-to-metabolite networks of Escherichia coli elucidated by integrative omics approach, OMICS. 15, 15-23 (2011)
Manabe K, Kageyama Y, Morimoto T, Shimizu E, Takahashi H, Kanaya S, Ara K, Ozaki K, Ogasawara N., Improved production of secreted heterologous enzyme in Bacillus subtilis strain MGB874 via modification of glutamate metabolism and growth conditions, Microb Cell Fact. 12, 18, (2013)

(4) Bioinformatics & Database

Nishi T, Ikemura T, Kanaya S., GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences. Gene. 346, 115-25, (2005)
Shinbo, Y., Nakamura, Y., Altaf-Ul-Amin, M, Asahi, H, Kurokawa, K, Arita M, Saito, K, Ohta, D,: KNApSAcK: A comprehensive species-metabolite relationship database. in Plant Metabolomics (Saito, K., Dixon, R. A., Willmitzer, L. eds), 165-184, Springer Verlag, Heidelberg (2006) .
Kinya O., Kanaya S., Asai, K., Accurate extraction of functional associations between proteins based on common interaction partners and common domains, Bioinformatics, 21, 2043-2048, (2005)
Tanaka, K., Nakamura, K., Saito, T., Osada, H., Hirai A., Takahashi, H., Kanaya.S., Md.Altaf-Ul-Amin, Metabolic pathway prediction based on inclusive relation between cyclic substructures, Plant Biotechnol., 26, 459–468 (2009)
Kanaya, S., Bioinformatics from MOURA to SHIKKAI, Plant Biotechnology 26, 443–444 (2009)
Matsuda, F., Redestig, H., Sawada, Y., Shinbo, Y., Hirai, MY., Kanaya, S., Saito, K., Visualization of metabolite identifier information, Plant Biotechnol. 26, 479–483 (2009)
Takahashi, H., Kawazoe, M., Wada, M., Hirai, A.,Nakamura, K., Md. Altaf-Ul-Amin, Sawada, Y., Hirai, MY., Kanaya, S., KNApSAcK gene classification system for Arabidopsis thaliana: Comparative genomic analysis of unicellular to seed plants, Plant Biotechnol., 26, 509-516, (2009)
Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S., Sequence-specific error profile of Illumina sequencers, Nucleic Acids Res. 39, e90, (2011)
Takahashi H, Morimoto T, Ogasawara N, Kanaya S., AMDORAP: non-targeted metabolic profiling based on high-resolution LC-MS, BMC Bioinformatics, 12, 259, (2011)
Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S., KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research, Plant Cell Physiol. 53, e1, (2012).
Ikeda S, Abe T, Nakamura Y, Kibinge N, Hirai Morita A, Nakatani A, Ono N, Ikemura T, Nakamura K, Altaf-Ul-Amin M, Kanaya S., Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database, Plant Cell Physiol. 54, 711-27 (2013)
Nakamura K, Shimura N, Otabe Y, Hirai-Morita A, Nakamura Y, Ono N, Ul-Amin MA, Kanaya S., KNApSAcK-3D: a three-dimensional structure database of plant metabolites, Plant Cell Physiol. 54 (2): e4(1–8) (2013)
Sakurai N, Ara T, Kanaya S, Nakamura Y, Iijima Y, Enomoto M, Motegi T, Aoki K, Suzuki H, Shibata D., An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values, Bioinformatics. 29, 290-1 (2013)
Nakamura Y, Afendi FM, Parvin AK, Ono N, Tanaka K, Hirai Morita A, Sato T, Sugiura T, Altaf-Ul-Amin M, Kanaya S., KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities., Plant Cell Physiol., 55:e7.1-9 (2014)

(5) Network Biology

Amin, M.A., Shinbo, U., Kenji Mihara, Kurokawa, K., Kanaya, S., Development and implementation of an algorithm for detection of protein complexes in large interaction networks, BMC Bioinformatics, 7, 207.1-13 (2006)
Arifuzzaman M., Maeda M., Itoh A., Nishikata K., Takita C., Saito R., Ara T., Nakahigashi K., Huang H.C., Hirai A., Tsuzuki K., Nakamura S., Altaf-Ul-Amin M., Oshima T., Baba T., Yamamoto N., Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H., Large-scale identification of protein–protein interaction of Escherichia coli K-12, Genome Res., 16, 686–691 (2006)
Amin, MA., Wada, M., Kanaya, S, Partitioning a PPI Network into OverlappingModules Constrained by High-Density and Periphery Tracking, ISRN Biomathematics, 1-11, (2012)
Kikugawa S, Nishikata K, Murakami K, Sato Y, Suzuki M, Altaf-Ul-Amin M, Kanaya S, Imanishi T., PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset, BMC Syst Biol. 6 Suppl 2:S7 (2012).

(6) Food, Edible & Medicinal Plant Informatics

Ikeda, T., Kanaya, S., Yonetani, T., Kobayashi, A., Fukusaki, E., Prediction of Japanese green tea ranking by fourier transform near-infrared reflectance, Spectroscopy, J Agric Food Chem. 55, 9908-12, (2007)
Afendi, FM, Sulistiyani, Hirai, A., Amin, MA, Takahashi, H., Nakamura, K., Kanaya, S., Modelling ingredient of Jamu to predict its efficacy, Forum Statistika dan Komputasi 15, 1-9, (2010)
Okada T, Afendi FM, Altaf-Ul-Amin M, Takahashi H, Nakamura K, Kanaya S. Metabolomics of medicinal plants: the importance of multivariate analysis of analytical chemistry data, Curr Comput Aided Drug Des. 6, 179-96, (2010)
Katoh, A., Fukuda, S., Fukusaki, E., Hashimoto, T., Hayasaki, T., Kanaya, S., Komura, H., Nomoto, K., Shojo, M., Takeno, KJ., Systems Biology in a Commercial Quality Study of the Japanese Angelica Radix: Toward an Understanding of Traditional Medicinal Plants, Am. J. Chin. Med. 39, 757 (2011)
Afendi, FM., 3 Darusman LK., Fukuyama, M., 1Amin, MA, Kanaya, S., A Bootstrapping Approach for Investigating the Consistency of Assignment of Plants to Jamu Efficacy by PLS-DA Model , Malaysian J. Math. Sci, 6, 147-164 (2012)
桂樹哲雄, 小野直亮, 森田(平井)晶, 中村由紀子, 金谷重彦, 料理のオミックス-食材からみえてくる雑煮とレトルト・カレーの構築原理, Foods & Food Ingredients J. Jpn., 218, 43-60, (2013),.
Afendi FM, Ono, N., Nakamura, Y., Nakamura K, Darusman LK, Kibinge N, Morita AH, Tanaka, Horai H, Amin MA , Kanaya S, Data mining methods for omics and knowledge of crude medicinal Plants toward Big Data Biology, Comput. Struct. Biotech. J., 4, e201301010.1-14
Afendi FM, Darusman LK, Morita AH, Altaf-Ul-Amin M, Takahashi H, Nakamura K, Tanaka K, Kanaya S, Efficacy prediction of jamu formulations by PLS modeling., Curr Comput Aided Drug Des. 9, 46-59, (2013)

Afendi, Farit Mochamad et al. “KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research.” Plant and Cell Physiology 53.2 (2012): e1–e1. Web. 10 June 2014.
Afendi, Farit M. et al. “Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology.” Computational and Structural Biotechnology Journal 4.5 (2013): n. pag. Web. 10 June 2014.

(7) Bio-Simulation

Katsuragi T, Ono N, Yasumoto K, Altaf-Ul-Amin M, Hirai MY, Sriyudthsak K, Sawada Y, Yamashita Y, Chiba Y, Onouchi H, Fujiwara T, Naito S, Shiraishi F, Kanaya S., SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks, Plant Cell Physiol. 54, 728-39 (2013)

(8) Biomedical Engineering

Mary-Clare D, Kanaya S, Sugiura T, “Localized cell stiffness measurement using axial movement of an optically trapped microparticle,” Journal of Biomedical Optics, vol.18, no.11, pp111411, 9 Aug. 2013
Kojima F, Sato T, Takahata H, Okada M, Sugiura T, Oshiro O, Date H, Nakamura H, “A novel surgical marking system for small peripheral lung nodules based on radio frequency identification technology: Feasibility study in a canine model,” The Journal of Thoracic and Cardiovascular Surgery, vol.ISSN 0022-5223, Jul. 2013
Ueda R, Sugiura T, Kume S, Ichikawa A, Larsen S, Miyoshi H, Hiramatsu H, Nagatsuka Y, Arai F, Suzuki Y, Hirabayashi Y, Fukuda T, Honda A, “A novel single virus infection system reveals that influenza virus preferetially infects cells in G1 phase,” PLoSOne, May. 2013
Punzalan FR, Sato T, Okada T, Kuhara S, Togashi K, Minato K, “Respiratory Motion and Correlation Simulation Platform for Coronary MR Angiography,” IEICE Trans. on Information and Systems, vol.E96-D, no.1, pp111-119, Jan. 2013
高畑裕美, 杉浦忠男, 岡田実, 佐藤寿彦, 小島史嗣, 井村誠孝, 黒田嘉宏, 大城理, “極小RFIDタグを用いた内視手術支援用微小腫瘍マーキングシステム,” 生体医工学, vol.50, no.6, 2012.11
Sugiura T, Miyoshi H, Nishio T, Honda A, “Cell palpation with an optically trapped particle,” Journal of Micro-Nano Mechatronics, vol.7, no.4, pp131-136, Nov. 2012
Sugiura T, Miyoshi H, Nishio T, Honda A, “Cell palpation with an optically trapped particle,” Journal of Micro-Bio Robotics, Oct. 2012
Nakazawa H, Sada T, Toriyama M, Tago K, Sugiura T, Fukuda M, Inagaki N, “Rab33a Mediates AnterogradeVesicular Transport for Membrane Exocytosis and Axon Outgrowth,” The Journal of Neuroscience, vol.32, pp12712-12725, 12 Sep. 2012
Maeda S, Sugiura T, Minato K, “Optical tweezers with assistance of sub-microsecond duration pulse laser beam,” Applied Physics Express, vol.5, no.4, Mar. 2012
Arief Z, Sato T, Okada T, Kuhara S, Kanao S, Togashi K, Minato K, “A Physician-specific Model for Cardiac Rest Period Determination of MR Coronary Angiography Using a Fuzzy Classifier,” Trans Jpn Soc Med Biol Eng, vol.49, no.5, pp712-719, Nov. 2011