研究業績

原著論文（査読有）

*Corresponding author

†Co-first author

2025

1. Yusuke Fukuda, Kohei Kawaguchi, Atsushi Fukushima*, "AtSRGA: A shiny application for retrieving and visualizing stress-responsive genes in Arabidopsis thaliana", Plant Physiology, in press [Abstract]. website AtSRGA.

2024

1. Kazuaki Kuwahata, Yukio Kawashima, Atsushi FuKushima, Masanori Tachikawa, Miyako Kusano, "Dependence of Substituents on UV-vis Spectra and Solvent Effect of Anthocyanins by Quantum Chemical Approach", Journal of Computer Chemistry, Japan 10: 2023-0045 (2024). [PDF]

2022

1. Atsushi Fukushima*, Mikiko Takahashi, Hideki Nagasaki, Yusuke Aono, Makoto Kobayashi, Miyako Kusano, Kazuki Saito, Norio Kobayashi, Masanori Arita,  Development of RIKEN Plant Metabolome MetaDatabase. Plant and Cell Physiology 63:433-440 (2022). [PDF]

2. Miyako Kusano, Kanjana Worarad, Atsushi Fukushima, Ken Kamiya, Yuka Mitani, Yozo Okazaki, Yasuhiro Higashi, Ryo Nakabayashi, Makoto Kobayashi, Tetsuya Mori, Tomoko Nishizawa, Yumiko Takebayashi, Mikiko Kojima, Hitoshi Sakakibara, Kazuki Saito, Shuhei Hao, Yoshihito Shinozaki, Yoshihiro Okabe, Junji Kimbara, Tohru Ariizumi, Hiroshi Ezura, Transcriptomic, Hormonomic and Metabolomic Analyses Highlighted the Common Modules Related to Photosynthesis, Sugar Metabolism and Cell Division in Parthenocarpic Tomato Fruits during Early Fruit Set. Cells 11:1420 (2022). [PDF]

2021

1. Yoshinori Utsumi, Maho Tanaka, Chikako Utsumi, Satoshi Takahashi, Akihiro Matsui, Atsushi Fukushima, Makoto Kobayashi, Ryosuke Sasaki, Akira Oikawa, Miyako Kusano, Kazuki Saito, Mikiko Kojima, Hitoshi Sakakibara, Punchapat Sojikul, Jarunya Narangajavana, Motoaki Seki, Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. Plant Molecular Biology 109:249-269 (2021). [Abstract]

2. Sandrien Desmet, Yvan Saeys, Kevin Verstaen, Rebecca Dauwe, Hoon Kim, Claudiu Niculaes, Atsushi Fukushima, Geert Goeminne, Ruben Vanholme, John Ralph, Wout Boerjan, Kris Morreela, Maize specialized metabolome networks reveal organ-preferential mixed glycosides. Comput Struct Biotechnol J19: 1127-1144 (2021). [PDF]

3.  Mostafa Abdelrahman, Rie Nishiyama, Cuong Duy Tran, Miyako Kusano, Ryo Nakabayashi, Yozo Okazaki, Fumio Matsuda, Ricardo A Chavez Montes, Mohammad Golam Mostofa, Weiqiang Li, Yasuko Watanabe, Atsushi Fukushima, Maho Tanaka, Motoaki Seki, Kazuki Saito, Luis Herrera-Estrella, Lam-Son Phan Tran, Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis.  Proceedings of the National Academy of Sciences USA118: e2105021118 (2021). [PDF]

2020年以前

1. Yoshihito Shinozaki, Bertrand P. Beauvoit, Masaru Takahara, Shuhei Hao, Kentaro Ezura, Marie-Helene Andrieu, Keiji Nishida, Kazuki Mori, Yutaka Suzuki, Satoshi Kuhara, Hirofumi Enomoto, Miyako Kusano, Atsushi Fukushima, Tetsuya Mori, Mikiko Kojima, Makoto Kobayashi, Hitoshi Sakakibara, Kazuki Saito, Yuya Ohtani, Camille Benard, Duyen Prodhomme, Yves Gibon, Hiroshi Ezura, Tohru Ariizumi, Fruit setting rewires central metabolism via gibberellin cascades. Proceedings of the National Academy of Sciences USA 117:23970-23981 (2020). [PDF]

2. Atsushi Fukushima, Takeshi Kuroha, Keisuke Nagai, Yoko Hattori, Makoto Kobayashi, Tomoko Nishizawa, Mikiko Kojima, Yoshinori Utsumi, Akira Oikawa, Motoaki Seki, Hitoshi Sakakibara, Kazuki Saito, Motoyuki Ashikari, Miyako Kusano, Metabolite and phytohormone profiling illustrates metabolic reprogramming as an escape strategy of deepwater rice during partially submerged stress. Metabolites 10:68 (2020). [PDF]

3. Keisuke Nagai, Yoshinao Mori, Shin Ishikawa, Tomoyuki Furuta, Rico Gamuyao, Yoko Niimi, Tokunori Hobo, Moyuri Fukuda, Mikiko Kojima, Yumiko Takebayashi, Atsushi Fukushima, Yasuyo Himuro, Masatomo Kobayashi, Wataru Ackley, Hiroshi Hisano, Kazuhiro Sato, Aya Yoshida, Jianzhong Wu, Hitoshi Sakakibara, Yutaka Sato, Hiroyuki Tsuji, Takashi Akagi, Motoyuki Ashikari, Antagonistic regulation of the gibberellic acid response during stem growth in rice. Nature 584:109-114 (2020). [Abstract]

4. Miyako Kusano, Atsushi Fukushima, Mayumi Tabuchi-Kobayashi, Kazuhiro Funayama, Soichi Kojima, Kyonoshin Maruyama, Yoshiharu Y. Yamamoto, Tomoko Nishizawa, Makoto Kobayashi, Mayumi Wakazaki, Mayuko Sato, Kiminori Toyooka, Kumiko Osanai-Kondo, Yoshinori Utsumi, Motoaki Seki, Chihaya Fukai, Kazuki Saito, Tomoyuki Yamaya, Cytosolic GLUTAMINE SYNTHETASE 1;1 modulates metabolism and chloroplast development in roots. Plant Physiology 182:1894-1909 (2020). [PDF]

5. Rutger A Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernandez-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander Garcia, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lutteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Nuria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi, BioHackathon 2015: semantics of data for life sciences and reproducible research. F1000Research 9:136 (2020). [PDF]

6. 桑畑和明，佐久間柚衣，川島雪生，福島敦史，長嶋雲兵，草野都，立川仁典，量子化学計算による植物が生産するUV-B防御物質の物性値予測．Journal of Computer Chemistry, Japan 18:108-114 (2019). [PDF]

7. Nam Tuan Vu, Ken Kamiya, Atsushi Fukushima, Shuhei Hao, Wang Ning, Tohru Ariizumi, Hiroshi Ezura, Miyako Kusano, Comparative co-expression network analysis extracts the SlHSP70 gene affecting to shoot elongation of tomato. Plant Biotechnology 36:143-153 (2019). [PDF]

8. Atsushi Fukushima, Shoko Hikosaka, Makoto Kobayashi, Tomoko Nishizawa, Kazuki Saito, Eiji Goto, Miyako Kusano, A systems analysis with “simplified source-sink model” reveals metabolic reprogramming in a pair of source-to-sink organs during early fruit development in tomato by LED light treatments. Frontiers in Plant Science 9:1439 (2018). [PDF]

9. Miwa Ohashi, Keiki Ishiyama, Miyako Kusano, Atsushi Fukushima, Soichi Kojima, Toshihiko Hayakawa, Tomoyuki Yamaya, Reduction in sucrose contents by downregulation of fructose-1,6-bisphosphatase 2 causes tiller outgrowth cessation in rice mutants lacking glutamine synthetase1;2. Rice 11:65 (2018). [PDF]

10. Eva Knoch, Satoko Sugawara, Tetsuya Mori, Christian Poulsen, Atsushi Fukushima, Jesper Harholt, Yoshinori Fujimoto, Naoyuki Umemoto, Kazuki Saito, Third DWF1 paralog in Solanaceae, sterol Δ24-isomerase, branches withanolide biosynthesis from the general phytosterol pathway. Proceedings of the National Academy of Sciences USA 115:E8096-E8103 (2018). [PDF]

11. Yasuhiro Higashi, Yozo Okazaki, Kouji Takano, Fumiyoshi Myouga, Kazuo Shinozaki, Eva Knoch, Atsushi Fukushima, Kazuki Saito, HEAT INDUCIBLE LIPASE1 remodels chloroplastic monogalactosyldiacylglycerol by liberating α-linolenic acid in Arabidopsis leaves under heat stress. Plant Cell 30:1887-1905 (2018). [PDF]

12. Kazuyoshi Kitazaki†, Atsushi Fukushima†, Ryo Nakabayashi, Yozo Okazaki, Makoto Kobayashi, Tetsuya Mori, Tomoko Nishizawa, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, Kazuki Saito, Kazuhiro Shoji, Miyako Kusano, Metabolic reprogramming in leaf lettuce grown under different light quality and intensity conditions using narrow-band LEDs. Scientific Reports 8:7914 (2018). [PDF]

13. Takeshi Kuroha, Keisuke Nagai, Yusuke Kurokawa, Yoshiaki Nagamura, Miyako Kusano, Hideshi Yasui, Motoyuki Ashikari, Atsushi Fukushima*, eQTLs regulating transcript variations associated with rapid internode elongation in deepwater rice. Frontiers in Plant Science 8:1753 (2017). [PDF]

14. Tomokazu Ushijima, Kousuke Hanada, Eiji Gotoh, Wataru Yamori, Yutaka Kodama, Hiroyuki Tanaka, Miyako Kusano, Atsushi Fukushima, Mutsutomo Tokizawa, Yoshiharu Y. Yamamoto, Yasuomi Tada, Yutaka Suzuki, Tomonao Matsushita, Light controls protein localization through phytochrome-mediated alternative promoter selection. Cell 171:1316-1325 (2017). [PDF]

15. Atsushi Fukushima, Mami Iwasa, Ryo Nakabayashi, Makoto Kobayashi, Tomoko Nishizawa, Yozo Okazaki, Kazuki Saito, Miyako Kusano, Effects of combined low glutathione with mild oxidative and low phosphorus stress on the metabolism of Arabidopsis thaliana. Frontiers in Plant Science 8:1464 (2017). [PDF]

16. Jong-Myong Kim, Taiko To, Akihiro Matsui, Keitaro Tanoi, Natsuko Kobayashi, Fumio Matsuda, Yoshiki Habu, Daisuke Ogawa, Takuya Sakamoto, Sachihiro Matsunaga, Khurram Bashir, Sultana Rasheed, Marina Ando, Hiroko Takeda, Kanako Kawaura, Miyako Kusano, Atsushi Fukushima, Takaho Endo, Takashi Kuromori, Junko Ishida, Taeko Morosawa, Maho Tanaka, Chieko Torii, Yumiko Takebayashi, Hitoshi Sakakibara, Yasunari Ogihara, Kazuki Saito, Kazuo Shinozaki, Alessandra Devoto, Motoaki Seki, Acetate-mediated novel survival strategy against drought in plants. Nature Plants 3:17097 (2017). [Abstract] [Erratum]

17. Atsushi Fukushima*, Michimi Nakamura, Hideyuki Suzuki, Mami Yamazaki, Eva Knoch, Tetsuya Mori, Naoyuki Umemoto, Masaki Morita, Go Hirai, Mikiko Sodeoka, Kazuki Saito, 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). [PDF]

18. Miyako Kusano, Makoto Kobayashi, Yumiko Iizuka, Atsushi Fukushima, Kazuki Saito, Unbiased profiling of volatile organic compounds in the headspace of Allium plants using an in-tube extraction device. BMC Research Notes 9:133 (2016). [PDF]

19. Yoshikazu Mikami, Atsushi Fukushima, Takao Kuwada-Kusunose, Tetsuya Sakurai, Taiichi Kitano, Yusuke Komiyama, Takashi Iwase, Kazuo Komiyama, Human uterus myoma and gene expression profiling: A novel in vitro model for studying secretory leukocyte protease inhibitor-mediated tumor invasion. Cancer Letters 379:84-93 (2016). [Abstract]

20. Emelda Rosseleena Rohani, Motoaki Chiba, Miki Kawaharada, Takashi Asano, Yoshimi Oshima, Nobutaka Mitsuda, Masaru Ohme-Takagi, Atsushi Fukushima, Amit Rai, Kazuki Saito, Mami Yamazaki, An MYB transcription factor regulating specialized metabolisms in Ophiorrhiza pumila. Plant Biotechnology 33:1-9 (2016). [PDF]

21. Atsushi Fukushima*, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito, Mami Yamazaki, High-throughput sequencing and de novo assembly of red and green forms of the Perilla frutescens var. crispa transcriptome. PLoS One 10:e0129154 (2015). [PDF]

22. Yoshikazu Mikami, Atsushi Fukushima, Takao Kuwada-Kusunose, Tetsuya Sakurai, Taiichi Kitano, Yusuke Komiyama, Takashi Iwase, Kazuo Komiyama, Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research. PLoS One 10:e0118587 (2015). [PDF]

23. Miwa Ohashi, Keiki Ishiyama, Miyako Kusano, Atsushi Fukushima, Soichi Kojima, Atsushi Hanada, Keiichi Kanno, Toshihiko Hayakawa, Yoshiya Seto, Junko Kyozuka, Shinjiro Yamaguchi, Tomoyuki Yamaya, Lack of cytosolic glutamine synthetase 1;2 in vascular tissues of axillary buds causes severe reduction in their outgrowth and disorder of metabolic balance in rice seedlings. The Plant Journal 81:347-356 (2015). [PDF]

24. Miyako Kusano, Ivan Baxter, Atsushi Fukushima, Akira Oikawa, Yozo Okazaki, Ryo Nakabayashi, Denise J. Bouvrette, Frederic Achard, Andrew R. Jakubowski, Joan M. Ballam, Jonathan R. Phillips, Angela H. Culler, Kazuki Saito, George G. Harrigan, Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding. Metabolomics 11:261-270 (2015). [Abstract]

25. Atsushi Fukushima*, Miyako Kusano, Ramon Francisco Mejia, Mami Iwasa, Makoto Kobayashi, Naomi Hayashi, Akiko Watanabe-Takahashi, Tomoko Narisawa, Takayuki Tohge, Manhoi Hur, Eve Syrkin Wurtele, Basil J. Nikolau, Kazuki Saito, Metabolomic characterization of knockout mutants in Arabidopsis: development of a metabolite profiling database for knockout mutants in Arabidopsis. Plant Physiology 165:948-961 (2014). [PDF]

26. Masakazu Satou, Harumi Enoki, Akira Oikawa, Daisaku Ohta, Kazunori Saito, Takushi Hachiya, Hitoshi Sakakibara, Miyako Kusano, Atsushi Fukushima, Kazuki Saito, Masatomo Kobayashi, Noriko Nagata, Fumiyoshi Myouga, Kazuo Shinozaki, Reiko Motohashi, Integrated analysis of transcriptome and metabolome of Arabidopsis albino or pale green mutants with disrupted nuclear-encoded chloroplast proteins. Plant Molecular Biology 85:411-428 (2014). [PDF]

27. Takeshi Furuhashi, Mikiko Kojima, Hitoshi Sakakibara, Atsushi Fukushima, Masami Yokota Hirai, Katsuhisa Furuhashi, Morphological and plant hormonal changes during parasitization by Cuscuta japonica on Momordica charantia. Journal of Plant Interactions 9:220-232 (2014). [PDF]

28. Miyako Kusano, Yumiko Iizuka, Makoto Kobayashi, Atsushi Fukushima, Kazuki Saito, Development of a direct headspace collection method from Arabidopsis seedlings using HS-SPME-GC-TOF-MS analysis. Metabolites 3:223-242 (2013). [PDF]

29. Atsushi Fukushima*, DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene 518:209-214 (2013). [PDF]

30. Atsushi Fukushima*, Tomoko Nishizawa, Mariko Hayakumo, Shoko Hikosaka, Kazuki Saito, Eiji Goto, Miyako Kusano, Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiology 158:1487-1502 (2012). [PDF]

31. Miyako Kusano, Atsushi Fukushima, Naoko Fujita, Yozo Okazaki, Makoto Kobayashi, Naoko Fujita Oitome, Kaworu Ebana, Kazuki Saito, Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis. Molecular Plant 5:442-451 (2012). [PDF]

32. Keiko Yonekura-Sakakibara, Atsushi Fukushima, Ryo Nakabayashi, Kousuke Hanada, Fumio Matsuda, Eri Inoue, Satoko Sugawara, Takashi Kuromori, Takuya Ito, Kazuo Shinozaki, Bunyapa Wangwattana, Mami Yamazaki, Kazuki Saito, Two glycosyltransferases involved in anthocyanin modification delimited by transcriptome independent component analysis in Arabidopsis thaliana. The Plant Journal 69:154-167 (2012). [PDF]

33. Takayuki Tohge, Miyako Kusano, Atsushi Fukushima, Kazuki Saito, Alisdair R. Fernie, Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. Plant Signaling & Behavior 6:1987-1992 (2011). [PDF]

34. Miyako Kusano, Par Jonsson, Jonas Gullberg, Atsushi Fukushima, Michael Sjostrom, Johan Trygg, Thomas Moritz, Metabolite signature during short-day induced growth cessation in Populus. Frontiers in Plant Science 2:29 (2011). [PDF]

35. Miyako Kusano†, Takayuki Tohge†, Atsushi Fukushima†, Makoto Kobayashi, Naomi Hayashi, Hitomi Otsuki, Youichi Kondou, Hiroto Goto, Mika Kawashima, Fumio Matsuda, Rie Niida, Minami Matsui, Kazuki Saito, Alisdair R. Fernie, Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to ultraviolet-B light. The Plant Journal 67:354-369 (2011). [PDF]

36. Miyako Kusano, Henning Redestig, Tadayoshi Hirai, Akira Oikawa, Fumio Matsuda, Atsushi Fukushima, Masanori Arita, Shin Watanabe, Megumu Yano, Kyoko Hiwasa-Tanase, Hiroshi Ezura, Kazuki Saito, Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. PLoS One 6:e16989 (2011). [PDF]

37. Miyako Kusano, Mayumi Tabuchi, Atsushi Fukushima, Kazuhiro Funayama, Celine Diaz, Makoto Kobayashi, Naomi Hayashi, Yumiko Tsuchiya, Hideki Takahashi, Atsuko Kamata, Tomoyuki Yamaya, Kazuki Saito, Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice. The Plant Journal 66:456-466 (2011). [PDF]

38. Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito, Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Systems Biology 5:1 (2011). [PDF]

39. Yoko Ide, Miyako Kusano, Akira Oikawa, Atsushi Fukushima, Hajime Tomatsu, Kazuki Saito, Masami Yokota Hirai, Toru Fujiwara, Effects of molybdenum deficiency and defects in molybdate transporter MOT1 on transcript accumulation and nitrogen/sulphur metabolisms in Arabidopsis thaliana. Journal of Experimental Botany 62:1483-1497 (2010). [PDF]

40. Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita, Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics 11:214 (2010). [PDF]

41. Miyako Kusano†, Atsushi Fukushima†, Henning Redestig, Makoto Kobayashi, Hitomi Otsuki, Hitoshi Onouchi, Satoshi Naito, Masami Yokota Hirai, Kazuki Saito, Comparative metabolomics charts the impact of genotype-dependent methionine accumulation in Arabidopsis thaliana. Amino Acids 39:1013-1021 (2010). [Abstract]

42. Doris Albinsky, Miyako Kusano, Mieko Higuchi, Naomi Hayashi, Makoto Kobayashi, Atsushi Fukushima, Masaki Mori, Takanari Ichikawa, Keiko Matsui, Hirofumi Kuroda, Yoko Horii, Yuko Tsumoto, Hitoshi Sakakibara, Hirohiko Hirochika, Minami Matsui, Kazuki Saito, Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism. Molecular Plant 3:125-142 (2010). [PDF]

43. Atsushi Fukushima, Shigehiko Kanaya, Masanori Arita, Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach. Plant Biotechnology 26:485-493 (2009). [PDF]

44. Henning Redestig, Atsushi Fukushima, Hans Stenlund, Thomas Moritz, Masanori Arita, Kazuki Saito, Miyako Kusano, Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Analytical Chemistry 81:7974-7980 (2009). [Abstract]

45. Norihito Nakamichi†, Atsushi Fukushima†, Miyako Kusano†, Hitoshi Sakakibara, Takeshi Mizuno, Kazuki Saito, Linkage between circadian clock and tricarboxylic acid cycle in Arabidopsis. Plant Signaling & Behavior 4:660-662 (2009). [PDF]

46. Atsushi Fukushima†, Miyako Kusano†, Norihito Nakamichi†, Makoto Kobayashi, Naomi Hayashi, Hitoshi Sakakibara, Takeshi Mizuno, Kazuki Saito, Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proceedings of the National Academy of Sciences USA 106:7251-7256 (2009) [PDF]; Correction 106:8791 (2009).

47. Norihito Nakamichi, Miyako Kusano, Atsushi Fukushima, Masanori Kita, Shogo Ito, Takafumi Yamashino, Kazuki Saito, Hitoshi Sakakibara, Takeshi Mizuno, Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant and Cell Physiology 50:447-462 (2009). [PDF]

48. Atsushi Fukushima, Masayoshi Wada, Shigehiko Kanaya, Masanori Arita, SVD-based anatomy of gene-expression for correlation analysis in Arabidopsis thaliana. DNA Research 15:367-374 (2008). [PDF]

49. Mutsumi Watanabe, Miyako Kusano, Akira Oikawa, Atsushi Fukushima, Masaaki Noji, Kazuki Saito, Physiological roles of the β-substituted alanine synthase gene family in Arabidopsis. Plant Physiology 146:310-320 (2008). [PDF]

50. Miyako Kusano†, Atsushi Fukushima†, Masanori Arita, Par Jonsson, Thomas Moritz, Makoto Kobayashi, Naomi Hayashi, Takayuki Tohge, Kazuki Saito, Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Systems Biology 1:53 (2007). [PDF]

51. Miyako Kusano, Atsushi Fukushima, Makoto Kobayashi, Naomi Hayashi, Par Jonsson, Thomas Moritz, Kaworu Ebana, Kazuki Saito, Application of a metabolomics method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice. Journal of Chromatography B 855:71-79 (2007).

52. Atsushi Fukushima, Toshimichi Ikemura, Shigehiko Kanaya, Comparative genome analysis focused on periodicity from prokaryote to higher eukaryote genomes based on power spectrum. Journal of Computer Chemistry, Japan 2:95-110 (2003).

53. Atsushi Fukushima, Toshimichi Ikemura, Makoto Kinouchi, Taku Oshima, Yoshihiro Kudo, Hirotada Mori, Shigehiko Kanaya, Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Gene 300:203-211 (2002).

総説（査読有）

1. Miyako Kusano, Zhigang Yang, Yozo Okazaki, Ryo Nakabayashi, Atsushi Fukushima, Kazuki Saito, Using metabolomic approaches to explore chemical diversity in rice. Molecular Plant 8:58-67 (2015). [PDF]

2. Atsushi Fukushima*, Shigehiko Kanaya, Kozo Nishida, Integrated network analysis and effective tools in plant systems biology. Frontiers in Plant Science 5:598 (2014). [PDF]

3. Atsushi Fukushima, Miyako Kusano, A network perspective on nitrogen metabolism from model to crop plants using integrated “omics” approaches. Journal of Experimental Botany 65:5619-5630 (2014). [PDF]

4. Atsushi Fukushima*, Miyako Kusano, Recent progress in the development of metabolome databases for plant systems biology. Frontiers in Plant Science 4:73 (2013). [PDF]

5. Keiko Yonekura-Sakakibara, Atsushi Fukushima, Kazuki Saito, Transcriptome data modeling for targeted plant metabolic engineering. Current Opinion in Biotechnology 24:285-290 (2013). [Abstract]

6. Miyako Kusano, Atsushi Fukushima, Current challenges and future potential of tomato breeding using omics approaches. Breeding Science 63:31-41 (2013). [PDF]

7. Miyako Kusano, Atsushi Fukushima, Henning Redestig, Kazuki Saito, Metabolomics approach toward the understanding of nitrogen metabolism in plants. Journal of Experimental Botany 62:1439-1453 (2011). [PDF]

8. Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito, Integrated omics approaches in plant systems biology. Current Opinion in Chemical Biology 13:532-538 (2009). [Abstract]

和文解説・総説（査読無）

1. 神谷健，草野都，福島敦史，メタボロームデータ解析および解釈に資する可視化手法．日本化学会情報化学部会誌 37:72-76 (2019). [PDF]

2. 福島敦史, 植物におけるオミックス統合ネットワークシステム生物学, SAR News No.31: 9-18 (2016). [PDF]

3. 市橋泰範，福島敦史, 植物科学におけるトランスクリプトーム解析の最前線, 植物科学の最前線 7:110 (2016). [PDF]

4. 福島敦史，草野都，植物代謝ネットワークの包括的理解に向けた複数オミクスデータの活用．バイオサイエンスとインダストリー 69:112-115 (2011).

5. 福島敦史，斉藤和季，植物システムバイオロジーの進展―マルチネットワークの視点から．バイオインダストリー 25:52-62 (2008).

6. 草野都，福島敦史，斉藤和季，メタボローム解析による植物代謝ネットワーク―多階層オミックスネットワークの現状と今後の展望．臨床化学 37:368-374 (2008). [PDF]

7. 福島敦史，草野都，有田正規，斉藤和季，植物メタボロミクス―代謝プロファイルからシステム解析へ．実験医学 26:13-17 (2008).

8. 金谷重彦，福島敦史，森浩禎，渡辺良久，市場勇太，池村淑道，ゲノム配列に潜む組織化された内部構造．数理科学 468:25-31 (2002).

著書（ブックチャプター等）

1. Miyako Kusano, Atsushi Fukushima, Plant Metabolomics: The Great Potential of Plant Metabolomics in Big Data Biology in Plant Omics: Advances in Big Data Biology, CABI Digital Library (2022). 

2. Yasunori Ichihashi, Atsushi Fukushima, Arisa Shibata, Ken Shirasu, High impact gene discovery: simple strand-specific mRNA library construction and differential regulatory analysis based on gene co-expression network. In: Nobutoshi Yamaguchi (ed) Plant Transcription Factors. Methods in Molecular Biology 1830, Humana Press, New York, pp. 163-189 (2018).

3. Atsushi Fukushima, Kozo Nishida, Using the DiffCorr package to analyze and visualize differential correlations in biological networks. In: Matthias Dehmer, Yongtang Shi, and Frank Emmert-Streib (eds) Computational Network Analysis with R: Applications in Biology, Medicine and Chemistry, Vol. 7, Wiley -VCH, Weinheim, pp. 1-34 (2016). [GitHub]

特許

1. 江面浩，有泉亨，篠崎良仁，金原淳司，草野都，福島敦史，斉藤和季，変異型植物．出願番号：特願2013-231495（出願日：2013年11月7日），公開番号：特開2015-089368（公開日：2015年5月11日）