発表論文 -Publication-


260. Naake T., Zhu F., Alseekh S., Scossa F., Perez de Souza L., Borghi M., Brotman Y., Mori T., Nakabayashi R., Tohge T., Alisdair R Fernie. (2023) Tenome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis. Plant Physiology, accepted. doi: 10.1093/plphys/kiad511. Online ahead of print. LINK

259. Khaksar G., Tohge T., Sirikantaramas S. (2023) Towards plant-based foods: from plant biodiversity to discovery of sensorially active compounds. Frontiers in Plant Science, accepted. doi: 10.3389/fpls.2023.1240745. Online ahead of print. LINK

258. Jing Y, Watanabe M., Aarabi F, Fernie AR, Borghi M, Tohge T.* (2023) Cross-species metabolomic analyses in the brassicaceae reveals common responses to ultraviolet-B exposure. Plant Cell Physiology, accepted. doi: 10.1093/pcp/pcad085. Online ahead of print. *corresponding author. LINK

257. Aghajanzadeh TA., Watanabe M., Tohge T., Hawkesford MJ., Fernie AR., Hoefgen R., Elzenga JTM., De Kok LJ. (2023) Necrotrophic fungal infection affects indolic glucosinolate metabolism in Brassica rapa. Acta Physiologiae Plantarum, 45, Article number: 64 LINK

256. Buelbuel S., Sakuraba Y., Sedaghatmehr M., Watanabe M., Hoefgen R., Balazadeh S., Mueller-Roeber B. (2023) Arabidopsis BBX14 negatively regulates nitrogen starvation- and dark-induced leaf senescence. The Plant Journalaccepted. doi: 10.1111/tpj.16374. Online ahead of print. LINK

255. Watanabe M.Tohge T.* (2023) Species-specific “specialized” genomic region provides the new insights into the functional genomics characterizing metabolic polymorphisms in plant. Current Opinion in Plant Biology, accepted*corresponding author. LINK

254. Perez de Souza L., Bitocchi E., Papa R., Tohge T., Fernie AR. (2023) Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking. The Plant Journal,  119, e2200108119. doi: 10.1111/tpj.16277. Online ahead of print. LINK


253. Komaki S., Tromer EC., De Jaeger G., De Winne N., Heese M., Schnittger A. (2022) Molecular convergence by differential domain acquisition is a hallmark of chromosomal passenger complex evolution. Proc Natl Acad Sci USA. 119, e2200108119.

252. Borghi M., Perez de Souza L., Tohge T., Mi J., Melandri G., Proost S., Martins MCM., Al-Babili S., Bouwmeester HJ., Fernie AR. (2022) High-energy-level metabolism and transport occur at the transition from closed to open flowers. Plant Physiology, 190, 319-339LINK

251. Zhu F., Jadhav SS., Tohge T., Salem MA., Li JM., Giovannoni JJ., Cheng Y., Alseekh S., Fernie AR. (2022) A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator. Plant Physiology190, 250-266LINK

250. Delfin JC., Kanno Y., Seo M., Kitaoka N., Matsuura H., Tohge T.Shimizu T. (2022) AtGH3.10 is another jasmonic acid-amido synthetase in Arabidopsis thaliana. The Plant Journal, 110, 1082-1096. LINK

249. Liu Y., Fernie AR., Tohge T.* (2022) Diversification of chemical structures of methoxylated flavonoids and genes encoding flavonoid-O-methyltransferases. Plants (Basel), 11, 1-18. *corresponding author. LINK

248. Ng LM., Komaki S., Takahashi H., Yamano T., Fukuzawa H., Hashimoto T. (2022) Hyperosmotic stress-induced microtubule disassembly in Chlamydomonas reinhardtii. BMC Plant Biol, 22, 46.

247. Lemaire-Chamley M., Koutouan C., Jorly J., Assali J., Yoshida T., Nogueira M., Tohge T., Ferrand C., Peres LEP., Asamizu E., Ezura H., Fraser PD., Hajirezaei MR., Fernie AR., Rothan C. (2022) A chimeric TGA repressor slows down fruit maturation and ripening in Tomato. Plant Cell Physiology, 63, 120-134. LINK

246. Okada T., Namiki T., Tohge T., Kanaya S. (2022) Cheminformatics modeling of the correlation between bupleurum root-formula medicines and excess and deficiency pattern in the diagnostic criteria of Sho in Kampo (traditional Japanese medicine) by non-targeted direct infusion mass spectrometry with machine learning. Journal of Natural Medicines, 76, 306-313. LINK

245. Romeiro Motta M., Zhao X., Pastuglia M., Belcram K., Roodbarkelari F., Komaki M., Harashima H., Komaki S., Kumar M., Bulankova P., Heese M., Riha K., Bouchez D., Schnittger A. (2022) B1-type cyclins control microtubule organization during cell division in Arabidopsis. EMBO Rep, 23, e53995.


244. Shen S., Peng M., Fang H., Wang Z., Zhou S., Jing X., Zhang M., Yang C., Guo H., Li Y., Lei L., Shi Y., Sun Y., Liu X., Xu C., Tohge T., Yuan M., Fernie AR., Ning Y., Wang GL., Luo J. (2021) An Oryza-specific hydroxycinnamoyl tyramine gene cluster contributes to enhanced disease resistance. Science Bulletin, 66, 2369-2380.  LINK

243. Aarabi F., Rakpenthai A., Barahimipour R., Gorka M., Alseekh S., Zhang Y., Salem MA., Brückner F., Omranian N., Watanabe M., Nikoloski Z., Giavalisco P., Tohge T., Graf A., Fernie AR., Hoefgen R. (2021) Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation. Plant Physiology, kiab386. LINK

242. Alseekh S., Aharoni A., Brotman Y., Contrepois K., D'Auria J., Ewald J., C Ewald J., Fraser PD., Giavalisco P., Hall RD., Heinemann M., Link H., Luo J., Neumann S, Nielsen J., Perez de Souza L., Saito K., Sauer U., Schroeder FC., Schuster S., Siuzdak G., Skirycz A., Sumner LW., Snyder MP., Tang H., Tohge T., Wang Y., Wen W., Wu S., Xu G., Zamboni N., Fernie AR. (2021) Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature Methods, 18, 747-756. LINK

241. Sangpong L., Khaksar G., Pinsorn P., Oikawa A., Sasaki R., Erban A., Watanabe M., Wangpaiboon K., Tohge T., Kopka J., Hoefgen R., Saito K., Sirikantaramas S. (2021) Assessing dynamic changes of taste-related primary metabolism during ripening of durian pulp using metabolomic and transcriptomic analyses. Frontiers in Plant Science, 12, 687799.  LINK

240. Watanabe M., Chiba Y., Hirai MY. (2021) Metabolism and regulatory functions of O-acetylserine, S-adenosylmethionine, homocysteine, and serine in plant development and environmental responses. Frontiers in Plant Science, 12, 643403. LINK

239. Bottcher A., Domingues-Junior AP., Perez de Souza L., Tohge T., Araújo WL. , Fernie AR., Mazzafera P. (2021) Sugarcane cell suspension reveals major metabolic changes under different nitrogen starvation regimes. Bragantia, 80, e2921. LINK

238. Israeli A., Burko Y., Shleizer-Burko S., Zelnik ID., Sela N., Hajirezaei MR., Fernie AR., Tohge T., Ori N., Bar M. (2021) Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium. PLoS Genetics, 17, e1009537. 

237. Liu Y., Watanabe M., Yasukawa S., Kawamura Y., Aneklaphakij C., Fernie AR., Tohge T.* (2021) Cross-species metabolic profiling of floral specialized metabolism facilitates understanding of evolutional aspects of metabolism among Brassicaceae species. Frontiers in Plant Science, 12, 640141. *corresponding author. LINK

236. Aneklaphakij C., Saigo T., Watanabe M., Naake T., Fernie AR., Bunsupa S., Satitpatipan V., Tohge T.* (2021) Diversity of chemical structures and biosynthesis of polyphenols in nut bearing species. Frontiers in Plant Science, 12, 642581. *corresponding author. LINK

235. Olas JJ., Apelt F., Watanabe M., Hoefgen R., Wahl V. (2021) Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation. Plant Science, 303, 110746. LINK

234. Schulz E., Tohge T., Winkler JB., Albert A., Schäffner AR., Fernie AR., Zuther E., Hincha DK. (2021) Natural variation among Arabidopsis accessions in the regulation of flavonoid metabolism and stress gene expression by combined UV radiation and cold. Plant Cell Physiolyology, 62, 502–514. LINK

233. Naake T., Maeda HA., Proost S., Tohge T., Fernie AR. (2021) Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily. Plant Physiology, 185, 857-875. LINK


232. Zhan C., Lei L., Liu Z., Zhou S., Yang C., Zhu X., Guo H., Zhang F., Peng M., Zhang M., Li Y., Yang Z., Sun Y., Shi Y., Li K., Liu L., Shen S., Wang X., Shao J., Jing X., Wang Z., Li Y., Czechowski T., Hasegawa M., Graham I., Tohge T., Qu L., Liu X., Fernie AR., Chen LL., Yuan M., Luo J. (2020) Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance. Nature Plants, 12, 1447-1454. LINK

231. Parry G., Provart NJ., Brady SM., Uzilday B., Multinational Arabidopsis Steering Committee. (2020) Current status of the multinational Arabidopsis community. Plant Direct, 4, e00248. LINK

230. Tohge T.* (2020) From Fruit-Omics to Fruiting Omics: Systematic Studies of Tomato Fruiting by Metabolic Networks. Molecular Plant, 13, 1114-1116*corresponding author. LINK

229. Alseekh S., Ofner I., Liu Z., Osorio S., Vallarino J., Last RL., Zamir D., Tohge T., Fernie AR. (2020) Quantitative trait loci analysis of seed‐specialized metabolites reveals seed‐specific flavonols and differential regulation of glycoalkaloid content in tomato. The Plant Journal, 103, 2007–2024

228. Calumpang CLF., Saigo T., Watanabe M., Tohge T.* (2020) Cross-species comparison of fruit-metabolomics to elucidate metabolic regulation of fruit polyphenolics in pepper (Capsicum annuum cv.) cultivars. Metabolites, 10, 209. *corresponding author. LINK

227. Tohge T.* and Fernie AR.* (2020) Co-regulation of clustered and neo-functionalized genes in plant specialized metabolism. Plants, 9, 622. *corresponding author. LINK

226. Watanabe M., Ueda Y., Kondo K., Ishikawa S., Tohge T., Burgos A., Brotman Y., Fernie AR., Walther D., Hoefgen R., Wissuwa M. (2020) Metabolomic markers and physiological adaptations for high phosphate utilization efficiency in rice. Plant, Cell & Environment, 43, 2066–2079. LINK

225. Richter AS., Tohge T., Fernie AR., Grimm B. (2020) The genomes uncoupled-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins. Philosophical Transactions of the Royal Society B: Biological Sciences, 375:20190403.

224. Tohge T., Scossa F., Wendenburg R., Frasse P., Balbo I., Watanabe M., Alseekh S., Jadhav SS., Delfin JC., Lohse M., Giavalisco P., Usadel B., Zhang Y., Luo J., Bouzayen M., Fernie AR. (2020) Exploiting the natural variation in tomato to define pathway structure and metabolic regulation of fruit polyphenolics in the lycopersicum complex. Molecular Plant, 13, 1027-1046LINK

223. Fichtner F., Olas JJ., Feil R., Watanabe M., Krause U., Hoefgen R., Stitt M., Lunn JE. (2020) Functional features of TREHALOSE-6-PHOSPHATE SYNTHASE1 - an essential enzyme in Arabidopsis thaliana. The Plant Cell, 32, 1949–1972

222. McQuinn RP., Gapper NE., Gray AG., Zhong S., Tohge T., Fei Z., Fernie AR., Giovannoni JJ. (2020) Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening. Plant Biotechnol Jounal, 18, 2210–2224.

221. Saigo T., Wang T., Watanabe M., Tohge T.* (2020) Diversity of anthocyanin and proanthocyanin biosynthesis in land plants. Current Opinion in Plant Biology, 55, 93-99*corresponding authorLINK

220. Hayashi S., Watanabe M., Kobayashi M., Tohge T., Hashimoto T., Shoji T. (2020) Genetic manipulation of transcriptional regulators alters nicotine biosynthesis in tobacco. Plant Cell Physiology, 61, 1041-1053. LINK

219. Correa Galvis V., Strand DD., Messer M., Thiele W., Bethmann S., Hübner D., Uflewski M., Kaiser E., Siemiatkowska B., Morris BA., Toth SZ., Watanabe M., Brückner F., Hoefgen R., Jahns P., Schöttler MA., Armbruster U. (2020) H+ transport by K+ EXCHANGE ANTIPORTER3 promotes photosynthesis and growth in chloroplast ATP synthase mutants. Plant Physiology, 182, 2126-2142.  

218. Ferrari C., Shivhare D., Hansen BO., Pasha A., Esteban E., Provart NJ., Kragler F., Fernie AR., Tohge T., Mutwil M. (2020) Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism, and roots. The Plant Cell, 32, 853-870. LINK

217. Hu C., Rao J., Song Y., Chan SA., Tohge T., Cui B., Lin H., Fernie AR., Zhang D., Shi J. (2020) Dissection of flag leaf metabolic shifts and their relationship with those occurring simultaneously in developing seed by application of non-targeted metabolomics. PLoS One, 15, e0227577. 

216. Scossa F., Roda F., Tohge T., Georgiev MI., Fernie AR. (2020) The Hot and the Colorful: Understanding the Metabolism, Genetics and Evolution of Consumer Preferred Metabolic Traits in Pepper and Related Species. Critical Reviews in Plant Sciences, 38, 339-381. LINK

215. Balboni M., Yang C., Komaki S., Brun J., Schnittger A. (2020) COMET functions as a PCH2 cofactor in regulating the HORMA domain protein ASY1. Current Biology, S0960-9822, 31148-31149.

214. Komaki S., Takeuchi H., Hamamura Y., Heese M., Hashimoto T., Schnittger A. (2020) Functional analysis of the plant chromosomal passenger complex. Plant Physiology, 183, 1586-1599.

213. Sofroni K., Takatsuka H., Yang C., Dissmeyer N., Komaki S., Hamamura Y., Böttger L., Umeda M., Schnittger A. (2020) CDKD-dependent activation of CKDA;1 controls microtubule dynamics and cytokinesis during meiosis. Journal of Cell Biology, 219.



212. Perez de Souza L., Garbowicz K., Brotman Y., Tohge T., Fernie AR. (2019) The acetate pathway supports flavonoid and lipid biosynthesis in Arabidopsis. Plant Physiology182, 857-869. LINK

211. Jorgea TF., Tohge T., Wendenburg R., Ramalho JC., Lidone FC., Ribeiro-Barros AI., Fernie AR., Antónioa C. (2019) Salt-stress secondary metabolite signatures involved in the ability of Casuarina glauca to mitigate oxidative stress. Environmental and Experimental Botany, 166, 103808. LINK

210. Watanabe M., Hoefgen R. (2019) Sulphur systems biology-making sense of omics data. Journal of Experimental Botany, 70, 4155-4170. LINK

209. Beshir WF., Tohge T., Watanabe M., Hertog MLATM., Fernie AR., Nicolaï BM. (2019) Non-aqueous fractionation revealed changing subcellular metabolite distribution during apple fruit development. Horticulture Research, 6, 98.

208. Mangel N., Fudge JB., Li KT., Wu TY., Tohge T., Fernie AR., Szurek B., Fitzpatrick TB., Gruissem W, Vanderschuren H. (2019) Enhancement of vitamin B6 levels in rice expressing Arabidopsis vitamin B6 biosynthesis de novo genes. The Plant Journal, 99, 1047-1065.

207. Heyneke E., Watanabe M., Erban A., Duan G., Buchner P., Walther D., Kopka J., Hawkesford MJ., Hoefgen R. (2019) Effect of senescence phenotypes and nitrate availability on wheat leaf metabolome during grain filling. Agronomy, 9, 305. LINK 

206. Riedel S., Siemiatkowska B., Watanabe M., Müller CS., Schünemann V., Hoefgen R., Leimkühler S. (2019) The ABCB7-like transporter PexA in Rhodobacter capsulatus is involved in the translocation of reactive sulfur species. Frontiers in Microbiology, 10, 406.

205. Ferrari C., Proost S., Janowski M., Becker J., Nikoloski Z., Bhattacharya D., Price D., Tohge T., Bar-Even A., Fernie A., Stitt M., Mutwil M. (2019) Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nature Communications, 10, 737. LINK

204. Battat M., Eitan A., Rogachev I., Hanhineva K., Fernie AR., Tohge T., Beekwilder J., Aharoni A. (2019) A MYB triad controls primary and phenylpropanoid metabolites for pollen coat patterning. Plant Physiology, 180, 87-108.

203. Casartelli A., Melino VJ., Baumann U., Riboni M., Suchecki R., Jayasinghe NS., Mendis H., Watanabe M., Erban A., Zuther E., Hoefgen R., Roessner U., Okamoto M., Heuer S. (2019) Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat. Plant molecular biology, 99, 477-497LINK

202. Matz JM., Watanabe M., Falade M., Tohge T., Hoefgen R., Matuschewski K. (2019) Plasmodium para-aminobenzoate synthesis and salvage resolve avoidance of folate competition and adaptation to host diet. Cell Reports, 26, 356-363. LINK

201. Cromer L., Jolivet S., Singh DK., Berthier F., De Winne N., De Jaeger G., Komaki S., Prusicki MA., Schnittger A., Guérois R., Mercier R. (2019) Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase. PNAS. 116, 16018-16027.

200. Prusicki MA., Keizer EM., van Rosmalen RP., Komaki S., Seifert F., Müller K., Wijnker E., Fleck C., Schnittger A. (2019) Live cell imaging of meiosis in Arabidopsis thaliana. eLife, 8, e42834.



199. Perez de Souza L., Scossa F., Proost S., Bitocchi E., Papa R., Tohge T.*, Fernie AR*. (2018) Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome.  The Plant Journal, 97, 1132-1153. *corresponding author. LINK

198. Fàbregas N., Lozano-Elena F., Blasco-Escámez D., Tohge T., Martínez-Andújar C., Albacete A., Osorio S., Bustamante M., Riechmann JL., Nomura T., Yokota T., Conesa A., Alfocea FP., Fernie AR., Caño-Delgado AI. (2018) Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth. Nature Communications, 9, 4680. 

197. Delfin JC., Watanabe M.,Tohge T.* (2019) Understanding the function and regulation of plant secondary metabolism through metabolomics approaches. Theoretical and Experimental Plant Physiology, 31, 127-138.*corresponding author.  LINK

196. da Fonseca-Pereira P., Daloso DM., Gago J., de Oliveira Silva FM., Condori-Apfata JA., Florez-Sarasa I., Tohge T., Reichheld JP., Nunes-Nesi A., Fernie AR., Araújo WL. (2018) The mitochondrial thioredoxin system contributes to the metabolic responses under drought episodes in Arabidopsis. Plant Cell Physiology, 60, 213-229.

195. Lortzing V., Oberländer J., Lortzing T., Tohge T., Steppuhn A., Kunze R., Hilker M. (2018) Insect egg deposition renders plant defense against hatching larvae more effective in a salicylic acid-dependent manner. Plant Cell Environment, 42, 1019-1032.

194. Naumann M., Hubberten HM., Watanabe M., Hänsch R., Schöttler MA., Hoefgen R. (2018) Sulfite reductase co-suppression in tobacco reveals detoxification mechanisms and downstream responses comparable to sulfate starvation.  Frontiers in Plant Science, 9, 1423. LINK

193. Watanabe M., Netzer F., Tohge T., Orf I., Brotman Y., Dubbert D., Fernie AR., Rennenberg H., Hoefgen R., Herschbach C. (2018) Metabolome and lipidome profiles of populus × canescens twig tissues during annual growth show phospholipid-linked storage and mobilization of C, N, and S. Frontiers in Plant Science, 9, 1292. LINK

192. Lorenz C., Brandt S., Borisjuk L., Rolletschek H., Heinzel N., Tohge T., Fernie AR., Braun HP., Hildebrandt TM. (2018) The role of persulfide metabolism during Arabidopsis seed development under light and dark conditions. Frontiers in Plant Science, 9, 1381. 

191. Brandt S., Fachinger S., Tohge T., Fernie AR., Braun HP., Hildebrandt TM. (2018) Extended darkness induces internal turnover of glucosinolates in Arabidopsis thaliana leaves. PLoS One, 13, e0202153.

190. Pinsorn P., Oikawa A., Watanabe M., Sasaki R., Ngamchuachit P., Hoefgen R, Saito K., Sirikantaramas S. (2018) Metabolic variation in the pulps of two durian cultivars: unraveling the metabolites that contribute to the flavor. Food Chemistry, 268, 118-125.

189. Watanabe M.*, Tohge T., Fernie AR., Hoefgen R.* (2018) The effect of single and multiple SERAT mutants on serine and sulfur metabolism. Frontiers in Plant Science, 9, 72. *corresponding authorLINK

188. de Souza LP., Fernie AR., Tohge T. (2018) Carbon atomic survey for identification of selected metabolic fluxes. Methods in Molecular Biology, 1778, 59-67. LINK

187. Shimizu T., Watanabe M., Fernie AR., Tohge T.* (2018) Targeted LC-MS analysis for plant secondary metabolites. Methods in Molecular Biology, 1778, 171-181. *corresponding authorLINK

186. Tohge T., de Souza LP., Fernie AR. (2018) On the natural diversity of phenylacylated-flavonoid and their in planta function under conditions of stress. Phytochemistry Reviews, 17, 279-290.

185. Salem MA., Li Y., Bajdzienko K., Fisahn J., Watanabe M., Hoefgen R., Schoettler MA., Giavalisco P. (2018) RAPTOR controls developmental growth transitions by altering the hormonal and metabolic balance. Plant Physiology, 177, 565-593.

184. Kamranfar I., Xue GP., Tohge T., Sedaghatmehr M., Fernie AR., Balazadeh S., Mueller-Roeber B. (2018) Transcription factor RD26 is a key regulator of metabolic reprogramming during dark-induced senescence. New Phytologist, 218, 1543-1557.

183. Tohge T.*, Borghi M., Fernie AR*. (2018) The natural variance of the Arabidopsis floral secondary metabolites. Scientific Data, 5, 180051. *corresponding author. LINK

182. Wu S., Tohge T., Cuadros-Inostroza Á., Tong H., Tenenboim H., Kooke R., Méret M., Keurentjes JB., Nikoloski Z., Fernie AR., Willmitzer L., Brotman Y. (2018) Mapping the Arabidopsis metabolic landscape by untargeted metabolomics at different environmental conditions. Molecular Plants, 11, 118-134.

181. Watanabe M., Tohge T., Balazadeh S., Erban A., Giavalisco P., Kopka J., Mueller-Roeber B., Fernie AR., Hoefgen R. (2018) Comprehensive metabolomics studies of plant developmental senescence. Methods in Molecular Biology, 1744, 339-358.

180. Yuan G, Ahootapeh BH, Komaki S, Schnittger A, Lillo C, De Storme N, Geelen D* (2018) PROTEIN PHOSHATASE 2A B'α and β Maintain Centromeric Sister Chromatid Cohesion during Meiosis in Arabidopsis. Plant Physiology. 178(1), 317-328.


179. Peng M., Shahzad R., Gul A., Subthain H., Shen S., Lei L., Zheng Z., Zhou J., Lu D., Wang S., Nishawy E., Liu X., Tohge T., Fernie AR., Luo J. (2017) Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance. Nature Communications, 8, 1975. LINK

178. Heyneke E., Watanabe M., Erban A., Duan G., Buchner P., Walther D., Kopka J., Hawkesford MJ., Hoefgen R. (2017) Characterization of the wheat leaf metabolome during grain filling and under varied N-supply. Frontiers in Plant Science, 8, 2048.

177. Dong Y., Silbermann M., Speiser A., Forieri I., Linster E., Poschet G., Allboje Samami A., Watanabe M., Sticht C., Teleman AA., Deragon JM., Saito K., Hell R., Wirtz M. (2017) Sulfur availability regulates plant growth via glucose-TOR signaling. Nature Communications, 8, 1174.

176. Alseekh S., Tong H., Scossa F., Brotman Y., Vigroux F., Tohge T., Ofner I., Zamir D., Nikoloski Z., Fernie AR. (2017) Canalization of Tomato Fruit Metabolism. The Plant Cell, 29, 2753-2765.

175. Gago J., Fernie AR., Nikoloski Z., Tohge T., Martorell S., Escalona JM., Ribas-Carbó M., Flexas J., Medrano H. (2017) Integrative field scale phenotyping for investigating metabolic components of water stress within a vineyard. Plant Methods, 13, 90. 

174. Fichtner F., Barbier FF., Feil R., Watanabe M., Annunziata MG., Chabikwa TG., Höfgen R., Stitt M., Beveridge CA., Lunn JE. (2017) Trehalose 6-phosphate is involved in triggering axillary bud outgrowth in garden pea (Pisum sativum L.). The Plant Journal, 92, 611-623.

173. Fernie AR., Tohge T. (2017) The genetics of plant metabolism. Annual Review of Genetics, 51, 287-310.

172. Zhu X., Yu J., Shi J., Tohge T., Fernie AR., Meir S., Aharoni A., Xu D., Zhang D., Liang W. (2017) The polyketide synthase OsPKS2 is essential for pollen exine and Ubisch body. Journal of Integrative Plant Biology, 59, 612-628. 

171. Han X., Tohge T., Lalor P., Dockery P., Devaney N., Esteves-Ferreira AA., Fernie AR., Sulpice R. (2017)  Phytochrome A and B Regulate Primary Metabolism in Arabidopsis Leaves in Response to Light. Frontiers in Plant Science, 8, 1394. 

170. Tohge T.*, de Souza LP., Fernie AR. (2017) Current understanding of the pathways of flavonoid biosynthesis in model and crop plants. Journal of Experimental Botany, 68, 4013-4028. *corresponding author.

169. Ishiga Y., Watanabe M., Ishiga T., Tohge T., Matsuura T., Ikeda Y., Hofgen R., Fernie AR., Mysore KS. (2017) The SAL-PAP chloroplast retrograde pathway contributes to plant immunity by regulating glucosinolate pathway and phytohormone signaling. Molecular Plant-Microbe Interactions, 30, 829-841.

168. Moschen S., Di Rienzo JA., Higgins J., Tohge T.Watanabe M., González S., Rivarola M., García-García F., Dopazo J., Hopp HE., Hoefgen R., Fernie AR., Paniego N., Fernández P., Heinz RA. (2017) Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.). Plant Molecular Biology, 94, 549-564.

167. Perez de Souza L., Naake T., Tohge T., Fernie AR. (2017) From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web-resources for mass spectral plant metabolomics. GigaScience, 6, 1-20.

166. Perez de Souza L., Szecowka M., Fernie AR., Tohge T.* (2017) 13CO2 labelling and mass spectral analysis of photorespiration. Methods in Molecular Biology, 1653:157-166. *corresponding author.

165. Prodhan MA., Jost R., Watanabe M., Hoefgen R., Lambers H., Finnegan PM. (2017) Tight control of sulfur assimilation: an adaptive mechanism for a plant from a severely phosphorus-impoverished habitat. New Phytologist, 215, 1068-1079.

164. Kohl K, Tohge T., Schottler, MA. (2017) Performance of Arabidopsis thaliana under LED compared to fluorescent lamp. Functional Plant Biology, 44, 727-738.

163. Ploetner B., Nurmi M., Fischer A., Watanabe M., Schneeberger K., Holm S., Vaid N., Schoettler MA., Walther D., Hoefgen R., Weigel D., Laitinen RA. (2017) Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. The Plant Journal, 91, 251-262.

162. Tohge T.*, Fernie AR.* (2017) Leveraging natural variance towards enhanced understanding of phytochemical sunscreens. Trends in Plant Science, 22, 308-315. *corresponding author.

161. Jin M., Zhang X., Zhao M., Deng M., Du Y., Zhou Y., Wang S., Tohge T., Fernie AR., Willmitzer L., Brotman Y., Yan J., Wen W. (2017) Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis. BMC Plant Biology, 17, 17.

160. Popławski P, Tohge T., Bogusawska J., Rybicka B., Taski Z., Fernie AR., Piekieko-Witkowska A. (2017) Integrated transcriptomic and metabolomic analysis shows that disturbances in metabolism of tumor cells contribute to poor survival of RCC patients. Biochimica et Biophysica Acta, 1863, 744-752.

159. Eisenhut M., Brautigam A., Timm S., Florian A., Tohge T., Fernie AR., Bauwe H., Weber APM. (2017) Photorespiration is crucial to the dynamic response of photosynthetic metabolism and stomatal movement to altered CO2 availability. Molecular Plant, 10, 47-61.

158. Tohge T.* and Fernie AR. (2017) An overview of medicinally important compounds derived from the shikimate and phenylpropanoid pathways. Mini-Reviews in Medicinal Chemistry, 17, 1013-1027. *corresponding author.

157. Ishimaru Y., Oikawa T., Suzuki T., Takeishi S., Matsuura H., Takahashi K., Hamamoto S., Uozumi N., Shimizu T., Seo M., Ohta H., Ueda M. (2017) GTR1 is a jasmonic acid and jasmonoyl-L-isoleucine transporter in Arabidopsis thaliana. Biosci. Biotechnol. Biochem., 81, 249-55.

156. Komaki S. and Schnittger A. (2017) The spindle assembly checkpoint in Arabidopsis is rapidly shut off during severe stress. Developmental Cell, 43, 172-185.

155. Zhao X., Bramsiepe J., Van Durme M., Komaki S., Prusicki MA., Maruyama D., Forner J., Medzihradszky A., Wijnker E., Harashima H., Lu Y, Schmidt A., Guthörl D., Logroño RS., Guan Y., Pochon G., Grossniklaus U., Laux T., Higashiyama T., Lohmann JU., Nowack MK., Schnittger A. (2017) RETINOBLASTOMA RELATED1 mediates germline entry in Arabidopsis. Science, 356, 6336. 


154. Tohge T. and Fernie AR. (2016) Specialized metabolites of the flavonol class mediate root phototropism and growth. Molecular Plant, 9, 1554-1555.

153. Aarabi F., Kusajima M., Tohge T., Konishi T., Gigolashvili T., Takamune M., Sasazaki Y., Watanabe M., Nakashita H., Fernie AR., Saito K., Takahashi H., Hubberten HM., Hoefgen R., Maruyama-Nakashita A. (2016) Sulfur-deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants. Science Advances, 2, e1601087.

152. Liu Z., Tavares R., Lugan R., Boutet-Mercey S., Forsythe ES., Tohge T., Beilstein M., Werck-Reichhart D., Renault H. (2016) Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism. Nature Communications, 7, 13026.

151. Schulz E., Tohge T., Zuther E., Fernie AR., Hincha DK. (2016) Flavonoids are determinants of freezing tolerance and cold acclimation in Arabidopsis thaliana. Scientific Reports, 6, 34027.

150. Inigo S., Durand AN., Ritter A., Le Gall S., Termathe M., Klassen R., Tohge T., De Coninck B., Van Leene J., De Clercq R., Cammue BPA., Fernie AR., Gevaert K., De Jaeger G., Leidel S., Schaffrath R., Van Lijsebettens M., Pauwels L., Goossen A. (2016) The monothiol glutaredoxin GRXS17 associates with the cytosolic iron-sulfur cluster assembly pathway in Arabidopsis. Plant Physiology, 172, 858-873.

149. Baetz U., Eisenach C., Tohge T., Martinoia E., De Angeli A. (2016) Vacuolar chloride fluxes impact ion content and distribution during early salinity in Arabidopsis. Plant Physiology, 172, 1167-1181.

148. Tohge T., Wendenburg R., Ishihara H., Nakabayashi R., Watanabe M., Sulpice R., Hofgen R., Takayama H., Saito K., Stitt M., Fernie AR. (2016) Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae. Nature Communications, 7, 12399.

147. Lu Y., Yasuda S., Li X., Fukao Y., Tohge T., Fernie AR., Matsukura C., Ezura H., Sato T., Yamaguchi J. (2016) Characterization of ubiquitin ligase SlATL31 and proteomic analysis of 14-3-3 targets in tomato fruit tissue (Solanum lycopersicum L). Journal of Proteomics, 143, 254-264.

146. Hofler S., Lorenz C., Busch T., Brinkkotter M., Tohge T., Fernie AR., Braun HP., Hildebrandt TM. (2016) Dealing with the sulfur part of cysteine: four enzymatic steps degrade L-cysteine to pyruvate and thiosulfate in Arabidopsis mitochondria. Physiologia Plantarum, 157, 352-366.

145. Montero R., Perez-Bueno ML., Baron M., Florez-Sarasa I., Tohge T., Fernie AR., El Aou Ouad H., Flexas J. and Bota J. (2016) Alterations in primary and secondary metabolism in Vitis vinifera 'Malvasia de Banyalbufar' upon infection with Grapevine Leafroll associated Virus 3 (GLRaV-3). Physiologia Plantarum, 157, 442-452.

144. Colinas M., Eisenhut M., Tohge T., Pesquera M., Fernie AR., Weber APM., Fitzpatrick TB. (2016) Balancing of B6 vitamers is essential for plant development and metabolism in Arabidopsis. The Plant Cell, 28, 439-453.

143. Hu C., Tohge T., Chan SA., Song Y., Rao J., Cui B., Lin H., Wang L., Fernie AR., Zhang D., Shi J. (2016) Identification of conserved and diverse metabolic shifts during rice grain development. Scientific Reports, 6, 1-12.

142. Sarnowska E., Gratkowska DM., Sacharowski SP., Cwiek P., Tohge T., Fernie AR., Siedlecki JA., Koncz C. and Sarnowski TJ. (2016) The role of SWI/SNF chromatin remodeling complexes in hormonal crosstalk. Trends in Plant Science, 21, 594-608.

141. Ruprecht C., Mendrinna A., Tohge T., Sampathkumar A., Klie S., Fernie AR., Nikoloski Z., Persson S., Mutwil M. (2016) FamNet: A framework to identify multiplied modules driving pathway diversification in plants. Plant Physiology, 170, 1878-1894.

140. Ishihara H., Tohge T., Viehoever P., Fernie AR., Weisshaar B., Stracke R. (2016) Natural variation in flavonol 3-O-gentiobioside 7-O-rhamnoside content in A. thaliana is determined by a glycoside hydrolase type flavonol glucosyltransferase BGLU6. Journal of Experimental Botany, 67, 1505-1517.

139. Wen W., Liu H., Zhou Y., Jin M., Yang N., Li D., Luo J., Xiao Y., Pan Q., Tohge T., Fernie AR., Yan J. (2016) Combining quantitative genetics approaches with regulatory network analysis to dissect complex metabolism in maize kernel. Plant Physiology, 170, 136-146.

138. Nietzsche M., Landgraf R., Tohge T., Bornke F. (2016) A protein-protein interaction network linking the energy-sensor kinase SnRK1 to multiple signaling pathways in Arabidopsis thaliana. Current Plant Biology, 5, 36-44.

137. Scossa F., Brotman Y., de Abreu e Lima F., Willmitzer L., Nikoloski Z., Tohge T., Fernie AR. (2016) Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. Plant Science, 242, 47-64.

136. Moschen S., Bengoa Luoni S., Rienzo JA., Pilar Caro M., Tohge T.Watanabe M., Hollmann J., Gonzalez S., Rivarola M., Garcia-Garcia F., Dopazo J., Esteban Hopp H., Hoefgen R., Fernie AR., Paniego N., Fernandez P., Heinz RA. (2016) Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower. Plant Biotechnology Journal, 14, 719-734.

135. Prodhan MA., Jost R., Watanabe M., Hoefgen R., Lambers H., Finnegan PM. (2016) Tight control of nitrate acquisition in a plant species that evolved in an extremely phosphorus-impoverished environment. Plant Cell and Environment, 39, 2754-2761.

134. Vicente R., Perez P., Martinez-Carrasco R., Feil R., Lunn JE., Watanabe M., Arrivault S., Stitt M., Hoefgen R., Morcuende R. (2016) Metabolic and transcriptional analysis of durum wheat responses to elevated CO2 at low and high nitrate supply. Plant and Cell Physiology, 57, 2133-2146.

133. Figueroa CM., Feil R., Ishihara H., Watanabe M., Kolling K., Krause U., Hoehne M., Encke B., Plaxton WC., Zeeman SC., Li Z., Schulze WX., Hoefgen R., Stitt M., Lunn JE. (2016) Trehalose 6-phosphate coordinates organic and amino acid metabolism with carbon availability. The Plant Journal, 85, 410-423.

132. Kanno Y., Oikawa T., Chiba Y., Ishimaru Y., Shimizu T., Sano N., Koshiba T., Kamiya Y., Seo M. (2016) AtSWEET13 and AtSWEET14 regulate gibberellin-mediated physiological processes. Nature Communications, 7, 13245.

131. Iwase A., Harashima H., Ikeuchi M., Rymen B., Ohnuma M., Komaki S., Morohashi K., Kurata T., Nakata M., Ohme-Takagi M., Grotewold E., Sugimoto K. (2016) WIND1 promotes shoot regeneration through transcriptional activation of ESR1 in Arabidopsis. The Plant Cell, 29, 54-69.

130. Komaki S., Schnittger A. (2016) The spindle checkpoint in plants - a green variation over a conserved theme? Current Opinion in Plant Biology, 34, 84-91. 


129. Zhang Y., Butelli E., Alseekh S., Tohge T., Rallapalli G., Luo J., Kawar PG., Hill L., Santino A., Fernie AR., Martin C. (2015) Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nature Communications, 6, 8635.

128. Lotkowska ME., Tohge T., Fernie AR., Xue GP., Balazadeh S., Mueller-Roeber B. (2015) The Arabidopsis transcription factor MYB112 promotes anthocyanin formation during salinity and under high light stress. Plant Physiology, 169, 1862-1880.

127. Pham PA., Wahl V., Tohge T., de Souza LR., Zhang Y., Do RT., Olas JJ., Stitt M., Araujo WL., Fernie AR. (2015) Analysis of knockout mutants reveals non-redundant functions of poly(ADP-ribose)polymerase isoforms in Arabidopsis. Plant Molecular Biology, 89, 319-338.

126. Tohge T.*, Scossa F., Fernie AR. (2015) Integrative approaches to enhance understanding of plant metabolic pathway structure and regulation. Plant Physiology, 163, 1499-1511. *corresponding author.

125. Harb JY., Alseekh S., Tohge T., Fernie AR. (2015) Profiling of primary metabolites and flavonols in leaves of two table grape varieties collected from semiarid and temperate regions. Phytochemistry, 117, 444-455.

124. Wang T., Tohge T., Ivakov A., Mueller-Roeber B., Fernie AR., Mutwil M., Schippers J., Persson S. (2015) Salt-related MYB1 (SRM1) coordinates abscisic acid biosynthesis and signaling during salt stress in Arabidopsis.Plant Physiology, 169, 1027-1041.

123 Tohge T., Zhang Y., Peterek S., Matros A., Rallapalli G., Tandron Y., Butelli E., Kallam K., Hertkorn N., Mock HP., Martin C., Fernie AR. (2015) Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato. The Plant Journal, 83, 686-704.

122. Tohge T.*, Fernie AR.* (2015) Metabolomics-derived insight into developmental, environmental and genetic aspects of tomato fruit chemical composition and quality. Plant and Cell Physiology, 56, 1681-1696. *corresponding author.

121. Colling J., Tohge T., De Clercq R., Brunoud G., Vernoux T., Fernie AR., Makunga NP, Goossens A., Pauwels L. (2015) Overexpression of the Arabidopsis thaliana signalling peptide TAXIMIN1 results in lateral organ fusion. Journal of Experimental Botany, 66, 5337-5349.

120. Fernie AR., Tohge T. (2015) Ascorbate biosynthesis: A cross-kingdom history. eLife, 4, e07527.

119. Omranian N., Kleessen S., Tohge T., Klie S., Basler G., Mueller-Roeber B., Fernie AR., Nikoloski Z. (2015) Differential metabolic and coexpression networks of plant metabolism. Trends in Plant Science, 20, 266-268.

118. Alseekh S.Tohge T.†, Wendenberg R., Scossa F., Omranian N., Li J., Kleessen S., Giavalisco P., Pleban T., Mueller-Roeber B., Zamir D., Nikoloski Z., Fernie AR. (2015) Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. Plant Cell, 27, 485-512. †equal first author.

117. Schulz E., Tohge T., Zuther E., Fernie AR., Hincha DK. (2015) Natural variation in flavonol and anthocyanin metabolism during cold acclimation in Arabidopsis thaliana accessions. Plant Cell and Environment, 68, 1658-1672.

116. Avin-Wittenberg T., Bajdzienko K., Wittenberg G., Alseekh S., Tohge T., Bock R., Giavalisco P. and Fernie AR. (2015) Global analysis of the role of autophagy on cellular metabolism and energy homeostasis in Arabidopsis seedlings under carbon starvation. The Plant Cell, 27, 306-322.

115. Daloso DM., Muller K., Obata T., Floriana A., Tohge T., Bottcher A., Riondet C., Bariat L., Carrari F., Nunes-Nesi A., Buchanan BB., Reichheld JP., Araujo WL., Fernie AR. (2015) Thioredoxin, a master regulator of the tricarboxylic acid cycle in plant mitochondria. Proc. Natl. Acad. Sci. USA, 112, E1392-E1400.

114. Bromke M., Hochmuth A., Tohge T., Fernie A., Giavalisco P., Burgos A., Willmitzer L., Brotman Y. (2015) Liquid chromatography high-resolution mass spectrometry for fatty acid profiling. The Plant Journal, 81, 529-536.

113. Fernie AR., Tohge T. (2015) Location, location, location - no more! The unravelling of chromatin remodeling regulatory aspects of plant metabolic gene clusters. New Phytologist, 205, 458-460.

112. Sade D., Shriki O., Cuadros-Inostroza A., Tohge T., Semel Y., Haviv Y., Willmitzer L., Fernie AR., Czosnek H., Brotman Y. (2015) Comparative metabolomics and transcriptomics of plant response to Tomato yellow leaf curl virus infection in resistant and susceptible tomato cultivars. Metabolomics, 1, 81-97.

111. Zuchi S., Watanabe M., Hubberten HM., Bromke M., Osorio S., Fernie AR., Celletti S., Paolacci AR., Catarcione G., Ciaffi M., Hoefgen R., Astolfi S. (2015) The interplay between sulfur and iron nutrition in tomato. Plant Physiology, 169, 2624-2639.

110. Speiser A., Haberland S., Watanabe M., Wirtz M., Dietz KJ., Saito K., Hell R. (2015) The significance of cysteine synthesis for acclimation to high light conditions. Frontiers in Plant Science, 5, 776.

109. Bielecka M., Watanabe M., Morcuende R., Scheible WR., Hawkesford MJ., Hesse H., Hoefgen R. (2015) Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis. Frontiers in Plant Science, 5, 805.

108. Mutuku JM., Yoshida S., Shimizu T., Ichihashi Y., Wakatake T., Takahashi A., Seo M., Shirasu K. (2015) The WRKY45-Dependent Signaling Pathway Is Required For Resistanceagainst Striga hermonthica Parasitism. Plant Physiol., 168, 1152-63.

107. Chiba Y., Shimizu T., Miyakawa S., Kanno Y., Koshiba T., Kamiya Y., Seo M. (2015) Identification of Arabidopsis thaliana NRT1/PTR FAMILY (NPF) proteins capable of transporting plant hormones. J Plant Res., 128, 679-86.

106. Shimizu T., Miyakawa S., Esaki T., Mizuno H., Masujima T., Koshiba T., Seo M. (2015) Live Single-Cell Plant Hormone Analysis by Video-Mass Spectrometry. Plant Cell Physiol., 56, 1287-96.

105. Narukawa H., Yokoyama R., Komaki S., Sugimoto K., Nishitani K. (2015) Stimulation of Cell Elongation by Tetraploidy in Hypocotyls of Dark-Grown Arabidopsis Seedlings. PLoS One. 10, e0134547.


104. Araujo WL., Martins AO., Fernie AR., Tohge T. (2014) 2-Oxoglutarate: linking TCA cycle function with amino acid, glucosinolate, flavonoid, alkaloid and gibberellin biosynthesis. Frontiers in Plant Science, 15, 552.

103. Schwahn K., Perez de Souza L., Fernie AR., Tohge T.* (2014) Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade. Journal of Integrative Plant Biology, 56, 864-875. *corresponding author.

102. Tohge T., Obata T., Fernie AR. (2014) Biosynthesis of the essential respiratory cofactor ubiquinone from phenylalanine in plants. Molecular Plant, 7, 1403-1405.

101. Bolger A., Scossa F., Bolger M., Lanz C., Maumus F., Tohge T., Quesneville H., Alseekh S., Sorensen I., Lichenstein G., Fich EA., Conte M., Keller H., Schneeberger K., Schwacke R., Osorio S., Alves Aflitos S., Schijlen E., Jiminez-Gomez J., Kimura S., Kumar R., Koenig D., Headland L., Maloof J., Sinha N., Van Ham R., Lankhorst RK., Mao L., Arsova B., Fei Z., Rose JCK., Zamir D., Carrari F., Giovannoni JJ., Weigel D, Usadel B., Fernie AR. (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, 46, 1034-1038.

100. Wang L., Czedik-Eysenberg A., Mertz RA., Si Y., Tohge T., Nunes-Nesi A., Arrivault S., Dedow LK., Bryant DW., Zhou W., Xu J., Weissmann S., Studer A., Li P., Zhang C., LaRue T., Shao Y., Ding Z., Sun Q., Patel RV., Turgeon R., Zhu X., Provart NJ., Mockler TC., Fernie AR., Stitt M., Liu P., Brutnell TP. (2014) Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nature Biotechnology, 32, 1158-1165.

99. Florian A., Timm S., Nikoloski Z., Tohge T., Bauwe H., Araujo WL., Fernie AR. (2014) Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures. Journal of Integrative Plant Biology, 56, 941-959.

98. Yonekura-Sakakibara K., Nakabayashi R., Sugawara S., Tohge T., Ito T., Koyanagi M., Kitajima M, Takayama H., Saito K. (2014) A flavonoid 3-O-glucoside:2"-O-glucosyltransferase responsible for terminal modification of pollen-specific flavonols in Arabidopsis thaliana. The Plant Journal, 79, 769-782.

97. Fukushima A, Kusano M, Mejia RF, Iwasa M, Kobayashi M, Hayashi N, Watanabe-Takahashi A, Narisawa T., Tohge T., Hur M., Wurtele ES., Nikolau BJ., Saito K. (2014) Metabolomic characterization of knock-out mutants in Arabidopsis - development of a metabolite profiling database for knock-out mutants in Arabidopsis (MeKO). Plant Physiology, 165, 948-961.

96. Tohge T., Perez de Souza L., Fernie AR. (2014) Genome-enabled plant metabolomics. Journal of Chromatography B: Analytical technologies in the biomedical and life sciences, 966, 7-20.

95. Heise R., Arrivault S., Szecowka M., Tohge T., Nunes-Nesi A., Stitt M., Nikoloski Z., Fernie AR. (2014) Flux profiling of photosynthetic carbon metabolism in intact plants. Nature Protocols, 8, 1803-1824.

94. Martins S., Araujo W., Fernie AR., Tohge T., Fabio D. (2014) In high-light-acclimated coffee plants the metabolic machinery is adjusted to avoid oxidative stress rather than to benefit from extra light enhancement in photosynthetic yield. PLOS ONE, 9, E94862.

93. Florian A., Nikoloski Z., Sulpice R., Timm S., Araujo W., Tohge T., Bauwe H., Fernie AR. (2014) Analysis of short-term metabolic alterations in Arabidopsis following changes in the prevailing environmental conditions. Molecular Plant, 7, 896-911.

92. Tohge T.*, Fernie AR. (2014) Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co-expression, co-response and protein locations to aid in identifying transport functions. Frontiers in Plant Science, 5, 75. *corresponding author.

91. Hu C., Shi J., Quan S., Cui B., Kleessen S., Nikoloski Z., Tohge T., Alexander D., Guo L., Lin H., Wang J., Cui X., Rao J., Luo Q., Fernie AR., Zhang D. (2014) Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics. Scientific Reports, 4, 5067.

90. Nakabayashi N., Yonekura-Sakakibara K., Urano K., Suzuki M., Yamada Y., Nishizawa T., Matsuda F., Kojima M., Sakakibara H., Shinozaki K., Michael A., Tohge T., Yamazaki M., Saito K. (2014) Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. The Plant Journal, 77, 367-379.

89. Klie S., Osorio S., Tohge T., Drincovich MF., Fait A., Giovannoni JJ., Fernie AR., Nikoloski Z. (2014) Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. Plant Physiology, 164, 55-68.

88. Tohge T.*, Alseekh S., Fernie AR. (2014) On the regulation and function of secondary metabolism during fruit development and ripening. Journal of Experimental Botany, 65, 4599-4611. *corresponding author.

87. Ruprecht C, Tohge T., Fernie AR., Mortimer CL., Kozlo A., Fraser PD., Funke N., Cesarino I., Vanholme R., Boerjan W., Morreel K., Burgert I, Gierlinger I., Bulone V., Schneider V., Stockero A., Navarro JP., Pudel F., Tambuyser B., Hygate J., Bumstead J., Notley L., Persson S. (2014) Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry. The Journal of Visualized Experiments, 87.

86. Lohse M., Nagel A., Herter T., May P., Schroda M., Zrenner R., Lunn J., Tohge T., Fernie AR., Stitt M., Usadel B. (2014) Mercator: A fast and simple functional annotation web server for genome scale sequence data. Plant Cell and Environment, 37, 1250-1258.

85. Araujo WL., Tohge T., Nunes-Nesi A., Obata T., Fernie AR. (2014) Analysis of kinetic labeling of amino acids and organic acids by GC-MS. Methods in Molecular Biology, 7, 107-120.

84. Weissgerber T.†, Watanabe M.†, Hoefgen R., Dahl C. (2014) Metabolomic profiling of the purple sulfur bacterium Allochromatium vinosum during growth on different reduced sulfur compounds and malate. Metabolomics, 10, 1094-1112. †equal first author.

83. Schmidt R., Schippers JH., Mieulet D., Watanabe M., Hoefgen R., Guiderdoni E., Mueller-Roeber B. (2014) SALT-RESPONSIVE ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice. Molecular Plant, 7, 404-421.

82. Chujo T., Miyamoto K., Ogawa S., Masuda Y., Shimizu T., Kishi-Kaboshi M., Takahashi A., Nishizawa Y., Minami E., Nojiri H., Yamane H., and Okada K. (2014) Overexpression of phosphomimic mutated OsWRKY53 leads to enhanced blast resistance in rice. PLoS One, 9, e98737.

81. Ruduś I., Terai H., Shimizu T., Kojima H., Hattori K., Nishimori Y., Tsukagoshi H., Kamiya Y., Seo M., Nakamura K., Kępczyński J., and Ishiguro S. (2014) Wound-induced expression of DEFECTIVE IN ANTHER DEHISCENCE1 and DAD1-like lipase genes is mediated by both CORONATINE INSENSITIVE1-dependent and independent pathways in Arabidopsis thaliana. Plant Cell Rep., 33, 849-860.

80. Toyomasu T., Usui M., Sugawara C., Otomo K., Hirose Y., Miyao A., Hirochika H., Okada K., Shimizu T., Koga J., Hasegawa M., Chuba M., Kawana Y., Kuroda M., Minami E., Mitsuhashi W., and Yamane H. (2014) Reverse-genetic approach to verify physiological roles of rice phytoalexins: characterization of a knockdown mutant of OsCPS4 phytoalexin biosynthetic gene in rice. Physiol Plant, 150, 55-62. 


79. Sarnowska EA., Rolicka AT., Bucior E., Cwiek P., Tohge T., Fernie AR., Jikumaru Y., Kamiya Y., Franzen R., Schmelzer E., Porri A., Sacharowski S., Gratkowska DM., Zugaj DL., Taff A., Zalewska A., Archacki R., Davis SJ., Coupland G., Koncz C., Jerzmanowski A., Sarnowski TJ. (2013) DELLA-interacting SWI3C core subunit of SWI/SNF chromatin remodeling complex modulates gibberellin responses and hormonal crosstalk in Arabidopsis. Plant Physiology, 163, 305-317.

78. Fernie AR., Tohge T. (2013) Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry. Genome Biology, 119.

77. Chen Y., Lee JH., Weber H., Tohge T., Witt S., Roje S., Fernie AR., Hellmann H. (2013) Arabidopsis BPM proteins function as substrate adaptors to a CUL3-based E3 ligase affecting fatty acid metabolism in plants. Plant Cell, 25, 2253-2264.

76. Koenig DP., Jimenez-Gomez JM., Kimura S., Fulop D., Chitwood DH., Headland LR., Kumar R., Covington MF., Devisetty UK., Tat AV., Tohge T., Bolger A., Schneeberger K., Ossowski S., Lanz C., Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D., Usadel B., Fernie AR., Peng J., Sinha NR., Maloof JN. (2013) Comparative transcriptomics in wild and domesticated tomato. Proc. Natl. Acad. Sci. USA, 110, E2655-2662.

75. Watanabe M.*, Balazadeh S., Tohge T., Erban A., Giavalisco P., Kopka J., Fernie AR., Mueller-Roeber B., Hoefgen R. (2013) Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in Arabidopsis. Plant Physiology, 162, 1290-1310. *corresponding author.

74. Tohge T.*Watanabe M., Hoefgen R., Fernie AR. (2013) Shikimate and phenylalanine biosynthesis in the green lineage. Frontiers in Plant Science, 4, 62. *corresponding author.

73. Tohge T.*Watanabe M., Hoefgen R., Fernie AR. (2013) The evolution of phenylpropanoid metabolism in the green lineage. Critical Reviews in Biochemistry and Molecular Biology, 48, 123-152. *corresponding author.

72. Archacki R., Buszewicz D., Sarnowski TJ., Sarnowska E., Rolicka AT., Tohge T., Fernie AR., Jikumaru Y., Kotlinski M., Iwanicka-Nowicka R., Kalisiak K., Patryn J., Halibart-Puzio J., Kamiya Y., Davis SJ., Koblowska MK., Jerzmanowski A. (2013) BRAHMA ATPase of the SWI/SNF chromatin remodeling complex acts as positive regulator of gibberellin - mediated responses in Arabidopsis. PLOS ONE, 8, e58588.

71. Brotman Y., Landau U., Cuadros-Inostroza A., Tohge T., Fernie AR., Chet I., Viterbo A., Willmitzer L. (2013) Trichoderma-plant root colonization: escaping early plant defense responses and activation of the antioxidant machinery for saline stress tolerance. PLOS Pathogens, 9, e1003221.

70. Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y., Yamazaki M., Tohge T., Fernie AR. (2013) The Flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Plant Physiology and Biochemistry, 72, 21-34.

69. Szecowka M., Heisse R, Tohge T., Nunes-Nesi A., Vorsloh D., Nikoloski Z., Stitt M., Fernie AR., Arrivault S. (2013) Metabolic fluxes of an illuminated Arabidopsis thaliana rosette. Plant Cell, 25, 694-714.

68. Antonio C., Mustaf NR., Osorio S., Tohge T., Giavalisco P., Willmitzer L., Rischerd H., Oksman-Caldentey SM., Verpoort R., Fernie AR. (2013) Analysis of the interface between primary and secondary metabolism in Catharanthus roseus cell cultures using 13C-stable isotope feeding and coupled mass spectrometry.Molecular Plant, 6, 581-584.

67. Tahir J.†, Watanabe M.†, Jing HC., Hunter D., Tohge T., Nunes-Nesi A., Brotman Y., Fernie AR, Hoefgen R., Dijkwel P. (2013) Activation of R-mediated innate immunity and disease susceptibility is affected by different mutations in a cytosolic O-acetylserine (thiol) lyase in Arabidopsis. The Plant Journal, 73, 118-120. †equal first author.

66. Gechev TS., Benina M., Obata T., Tohge T., Sujeeth N., Minkov I., Hille J., Temanni MR., Marriott AS., Bergstrom E., Thomas-Oates J., Antonio C., Mueller-Roeber B., Schippers JH., Fernie AR., Toneva V. (2013) Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis. Cellular and Molecular Life Sciences, 70, 689-709.

65. Sieh D., Watanabe M., Devers EA., Brueckner F., Hoefgen R., Krajinski F. (2013) The arbuscular mycorrhizal symbiosis influences sulfur starvation responses of Medicago truncatula. New Phytologist, 197, 606-616.

64. Yokotani N., Sato Y., Tanabe S., Chujo T., Shimizu T., Okada K., Yamane H., Shimono M., Sugano S., Takatsuji H., Kaku H., Minami E., and Nishizawa Y. (2013) WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance. Journal of Experimental Botany, 64, 5085-5097.

63. Shimizu T., Miyamoto K., Miyamoto K., Minami E., Nishizawa Y., Iino M., Nojiri H., Yamane Y., and Okada K. (2013) OsJAR1 mainly contributes to biosynthesis of the stress-induced jasmonoyl-isoleucine that is involved in defense responses in rice. Biosci. Biotechnol. Biochem., 77, 1556-1564.

62. Riemann M., Haga K., Shimizu T., Okada K., Ando S., Mochizuki S., Nishizawa Y., Yamanouchi U., Nick P., Yano M., Minami E., Takano M., Yamane H., and Iino M. (2013) Identification of rice ALLENE OXIDE CYCLASE mutants and the function of jasmonate for defence against Magnaporthe oryzae. The Plant Journal, 74, 226-238.

61. Miyamoto K., Shimizu T., Mochizuki S., Nishizawa Y., Minami E., Nojiri H., Yamane H., and Okada K. (2013) Stress-induced expression of the transcription factor RERJ1 is tightly regulated in the response to jasmonic acid accumulation in rice. Protoplasma, 250, 241-249.

60. Chujo T., Miyamoto K., Shimogawa T., Shimizu T., Otake Y., Yokotani N., Nishizawa Y., Shibuya N., Nojiri H., Yamane H., Minami E., and Okada K. (2013) OsWRKY28, a PAMP-responsive transrepressor, negatively regulates innate immune responses in rice against rice blast fungus. Plant Mol Biol, 82, 23-37.


59. Rohrmann J., McQuinn R., Giovannoni JJ., Fernie AR., Tohge T.* (2012) Tissue specificity and differential expression of transcription factors in tomato provide hints of conserved and unique regulatory networks.Plant Signaling and Behavior, 7, 1639-1647. *corresponding author.

58. Tohge T., Fernie AR. (2012) Co-expression and co-responses: within and beyond transcription. Frontiers in Plant Science, 3, 248.

57. Araujo WL., Tohge T., Osorio S., Lohse M., Balbo I., Krahnert I., Sienkiewicz-Porzucek A., Usadel B., Nunes-Nesi A., Fernie AR. (2012) Antisense inhibition of the 2-oxoglutarate dehydrogenase complex in tomato demonstrates its importance for plant respiration and during leaf senescence and fruit maturation. Plant Cell, 24, 2328-2351.

56. Alejandro S. †*, Lee Y.*, Tohge T.†*, Sudre D., Osorio S., Park J., Bovet L., Lee Y., Geldner N., Fernie AR., Martinoia E. (2012) AtABCG29 is a monolignol transporter involved in lignin biosynthesis. Current Biology, 22, 1207-1212. †equal first author, *corresponding author.

55. Tohge T.*, Fernie AR. (2012) Annotation of plant gene function via combined genomics, metabolomics and informatics. The Journal of Visualized Experiments, 17, e3487. *corresponding author.

54. Araujo WL., Tohge T., Nunes-Nesi A., Nimick M., Krahnert I., Bunik VI., Moorhead GBG., Fernie AR. (2012) Phosphonate analogs of 2-oxoglutarate perturb metabolism and gene expression in the illuminated leaf in a manner independent of the PII sensor. Frontiers in Plant Science, 3, 114.

53. Toubiana D., Semel Y., Tohge T., Beleggi R., Cattivelli L., Rosental L., Nikoloski Z., Zamir D., Fernie AR., Fait A (2012) Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit and plant relations. PLOS Genetics, 8, e1002612.

52. Wu A., Balazadeh S., Allu AD., Garapati P., Siddiqui H., Dortay H., Zanor MI., Asensi-Fabado MA., Bosch SM, Antonio C., Tohge T., Fernie AR., Kaufmann K., Xue GP., Mueller-Roeber B. (2012) Control of juvenility by JUNBGRUNNEN 1, a ROS-responsive NAC transcription factor, in Arabidopsis thaliana. Plant Cell, 24, 482-506.

51. Shimizu T., Lin F., Hasegawa M., Nojiri H., Yamane H., and Okada K. (2012) The potential bioproduction of the pharmaceutical agent sakuranetin, a flavonoid phytoalexin in rice. Bioengineered, 3, 352-357.

50. Shimizu T., Lin F., Okada K., Hasegawa M., Nojiri H., and Yamane H. (2012) Purification and identification of naringenin 7-O-methyltransferase, a key enzyme in the biosynthesis of the flavonoid phytoalexin sakuranetin in rice. J Biol Chem, 287, 19315-19325.

49. Miyamoto K., Shimizu T., Lin F., Sainsbury F., Thuenemann E., Lomonossoff G., Nojiri H., Yamane H., and Okada K. (2012) Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice. J Plant Physiol, 169, 621-627.

48. Komaki S., Sugimoto K. (2012) Control of the Plant Cell Cycle by Developmental and Environmental Cues. Plant and Cell Physiology. 53, 953-964.


47. Tohge T.*, Kusano M, Fukushima A, Saito K., Fernie AR. (2011) Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. Plant Signaling and Behavior, 6, 1987-1992. *corresponding author.

46. Matas AJ., Yeats TH., Buda GJ., Zheng Y., Chatterjee S., Tohge T., Ponnala L., Fernie AR., Stark R., Fei Z., Giovannoni JJ., Rose JKC. (2011) Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell, 23, 3893-3910.

45. Tohge T., Schnell Ramos M., Nunes-Nesi1 A., Giavalisco P., Steinhauser D., Schellenberg M, Willmitzer L., Martinoia E., Fernie AR. (2011) Towards the storage metabolome: profiling the barley vacuole. Plant Physiology, 157, 1469-1482.

44. Lytovchenko A., Eickmeier I., Pons C., Szecowka M., Lehmberg K., Arrivault S., Tohge T., Hedtke B., Lu Y., Gupta KL., Fisahn J., Bock R., Stitt M., Grimm B., Granell A., Fernie AR. (2011) Tomato fruit photosynthesis is seemingly unimportant in primary metabolism and ripening but plays a considerable role in seed development. Plant Physiology, 157, 1650-1663.

43. Djamei A., Schipper K., Rabe F., Vincon V., Kahnt J., Osorio S., Tohge T., Fernie AR., Johannsen M., Maier U., Morschel E., Feussner6 I., Feussner K., Stierhoff Y., Schwarz H., Marek B., Mann M., Kahmann R. (2011) Metabolomic priming by a secreted fungal effector. Nature, 478, 395-398.

42. Tohge T.*, Mettler T., Arrivault S., Carroll AJ., Stitt M., Fernie AR. (2011) From models to crop species: solutions and caveats for translational metabolomics. Frontiers in Plant Science, 2, 61. *corresponding author.

41. Araujo WL., Ishizaki K., Nunes-Nesi A., Tohge T., Larson TR., Krahnert I., Balbo I., Witt S., Dormann P., Graham IA., Leaver CJ., Fernie AR. (2011) Analysis of a range of catabolic mutants provides evidence that phytanoyl-coenzyme A does not act as a substrate of the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex in Arabidopsis during dark-induced senescence. Plant Physiology, 157, 55-69.

40. Dal Cin V., Tieman DM., Tohge T., McQuinn R., de Vos RC., Osorio S., Schmelz EA., Taylor MG., Smits-Kroon MT., Schuurink RC., Haring MA., Giovannoni J., Fernie AR., Klee HJ. (2011) Identification of genes in the phenylalanine metabolic pathway by ectopic expression of a MYB transcription factor in tomato fruit. Plant Cell, 23, 2738-2753.

39. Fernie AR., Aharoni A., Willmitzer L., Stitt M., Tohge T., Kopka J., Carroll AJ., Saito K., Fraser PD., DeLuca V. (2011) Recommendations for reporting metabolite data. Plant Cell, 23, 2477-2482.

38. Bazzini A., Tohge T., Manacorda CA., Conti G., Nunes-Nesi A., Fernie A., Carrari F., Asurmendi S. (2011) Metabolic profiling of Tobacco mosaic virus infected plants across the infection reveals biphasic temporal changes in the metabolome. PLOS ONE, 6, e28466.

37. Araujo WL., Tohge T., Ishizaki K., Leaver CJ., Fernie AR. (2011) Protein degradation - an alternative respiratory substrate for stressed plants. Trends in Plant Science, 16, 489-498.

36. Rohrmann J.†, Tohge T.†, Alba R., Osorio S., Caldana C., McQuinn R., Arvidsson S., van der Merwe MJ., Riano-Pachon DM., Mueller-Roeber B., Fei Z., Nunes-Nesi A., Giovannoni JJ., Fernie AR. (2011) Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. The Plant Journal, 68, 999-1013. †equal first author.

35. Osorio S., Alba R., Damasceno CMR., Lopez-Casado G., Lohse M., Zanora MI., Tohge T., Usadel B., Rose JKC., Fernie AR., Giovannoni JJ. (2011) Systems biology of tomato fruit development: combined transcript, protein and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiology, 157, 405-425.

34. Kusano M.†, Tohge T.†, Fukushima A.†, Kobayashi M., Hayashi N., Otsuki H., Kondou Y., Goto H., Kawashima M., Matsuda F., Niida R., Matsui M., Saito K., Fernie AR. (2011) Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to ultraviolet-B light. The Plant Journal, 67, 354-369. †equal first author.

33. Mutwil M., Klie S, Tohge T., Giorgi FM., Fernie AR., Usadel B., Persson S. (2011) PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell, 23, 895-910.

32. Araujo WL., Nunes-Nesi A., Osorio S., Usadel B., Fuentes D., Balbo I., Lehmann M., Studart-Witkowski C., Tohge T., Jordana X., DaMatta FM., Fernie AR. (2011) The antisense inhibition of the iron-sulphur subunit of succinate dehydrogenase results in elevated photosynthesis and plant growth in tomato via an organic acid-mediated effect on stomatal aperture. Plant Cell, 23, 600-627.

31. Ando S., Sato Y., Shigemori H., Shimizu T., Okada K., Yamane H., Jikumaru Y., Kamiya Y., Yamada K., Akimoto-Tomiyama C., Tanabe S., Nishizawa Y., and Minami E. (2011) Identification and characterization of 2’-deoxyuridine from the supernatant of conidial suspension of rice blast fungus as an infection-promoting factor in rice plants. Mol Plant Microbe Interact, 24:519-532.


30. Stracke R., Keck M., Tohge T., Blumke A., Niehaus K., Fernie AR., Weisshaar B. (2010) Analysis of PRODUCTION OF FLAVONOL GLYCOSIDES-dependent flavonol glycoside accumulation in Arabidopsis thaliana plants reveals MYB11-, MYB12- and MYB111-independent flavonol glycoside accumulation. New Phytologist, 188, 985-1000.

29. Horai H., Arita M., Kanaya S., Nihei Y., Ikeda T., Suwa K., Ojima Y., Tanaka K., Tanaka S., Aoshima K., Oda Y., Kakazu Y., Kusano M., Tohge T., Matsuda F., Sawada Y., Hirai MY., Nakanishi H., Ikeda K., Akimoto N., Maoka T., Takahashi H., Ara T., Sakurai N., Suzuki H., Shibata D., Neumann S., Iida T., Tanaka K., Funatsu K., Matsuura F., Soga T., Taguchi R., Saito K., Nishioka T. (2010) MassBank: a public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry, 45, 703-714.

28. Huang T., Tohge T., Lytovchenko A., Fernie AR., Jander G. (2010) Pleiotropic physiological consequences of feedback-insensitive phenylalanine biosynthesis in Arabidopsis thaliana. The Plant Journal, 63, 823-835.

27. Tohge T., Fernie AR. (2010) Combining genetic diversity, informatics, and metabolomics to facilitate annotation of plant gene function. Nature Protocols, 5, 1210-1227.

26. Araujo WL., Ishizaki K., Nunes-Nesi A., Larson TR., Tohge T., Krahnert I., Witt S., Obata T., Schauer N., Graham IA., Leaver CJ., Fernie AR. (2010) Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of plant mitochondria. Plant Cell, 22, 1549-1563.

25. Maloney GS., Kochevenko A., Tieman D., Tohge T., Krieger U., Zamir D., Taylor MG., Fernie AR., Klee HJ. (2010) Characterization of the branched-chain amino acid aminotransferase enzyme family in Solanum lycopersicumPlant Physiology, 153, 925-936.

24. Kitamura S., Matsuda F., Tohge T., Yonekura-Sakakibara K., Yamazaki M., Saito K., Narumi I. (2010) Metabolic profiling and cytological analysis of proanthocyanidins in immature seeds of flavonoid accumulation mutants of Arabidopsis thaliana. The Plant Journal, 62, 549-559.

23. Watanabe M., Hubberten HM., Saito K., Hoefgen R. (2010) General regulatory patterns of plant mineral nutrient depletion as revealed by serat quadruple mutants disturbed in cysteine synthesis. Molecular Plant, 3, 438-466.

22. Komaki S., Abe T., Coutuer S., Inzé D., Russinova E., Hashimoto T. (2010) Nuclear-localized subtype of end-binding 1 protein regulates spindle organization in Arabidopsis. Journal of Cell Science, 123, 451-459.


21. Rubin G., Tohge T., Matsuda F., Saito K., Scheible WR. (2009) Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell, 21, 3567-3584.

20. Tohge T.*, Fernie AR. (2009) Web-based resources for mass-spectrometry-based metabolomics: A user’s guide. Phytochemistry, 70, 450-456. *corresponding author.

19. Wirth J., Poletti S., Aeschlimann B., Drosse B., Osorio S., Nandadela Y., Tohge T., Fernie AR., Guenther D., Gruissem W., Sautter C. (2009) Rice endosperm iron biofortification by targeted and synergistic action of nicotianamine synthase and ferritin. Plant Biotechnology Journal, 7, 631-644.

18. Nakabayashi R., Kusano M., Kobayashi M., Tohge T., Yonekura-Sakakibara K., Kogure N., Yamazaki M., Kitajima M., Saito K., Takayama H. (2009) Metabolomics-oriented isolation and structure elucidation of 37 compounds including two new anthocyanins from Arabidopsis thaliana. Phytochemistry, 70, 1017-1029.

17. Lehmann M., Schwarzlaender M., Obata T., Sinkantaramas S., Burow M., Olsen CE., Tohge T., Mark D., Fricker MD., Moller BL., Fernie AR., Sweetlove LJ., Laxa M. (2009) The metabolic response of Arabidopsis roots to oxidative stress is distinct from that of heterotrophic cells in culture and highlights a complex relationship between the levels of transcripts, metabolites and flux. Molecular Plant, 2, 390-460.

16. Kato T., Tanabe S., Nishimura M., Ohtake Y., Nishizawa Y., Shimizu T., Jikumaru Y., Koga J., Okada K., Yamane H., and Minami E. (2009) Differential responses of rice to inoculation with wild-type and non-pathogenic mutants of Magnaporthe oryzae. Plant Mol Biol, 70, 617-625. 

15. Nonomura T., Komaki S., Xu L., Moriura N., Ioroi H., Takashima S., Kakutani K., Takikawa Y., Matsuda Y., Toyoda H. (2009) Tryptophan synthesis block‐associated sugar response, a physiological marker for rapid selection of Arabidopsis thaliana transformants, marked with feedback‐inhibition‐insensitive anthranilate synthase gene. Plant Breeding, 128, 282-289.


14. Yonekura-Sakakibara K.†, Tohge T.†, Matsuda F., Nakabayashi R., Takayama H., Niida R. Watanabe-Takahashi A., Inoue E., Saito K. (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene?metabolite correlations in Arabidopsis. Plant Cell, 20, 2160-2176. †equal first author.

13. Akiyama K., Chikayama E., Yuasa H., Shimada Y., Tohge T., Shinozaki K., Hirai MY., Sakurai T., Kikuchi J., Saito K. (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biology, 8, 339-345.

12. Watanabe M., Mochida K., Kato T., Tabata S., Yoshimoto N., Noji M., Saito K. (2008) Comparative genomics and reverse genetics analysis reveal indispensable functions of the serine acetyltransferase gene family in Arabidopsis. Plant Cell, 20, 2484-2496.

11. Watanabe M., Kusano M., Oikawa A., Fukushima A., Noji M., Saito K. (2008) Physiological roles of the beta-substituted alanine synthase gene family in Arabidopsis. Plant Physiology, 146, 310-320.

10. Shimizu T., Jikumaru Y., Okada A., Okada K., Koga J., Umemura K., Minami E., Shibuya N., Hasegawa M., Kodama O., Nojiri H., and Yamane H. (2008) Effect of a bile acid elicitor, cholic acid, on the biosynthesis of diterpenoid phytoalexins in suspension-cultured rice cells. Phytochemistry, 69, 973-981.


9. Kusano M., Fukushima A., Arita M., Jonsson P., Moritz T., Kobayashi M., Hayashi N., Tohge T., Saito K. (2007) Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Systems Biology, 21, 53.

8. Yonekura-Sakakibara K.Tohge T., Niida R., Saito K. (2007) Identification of a flavonol 7-O-rhamnosyltranserase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression and reverse genetics. Journal of Biological Chemistry, 282, 14932-14941. †equal first author.

7. Tohge T., Yonekura-Sakakibara K., Niida R., Watanabe-Takahashi A., Saito K. (2007) Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes. Pure and Applied Chemistry, 79, 811-823.

6. Hirai MY., Sugiyama K., Sawada Y., Tohge T., Obayashi T., Suzuki A., Araki R., Sakurai N., Suzuki H., Aoki K., Nishizawa O., Shibata D., Saito K. (2007) Omics-based identification of Arabidopsis Myb transcription factor genes which regulate aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci. USA, 104, 6478-6483.

5. Okada A., Shimizu T., Okada K., Kuzuyama T., Koga J., Shibuya N., Nojiri H., and Yamane H. (2007) Elicitor induced activation of the methylerythritol phosphate pathway toward phytoalexins biosynthesis in rice. Plant Mol Biol, 65:177-187.


4. Maruyama-Nakashita A., Nakamura Y., Tohge T., Saito K., Takahashi H. (2006) Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. Plant Cell, 18, 3235-3251.


3. Tohge T., Matsui K., Ohme-Takagi M., Yamazaki M., Saito K. (2005) Enhanced radical scavenging activity of genetically modified Arabidopsis seeds. Biotechnology Letters, 27, 297-3.

2. Tohge T., Nishiyama Y., Hirai MY., Yano M., Nakajima J., Awazuhara M., Inoue E., Takahashi H., Goodenowe DB., Kitayama M., Noji M., Yamazaki M., Saito K. (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing a MYB transcription factor. The Plant Journal, 42, 218-235. + the top-cited paper of amongst the papers in the field of “plant biotechnology” published in 2005 [Nature Biotechnology. (2007): Trend in biotech literature 2006. 27, 961].


1. Fukumoto T., Nonomura T., Matsuda Y., Komaki S., Moriura N., Kakutani K., Sawabe A., Toyoda H. (2003) Evaluation for Efficient Hairy Root Production Assessed by GFP-gene Expression in Tomato Cultivars Inoculated with Agrobacterium rhizogenes MAFF07-20001. Plant Biotechnology. 20, 257-261.

BOOKS and Others

16. Watanabe M., Hoefgen R. (2017) Expression profile of the serine acetyltransferase (SERAT) and O-acetylserine (thiol)lyase (OASTL) gene families in Arabidopsis. In “Sulfur Nutrition and Assimilation in Higher Plants: Fundamental, Environmental and Agricultural Aspects”, De Kok LJ., Hawkesford MJ., Haneklaus SH., Schnug E., eds: pp 31-38, Springer, Dordrecht.

15. Hoefgen R, Watanabe M. (2017) Re-assessing systems biology approaches on analyzing sulfate metabolism. In “Sulfur Nutrition and Assimilation in Higher Plants: Fundamental, Environmental and Agricultural Aspects”, De Kok LJ., Hawkesford MJ., Haneklaus SH., Schnug E., eds: pp 123-133, Springer, Dordrecht.

14. Watanabe M., Hubberten HM., Saito K., Hoefgen R. (2015) Chapter 11: Serine acetyltransferase. In “Amino Acids in Higher Plants” D'Mello JPF., eds: pp 195-218, CPI Group (UK) Ltd, Croydon.

13. Watanabe M., Hoefgen R. (2015) Metabolic analysis of sulfur metabolism during leaf senescence. In “Molecular Physiology and Ecophysiology of Sulfur” De Kok LJ., Hawkesford MJ., Rennenberg H., Saito K., Schnug E., eds: pp 99-105, Springer, Dordrecht.

12. Heyneke E., Watanabe M., Aarabi F., Hoefgen R. (2015) The CBL-SnRK3 network: connections to sulfur metabolism. In “Molecular Physiology and Ecophysiology of Sulfur” De Kok LJ., Hawkesford MJ., Rennenberg H., Saito K., Schnug E., eds: pp 145-152, Springer, Dordrecht.

11. Hubberten HM., Watanabe M., Bielecka M., Heyneke E., Aarabi F., Hoefgen R. (2015) More than a substrate: the O-acetylserine responsive transcriptome. In “Molecular Physiology and Ecophysiology of Sulfur” De Kok LJ., Hawkesford MJ., Rennenberg H., Saito K., Schnug E., eds: pp 133-143, Springer, Dordrecht.

10. Aarabi F., Hubberten HM., Heyneke E., Watanabe M., Hoefgen R. (2015) OAS cluster genes: a tightly co-regulated network. In “Molecular Physiology and Ecophysiology of Sulfur” De Kok LJ., Hawkesford MJ., Rennenberg H., Saito K., Schnug E., eds: pp 125-132, Springer, Dordrecht.

9. Whitcomb SJ., Heyneke E., Aarabi F., Watanabe M., Hoefgen R. (2014) Mineral nutrient depletion affects plant development and crop yield. In “Nutrient Use Efficiency in Plants: Concepts and Approaches” Hawkesford MJ., Kopriva S., De Kok LJ., eds: pp 205-228, Springer, Dordrecht.

8. Watanabe M., Hubberten HM., Hoefgen R. (2012) Plant response to mineral ion availability: transcriptome responses to sulfate, selenium and iron. In “Sulfur Metabolism in Plants, Proceedings of the International Sulfur Workshop” De Kok LJ., Tabe L., Tausz M., Hawkesford MJ., Hoefgen R., McManus MT., Norton RM., Rennenberg H., Saito K., Schnug E., eds: pp 123-134, Springer, Dordrecht.

7. Tohge T., Nunes-Nesi A., Fernie AR. (2009) Finding the paths-metabolomics and approaches to metabolic flux analysis for defining metabolic pathways and their regulation. BIOCHEMIST, 31, 2-6.

6. Osorio S., Tohge T., Fernie AR. (2009) Application of metabolomic profiling for identififying valuable traits in tomato. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 4, 024, 1-9.

5. Watanabe M., Kusano M., Oikawa A., Fukushima A., Mochida K., Kato T., Tabata S., Yoshimoto N., Noji M., Saito K. (2009) Cysteine biosynthesis in Arabidopsis: comprehensive reverse genetic study on the functions of BSAS and SERAT gene families. In "Sulfur Metabolism in Plants Regulatory Aspects Significance of Sulfur in the Food Chain, Agriculture and the Environment" Sirko A., De Kok LJ., Haneklaus S., Hawkesford MJ., Rennenberg H., Saito K., Schnug E., Stulen I., eds: pp 201-206, Backhuys Publishers, Leiden.

4. Tohge T., Nishiyama Y., Hirai MY., Yano M., Nakajima J., Awazuhara M., Inoue E., Takahashi H., Goodenowe DB., Kitayama M., Noji M., Yamazaki M., Saito K. (2007) Identification of genes involved in anthocyanin accumulation by integrated analysis of metabolome and transcriptome in pap1-overexpressing Arabidopsis plants. In "Concepts in Plant Metabolomics" Basil J. Nikolau, Eve Syrkin Wurtele, eds: pp. 159-168, Springer Verlag, Heidelberg.

3. Yokota-Hirai M., Tohge T., Saito K. (2006) Systems-based analysis of plant metabolism by integration of metabolomics with transcriptomics. In: Biotechnology in Agriculture and Forestry, "Plant Metabolomics", edited by Saito, K., Dixon R.A., Willmitzer, L. Springer, pp. 199-209.

2. Noji M., Higashi Y., Watanabe M., Saito K. (2005) T-DNA insertion mutant of ATP sulfurylase, the first enzyme of sulfur assimilatory metabolism, in Arabidopsis thaliana. In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras” Saito K., De Kok LJ., Stulen I., Hawkesford MJ., Schnug E., Sirko A., Rennenberg H., eds: pp 81-82, Backhuys Publishers, Leiden.

1. Watanabe M., Noji M., Kusano M., Kato T., Tabata S., Saito K. (2005) Functional analysis of serine acetyltransferase genes (Serat) involved in sulfur assimilation in Arabidopsis thaliana. In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras” Saito K., De Kok LJ., Stulen I., Hawkesford MJ., Schnug E., Sirko A., Rennenberg H., eds: pp 99-101, Backhuys Publishers, Leiden.

Japanese article

9. 峠隆之 (2021) 「オミクス科学を活用した作物の分子育種に向けて」FFIジャーナル, 226 巻 4 号 p342-350 LINK

8. 西郷知樹峠隆之 (2019) 「植物の天然物化学構造情報のデータマイニングを起点とした機能ゲノミクス」日本化学会情報化学部会誌, 37 巻 2 号 LINK

7. 小牧伸一郎, 橋本隆 (2018) 植物におけるSpindle assembly checkpoint. BSJ-Review. vol. 9: 169-177.

6. 峠隆之 (2016) 「オミクス統合解析を用いた植物二次代謝機能ゲノミクスについて」 SAR News

5. 清水崇史、瀬尾光範(2015)「一細胞からの植物ホルモン質量分析法」 化学と生物, 54(7):454-6.

4. 清水崇史、瀬尾光範(2014)「輸送体研究における新たなアプローチ」 植物の生長調節, 49: 74-80

3. 小牧伸一郎, 杉本慶子 (2011) 細胞増殖から見た個体サイズの制御機構. 植物の生長調節, 49: 363-372.

2. 草野都、峠隆之、松田史生、岡咲洋三、及川彰、斉藤和季 (2007) "マススペクトロメトリーによる植物メタボローム解析""細胞工学別冊 最新プロテオミクス・メタボロミクス 質量分析の基礎からバイオ医薬への応用"丹羽利充 監修、pp. 146-156 秀潤社

1. 平井優美、峠隆之、斉藤和季 (2006)“ツールとしてのメタボロミクス―ゲノム機能科学への応用と今後の展望”ブレイン テクノニュース、114, 7-12