原著論文（1998年以降）

  1. Kanesaka, Y., Inoue, K., Tomita, Y., Yamaoka, S., and Araki, T.* (2023)
    Circadian clock does not play an essential role in daylength measurement for growth-phase transition in Marchantia polymorpha.
    Frontiers in Plant Science 14, 1275503.
    PubMed
  2. Saito, M., Momiki, R., Ebine, K., Yoshitake, Y., Nishihama, R., Miyakawa, T., Nakano, T., Mitsuda, N., Araki, T., Kohchi, T., Yamaoka, S.* (2023)
    A bHLH heterodimer regulates germ cell differentiation in land plant gametophytes.
    Current Biology 33(20 Nov. issue) 1-8, e1-e6.
    PubMed
    京都大学HP
    研究科HP
  3. Torii, K., Inoue, K., Bekki, K., Haraguchi, K., Kubo, M., Kondo, Y., Suzuki, T., Kubota, A., Uemoto, K., Shimizu, H., Saito, M., Fukuda, H., Araki, T., and Endo, M.* (2022)
    A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing.
    Cell Reports 40(2), 111059.
    K.T. and K.I. are co-first authors.
    PubMed
  4. Uemoto, K, Mori, E, Yamauchi, S, Kubota, A, Takahashi, N, Egashira, H, Kunimoto, Y, Araki, T, Takemiya, A, Ito, H, Endo, M* (2021)
    Root PRR7 improves the accuracy of the shoot circadian clock through nutrient transport.
    Plant & Cell Physiology 64(3), 352-362.
    PubMed
  5. Yamaoka, S.*, Inoue, K., and Araki, T.* (2021)
    Regulation of gametangia and gametangiophore initiation in the liverwort Marchantia polymorpha.
    Plant Reproduction 34(4), 297-306.
    PubMed
  6. Torii, K., Kubota, A., Araki, T., and Endo, M.* (2020)
    Time-series single-cell RNA-seq data reveals auxin fluctuation during endocycle.
    Plant & Cell Physiology 61(2), 243-254.
    PubMed
    Featured in Research Highlight of the issue.
  7. Tuzuki, M., Futagami, K., Shimamura, M., Inoue, C., Kunimoto, K., Oogami, T., Tomita, Y., Inoue, K., Kohchi, T., Yamaoka, S., Araki, T., Hamada, T*., and Watanabe, Y. (2019)
    An early arising role of microRNA156/529c-SPL module in reproductive development revealed by the liverwort Marchantia polymorpha.
    Current Biology 29(19), 3307-3314., e1-e5.
    PubMed
    プレスリリース
  8. Hisanaga, T., Yamaoka, S., Kawashima, T., Higo, A., Nakajima, K., Araki, T., Kohchi, T., and Berger, F. (2019)
    Building new insights in plant gametogenesis from an evolutionary perspective.
    Nature Plants 5(7), 663-669.
    T.H., S.Y., and T.Ka. are co-first authors.
    PubMed
  9. Inoue, K., Nishihama, R., Araki, T., and Kohchi, T. (2019)
    Reproductive induction is a far-red high irradiance response that is mediated by phytochrome and PHYTOCHROME INTERACTING FACTOR in Marchantia polymorpha.
    Plant & Cell Physiology 60(5), 1136-1145.
    K.I. and T.K. are co-corresponding authors.
    PubMed
    Featured in Research Highlight of the issue.
  10. Higo, A., Kawashima, T., Borg, M., Zhao, M., López-Vidriero, I., Sakayama, H., Montgomery, S. A., Sekimoto, H., Hackenberg, D., Shimamura, M., Nishiyama, T., Sakakibara, K., Tomita, Y., Togawa, T., Kunimoto, K., Osakabe, A., Suzuki, Y., Yamato, K. T., Ishizaki, K., Nishihama, R., Kohchi, T., Franco-Zorrilla, J. M., Twell, D., Berger, F., and Araki, T. (2018)
    Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants.
    Nature Communications 9, 5283, 1-13.
    A.H. and T.K. are co-first authors, F.B. and T.A. are co-corresponding authors
    PubMed
    プレスリリース
  11. Inoue, K., Araki, T., and Endo, M. (2018)
    Oscillator networks with tissue-specific circadian clocks in plants.
    Seminars in Cell and Developmental Biology 83, 78-85.
    PubMed
  12. Endo, M., Yoshida, M., Sasaki, Y., Negishi, K., Horikawa, K., Daimon, Y., Kurotani, K.-i., Notaguchi, M., Abe, M., and Araki, T. (2018)
    Reevaluation of florigen transport kinetics with separation of function by mutations that uncouple flowering initiation and long-distance transport.
    Plant & Cell Physiology 59, (8), 1621-1629.
    PubMed
    Featured in Research Highlight of the issue.
    Commentary by Lee and Imaizumi (2018): Plant & Cell Physiology 59 (8), 1487-1489.
    PubMed
  13. Uemoto, K., Araki, T., and Endo, M. (2018)
    Isolation of Arabidopsis palisade and spongy mesophyll cells.
    Yamaguchi, N. (ed.) Plant Transcription Factors. Methods and Protocols. Methods in Molecular Biology 1830, 141-148.
    PubMed
  14. Negishi, K., Endo, M., Abe, M., and Araki, T. (2018)
    SODIUM POTASSIUM ROOT DEFECTIVE1 regulates FLOWERING LOCUS T expression via microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module in response to potassium conditions.
    Plant & Cell Physiology 59, (2), 404-413.
    PubMed
    Featured in Research Highlight of the issue.
  15. Inoue, K., Araki, T., and Endo, M. (2018)
    Circadian clock during plant development.
    Journal of Plant Research 131, (1), 59-66.
    PubMed
    Correction: Journal of Plant Research 131 (3), 571 (2018).
    PubMed
  16. Bowman, J.L., Kohchi, T., Yamato, K.T., Jenkins, J., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., Nakamura, Y., Berger, F., Adam, C., Aki, S.S., Althoff, F., Araki, T., Arteaga-Vazquez, M.A., Balasubrmanian, S., Barry, K., Bauer, D., Boehm, C.R., Briginshaw, L., Caballero-Perez, J., Catarino, B., Chen, F., Chiyoda, S., Chovatia, M., Davies, K.M., Delmans, M., Demura, T., Dierschke, T., Dolan, L., Dorantes-Acosta, A.E., Eklund, D. M., Florent, S.N., Flores-Sandoval, E., Fujiyama, A., Fukuzawa, H., Galik, B., Grimanelli, D., Grimwood, J., Grossniklaus, U., Hamada, T., Haseloff, J., Hetherington, A.J., Higo, A., Hirakawa, Y., Hundley, H.N., Ikeda, Y., Inoue, K., Inoue, S.-i., Ishida, S., Jia, Q., Kakita, M., Kanazawa, T., Kawai, Y., Kawashima, T., Kennedy, M., Kinose, K., Kinoshita, T., Kohara, Y., Koide, E., Komatsu, K., Kopischke, S., Kubo, M., Kyozuka, J., Lagercrantz, U., Lin, S.-S., Lindquist, E., Lipzen, A.M., Lu, C.-W., De Luna, E., Martienssen, R.A., Minamino, N., Mizutani, M., Mizutani, M., Mochizuki, N., Monte, I., Mosher, R., Nagasaki, H., Nakagami, H., Naramoto, S., Nishitani, K., Ohtani, M., Okamoto, T., Okumura, M., Phillips, J., Pollak, B., Reinders, A., Rövekamp, M., Sano, R., Sawa, S., Schmid, M.W., Shirakawa, M., Solano, R., Spunde, A., Suetsugu, N., Sugano, S., Sugiyama, A., Sun, R., Suzuki, Y., Takenaka, M., Takezawa, D., Tomogane, H., Tsuzuki, M., Ueda, T., Umeda, M., Ward, J.M., Watanabe, Y., Yazaki, K., Yokoyama, R., Yoshitake, Y., Yotsui, I., Zachgo, S., and Schmutz, J. (2017)
    Insights into land plant evolution garnered from the Marchantia polymorpha genome.
    Cell 171, (2), 287-304.
    PubMed
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  17. Inoue, K., Araki, T., and Endo, M. (2017)
    Integration of input signals into the gene network in the plant circadian clock.
    Plant & Cell Physiology 58, (6), 977-982.
    PCP
    Featured in Research Highlight of the issue.
  18. Endo, M., Shimizu, H., and Araki, T. (2016)
    Rapid and simple isolation of vascular, epidermal and mesophyll cells from plant leaf tissue.
    Nature Protocols 11, (8), 1388-1395.
    PubMed
  19. Endo, M., Araki, T., and Nagatani, A. (2016)
    Tissue-specific regulation of flowering by photoreceptors.
    Cellular and Molecular Life Sciences 73, (4), 829-839.
    PubMed
  20. Shimizu, H., Torii, K., Araki, T., and Endo, M. (2016)
    Importance of epidermal clocks for regulation of hypocotyl elongation through PIF4 and IAA2.
    Plant Signaling & Behavior 11, (2), e1143999, 1-2.
    PubMed
  21. Higo, A., Niwa, M., Yamato, K. T., Yamada, L., Sawada, H., Sakamoto, T., Kurata, T., Shirakawa, M., Endo, M., Shigenobu, S., Ishizaki, K., Nishihama, R., Kohchi, T., and Araki, T. (2016)
    Transcriptional framework of male gametogenesis in the liverwort Marchantia polymorpha L.
    Plant & Cell Physiology 57, (2), 325-338.
    PubMed
  22. Bowman, J.L., Araki, T., Arteaga-Vazquez, M., Berger, F., Dolan, L., Haseloff, J., Ishizaki, K., Kyozuka, J., Lin, S.-S., Nagasaki, H., Nakagami, H., Nakajima, K., Nakamura, Y., Ohashi-Ito, K., Sawa, S., Shimamura, M., Solano, R., Tsukaya, H., Ueda, T., Watanabe, Y., Yamato, K.T., Zachgo, S., and Kohchi, T. (2016)
    The naming of names: guidelines for gene nomenclature in Marchantia.
    Plant & Cell Physiology 57, (2), 257-261.
    PubMed
  23. Bowman, J.L., Araki, T., and Kohchi, T. (2016)
    Marchantia: past, present and future.
    Plant & Cell Physiology 57, (2), 205-209.
    PubMed
  24. Kawamoto, N., Endo, M., and Araki, T. (2015)
    Expression of a kinase-dead form of CPK33 involved in florigen complex formation causes delayed flowering.
    Plant Signaling & Behavior 10, (12), e1143999, 1-2.
    PubMed
  25. Shimizu, H., Katayama, K., Koto, T., Torii, K., Araki, T., and Endo, M. (2015)
    Decentralized circadian clocks process thermal and photoperiodic cues in specific tissues.
    Nature Plants 1, Article Number 15163, 1-6.
    PubMed
    Author Correction: Nature Plants 4 (12), 1126 (2018).
    Commentary by McClung (2015): Nature Plants 1 Article Number: 15172.
    PubMed
    プレスリリース
  26. Abe, M., Kaya, H., Watanabe-Taneda, A., Shibuta, M., Yamaguchi, A., Sakamoto, T., Kurata, T., Ausin, I., Araki, T., and Alonso-Blanco, C. (2015)
    FE, a phloem-specific Myb-related protein, promotes flowering through transcriptional activation of FLOWERING LOCUS T and FLOWERING LOCUS T INTERACTING PROTEIN 1.
    Plant Journal 83, (6), 1059-1068.
    PubMed
  27. Shimizu, H., Araki, T., and Endo, M. (2015)
    Photoperiod sensitivity of the Arabidopsis circadian clock is tissue-specific.
    Plant Signaling & Behavior 10, (6), e1010933, 1-2.
    PubMed
  28. Kawamoto, N., Sasabe, M., Endo, M., Machida, Y., and Araki, T. (2015)
    Calcium-dependent protein kinases responsible for the phosphorylation of a bZIP transcription factor FD crucial for the florigen complex formation.
    Scientific Reports 5, 8341. 1-9.
    PubMed
  29. Endo, M., Shimizu, H., Nohales, M.A., Araki, T., and Kay, S.A. (2014)
    Tissue-specific clocks in Arabidopsis show asymmetric coupling.
    Nature 515, (7527), 419-422.
    PubMed
    Commentary by Martí and Webb (2015): Nature 515 (7527), 352-353.
    PubMed
    プレスリリース
    30. Access the recommendation on F1000Prime
  30. Endo, M., Kudo, D., Koto, T., Shimizu, H., and Araki, T. (2014)
    Light-dependent destabilization of PHL in Arabidopsis.
    Plant Signaling & Behavior 9 (2), e28118.
    ME and TA are co-corresponding authors.
    PubMed
  31. Niwa, M., Endo, M., and Araki, T. (2013)
    Florigen is involved in axillary bud development at multiple stages in Arabidopsis.
    Plant Signaling & Behavior 8 (11), e27167.
    PubMed
  32. Endo, M., Tanigawa, Y., Murakami, T., Araki, T., and Nagatani, A. (2013)
    PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering through physical interactions with phytochrome B and CONSTANS.
    Proceedings of the National Academy of Sciences of the United States of America 110 (44), 18017-18022.
    ME, TA, and NA are co-corresponding authors.
    PubMed
    京都大学 HP の紹介記事
  33. Yoo, S.-C., Chen, C., Rojas, M., Daimon, Y., Ham, B.-K., Araki, T., and Lucas, W. (2013)
    Phloem long-distance delivery of FLOWERING LOCUS T (FT) to the apex.
    Plant Journal 75 (3), 456-468.
    TA and WL are co-corresponding authors.
    PubMed
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  34. Niwa, M., Daimon, Y., Kurotani, K., Higo, A., Pruneda-Paz, J.L., Breton, G., Mitsuda, N., Kay, S.A., Ohme-Takagi, M., Endo, M., and Araki, T. (2013)
    BRANCHED1 interacts with FLOWERING LOCUS T to repress the floral transition of the axillary meristems in Arabidopsis.
    Plant Cell 25 (4), 1228-1242.
    PubMed Free Full Text (Open Access) Featured in "In Brief" section of the issue.
    "Author profile (Masaki Niwa)"
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  35. Hiraoka, K., Yamaguchi, A., Abe, M., and Araki, T. (2013)
    The florigen genes FT and TSF modulate lateral shoot outgrowth in Arabidopsis thaliana.
    Plant & Cell Physiology 54 (3), 352-368. PubMed Free Full Text
  36. Machida, Y., Fukaki, H., and Araki, T. (2013)
    Plant meristems and organogenesis: the new era of plant developmental research. (Editorial)
    Plant & Cell Physiology 54 (3), 295-301. PubMed Free Full Text
  37. Imura, Y., Kobayashi, Y., Yamamoto, S., Furutani, M., Tasaka, M., Abe, M., and Araki, T. (2012)
    CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis.
    Plant & Cell Physiology 53 (2), 287-303. PubMed Free Full Text (Open Access)
    Selected as an "Editor-in-Chief's Choice Article"
  38. Iwata, H., Gaston, A., Remay, A., Thouroude, T., Jeauffre, J., Kawamura, K., Oyant, L.H., Araki, T., Denoyes, B., and Foucher, F. (2012)
    The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry.
    Plant Journal 69 (1), 116-125. PubMed
  39. Nishikawa, F., Endo, T., Shimada, H., Fujii, H., Shimizu, T., Kobayashi, Y., Araki, T., and Omura, M. (2010)
    Transcriptional changes in CiFT-introduced transgenic trifoliate orange (Poncirus trifoliata L. Raf.).
    Tree Physiology 30 (3), 431-439. PubMed
  40. Notaguchi, M., Daimon, Y., Abe, M., and Araki, T. (2009)
    Adaptation of a seedling micro-grafting technique to the study of long-distance signaling in flowering of Arabidopsis thaliana.
    Journal of Plant Research 122 (2), 201-214. PubMed
    2010 年度 日本植物学会 JPR 論文賞 講評（日本植物学会 HP） 賞状
  41. Endo, T., Shimada, T., Fujii, H., Nishikawa, F., Sugiyama, A., Nakano, M., Shimizu, T., Kobayashi, Y., Araki, T., Pena, L., and Omura, M. (2009)
    Development of a CiFT co-expression system for functional analysis of genes in Citrus flowers and fruit.
    Journal of the Japanese Society for Horticultural Science 78 (1), 74-83. Abstract (journal HP)
    平成22年度 園芸学会年間優秀論文賞　賞状
  42. Notaguchi, M., Daimon, Y., Abe, M., and Araki, T. (2009)
    Graft-transmissible action of Arabidopsis FLOWERING LOCUS T protein to promote flowering.
    Plant Signaling & Behavior 4 (2), 123-125.
    Addendum to: Notaguchi, M. et. al. (2008) Plant & Cell Physiology 49 (11), 1645-1658. PubMed Free Full Text
  43. Notaguchi, M., Abe, M., Kimura, T., Daimon, Y., Kobayashi, T., Yamaguchi, A., Tomita, Y., Dohi, K., Mori, M., and Araki, T. (2008)
    Long-distance, graft-transmissible action of Arabidopsis FLOWERING LOCUS T protein to promote flowering.
    Plant & Cell Physiology 49 (11), 1645-1658. PubMed Free Full Text (Open Access)
    Corrigendum (copyright information): Plant & Cell Physiology 49 (12), 1922.
  44. Tsukaya, H., Tsujino, R., Ikeuchi, M., Isshiki, Y., Kono, M. Takeuchi, T., and Araki, T. (2007)
    Morphological variation in leaf shape in Ainsliaea apiculata with special reference to the endemic characters of populations on Yakushima Island, Japan.
    Journal of Plant Research 120 (3), 351-358. PubMed
  45. Ikeda, Y., Kobayashi, Y., Yamaguchi, A., Abe, M., and Araki, T. (2007)
    Molecular basis of late-flowering phenotype caused by dominant epi-alleles of the FWA locus in Arabidopsis.
    Plant & Cell Physiology 48 (2), 205-220. PubMed Free Full Text
    Erratum: Plant & Cell Physiology 48 (3), 562.
  46. Endo, M., Ishikawa, Y., Osakabe, K., Nakayama, S., Kaya, H., Araki, T., Shibahara, K., Abe, K., Ichikawa, H., Valentine, L., Hohn, B., and Toki, S. (2006)
    Increased frequency of homologous recombination and T-DNA integration in Arabidopsis CAF-1 mutants.
    EMBO Journal 25 (23), 5579-5590. PubMed
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  47. Kieber, J. and Araki, T. (2006)
    Cell signaling and gene regulation (Editorial Overview).
    Current Opinion Plant Biology 9 (5), 445-447.
  48. Ono, T., Kaya, H., Takeda, S., Abe, M., Ogawa, Y., Kato, M., Kakutani, T., Mittelsten Scheid, O., Araki, T., and Shibahara, K. (2006)
    Chromatin assembly factor-1 insures the stable maintenance of silent chromatin states in Arabidopsis.
    Genes to Cells 11 (2), 153-162. PubMed Cover
  49. Endo, T., Shimada, T., Fujii, H., Kobayashi, Y., Araki, T., and Omura, M. (2005)
    Ectopic expression of an FT homolog from Citrus confers an early flowering phenotype on trifoliate orange (Poncirus trifoliata L. Raf.).
    Transgenic Research 14 (5), 703-712. PubMed
  50. Abe, M., Kobayashi, Y., Yamamoto, S., Daimon, Y., Yamaguchi, A., Ikeda, Y., Ichinoki, H., Notaguchi, M., Goto, K., and Araki, T. (2005)
    FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex.
    Science 309 (5737), 1052-1056.
    First three authors (MA, YK, SY) are co-first authors. PubMed
    プレスリリース
    科学技術振興機構 CREST プレス発表
    Science誌が選ぶ2005年の十大"Breakthrough of the Year"の３番目（"Blooming marvelous"）に選ばれました
    朝日新聞の記事（2005年12月31日）
    featured by Science（August 12 2005）
    featured by Nature Genetics（October 2005）
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  51. Yamaguchi, A., Kobayashi, Y., Goto, K., Abe, M., and Araki, T. (2005)
    TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT.
    Plant & Cell Physiology 46 (8), 1175-1189. PubMed Free Full Text Cover 日本植物生理学会論文賞
  52. Endo, M., Nakamura, S., Araki, T., Mochizuki, N., and Nagatani, A. (2005)
    Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles.
    Plant Cell 17 (7), 1941-1952. PubMed
  53. Takeda, S., Tadele, Z., Hofmann, I., Probst, A. V., Angelis, K. J., Kaya, H., Araki, T., Mengiste, T., Mittelsten Scheid, O., Shibahara, K., Scheel, D. and Paszkowski, J. (2004)
    BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis.
    Genes & Development 18 (7), 782-793. PubMed
  54. Kojima, S., Takahashi, Y., Kobayashi, Y., Monna, L., Sasaki, T., Araki, T., and Yano, M. (2002)
    Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day condition.
    Plant & Cell Physiology 43 (10), 1096-1105. PubMed Cover 日本植物生理学会論文賞
    Most cited article of the journal
  55. Eckardt, N. A., Araki, T., Benning, C., Cubas, P., Goodrich, J. Jacobsen, S., Masson, P., Nambara, E., Simon, R., Somerville, S., and Wasteneys, G. (2001)
    Meeting Report Arabidopsis Research 2001.
    Plant Cell 13 (9), 1973-1982. PubMed
  56. Ohto, M., Onai, K., Furukawa, Y., Aoki, E., Araki, T. and Nakamura, K. (2001)
    Effects of sugar on vegetative development and floral transition in Arabidopsis thaliana.
    Plant Physiology 127 (1), 252-261. PubMed
  57. Mimida, N., Goto, K., Kobayashi, Y., Araki, T., Ahn, J. H., Weigel, D., Murata, M., Motoyoshi, F. and Sakamoto, W. (2001)
    Functional divergence of the TFL1-like gene family in Arabidopsis revealed by characterization of a novel homologue.
    Genes to Cells 6 (4), 327-336. PubMed
  58. Araki, T. (2001)
    Transition from vegetative to reproductive phase.
    Current Opinion in Plant Biology 4 (1), 63-68. PubMed
  59. Kaya, H., Shibahara, K., Taoka, K., Iwabuchi, M., Stillman, B. and Araki, T. (2001)
    FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems.
    Cell 104 (1), 131-142. PubMed
  60. Kaya, H., Sato, S., Tabata, S., Kobayashi, Y., Iwabuchi, M. and Araki, T. (2000)
    hosoba toge toge, a syndrome caused by a large chromosomal deletion associated with a T-DNA insertion in Arabidopsis.
    Plant & Cell Physiology 41 (9), 1055-1066. PubMed
  61. Sakamoto, H., Araki, T., Meshi, T. and Iwabuchi, M. (2000)
    Expression of a subset of the Arabidopsis Cys2/His2-type zinc-finger protein gene family under water stress.
    Gene 248 (1-2), 23-32. PubMed
  62. Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M. and Araki, T. (1999)
    A pair of related genes with antagonistic roles in mediating flowering signals.
    Science 286 (5446), 1960-1962. PubMed
  63. Taoka, K., Kaya, H., Nakayama, T., Araki, T., Meshi, T. and Iwabuchi, M. (1999)
    Identification of three kinds of mutually related composite elements conferring S phase-specific transcriptional activation.
    Plant Journal 18 (6), 611-623. PubMed
  64. Araki, T., Kaya, H., Kobayashi, Y. and Iwabuchi, M. (1998)
    The flowering-time gene FT and regulation of flowering in Arabidopsis.
    Journal of Plant Research 111 (1102), 277-281. Abstract Cover