Laboratory of Embryology

• Inoue Y., Suzuki Y., Kunishima Y., Washio T., Morishita S., Takeda H. (2023). High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes). BMC Genomics, 24(1):472
• Inoue Y., Takeda H. (2023). Teratorn and its relatives – a cross-point of distinct mobile elements, transposons and viruses. Frontiers in Veterinary Science, 10:1158023.
• Fukushima H.S., Takeda H., Nakamura R. (2023). Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development. Genome Research, 33(4): 572–586. (selected as the cover picture)
• Yusuke Inoue, Hiroyuki Takeda. (2023). Teratorn and Its Related Elements – a Novel Group of Herpesviruses Widespread in Teleost Genomes. Zoological Science, 40(2):83-90.
• Mikami T., Ikeda T., Muramiya Y., Hirasawa T. and Iwasaki W. (2023). Three-dimensional anatomy of the Tully monster casts doubt on its presumed vertebrate affinities. Palaeontology, e12646.
• Fukushima, H.S., Takeda, H., Nakamura, R. (2023). Targeted Manipulation of Histone Modification in Medaka Embryos. In: Hatada, I., Horii, T. (eds) Epigenomics. Methods in Molecular Biology, vol 2577. Humana, New York, NY.
• Ann Kathrin Heilig, Ryohei Nakamura, Atsuko Shimada, Yuka Hashimoto, Yuta Nakamura, Joachim Wittbrodt, Hiroyuki Takeda, Toru Kawanishi, Wnt11 acts on dermomyotome cells to guide epaxial myotome morphogenesis. Elife, May 6;11:e71845. (2022).
• Takafumi Ikeda, Kiichi Inamori, Toru Kawanishi, Hiroyuki Takeda, Reemployment of Kupffer’s vesicle cells into axial and paraxial mesoderm via transdifferentiation. Development, Growth & Differentiation, 64:163–177. (2022). (selected as the cover picture)
• Xiaotong Wu, Hongmei Zhang, Bingjie Zhang, Yu Zhang, Qiuyan Wang, Weimin Shen, Xi Wu, Lijia Li, Weikun Xia, Ryohei Nakamura, Bofeng Liu, Feng Liu, Hiroyuki Takeda, Anming Meng, Wei Xie, Methylome inheritance and enhancer dememorization reset an epigenetic gate safeguarding embryonic programs. Science Advances, Dec 24;7(52):eabl3858. (2021).
• Ryohei Nakamura, Yuichi Motai, Masahiko Kumagai, Candice L. Wike, Haruyo Nishiyama, Yoichiro Nakatani, Neva C. Durand, Kaori Kondo, Takashi Kondo, Tatsuya Tsukahara, Atsuko Shimada, Bradley R. Cairns, Erez Lieberman Aiden, Shinichi Morishita, Hiroyuki Takeda, CTCF looping is established during gastrulation in medaka embryos. Genome Research, 31:968-980. (2021).
• Candice L. Wike, Yixuan Guo, Mengyao Tan, Ryohei Nakamura, Dana Klatt Shaw, Noelia Díaz, Aneasha F. Whittaker-Tademy, Neva C. Durand, Erez Lieberman Aiden, Juan M. Vaquerizas, David Grunwald, Hiroyuki Takeda, Bradley R. Cairns, Chromatin architecture transitions from zebrafish sperm through early embryogenesis. Genome Research, 31:981-994. (2021).
• Yu Nakagama, Norihiko Takeda, Seishi Ogawa, Hiroyuki Takeda, Yoshiyuki Furutani, Toshio Nakanishi, Tatsuyuki Sato, Yoichiro Hirata, Akira Oka, Ryo Inuzuka, Noonan syndrome-associated biallelic LZTR1 mutations cause cardiac hypertrophy and vascular malformations in zebrafish. Mol Genet Genomic Med, 8(3). (2020).
• Mulholland, Christopher B., Atsuya Nishiyama, Joel Ryan, Ryohei Nakamura, Merve Yiğit, Ivo M. Glück, Carina Trummer, Weihua Qin, Michael D. Bartoschek, Franziska R. Traube, Edris Parsa, Enes Ugur, Miha Modic, Aishwarya Acharya, Paul Stolz, Christoph Ziegenhain, Michael Wierer, Wolfgang Enard, Thomas Carell, Don C. Lamb, Hiroyuki Takeda, Makoto Nakanashi, Sebastian Bultmann, & Heinrich Leonhardt, Recent Evolution of a TET-Controlled and DPPA3/STELLA-Driven Pathway of Passive DNA Demethylation in Mammals. Nature Communications, 11(1). (2020).
• Satou, Yutaka, Ryohei Nakamura, Deli Yu, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, Noriyuki Satoh, & Rachel O’Neill. A Nearly Complete Genome of Ciona Intestinalis Type A (C. Robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. Genome Biology and Evolution, 11(11):3144–57. (2019).
• Abe K., Shimada S., Tayama S., Nishikawa S., Kaneko T., Tsuda S., Karaiwa A., Matsui T., Ishitani T., & Takeda, H., Horizontal boundary cells, a special group of dermomyotomal cells, play crucial roles in the formation of dorsoventral compartments in teleost somite. Cell Reports, 27, 928–939. (2019).
• Fukushima HS., Takeda H., & Nakamura R., Targeted in vivo epigenome editing of H3K27me3. Epigenetics & Chromatin, 12(1):17 (2019).
• Yamaguchi H., Oda T., Kikkawa M., & Takeda H., Systematic studies of all PIH proteins in zebrafish reveal their distinct roles in axonemal dynein assembly. eLife, 9(7)(2018) pii: e36979. doi: 10.7554/eLife.36979.
• Yui Uchida Y, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda & Naoki Irie, Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos. EvoDevo, 9(7)(2018)
• Inoue Y., Kumagai M., Zhang X., Saga T., Wang D., Koga A. & Takeda H., Fusion of piggyBac-like transposons and herpesviruses occurs frequently in teleosts. Zoological Letters, 4:6 (2018)
• Napo K. M. Cheung, Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Hiroto S. Fukushima, Shinichi Morishita & Hiroyuki Takeda, Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish. PLoS Genet., 13(12):e1007123 (2017)
• Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda & Shinich Morishita, Centromere evolution and CpG methylation during vertebrate speciation. Nat Commun., 8,1833 (2017)
• Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Shinichi Morishita & Hiroyuki Takeda, Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts. Epigenetics & Chromatin, 10:44 (2017)
• Inoue, Y., Saga, T., Aikawa, T., Kumagai, M., Shimada, A., Kawaguchi, Y., Naruse, K., Morishita, S., Koga, A. & Takeda, H., Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish. Nat Commun. 8, 551 (2017)
• Qu, Wei, Tatsuya Tsukahara, Ryohei Nakamura, Hideaki Yurino, Shin Ichi Hashimoto, Shoji Tsuji, Hiroyuki Takeda, & Shinichi Morishita. Assessing Cell-to-Cell DNA Methylation Variability on Individual Long Reads. Scientific Reports 6(February):1–7 (2016).
• Ayako Uno, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Sumio Sugano, Yutaka Suzuki, Shinichi Morishita & Takeda, H., Comparative analysis of genome and epigenome in the closely related medaka species identifies conserved sequence preferences for DNA hypomethylated domains. Zoological Science, 33 (4), 358-365 (2016).
• Nakatani, Yoichiro, Cecilia C. Mello, Shin Ichi Hashimoto, Atsuko Shimada, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Jun Yoshimura, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Andrew Fire, & Shinichi Morishita. Associations between Nucleosome Phasing, Sequence Asymmetry, and Tissue-Specific Expression in a Set of Inbred Medaka Species. BMC Genomics 16(1):1–14 (2015).
• Takayoshi Otsuka, Tatsuya Tsukahara & Takeda, H., Development of the pancreas in medaka, Oryzias latipes, from embryo to adult. Dev Growth Differ. , 57(8), 557-69 (2015)
• Yamamoto, T., Tsukahara, T., Ishiguro, T., Hagiwara, H., Taira, M. & Takeda, H., The medaka dhc2 mutant reveals conserved and distinct mechanisms of Hedgehog signaling in teleosts. BMC Developmental Biology, 15:9 (2015)
• Hojo, M., Omi, A., Hamanaka, G., Shindo, K., Shimada, A., Kondo, M., Narita, T., Kiyomoto, M., Katsuyama, Y., Ohnishi, Y., Irie, N. & Takeda, H., Unexpected link between polyketide synthase and calcium carbonate biomineralization. Zoological Letters, 1:3 (2015)
• Nakamura, R., Tsukahara, T., Qu, W., Ichikawa, K., Otsuka, T., Ogoshi, K., Saito, T.L., Matsushima, K., Sugano, S., Hashimoto, S., Suzuki, Y., Morishita, S. & Takeda, H. Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates. Development 141, 2568-2580 (2014).
• Matsuo, M., Shimada, A., Koshida, S., Saga, Y. & Takeda, H. The establishment of rotational polarity in the airway and ependymal cilia: analysis with a novel cilium motility mutant mouse. Am J Physiol Lung Cell Mol Physiol, 304, L736-45 (2013).
• Shimada, A., Kawanishi, T., Kaneko, T., Yoshihara, H., Yano, T., Inohaya, K., Kinoshita, M., Kamei, Y., Tamura, K. & Takeda, H. Trunk exoskeleton in teleosts is mesodermal in origin. Nat Commun, 4, 1639 (2013).
• Kawanishi, T., Kaneko, T., Moriyama, Y., Kinoshita, M., Yokoi, H., Suzuki, T., Shimada, A. & Takeda, H. Modular development of the teleost trunk along the dorsoventral axis and zic1/zic4 as selector genes in the dorsal module. Development, 140, 1486-96 (2013).
• Sato, A. & Takeda, H. Neuronal subtypes are specified by the level of neurod expression in the zebrafish lateral line.
  J Neurosci, 33, 556-62 (2013).
  
• Moriyama, Y., Kawanishi, T., Nakamura, R., Tsukahara, T., Sumiyama, K., Suster, M.L., Kawakami, K., Toyoda, A., Fujiyama, A., Yasuoka, Y., Nagao, Y., Sawatari, E., Shimizu, A., Wakamatsu, Y., Hibi, M., Taira, M., Okabe, M., Naruse, K., Hashimoto, H., Shimada, A. & Takeda, H. The medaka zic1/zic4 mutant provides molecular insights into teleost caudal fin evolution. Curr Biol, 22, 601-7 (2012).
• Kamura, K., Kobayashi, D., Uehara, U., Koshida, S., Iijima, N., Kudo, A., Yokoyama T. & Takeda, H. Pkd1l1 complexes with Pkd2 on motile cilia and functions to establish the left-right axis. Development, 138, 1121-9 (2011).
• Takeda H. & Shimada, A. The art of medaka genetics and genomics:what makes them so unique? Ann Rev Genet, 44, 217 - 241. (2010)
• Sato, A., Koshida, S. & Takeda, H. Single-cell analysis of somatotopic map formation in the zebrafish lateral line system. Dev Dyn, 239, 2058-65. (2010).
• Ishimatsu, K., Takamatsu, A. & Takeda, H. Emergence of traveling wave in the zebrafish segmentation clock. Development, 137, 1595-9. (2010).
• Tsuda, S., Kitagawa, T., Takashima, S., Asakawa, S., Shimizu, N., Mitani, H., Shima, A., Tsutsumi, M., Hori, H., Naruse, K., Ishikawa, Y. & Takeda, H. FAK-mediated extracellular signals are essential for interkinetic nuclear migration and planar divisions in the neuroepithelium. J Cell Sci, 123, 484-96. (2010).
• Sano, S., Takashima, S., Niwa, H., Yokoi, H., Shimada, A., Arenz, A., Wittbrodt, J. & Takeda, H. Characterization of teleost Mdga1 using a gene-trap approach in medaka (Oryzias latipes). Genesis, 47, 505-513. (2009).
• Sasaki, S., Mello, C. C., Shimada, A., Nakatani, Y., Hashimoto, S., Ogawa, M., Matsushima, K., Gu, S. G., Kasahara, M., Ahsan, B., Sasaki, A., Saito, T., Suzuki, Y., Sugano, S., Kohara, Y., Takeda, H., Fire, A. & Morishita, S. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science, 323, 401-4. (2009).
  
• Omran, H., Kobayashi, D., Olbrich, H., Tsukahara, T., Loges, N. T., Hagiwara, H., Zhang, Q., Leblond, G., Toole, E. O’, Hara, C., Mizuno, H., Kawano, H., Fliegauf, M., Yagi, T., Koshida, S., Miyawaki, A., Zentgraf, H., Seithe, H., Reinhardt, R. , Watanabe, Y., Kamiya, R., Mitchell, D. R., & Takeda, H. Ktu/PF13 is required for cytoplasmic pre-assembly of axonemal dyneins. Nature , 456, 611-616, (2008).
• Takashima, S., Kage, T., Yasuda, T., Inohaya, K., Maruyama, K., Araki, K., Takeda, H., & Ishikawa, Y. Phenotypic analyses of a medaka mutant reveal the importance of bilaterally synchronized expression of isthmic fgf8 for bilaterally symmetric formation of the optic tectum. Genesis, 46, 537-45. (2008).
• Miyake, A., Higashijima, S., Kobayashi, D., Narita, T., Jindo, T., Setiamarga, D.,H., E., Ohisa, S., Orihara, N., Hibiya, K., Konno, S., Sakaguchi, S., Horie, K., Imai, Y., Naruse, K., Kudo, A., & Takeda, H. A mutation in the abcb7 gene causes abnormal iron and fatty acid metabolism in developing medaka fish. Dev Growth Differ, 50, 703-16. (2008).
• Shimada, A. & Takeda, H. Production of a maternal-zygotic medaka mutant using hybrid sterility. Dev Growth Differ, 50, 421-426. (2008).
  
• Takeda, H. Draft genome of the medaka fish: A comprehensive resource for medaka developmental genetics and vertebrate evolutionary biology. Develop. Growth Differ. 50, S157?S166. (2008).
  
• Shimada, A., Yabusaki, M., Niwa, H., Yokoi, H., Hatta, K., Kobayashi, D. & Takeda, H. Maternal-zygotic medaka mutants for fgfr1 reveal its essential role in the migration of the axial mesoderm but not the lateral mesoderm. Development, 135, 281-90. (2008).
• Nagayoshi, S., Hayashi, E., Abe, G., Osato, N., Asakawa, K., Urasaki, A., Horikawa, K., Ikeo, K., Takeda, H. & Kawakami, K. Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes: tcf7 and synembryn-like. Development, 135, 159-69. (2008).
• Ahsan, B., Kobayashi, D., Yamada, T., Kasahara, M., Sasaki, S., Saito, T. L., Nagayasu, Y., Doi, K., Nakatani, Y., Qu, W., Jindo, T., Shimada, A., Naruse, K., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu, N., Hashimoto, S., Yang, J., Lee, Y., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T., Shin, I. T., Takeda, H., Kohara, Y. & Morishita, S. UTGB/medaka: genomic resource database for medaka biology. Nucleic Acids Res, 36, D747-52. (2008).
• Yokoi, H., Shimada, A., Carl, M., Takashima, S., Kobayashi, D., Narita, T., Jindo, T., Kimura, T., Kitagawa, T., Kage, T., Sawada, A., Naruse, K., Asakawa, S., Shimizu, N., Mitani, H., Shima, A., Tsutsumi, M., Hori, H., Wittbrodt, J., Saga, Y., Ishikawa, Y., Araki, K. & Takeda, H. Mutant analyses reveal different functions of fgfr1 in medaka and zebrafish despite conserved ligand-receptor relationships. Dev Biol, 304, 326-37. (2007).
• Takashima, S., Shimada, A., Kobayashi, D., Yokoi, H., Narita, T., Jindo, T., Kage, T., Kitagawa, T., Kimura, T., Sekimizu, K., Miyake, A., Setiamarga, D. H., Murakami, R., Tsuda, S., Ooki, S., Kakihara, K., Hojo, M., Naruse, K., Mitani, H., Shima, A., Ishikawa, Y., Araki, K., Saga, Y. & Takeda, H. Phenotypic analysis of a novel chordin mutant in medaka. Dev Dyn, 236, 2298-310. (2007).
• Sekimizu, K., Tagawa, M. & Takeda, H. Defective Fin Regeneration in Medaka Fish (Oryzias latipes) with Hypothyroidism. Zoolog Sci, 24, 693-9. (2007).
• Sasaki, T., Shimizu, A., Ishikawa, S. K., Imai, S., Asakawa, S., Murayama, Y., Khorasani, M. Z., Mitani, H., Furutani-Seiki, M., Kondoh, H., Nanda, I., Schmid, M., Schartl, M., Nonaka, M., Takeda, H., Hori, H., Himmelbauer, H., Shima, A. & Shimizu, N. The DNA sequence of medaka chromosome LG22. Genomics, 89, 124-33. (2007).
• Nakatani, Y., Takeda, H., Kohara, Y. & Morishita, S. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res, 17, 1254-65. (2007).
• Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan, B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo, T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu, N., Hashimoto, S., Yang, J., Lee, Y., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T., Shin, I. T., Takeda, H., Morishita, S. & Kohara, Y. The medaka draft genome and insights into vertebrate genome evolution. Nature, 447, 714-9. (2007).
• Ishimatsu, K., Horikawa, K. & Takeda, H. Coupling cellular oscillators: a mechanism that maintains synchrony against developmental noise in the segmentation clock. Dev Dyn, 236, 1416-21. (2007).
• Ishikawa, Y., Yamamoto, N., Yoshimoto, M., Yasuda, T., Maruyama, K., Kage, T., Takeda, H. & Ito, H. Developmental origin of diencephalic sensory relay nuclei in teleosts. Brain Behav Evol, 69, 87-95. (2007).
• Hojo, M., Takashima, S., Kobayashi, D., Sumeragi, A., Shimada, A., Tsukahara, T., Yokoi, H., Narita, T., Jindo, T., Kage, T., Kitagawa, T., Kimura, T., Sekimizu, K., Miyake, A., Setiamarga, D., Murakami, R., Tsuda, S., Ooki, S., Kakihara, K., Naruse, K. & Takeda, H. Right-elevated expression of charon is regulated by fluid flow in medaka Kupffer's vesicle. Dev Growth Differ, 49, 395-405. (2007).
• Terasaki, H., Murakami, R., Yasuhiko, Y., Shin, I. T., Kohara, Y., Saga, Y. & Takeda, H. Transgenic analysis of the medaka mesp-b enhancer in somitogenesis. Dev Growth Differ, 48, 153-68. (2006).
• Sakaguchi, T., Kikuchi, Y., Kuroiwa, A., Takeda, H. & Stainier, D. Y. The yolk syncytial layer regulates myocardial migration by influencing extracellular matrix assembly in zebrafish. Development, 133, 4063-72. (2006).
• Okuda, Y., Yoda, H., Uchikawa, M., Furutani-Seiki, M., Takeda, H., Kondoh, H. & Kamachi, Y. Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution. Dev Dyn. (2006).
• Kobayashi, D., Jindo, T., Naruse, K. & Takeda, H. Development of the endoderm and gut in medaka, Oryzias latipes. Dev Growth Differ, 48, 283-95. (2006).
• Islam, M. E., Kikuta, H., Inoue, F., Kanai, M., Kawakami, A., Parvin, M. S., Takeda, H. & Yamasu, K. Three enhancer regions regulate gbx2 gene expression in the isthmic region during zebrafish development. Mech Dev, 123, 907-24. (2006).
• Horikawa, K., Ishimatsu, K., Yoshimoto, E., Kondo, S. & Takeda, H. Noise-resistant and synchronized oscillation of the segmentation clock. Nature, 441, 719-23. (2006).
• Shimoda, N., Yamakoshi, K., Miyake, A. & Takeda, H. Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene. Dev Dyn, 233, 1509-16. (2005).
• Murayama, E., Herbomel, P., Kawakami, A., Takeda, H. & Nagasawa, H. Otolith matrix proteins OMP-1 and Otolin-1 are necessary for normal otolith growth and their correct anchoring onto the sensory maculae. Mech Dev, 122, 791-803. (2005).
• Kimura, T., Yoshida, K., Shimada, A., Jindo, T., Sakaizumi, M., Mitani, H., Naruse, K., Takeda, H., Inoko, H., Tamiya, G. & Shinya, M. Genetic linkage map of medaka with polymerase chain reaction length polymorphisms. Gene, 363, 24-31. (2005).
• Kawakami, A., Nojima, Y., Toyoda, A., Takahoko, M., Satoh, M., Tanaka, H., Wada, H., Masai, I., Terasaki, H., Sakaki, Y., Takeda, H. & Okamoto, H. The zebrafish-secreted matrix protein you/scube2 is implicated in long-range regulation of hedgehog signaling. Curr Biol, 15, 480-8. (2005).
• Kawahara, A., Che, Y. S., Hanaoka, R., Takeda, H. & Dawid, I. B. Zebrafish GADD45beta genes are involved in somite segmentation. Proc Natl Acad Sci U S A, 102, 361-6. (2005).
• Tanaka, K., Ohisa, S., Orihara, N., Sakaguchi, S., Horie, K., Hibiya, K., Konno, S., Miyake, A., Setiamarga, D., Takeda, H., Imai, Y. & Kudo, A. Characterization of mutations affecting embryonic hematopoiesis in the medaka, Oryzias latipes. Mech Dev, 121, 739-46. (2004).
• Sekimizu, K., Nishioka, N., Sasaki, H., Takeda, H., Karlstrom, R. O. & Kawakami, A. The zebrafish iguana locus encodes Dzip1, a novel zinc-finger protein required for proper regulation of Hedgehog signaling. Development, 131, 2521-32. (2004).
• Ohtsuka, M., Kikuchi, N., Yokoi, H., Kinoshita, M., Wakamatsu, Y., Ozato, K., Takeda, H., Inoko, H. & Kimura, M. Possible roles of zic1 and zic4, identified within the medaka Double anal fin (Da) locus, in dorsoventral patterning of the trunk-tail region (related to phenotypes of the Da mutant). Mech Dev 121, 873-82. (2004).
• Naruse, K., Hori, H., Shimizu, N., Kohara, Y. & Takeda, H. Medaka genomics: a bridge between mutant phenotype and gene function. Mech Dev, 121, 619-28. (2004).
• Kimura, T., Jindo, T., Narita, T., Naruse, K., Kobayashi, D., Shin, I. T., Kitagawa, T., Sakaguchi, T., Mitani, H., Shima, A., Kohara, Y. & Takeda, H. Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics. Mech Dev, 121, 915-32. (2004).
• Kawakami, A., Fukazawa, T. & Takeda, H. Early fin primordia of zebrafish larvae regenerate by a similar growth control mechanism with adult regeneration. Dev Dyn, 231, 693-9. (2004).
• Kage, T., Takeda, H., Yasuda, T., Maruyama, K., Yamamoto, N., Yoshimoto, M., Araki, K., Inohaya, K., Okamoto, H., Yasumasu, S., Watanabe, K., Ito, H. & Ishikawa, Y. Morphogenesis and regionalization of the medaka embryonic brain. J Comp Neurol, 476, 219-39. (2004).
• Takeuchi, M., Nakabayashi, J., Sakaguchi, T., Yamamoto, T. S., Takahashi, H., Takeda, H. & Ueno, N. The prickle-related gene in vertebrates is essential for gastrulation cell movements. Curr Biol, 13, 674-9. (2003).
• Yokoi, H., Kobayashi, T., Tanaka, M., Nagahama, Y., Wakamatsu, Y., Takeda, H., Araki, K., Morohashi, K. & Ozato, K. Sox9 in a teleost fish, medaka (Oryzias latipes): evidence for diversified function of Sox9 in gonad differentiation. Mol Reprod Dev, 63, 5-16. (2002).
• Tonou-Fujimori, N., Takahashi, M., Onodera, H., Kikuta, H., Koshida, S., Takeda, H. & Yamasu, K. Expression of the FGF receptor 2 gene (fgfr2) during embryogenesis in the zebrafish Danio rerio. Gene Expr Patterns, 2, 183-8. (2002).
• Picker, A., Scholpp, S., Bohli, H., Takeda, H. & Brand, M. A novel positive transcriptional feedback loop in midbrain-hindbrain boundary development is revealed through analysis of the zebrafish pax2.1 promoter in transgenic lines. Development, 129, 3227-39. (2002).
• Nomura-Kitabayashi, A., Takahashi, Y., Kitajima, S., Inoue, T., Takeda, H. & Saga, Y. Hypomorphic Mesp allele distinguishes establishment of rostrocaudal polarity and segment border formation in somitogenesis. Development, 129, 2473-81. (2002).
• Nikaido, M., Kawakami, A., Sawada, A., Furutani-Seiki, M., Takeda, H. & Araki, K. Tbx24, encoding a T-box protein, is mutated in the zebrafish somite-segmentation mutant fused somites. Nat Genet, 31, 195-9. (2002).
• Koshida, S., Shinya, M., Nikaido, M., Ueno, N., Schulte-Merker, S., Kuroiwa, A. & Takeda, H. Inhibition of BMP activity by the FGF signal promotes posterior neural development in zebrafish. Dev Biol, 244, 9-20. (2002).
• Holley, S. A. & Takeda, H. Catching a wave: the oscillator and wavefront that create the zebrafish somite. Semin Cell Dev Biol, 13, 481-8. (2002).
• Fujii, H., Nagai, T., Shirasawa, H., Doi, J. Y., Yasui, K., Nishimatsu, S., Takeda, H. & Sakai, M. Anteroposterior patterning in Xenopus embryos: egg fragment assay system reveals a synergy of dorsalizing and posteriorizing embryonic domains. Dev Biol, 252, 15-30. (2002).
• Shinya, M., Koshida, S., Sawada, A., Kuroiwa, A. & Takeda, H. Fgf signalling through MAPK cascade is required for development of the subpallial telencephalon in zebrafish embryos. Development, 128, 4153-64. (2001).
• Sawada, A., Shinya, M., Jiang, Y. J., Kawakami, A., Kuroiwa, A. & Takeda, H. Fgf/MAPK signalling is a crucial positional cue in somite boundary formation. Development, 128, 4873-80. (2001).
• Sakaguchi, T., Kuroiwa, A. & Takeda, H. A novel sox gene, 226D7, acts downstream of Nodal signaling to specify endoderm precursors in zebrafish. Mech Dev, 107, 25-38. (2001).
  
• Sakaguchi, T., Kuroiwa, A. & Takeda, H. Expression of zebrafish btg-b, an anti-proliferative cofactor, during early embryogenesis. Mech Dev, 104, 113-5. (2001).
• Saga, Y. & Takeda, H. The making of the somite: molecular events in vertebrate segmentation. Nat Rev Genet, 2, 835-45. (2001).
• Haraguchi, S., Kitajima, S., Takagi, A., Takeda, H., Inoue, T. & Saga, Y. Transcriptional regulation of Mesp1 and Mesp2 genes: differential usage of enhancers during development. Mech Dev, 108, 59-69. (2001).
• Sawada, A., Fritz, A., Jiang, Y. J., Yamamoto, A., Yamasu, K., Kuroiwa, A., Saga, Y. & Takeda, H. Zebrafish Mesp family genes, mesp-a and mesp-b are segmentally expressed in the presomitic mesoderm, and Mesp-b confers the anterior identity to the developing somites. Development, 127, 1691-702. (2000).
• Kondoh, H., Uchikawa, M., Yoda, H., Takeda, H., Furutani-Seiki, M. & Karlstrom, R. O. Zebrafish mutations in Gli-mediated hedgehog signaling lead to lens transdifferentiation from the adenohypophysis anlage. Mech Dev, 96, 165-74. (2000).
• Amanuma, K., Takeda, H., Amanuma, H. & Aoki, Y. Transgenic zebrafish for detecting mutations caused by compounds in aquatic environments. Nat Biotechnol, 18, 62-5. (2000).
• Shinya, M., Furutani-Seiki, M., Kuroiwa, A. & Takeda, H. Mosaic analysis with oep mutant reveals a repressive interaction between floor-plate and non-floor-plate mutant cells in the zebrafish neural tube. Dev Growth Differ, 41, 135-42. (1999).
• Rodaway, A., Takeda, H., Koshida, S., Broadbent, J., Price, B., Smith, J. C., Patient, R. & Holder, N. Induction of the mesendoderm in the zebrafish germ ring by yolk cell-derived TGF-beta family signals and discrimination of mesoderm and endoderm by FGF. Development, 126, 3067-78. (1999).
• Nikaido, M., Tada, M., Takeda, H., Kuroiwa, A. & Ueno, N. In vivo analysis using variants of zebrafish BMPR-IA: range of action and involvement of BMP in ectoderm patterning. Development, 126, 181-90. (1999).
• Mizuno, T., Yamaha, E., Kuroiwa, A. & Takeda, H. Removal of vegetal yolk causes dorsal deficencies and impairs dorsal-inducing ability of the yolk cell in zebrafish. Mech Dev, 81, 51-63. (1999).
• Mizuno, T., Shinya, M. & Takeda, H. Cell and tissue transplantation in zebrafish embryos. Methods Mol Biol, 127, 15-28. (1999).
  
• Yamanaka, Y., Mizuno, T., Sasai, Y., Kishi, M., Takeda, H., Kim, C. H., Hibi, M., Hirano, T. A novel homeobox gene, dharma, can induce the organizer in a non-cell-autonomous manner. Genes Dev, 12, 2345-53. (1998).
• Yamaha, E., Mizuno, T., Hasebe, Y., Takeda, H. & Yamazaki, F. Dorsal specification in blastoderm at the blastula stage in the goldfish, Carassius auratus. Dev Growth Differ, 40, 267-75. (1998).
• Makita, R., Mizuno, T., Koshida, S., Kuroiwa, A. & Takeda, H. Zebrafish wnt11: pattern and regulation of the expression by the yolk cell and No tail activity. Mech Dev, 71, 165-76. (1998).
• Koshida, S., Shinya, M., Mizuno, T., Kuroiwa, A. & Takeda, H. Initial anteroposterior pattern of the zebrafish central nervous system is determined by differential competence of the epiblast. Development, 125, 1957-66. (1998).
• Kobayashi, M., Toyama, R., Takeda, H., Dawid, I. B. & Kawakami, K. Overexpression of the forebrain-specific homeobox gene six3 induces rostral forebrain enlargement in zebrafish. Development, 125, 2973-82. (1998).
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• Miyagawa, T., Amanuma, H., Kuroiwa, A. & Takeda, H. Specification of posterior midbrain region in zebrafish neuroepithelium. Genes Cells 1, 369-77. (1996).
• Takeda, H., Matsuzaki, T., Oki, T., Miyagawa, T. & Amanuma, H. A novel POU domain gene, zebrafish pou2: expression and roles of two alternatively spliced twin products in early development. Genes Dev 8, 45-59. (1994).
• Matsuzaki, T., Amanuma, H. & Takeda, H. A POU-domain gene of zebrafish, ZFPOU1, specifically expressed in the developing neural tissues. Biochem Biophys Res Commun 187, 1446-53. (1992).
  

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