動物発生学研究室

2023

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.

2022

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)

2021

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).

2020

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).

2019

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).

2018

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)

2017

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)

2016

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).

2015

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)

2014

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).

2013

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).

2012

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).

2011

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).

2010

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).

2009

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).


2008

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).

2007

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).

2006

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).

2005

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).

2004

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).

2003

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).

2002

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).

2001

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).

before 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).

Mizuno, T., Yamaha, E., Wakahara, M., Kuroiwa, A. & Takeda, H. Mesoderm induction in zebrafish. Nature, 383, 131-132. (1996).

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).

Publications from Irie group can be found here.

• 武田洋幸、相賀裕美子著　発生遺伝学　－脊椎動物のからだと器官のなりたち－　東大出版会　（2007）197頁
• 浅島誠・武田洋幸共編　「発生」　シリーズ21世紀の動物科学　5巻　培風館　237頁　　(2007）．　武田洋幸 - 小型魚類をモデルとした発生遺伝学の展開－初期体軸形成と分節性の確立を中心に - p. 74-112　（培風館）
• 武田洋幸　著　動物のからだづくり　－形態発生の分子メカニズム－　シリーズ応用動物科学・バイオサイエンス２　朝倉書店　（2001） (138頁)
  

• 武田洋幸、廣野雅文監修　細胞工学 vol.28 No.10 2009年10月号. 動くだけではない!? 繊毛の多彩な機能.
• 武田洋幸. メダカ変異体から軸糸ダイニン形成の普遍的メカニズムへ. 細胞工学 28. (2009).
• 武田洋幸. メダカゲノムの解読 - 進化・種分化の研究に光をあてる. 遺伝 62, 2-5. (2008).
• 武田洋幸. 小型魚類を通してみる脊椎動物の左右非対称性形成の遺伝的機構. 細胞工学 27, 559-563. (2008).
• 武田洋幸. メダカゲノムの解読. 蛋白質核酸酵素 53, 227-234. (2008).
• 武田洋幸、 堀川一樹. 分節時計が正確に時を刻むメカニズム－同調性とノイズ耐性. 蛋白質核酸酵素 52, 236-242. (2007).
• 武田洋幸, 成田貴則 and 小林大介. 小型魚類における発生遺伝学とゲノミクス. 実験医学増刊号 23, 175-180. (2005).
• 工藤明 and 武田洋幸. 序　注目を浴びる器官形成・疾患モデル：ゼブラフィッシュ＆メダカ。特集「ヒト疾患モデルとしてのゼブラフィッシュ＆メダカ」. 細胞工学 23, 14-16. (2004).
• 武田洋幸. 小型魚類の初期発生-ゼブラフィッシュの中・内胚葉形成を中心として. 「発生生物学がわかる」（羊土社）, 168-173. (2003).
• 武田洋幸 and 相賀裕美子. FGFとNotchシグナルによる体節形成の制御. 細胞工学 21, 486-492. (2002).
• 武田洋幸 and 影山龍一郎. 特集「位置情報と境界形成を担うシグナル：器官形成の基本原理」“序：組織の中にコンパートメントを作る－位置情報と境界形成. 細胞工学 21, 465-463. (2002).
• 武田洋幸. 波と分節. 蛋白質核酸酵素 47, 2017-2023. (2002).
• 成瀬清 and 武田洋幸. ゲノム時代を泳ぎ抜く－　小型魚類. 細胞工学 22, 55-62. (2002).
  澤田篤志, 相賀裕美子 and 武田洋幸. 体節の形成と分化. 蛋白質核酸酵素 45, 2766-2773. (2000).
• 新屋みのり, 武田洋幸 and 恭, 弥. 神経誘導と神経組織の体軸に沿ったパターニン. 蛋白質核酸酵素 45, 2738-2744. (2000).
• 武田洋幸. ゼブラフィッシュの系統保存. 蛋白質核酸酵素 44, 803-806. (1999).
• 武田洋幸. ゼブラフィッシュの現状 - 突然変異体から遺伝子へ. 医学のあゆみ 185, 395-398. (1999).
• 武田洋幸. ゼブラフィッシュ. 遺伝 52, 68-71. (1998).
• 武田洋幸, 新屋みのり and 越田澄人. 頭部神経は外胚葉の前方でしか誘導されない－ゼブラフィッシュ外胚葉の応答能の差－. 細胞工学 16, 373-381. (1997).
• 天沼喜美子, 浜田康夫 and 武田洋幸. ゼブラフィッシュにおける外来遺伝子導入系. 蛋白質核酸酵素 40, 2257-2264. (1995).
• 武田洋幸. 実験動物としてのゼブラフィッシュと遺伝子導入. Molecular Medicine 増刊号「疾患モデルマウス」, 21. (1994).
• 武田洋幸. コールドスプリングハーバー Lab. ミーティング「Zebrafish Development and Genetics」に参加して. 実験医学 12, 1676-1677. (1994).
• 武田洋幸, 松崎貴 and 天沼宏. ゼブラフィッシュ初期発生と POU 転写因子. 実験医学 11, 1619-1625. (1993).
• 武田洋幸. ゼブラフィッシュ－中枢神経系発生の脊椎モデル動物として. 実験医学 11, 65-68. (1991).
  
  

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