Research Center for Transomics Medicine

Research Output

The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis

Abdalla, M. O. A., Yamamoto, T., Maehara, K., Nogami, J., Ohkawa, Y., Miura, H., Poonperm, R., Hiratani, I., Nakayama, H., Nakao, M. & Saitoh, N., Dec 1 2019, In : Nature communications. 10, 1, 3778.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

The finding of a group IIE phospholipase A2 gene in a specified segment of Protobothrops flavoviridis genome and its possible evolutionary relationship to group IIA phospholipase A2 genes

Yamaguchi, K., Chijiwa, T., Ikeda, N., Shibata, H., Fukumaki, Y., Oda-Ueda, N., Hattori, S. & Ohno, M., Jan 1 2014, In : Toxins. 6, 12, p. 3471-3487 17 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

The habu genome reveals accelerated evolution of venom protein genes

Shibata, H., Chijiwa, T., Oda-Ueda, N., Nakamura, H., Yamaguchi, K., Hattori, S., Matsubara, K., Matsuda, Y., Yamashita, A., Isomoto, A., Mori, K., Tashiro, K., Kuhara, S., Yamasaki, S., Fujie, M., Goto, H., Koyanagi, R., Takeuchi, T., Fukumaki, Y., Ohno, M. & 4 others, Shoguchi, E., Hisata, K., Satoh, N. & Ogawa, T., Dec 1 2018, In : Scientific reports. 8, 1, 11300.

Research output: Contribution to journalArticle

13 Citations (Scopus)

The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family

Goto, H., Watanabe, K., Araragi, N., Kageyama, R., Tanaka, K., Kuroki, Y., Toyoda, A., Hattori, M., Sakaki, Y., Fujiyama, A., Fukumaki, Y. & Shibata, H., Oct 12 2009, In : BMC Evolutionary Biology. 9, 1, 224.

Research output: Contribution to journalArticle

11 Citations (Scopus)

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

Suryamohan, K., Krishnankutty, S. P., Guillory, J., Jevit, M., Schröder, M. S., Wu, M., Kuriakose, B., Mathew, O. K., Perumal, R. C., Koludarov, I., Goldstein, L. D., Senger, K., Dixon, M. D., Velayutham, D., Vargas, D., Chaudhuri, S., Muraleedharan, M., Goel, R., Chen, Y. J. J., Ratan, A. & 22 others, Liu, P., Faherty, B., de la Rosa, G., Shibata, H., Baca, M., Sagolla, M., Ziai, J., Wright, G. A., Vucic, D., Mohan, S., Antony, A., Stinson, J., Kirkpatrick, D. S., Hannoush, R. N., Durinck, S., Modrusan, Z., Stawiski, E. W., Wiley, K., Raudsepp, T., Kini, R. M., Zachariah, A. & Seshagiri, S., Jan 1 2020, In : Nature genetics. 52, 1, p. 106-117 12 p.

Research output: Contribution to journalArticle

Open Access

The jpost environment: An integrated proteomics data repository and database

Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Matsumoto, M., Takami, T., Kobayashi, D., Yamanouchi, Y., Araki, N., Yoshizawa, A. C., Tabata, T., Iwasaki, M., Sugiyama, N., Tanaka, S., Goto, S. & Ishihama, Y., Jan 8 2019, In : Nucleic acids research. 47, D1, p. D1218-D1224

Research output: Contribution to journalArticle

8 Citations (Scopus)

The LTB4-BLT1 axis mediates neutrophil infiltration and secondary injury in experimental spinal cord injury

Saiwai, H., Ohkawa, Y., Yamada, H., Kumamaru, H., Harada, A., Okano, H., Yokomizo, T., Iwamoto, Y. & Okada, S., May 2010, In : American Journal of Pathology. 176, 5, p. 2352-2366 15 p.

Research output: Contribution to journalArticle

98 Citations (Scopus)

The novel heart-specific RING finger protein 207 is involved in energy metabolism in cardiomyocytes

Mizushima, W., Takahashi, H., Watanabe, M., Kinugawa, S., Matsushima, S., Takada, S., Yokota, T., Furihata, T., Matsumoto, J., Tsuda, M., Chiba, I., Nagashima, S., Yanagi, S., Matsumoto, M., Nakayama, K. I., Tsutsui, H. & Hatakeyama, S., Nov 1 2016, In : Journal of Molecular and Cellular Cardiology. 100, p. 43-53 11 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

The novel heme-dependent inducible protein, SRRD regulates heme biosynthesis and circadian rhythms

Adachi, Y., Umeda, M., Kawazoe, A., Sato, T., Ohkawa, Y., Kitajima, S., Izawa, S., Sagami, I. & Taketani, S., Oct 1 2017, In : Archives of Biochemistry and Biophysics. 631, p. 19-29 11 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

The ortholog of human ataxin-2 is essential for early embryonic patterning in C. elegans

Kiehl, T. R., Shibata, H. & Pulst, S. M., Jan 1 2000, In : Journal of Molecular Neuroscience. 15, 3, p. 231-241 11 p.

Research output: Contribution to journalArticle

41 Citations (Scopus)

The pericentromeric protein shugoshin 2 cooperates with HSF1 in heat shock response and RNA Pol II recruitment

Takii, R., Fujimoto, M., Matsumoto, M., Srivastava, P., Katiyar, A., Nakayama, K. I. & Nakai, A., Dec 16 2019, In : EMBO Journal. 38, 24, e102566.

Research output: Contribution to journalArticle

1 Citation (Scopus)

The PPARγ locus makes long-range chromatin interactions with selected tissue-specific gene loci during adipocyte differentiation in a protein kinase a dependent manner

LeBlanc, S. E., Wu, Q., Barutcu, A. R., Xiao, H., Ohkawa, Y. & Imbalzano, A. N., Jan 20 2014, In : PloS one. 9, 1, e86140.

Research output: Contribution to journalArticle

10 Citations (Scopus)

The prehistoric peopling of Southeast Asia

McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Víctor Moreno-Mayar, J., Van Driem, G., Wilken, U. G., Seguin-Orlando, A., De la Fuente Castro, C., Wasef, S., Shoocongdej, R., Souksavatdy, V., Sayavongkhamdy, T., Saidin, M. M., Allentoft, M. E., Sato, T., Malaspinas, A. S., Aghakhanian, F. A., Korneliussen, T. & 46 others, Prohaska, A., Margaryan, A., De Barros Damgaard, P., Kaewsutthi, S., Lertrit, P., Nguyen, T. M. H., Hung, H. C., Tran, T. M., Truong, H. N., Nguyen, G. H., Shahidan, S., Wiradnyana, K., Matsumae, H., Shigehara, N., Yoneda, M., Ishida, H., Masuyama, T., Yamada, Y., Tajima, A., Shibata, H., Toyoda, A., Hanihara, T., Nakagome, S., Deviese, T., Bacon, A. M., Duringer, P., Ponche, J. L., Shackelford, L., Patole-Edoumba, E., Nguyen, A. T., Bellina-Pryce, B., Galipaud, J. C., Kinaston, R., Buckley, H., Pottier, C., Rasmussen, S., Higham, T., Foley, R. A., Lahr, M. M., Orlando, L., Sikora, M., Phipps, M. E., Oota, H., Higham, C., Lambert, D. M. & Willerslev, E., Jul 6 2018, In : Science. 361, 6397, p. 88-92 5 p.

Research output: Contribution to journalArticle

36 Citations (Scopus)

The promise of targeted proteomics for quantitative network biology

Matsumoto, M. & Nakayama, K., Dec 1 2018, In : Current Opinion in Biotechnology. 54, p. 88-97 10 p.

Research output: Contribution to journalReview article

7 Citations (Scopus)

Therapeutic activities of engrafted neural stem/precursor cells are not dormant in the chronically injured spinal cord

Kumamaru, H., Saiwai, H., Kubota, K., Kobayakawa, K., Yokota, K., Ohkawa, Y., Shiba, K., Iwamoto, Y. & Okada, S., Aug 1 2013, In : STEM CELLS. 31, 8, p. 1535-1547 13 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

The requirement of Mettl3-promoted MyoD mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation

Kudou, K., Komatsu, T., Nogami, J., Maehara, K., Harada, A., Saeki, H., Oki, E., Maehara, Y. & Ohkawa, Y., Jan 1 2017, In : Open Biology. 7, 9, 170119.

Research output: Contribution to journalArticle

12 Citations (Scopus)

The role of galanin in the differentiation of mucosal mast cells in mice

Yamaguchi, T., Ikeda, Y., Tashiro, K., Ohkawa, Y. & Kawabata, K., Jan 1 2020, In : European Journal of Immunology. 50, 1, p. 110-118 9 p.

Research output: Contribution to journalArticle

The role of Mediator and Little Elongation Complex in transcription termination

Takahashi, H., Ranjan, A., Chen, S., Suzuki, H., Shibata, M., Hirose, T., Hirose, H., Sasaki, K., Abe, R., Chen, K., He, Y., Zhang, Y., Takigawa, I., Tsukiyama, T., Watanabe, M., Fujii, S., Iida, M., Yamamoto, J., Yamaguchi, Y., Suzuki, Y. & 10 others, Matsumoto, M., Nakayama, K. I., Washburn, M. P., Saraf, A., Florens, L., Sato, S., Tomomori-Sato, C., Conaway, R. C., Conaway, J. W. & Hatakeyama, S., Dec 1 2020, In : Nature communications. 11, 1, 1063.

Research output: Contribution to journalArticle

Open Access

The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands

Shibata, H., Chijiwa, T., Hattori, S., Terada, K., Ohno, M. & Fukumaki, Y., Aug 1 2016, In : Molecular Phylogenetics and Evolution. 101, p. 91-100 10 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Thymine DNA glycosylase modulates DNA damage response and gene expression by base excision repair-dependent and independent mechanisms

Nakamura, T., Murakami, K., Tada, H., Uehara, Y., Nogami, J., Maehara, K., Ohkawa, Y., Saitoh, H., Nishitani, H., Ono, T., Nishi, R., Yokoi, M., Sakai, W. & Sugasawa, K., Apr 1 2017, In : Genes to Cells. 22, 4, p. 392-405 14 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Tissue-specific expression of histone H3 variants diversified after species separation

Maehara, K., Harada, A., Sato, Y., Matsumoto, M., Nakayama, K. I., Kimura, H. & Ohkawa, Y., Sep 17 2015, In : Epigenetics and Chromatin. 8, 1, 35.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding

Hosokawa, H., Ungerbäck, J., Wang, X., Matsumoto, M., Nakayama, K. I., Cohen, S. M., Tanaka, T. & Rothenberg, E. V., Jun 19 2018, In : Immunity. 48, 6, p. 1119-1134.e7

Research output: Contribution to journalArticle

20 Citations (Scopus)

Transcriptome profiling of refractory atopic keratoconjunctivitis by RNA sequencing

Matsuda, A., Asada, Y., Suita, N., Iwamoto, S., Hirakata, T., Yokoi, N., Ohkawa, Y., Okada, Y., Yokomizo, T. & Ebihara, N., Apr 2019, In : Journal of Allergy and Clinical Immunology. 143, 4, p. 1610-1614.e6

Research output: Contribution to journalArticle

1 Citation (Scopus)

Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks

Kawata, K., Hatano, A., Yugi, K., Sano, T., Fujii, M., Tomizawa, Y., Kokaji, T., Tanaka, K. Y., Uda, S., Suzuki, Y., Matsumoto, M., Nakayama, K., Saitoh, K., Kato, K., Ueno, A., Ohishi, M., Hirayama, A., Soga, T. & Kuroda, S., 2018, In : iScience. 7, p. 212-229

Research output: Contribution to journalArticle

Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks

Kawata, K., Hatano, A., Yugi, K., Kubota, H., Sano, T., Fujii, M., Tomizawa, Y., Kokaji, T., Tanaka, K. Y., Uda, S., Suzuki, Y., Matsumoto, M., Nakayama, K. I., Saitoh, K., Kato, K., Ueno, A., Ohishi, M., Hirayama, A., Soga, T. & Kuroda, S., Sep 28 2018, In : iScience. 7, p. 212-229 18 p.

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers

Yugi, K., Kubota, H., Hatano, A. & Kuroda, S., Apr 1 2016, In : Trends in biotechnology. 34, 4, p. 276-290 15 p.

Research output: Contribution to journalReview article

94 Citations (Scopus)

Trans-omics Impact of Thymoproteasome in Cortical Thymic Epithelial Cells

Ohigashi, I., Tanaka, Y., Kondo, K., Fujimori, S., Kondo, H., Palin, A. C., Hoffmann, V., Kozai, M., Matsushita, Y., Uda, S., Motosugi, R., Hamazaki, J., Kubota, H., Murata, S., Tanaka, K., Katagiri, T., Kosako, H. & Takahama, Y., Nov 26 2019, In : Cell Reports. 29, 9, p. 2901-2916.e6

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

Tricarboxylic acid cycle activity suppresses acetylation of mitochondrial proteins during early embryonic development in Caenorhabditis elegans

Hada, K., Hirota, K., Inanobe, A., Kako, K., Miyata, M., Araoi, S., Matsumoto, M., Ohta, R., Arisawa, M., Daitoku, H., Hanada, T. & Fukamizu, A., Mar 1 2019, In : Journal of Biological Chemistry. 294, 9, p. 3091-3099 9 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

TRIM8 regulates Nanog via Hsp90β-mediated nuclear translocation of STAT3 in embryonic stem cells

Okumura, F., Okumura, A. J., Matsumoto, M., Nakayama, K. I. & Hatakeyama, S., Oct 1 2011, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1813, 10, p. 1784-1792 9 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Truncation mutants of ASXL1 observed in myeloid malignancies are expressed at detectable protein levels

Inoue, D., Matsumoto, M., Nagase, R., Saika, M., Fujino, T., Nakayama, K. I. & Kitamura, T., Mar 1 2016, In : Experimental Hematology. 44, 3, p. 172-176.e1

Research output: Contribution to journalArticle

24 Citations (Scopus)

Tyrosine pre-transfer RNA fragments are linked to p53-dependent neuronal cell death via PKM2

Inoue, M., Hada, K., Shiraishi, H., Yatsuka, H., Fujinami, H., Morisaki, I., Nishida, Y., Matsubara, E., Ishitani, T., Hanada, R., Matsumoto, M., Penninger, J. M., Ihara, K. & Hanada, T., May 7 2020, In : Biochemical and Biophysical Research Communications. 525, 3, p. 726-732 7 p.

Research output: Contribution to journalArticle

Ubiquitin-dependent degradation of IκBα is mediated by a ubiquitin ligase Skp1/Cul 1/F-box protein FWD1

Hatakeyama, S., Kitagawa, M., Nakayama, K., Shirane, M., Matsumoto, M., Hattori, K., Higashi, H., Nakano, H., Okumura, K., Onoé, K., Good, R. A. & Nakayama, K. I., Mar 30 1999, In : Proceedings of the National Academy of Sciences of the United States of America. 96, 7, p. 3859-3863 5 p.

Research output: Contribution to journalArticle

168 Citations (Scopus)

U-box protein carboxyl terminus of Hsc70-interacting protein (CHIP) mediates poly-ubiquitylation preferentially on four-repeat Tau and is involved in neurodegeneration of tauopathy

Hatakeyama, S., Matsumoto, M., Kamura, T., Murayama, M., Chui, D. H., Planel, E., Takahashi, R., Nakayama, K. I. & Takashima, A., Oct 1 2004, In : Journal of Neurochemistry. 91, 2, p. 299-307 9 p.

Research output: Contribution to journalArticle

91 Citations (Scopus)

Unique structure (construction and configuration) and evolution of the array of small serum protein genes of Protobothrops flavoviridis snake

Chijiwa, T., Inamaru, K., Takeuchi, A., Maeda, M., Yamaguchi, K., Shibata, H., Hattori, S., Oda-Ueda, N. & Ohno, M., Jul 5 2019, In : Bioscience reports. 39, 7, BSR20190560.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Use of on-line supercritical fluid extraction-supercritical fluid chromatography/tandem mass spectrometry to analyze disease biomarkers in dried serum spots compared with serum analysis using liquid chromatography/tandem mass spectrometry

Suzuki, M., Nishiumi, S., Kobayashi, T., Sakai, A., Iwata, Y., Uchikata, T., Izumi, Y., Azuma, T., Bamba, T. & Yoshida, M., May 30 2017, In : Rapid Communications in Mass Spectrometry. 31, 10, p. 886-894 9 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

UV damage-induced phosphorylation of HBO1 triggers CRL4DDB2-mediated degradation to regulate cell proliferation

Matsunuma, R., Niida, H., Ohhata, T., Kitagawa, K., Sakai, S., Uchida, C., Shiotani, B., Matsumoto, M., Nakayama, K. I., Ogura, H., Shiiya, N. & Kitagawa, M., Jan 1 2016, In : Molecular and cellular biology. 36, 3, p. 394-406 13 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Vascular remodeling induced by naturally occurring unsaturated lysophosphatidic acid in vivo

Yoshida, K., Nishida, W., Hayashi, K., Ohkawa, Y., Ogawa, A., Aoki, J., Arai, H. & Sobue, K., Oct 7 2003, In : Circulation. 108, 14, p. 1746-1752 7 p.

Research output: Contribution to journalArticle

88 Citations (Scopus)

VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases

Kamura, T., Maenaka, K., Kotoshiba, S., Matsumoto, M., Kohda, D., Conaway, R. C., Conaway, J. W. & Nakayama, K. I., Dec 15 2004, In : Genes and Development. 18, 24, p. 3055-3065 11 p.

Research output: Contribution to journalArticle

316 Citations (Scopus)

Widely-targeted quantitative lipidomics method by supercritical fluid chromatography triple quadrupole mass spectrometry

Takeda, H., Izumi, Y., Takahashi, M., Paxton, T., Tamura, S., Koike, T., Yu, Y., Kato, N., Nagase, K., Shiomi, M. & Bamba, T., Jan 1 2018, In : Journal of Lipid Research. 59, 7, p. 1283-1293 11 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)
2 Citations (Scopus)

Wnt signaling regulates left-right axis formation in the node of mouse embryos

Kitajima, K., Oki, S., Ohkawa, Y., Sumi, T. & Meno, C., Aug 15 2013, In : Developmental Biology. 380, 2, p. 222-232 11 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway

Adachi, S., Homoto, M., Tanaka, R., Hioki, Y., Murakami, H., Suga, H., Matsumoto, M., Nakayama, K. I., Hatta, T., Iemura, S. I. & Natsume, T., Jan 1 2014, In : Nucleic acids research. 42, 15, p. 10037-10049 13 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation

Villacorte, M., Suzuki, K., Hirasawa, A., Ohkawa, Y., Suyama, M., Maruyama, T., Aoki, D., Ogino, Y., Miyagawa, S., Terabayashi, T., Tomooka, Y., Nakagata, N. & Yamada, G., Jul 18 2013, In : Oncogene. 32, 29, p. 3477-3482 6 p.

Research output: Contribution to journalArticle

32 Citations (Scopus)