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ArticlesPeer ReviewedFull Text
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation
Author / Creator:Nakato, Ryuichiro ; Shirahige, Katsuhiko
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2017-03, Vol.18 (2), p.279-290
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HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data
Author / Creator:Wang, Jiankang ; Nakato, Ryuichiro
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2022-01, Vol.23 (1)
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Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity
Author / Creator:Tanaka, Shinya ; Ise, Wataru ; Inoue, Takeshi ; Ito, Ayako ; Ono, Chisato ; Shima, Yoshihito ; Sakakibara, Shuhei ; Nakayama, Manabu ; Fujii, Kentaro ; Miura, Ikuo ; Sharif, Jafar ; Koseki, Haruhiko ; Koni, Pandelakis A. ; Raman, Indu ; Li, Quan-Zhen ; Kubo, Masato ; Fujiki, Katsunori ; Nakato, Ryuichiro ; Shirahige, Katsuhiko ; Araki, Hiromitsu ; Miura, Fumihito ; Ito, Takashi ; Kawakami, Eiryo ; Baba, Yoshihiro ; Kurosaki, Tomohiro
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2020-08, Vol.21 (8), p.950-961
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PHOSPHATE exporter XPR1/SLC53A1 is required for the tumorigenicity of epithelial ovarian cancer
Author / Creator:Akasu‐Nagayoshi, Yoko ; Hayashi, Tomoatsu ; Kawabata, Ayako ; Shimizu, Naomi ; Yamada, Ai ; Yokota, Naoko ; Nakato, Ryuichiro ; Shirahige, Katsuhiko ; Okamoto, Aikou ; Akiyama, Tetsu
Publisher:England: John Wiley & Sons, Inc
Journal title:Cancer science, 2022-06, Vol.113 (6), p.2034-2043
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The HSF1–PARP13–PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis
Author / Creator:Fujimoto, Mitsuaki ; Takii, Ryosuke ; Takaki, Eiichi ; Katiyar, Arpit ; Nakato, Ryuichiro ; Shirahige, Katsuhiko ; Nakai, Akira
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2017-11, Vol.8 (1), p.1638-16, Article 1638
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Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation
Author / Creator:Wang, Jiankang ; Bando, Masashige ; Shirahige, Katsuhiko ; Nakato, Ryuichiro
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-06, Vol.13 (1), p.3218-3218, Article 3218
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HSF1 phosphorylation establishes an active chromatin state via the TRRAP–TIP60 complex and promotes tumorigenesis
Author / Creator:Fujimoto, Mitsuaki ; Takii, Ryosuke ; Matsumoto, Masaki ; Okada, Mariko ; Nakayama, Keiich I. ; Nakato, Ryuichiro ; Fujiki, Katsunori ; Shirahige, Katsuhiko ; Nakai, Akira
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-07, Vol.13 (1), p.4355-4355, Article 4355
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Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Author / Creator:Nakato, Ryuichiro ; Sakata, Toyonori ; Wang, Jiankang ; Nagai, Luis Augusto Eijy ; Nagaoka, Yuya ; Oba, Gina Miku ; Bando, Masashige ; Shirahige, Katsuhiko
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-09, Vol.14 (1), p.5647-5647, Article 5647
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Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin
Author / Creator:Izumi, Kosuke ; Nakato, Ryuichiro ; Zhang, Zhe ; Edmondson, Andrew C ; Noon, Sarah ; Dulik, Matthew C ; Rajagopalan, Ramakrishnan ; Venditti, Charles P ; Gripp, Karen ; Samanich, Joy ; Zackai, Elaine H ; Deardorff, Matthew A ; Clark, Dinah ; Allen, Julian L ; Dorsett, Dale ; Misulovin, Ziva ; Komata, Makiko ; Bando, Masashige ; Kaur, Maninder ; Katou, Yuki ; Shirahige, Katsuhiko ; Krantz, Ian D
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2015-04, Vol.47 (4), p.338-344
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MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress
Author / Creator:Bleuyard, Jean-Yves ; Fournier, Marjorie ; Nakato, Ryuichiro ; Couturier, Anthony M. ; Katou, Yuki ; Ralf, Christine ; Hester, Svenja S. ; Dominguez, Daniel ; Rhodes, Daniela ; Humphrey, Timothy C. ; Shirahige, Katsuhiko ; Esashi, Fumiko
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2017-07, Vol.114 (29), p.7671-7676
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A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS
Author / Creator:Zuin, Jessica ; Franke, Vedran ; van IJcken, Wilfred F. J. ; van der Sloot, Antoine ; Krantz, Ian D. ; van der Reijden, Michael I. J. A. ; Nakato, Ryuichiro ; Lenhard, Boris ; Wendt, Kerstin S.
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2014-02, Vol.10 (2), p.e1004153-e1004153
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ArticlesPeer ReviewedFull Text
Publisher Correction: Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity
Author / Creator:Tanaka, Shinya ; Ise, Wataru ; Inoue, Takeshi ; Ito, Ayako ; Ono, Chisato ; Shima, Yoshihito ; Sakakibara, Shuhei ; Nakayama, Manabu ; Fujii, Kentaro ; Miura, Ikuo ; Sharif, Jafar ; Koseki, Haruhiko ; Koni, Pandelakis A. ; Raman, Indu ; Li, Quan-Zhen ; Kubo, Masato ; Fujiki, Katsunori ; Nakato, Ryuichiro ; Shirahige, Katsuhiko ; Araki, Hiromitsu ; Miura, Fumihito ; Ito, Takashi ; Kawakami, Eiryo ; Baba, Yoshihiro ; Kurosaki, Tomohiro
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2020-12, Vol.21 (12), p.1611-1612
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The metabolic stress-activated checkpoint LKB1-MARK3 axis acts as a tumor suppressor in high-grade serous ovarian carcinoma
Author / Creator:Machino, Hidenori ; Kaneko, Syuzo ; Komatsu, Masaaki ; Ikawa, Noriko ; Asada, Ken ; Nakato, Ryuichiro ; Shozu, Kanto ; Dozen, Ai ; Sone, Kenbun ; Yoshida, Hiroshi ; Kato, Tomoyasu ; Oda, Katsutoshi ; Osuga, Yutaka ; Fujii, Tomoyuki ; von Keudell, Gottfried ; Saloura, Vassiliki ; Hamamoto, Ryuji
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2022-01, Vol.5 (1), p.39-39, Article 39
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The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement
Author / Creator:Jeppsson, Kristian ; Carlborg, Kristian K. ; Nakato, Ryuichiro ; Berta, Davide G. ; Lilienthal, Ingrid ; Kanno, Takaharu ; Lindqvist, Arne ; Brink, Maartje C. ; Dantuma, Nico P. ; Katou, Yuki ; Shirahige, Katsuhiko ; Sjögren, Camilla
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2014-10, Vol.10 (10), p.e1004680-e1004680
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The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR‐Cas9 screen
Author / Creator:Cona, Brandon ; Hayashi, Tomoatsu ; Yamada, Ai ; Shimizu, Naomi ; Yokota, Naoko ; Nakato, Ryuichiro ; Shirahige, Katsuhiko ; Akiyama, Tetsu
Publisher:England: John Wiley & Sons, Inc
Journal title:FEBS open bio, 2022-03, Vol.12 (3), p.582-593
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Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells
Author / Creator:Seong, Ki-Hyeon ; Ly, Nhung Hong ; Katou, Yuki ; Yokota, Naoko ; Nakato, Ryuichiro ; Murakami, Shinnosuke ; Hirayama, Akiyoshi ; Fukuda, Shinji ; Kang, Siu ; Soga, Tomoyoshi ; Shirahige, Katsuhiko ; Ishii, Shunsuke
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2020-05, Vol.3 (1), p.208-208, Article 208
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Cgaln: fast and space-efficient whole-genome alignment
Author / Creator:Nakato, Ryuichiro ; Gotoh, Osamu
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2010-04, Vol.11 (1), p.224-224, Article 224
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CRISPR/Cas9 Screening for Identification of Genes Required for the Growth of Ovarian Clear Cell Carcinoma Cells
Author / Creator:Kawabata, Ayako ; Hayashi, Tomoatsu ; Akasu-Nagayoshi, Yoko ; Yamada, Ai ; Shimizu, Naomi ; Yokota, Naoko ; Nakato, Ryuichiro ; Shirahige, Katsuhiko ; Okamoto, Aikou ; Akiyama, Tetsu
Publisher:MDPI
Journal title:Current issues in molecular biology, 2022-04, Vol.44 (4), p.1587-1596
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Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Author / Creator:Nakato, Ryuichiro ; Wada, Youichiro ; Nakaki, Ryo ; Nagae, Genta ; Katou, Yuki ; Tsutsumi, Shuichi ; Nakajima, Natsu ; Fukuhara, Hiroshi ; Iguchi, Atsushi ; Kohro, Takahide ; Kanki, Yasuharu ; Saito, Yutaka ; Kobayashi, Mika ; Izumi-Taguchi, Akashi ; Osato, Naoki ; Tatsuno, Kenji ; Kamio, Asuka ; Hayashi-Takanaka, Yoko ; Wada, Hiromi ; Ohta, Shinzo ; Aikawa, Masanori ; Nakajima, Hiroyuki ; Nakamura, Masaki ; McGee, Rebecca C. ; Heppner, Kyle W. ; Kawakatsu, Tatsuo ; Genno, Michiru ; Yanase, Hiroshi ; Kume, Haruki ; Senbonmatsu, Takaaki ; Homma, Yukio ; Nishimura, Shigeyuki ; Mitsuyama, Toutai ; Aburatani, Hiroyuki ; Kimura, Hiroshi ; Shirahige, Katsuhiko
Publisher:England: BioMed Central Ltd
Journal title:Epigenetics & chromatin, 2019-12, Vol.12 (1), p.77-77, Article 77
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Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
Author / Creator:Sakai, Akiko ; Nakato, Ryuichiro ; Ling, Yiwei ; Hou, Xubin ; Hara, Norikazu ; Iijima, Tomoya ; Yanagawa, Yuchio ; Kuwano, Ryozo ; Okuda, Shujiro ; Shirahige, Katsuhiko ; Sugiyama, Sayaka
Publisher:Switzerland: Frontiers Research Foundation
Journal title:Frontiers in neuroscience, 2017-05, Vol.11, p.307-307
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Showing 1 to 20 of 38 results

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Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation

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HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data

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Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity

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PHOSPHATE exporter XPR1/SLC53A1 is required for the tumorigenicity of epithelial ovarian cancer

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The HSF1–PARP13–PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis

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Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation

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HSF1 phosphorylation establishes an active chromatin state via the TRRAP–TIP60 complex and promotes tumorigenesis

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Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

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Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin

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MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress

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A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS

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Publisher Correction: Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity

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The metabolic stress-activated checkpoint LKB1-MARK3 axis acts as a tumor suppressor in high-grade serous ovarian carcinoma

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The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement

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The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR‐Cas9 screen

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Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells

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Cgaln: fast and space-efficient whole-genome alignment

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CRISPR/Cas9 Screening for Identification of Genes Required for the Growth of Ovarian Clear Cell Carcinoma Cells

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Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells

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Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex

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