Methods for ChIP-seq analysis: A practical workflow and advanced applications von Nakato, Ryuichiro, Sakata, Toyonori

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Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation von Nakato, Ryuichiro, Shirahige, Katsuhiko

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HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data von Wang, Jiankang, Nakato, Ryuichiro

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Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile von Nakato, Ryuichiro, Shirahige, Katsuhiko

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Computational Methods for 3D Genome Analysis

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Origin Association of Sld3, Sld7, and Cdc45 Proteins Is a Key Step for Determination of Origin-Firing Timing von Tanaka, Seiji, Nakato, Ryuichiro, Katou, Yuki, Shirahige, Katsuhiko, Araki, Hiroyuki

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PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells von Yamaji, Masashi, Ueda, Jun, Hayashi, Katsuhiko, Ohta, Hiroshi, Yabuta, Yukihiro, Kurimoto, Kazuki, Nakato, Ryuichiro, Yamada, Yasuhiro, Shirahige, Katsuhiko, Saitou, Mitinori

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PHOSPHATE exporter XPR1/SLC53A1 is required for the tumorigenicity of epithelial ovarian cancer von Akasu‐Nagayoshi, Yoko, Hayashi, Tomoatsu, Kawabata, Ayako, Shimizu, Naomi, Yamada, Ai, Yokota, Naoko, Nakato, Ryuichiro, Shirahige, Katsuhiko, Okamoto, Aikou, Akiyama, Tetsu

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Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation von Wang, Jiankang, Bando, Masashige, Shirahige, Katsuhiko, Nakato, Ryuichiro

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The HSF1–PARP13–PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis von Fujimoto, Mitsuaki, Takii, Ryosuke, Takaki, Eiichi, Katiyar, Arpit, Nakato, Ryuichiro, Shirahige, Katsuhiko, Nakai, Akira

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

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Replication-Coupled PCNA Unloading by the Elg1 Complex Occurs Genome-wide and Requires Okazaki Fragment Ligation von Kubota, Takashi, Katou, Yuki, Nakato, Ryuichiro, Shirahige, Katsuhiko, Donaldson, Anne D.

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Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior von Fujita, Yuki, Masuda, Koji, Bando, Masashige, Nakato, Ryuichiro, Katou, Yuki, Tanaka, Takashi, Nakayama, Masahiro, Takao, Keizo, Miyakawa, Tsuyoshi, Tanaka, Tatsunori, Ago, Yukio, Hashimoto, Hitoshi, Shirahige, Katsuhiko, Yamashita, Toshihide

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HSF1 phosphorylation establishes an active chromatin state via the TRRAP–TIP60 complex and promotes tumorigenesis von Fujimoto, Mitsuaki, Takii, Ryosuke, Matsumoto, Masaki, Okada, Mariko, Nakayama, Keiich I., Nakato, Ryuichiro, Fujiki, Katsunori, Shirahige, Katsuhiko, Nakai, Akira

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Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells von Wang, Jiankang, Nakato, Ryuichiro

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Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data von Nakajima, Natsu, Hayashi, Tomoatsu, Fujiki, Katsunori, Shirahige, Katsuhiko, Akiyama, Tetsu, Akutsu, Tatsuya, Nakato, Ryuichiro

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Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors von Nakato, Ryuichiro, Sakata, Toyonori, Wang, Jiankang, Nagai, Luis Augusto Eijy, Nagaoka, Yuya, Oba, Gina Miku, Bando, Masashige, Shirahige, Katsuhiko

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DROMPA: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data von Nakato, Ryuichiro, Itoh, Tahehiko, Shirahige, Katsuhiko

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Histone Variants Enriched in Oocytes Enhance Reprogramming to Induced Pluripotent Stem Cells von Shinagawa, Toshie, Takagi, Tsuyoshi, Tsukamoto, Daisuke, Tomaru, Chinatsu, Huynh, Linh My, Sivaraman, Padavattan, Kumarevel, Thirumananseri, Inoue, Kimiko, Nakato, Ryuichiro, Katou, Yuki, Sado, Takashi, Takahashi, Satoru, Ogura, Atsuo, Shirahige, Katsuhiko, Ishii, Shunsuke

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The Deubiquitinating Enzyme USP7 Regulates Androgen Receptor Activity by Modulating Its Binding to Chromatin von Chen, Shu-Ting, Okada, Maiko, Nakato, Ryuichiro, Izumi, Kosuke, Bando, Masashige, Shirahige, Katsuhiko

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