Teaching

"Basic Bioinformatics I", (Department of Computational Biology and Medical Science, 2014-2017 Summer Semester)
"DNA Methylation and Genome Evolution", GCOE Lecture I (Graduate School of Frontier Sciences, 2012/5/30)

Publications Google Scholar

• Hiroki Hongo, Satoru Miyawaki, Hideaki Imai, Masahiro Shimizu, Shinichi Yagi, Jun Mitsui, Hiroyuki Ishiura, Jun Yoshimura, Koichiro Doi, Wei Qu, Yu Teranishi, Atsushi Okano, Hideaki Ono, Hirofumi Nakatomi, Tsuneo Shimizu, Shinichi Morishita, Shoji Tsuji, Nobuhito Saito. Comprehensive investigation of RNF213 nonsynonymous variants associated with intracranial artery stenosis.
  Scientific Reports doi:10.1038/s41598-020-68888-1 (2020)
• Hiroyuki Ishiura, Shota Shibata, Jun Yoshimura, Yuta Suzuki, Wei Qu, Koichiro Doi, M. Asem Almansour, Junko Kanda Kikuchi, Makiko Taira, Jun Mitsui, Yuji Takahashi, Yaeko Ichikawa, Tatsuo Mano, Atsushi Iwata, Yasuo Harigaya, Miho Kawabe Matsukawa, Takashi Matsukawa, Masaki Tanaka, Yuichiro Shirota, Ryo Ohtomo, Hisatomo Kowa, Hidetoshi Date, Aki Mitsue, Hiroyuki Hatsuta, Satoru Morimoto, Shigeo Murayama, Yasushi Shiio, Yuko Saito, Akihiko Mitsutake, Mizuho Kawai, Takuya Sasaki, Yusuke Sugiyama, Masashi Hamada, Gaku Ohtomo, Yasuo Terao, Yoshihiko Nakazato, Akitoshi Takeda, Yoshio Sakiyama, Yumi Umeda-Kameyama, Jun Shinmi, Katsuhisa Ogata, Yutaka Kohno, Shen-Yang Lim, Ai Huey Tan, Jun Shimizu, Jun Goto, Ichizo Nishino, Tatsushi Toda, Shinichi Morishita & Shoji Tsuji. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease.
  Nature Genetics doi:10.1038/s41588-019-0458-z (2019)
• Hiroyuki Ishiura, Koichiro Doi, Jun Mitsui, Jun Yoshimura, Miho Kawabe Matsukawa, Asao Fujiyama, Yasuko Toyoshima, Akiyoshi Kakita, Hitoshi Takahashi, Yutaka Suzuki, Sumio Sugano, Wei Qu, Kazuki Ichikawa, Hideaki Yurino, Koichiro Higasa, Shota Shibata, Aki Mitsue, Masaki Tanaka, Yaeko Ichikawa, Yuji Takahashi, Hidetoshi Date, Takashi Matsukawa, Junko Kanda, Fumiko Kusunoki Nakamoto, Mana Higashihara, Koji Abe, Ryoko Koike, Mutsuo Sasagawa, Yasuko Kuroha, Naoya Hasegawa, Norio Kanesawa, Takayuki Kondo, Takefumi Hitomi, Masayoshi Tada, Hiroki Takano, Yutaka Saito, Kazuhiro Sanpei, Osamu Onodera, Masatoyo Nishizawa, Masayuki Nakamura, Takeshi Yasuda, Yoshio Sakiyama, Mieko Otsuka, Akira Ueki, Ken-ichi Kaida, Jun Shimizu, Ritsuko Hanajima, Toshihiro Hayashi, Yasuo Terao, Satomi Inomata-Terada, Masashi Hamada, Yuichiro Shirota, Akatsuki Kubota, Yoshikazu Ugawa, Kishin Koh, Yoshihisa Takiyama, Natsumi Ohsawa-Yoshida, Shoichi Ishiura, Ryo Yamasaki, Akira Tamaoka, Hiroshi Akiyama, Taisuke Otsuki, Akira Sano, Akio Ikeda, Jun Goto, Shinichi Morishita & Shoji Tsuji. Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy.
  Nature Genetics doi:10.1038/s41588-018-0067-2 (2018)
• Masahito Kawazu , Shinya Kojima, Toshihide Ueno, Yasushi Totoki, Hiromi Nakamura, Akiko Kunita, Wei Qu, Jun Yoshimura, Manabu Soda, Takahiko Yasuda, Natsuko Hama, Mihoko Saito-Adachi, Kazuhito Sato, Shinji Kohsaka, Eirin Sai, Masako Ikemura, Shigeru Yamamoto, Tomoko Ogawa, Masashi Fukayama, Keiichiro Tada, Yasuyuki Seto, Shinichi Morishita, Shoichi Hazama, Tatsuhiro Shibata, Yoshihiro Yamashita, Hiroyuki Mano. Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency.
  PLOS Genetics 13(6): e1006853 (2017)
• Ayako Uno, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Sumio Sugano, Yutaka Suzuki, Shinichi Morishita and Hiroyuki Takeda. 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)
• Yuta Suzuki, Jonas Korlach, Stephen W. Turner, Tatsuya Tsukahara, Junko Taniguchi, Wei Qu, Kazuki Ichikawa, Jun Yoshimura, Hideaki Yurino, Yuji Takahashi, Jun Mitsui, Hiroyuki Ishiura, Shoji Tsuji, Hiroyuki Takeda, and Shinichi Morishita. AgIn: Measuring the Landscape of CpG Methylation of Individual Repetitive Elements.
  Bioinformatics doi:10.1093 (2016)
• Wei Qu, 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 (2016)
• Yoichiro Nakatani, 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), 978 (2015)
• Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Kazuki Ichikawa, Takayoshi Otsuka, Katsumi Ogoshi, Taro L Saito, Kouji Matsushima, Sumio Sugano, Shinichi Hashimoto, Yutaka Suzuki, Shinichi Morishita, and Hiroyuki Takeda. Large hypomethylated domain serves as strong repressive machinery for key developmental genes in vertebrate.
  Development 10.1242/dev.108548 (2014)
• Shin-ichi Hashimoto, Katsumi Ogoshi, Atsushi Sasaki, Jun Abe, Wei Qu, Yoichiro Nakatani, Budrul Ahsan, Kenshiro Oshima, Francis HW Shand, Akio Ametani, Yutaka Suzuki, Shuichi Kaneko, Takashi Wada, Masahira Hattori, Sumio Sugano, Shinichi Morishita, Kouji Matsushima. Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells.
  the Journal of Immunology (2013)
• Wei Qu, Shin-ichi Hashimoto, Atsuko Shimada, Yoichiro Nakatani, Kazuki Ichikawa, Taro L Saito, Katsumi Ogoshi, Kouji Matsushima, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Shinichi Morishita. Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns.
  Genome Research 22:1419-1425 (2012)
• Katsumi Ogoshi, Shin-Ichi Hashimoto, Yoichiro Nakatani, Wei Qu, Kenshiro Oshima, Katsushi Tokunaga, Sumio Sugano, Masahira Hattori, Shinichi Morishita, Kouji Matsushima. Genome-wide profiling of DNA methylation in human cancer cells.
  Genomics 98(4):280-7 (2011)
• Wei Qu,Shin-ichi Hashimoto, Shinichi Morishita. Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing.
  Genome Research 19:1309-1315 (2009)
• Shin-ichi Hashimoto(*), Wei Qu(*), Budrul Ahsan, Katsumi Ogoshi, Atsushi Sasaki, Yoichiro Nakatani, Yongjun Lee, Masako Ogawa, Akio Ametani, Yutaka Suzuki, Sumio Sugano, Clarence C Lee, Robert C Nutter, Shinichi Morishita, Kouji Matsushima. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.
  PLoS One 4(1):e4108. Epub (2009)
  * joint first authors.
• The International Silkworm Genome Consortium. The genome of a lepidopteran model insect, the silkworm Bombyx mori.
  Insect Biochemistry and Molecular Biology, Vol. 38, Issue 12, 1036-1045 (2008)
• Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro L. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita. UTGB/medaka: genomic resource database for medaka biology.
  Nucleic Acids Research, Vol. 36, Database issue D747-D752, (2008)
• Masahiro Kasahara(*), Kiyoshi Naruse(*), Shin Sasaki(*), Yoichiro Nakatani(*), Wei Qu, Budrul Ahsan, Tomoyuki Yamada, Yukinobu Nagayasu, Koichiro Doi, Yasuhiro Kasai, Tomoko Jindo, Daisuke Kobayashi, Atsuko Shimada, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda(#), Shinichi Morishita(#), and Yuji Kohara(#). The medaka draft genome and insights into vertebrate genome evolution.
  Nature 447, 714-719 (2007)
  * joint first authors. # joint corresponding authors.