Motomu Matsui, Ph.D.


Research Associate
    Department of Biological Sciences,
    Graduate School of Science,
    The University of Tokyo, Japan

助教
    東京大学
    大学院理学系研究科
    生物科学専攻

E-mail: qm at bs.s.u-tokyo.ac.jp

Research Topics
  1. Molecular Evolution; Phylogenetic networks, Genome evolution
  2. Japanese Archery; Ogasawara-ryu, 4th dan level
  3. RNA biology; non-coding RNA, post-transcriptional regulation
  1. 分子進化; 進化ネットワーク, ゲノム進化
  2. 弓道; 四段 (小笠原流)
  3. RNA; non-coding RNA, 転写後制御
Work experience
    2017-present Research Associate; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan (Wataru Iwasaki Laboratory)
    2015-2017 Postdoctral Fellow, Japan Society for the Promotion of Science (PD); Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan (Wataru Iwasaki Laboratory)
    2014-2015 Postdoctral Fellow, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan (Wataru Iwasaki Laboratory)
    2009-2011 Research Fellow, Japan Society for the Promotion of Science (DC1)
    2009-2012 Part-time lecturer, Faculty of Environment and Information Studies, Keio University, Japan (Genetic Analysis Laboratory)

    2017-現在 助教, 東京大学大学院理学系研究科生物科学専攻 (岩崎渉研究室)
    2015-2017 日本学術振興会 特別研究員 (PD), 東京大学大学院理学系研究科生物科学専攻 (岩崎渉研究室)
    2014-2015 特任研究員, 東京大学大学院理学系研究科 生物科学専攻 (岩崎渉研究室)
    2009-2011 日本学術振興会 特別研究員 (DC1)慶應義塾大学 政策・メディア研究科 (冨田勝研究室)
    2009-2012 非常勤講師, 慶應義塾大学 環境情報学部 (遺伝子解析実習)
Education
    2014 Ph.D., Graduate School of Media and Governance, Keio University, Japan
    2009 M.A. in Systems Biology, Graduate School of Media and Governance, Keio University, Japan
    2007 B.S., Faculty of Environment and Information Studies, Keio University, Japan

    2014 慶應義塾大学 政策・メディア研究科 博士課程 修了
    2009 慶應義塾大学 政策・メディア研究科 修士課程 修了
    2007 慶應義塾大学 環境情報学部 卒業
    2003 筑波大学附属駒場高等学校 卒業
Texts
  1. Motomu MatsuiBasic Theories for Bioinformatics lecture note I, PDF
  2. Motomu Matsui, Rintaro Saito, Masaru Tomita, 初学者のためのPerlによるバイオプログラミング演習, PDF
Tools
Escherichia coli sRNA Browser
http://rna.iab.keio.ac.jp/
Publications (Peer-reviewed papers)
The publication list in PubMed

1.
Motomu Matsui, Masaru Tomita and Akio Kanai
Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks
Genome Biol. Evol. 2013, 5(2), 267-282
 Adopted as the cover art of Genome Biology and Evolution, 5(4), 2013.

2.
Atsuko Shinhara, Motomu Matsui, Kiriko Hiraoka, Wataru Nomura, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori and Akio Kanai
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli
BMC Genomics 2011, 12, 428
Certified as
 in BMC Genomics, 12.

3.
Motomu Matsui, Nozomu Yachie, Yuki Okada, Rintaro Saito and Masaru Tomita.
Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse.
FEBS Lett. 2007, 581, 4184-4188

4.
Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita and Akio Kanai.
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level
In Silico Biol. 2006, 6, 411-418

5.
Kazuharu Arakawa, Haruo Suzuki, Kosuke Fujishima, Kenji Fujimoto, Shou Ueda, Motomu Matsui and Masaru Tomita.
A comprehensive software suite for the analysis of cDNAs.
Genomics Proteomics Bioinformatics 2005, 3, 179-188
Others
        1. 表紙
        Motomu Matsui
        大腸菌の転写因子ネットワーク
        日本ゲノム微生物学会ニュースレター, 9, 2014
        PDF

        2. 表紙
        Motomu Matsui
        Cover image
        Genome Biology and Evolution, 5(4), 2013.
        GBE
Talks
[English]
  1. Motomu Matsui, Nozomu Yachie, Kosaku Shinoda, Naoyuki Sugiyama, Fumio Ando, Yuki Okada, Martin Robert, Rintaro Saito, Masaru Tomita, Genome-wide Analysis of novel small Peptide in Escherichia coli, CBI2006 (07/25/06)
[Japanese]
  1. Motomu Matsui and Wataru Iwasaki, Graph Splitting Method: Novel Phylogenetic Approach Beyond the Twilight Zone

    , JSBi2015 (10/29/15)

  2. Motomu Matsui and Wataru Iwasaki, Graph Splitting法: トワイライトゾーンを越える新たな系統解析手法, 第17回日本進化学会 (08/20/15)
  3. Motomu Matsui, Masaru Tomita and Akio Kanai, バクテリアにおける転写制御ネットワークの包括的進化解析, 第8回日本ゲノム微生物学会 (03/07/14)
  4. Reina Fukuzawa, Motomu Matsui, Masaru Tomita and Mitsuhiro Itaya, 大規模な比較ゲノム解析から見えるTrypanosomaとバクテリア間の水平伝播の考察, 第8回日本ゲノム微生物学会 (03/09/14)
  5. Motomu Matsui, Masaru Tomita and Akio Kanai, Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks, JSBi2013 (2013年度・生命医薬情報学連合大会, ハイライトトラック, 10/29/13)
  6. Motomu Matsui, Masaru Tomita and Akio Kanai, バクテリアにおける全転写因子の進化プロセス解析, 第15回日本進化学会 (08/28/13)
  7. Motomu Matsui, Masaru Tomita and Akio Kanai, Stepwise evolution of bacterial CRP/FNR-type transcription factors and their transcriptional networks, 第35回日本分子生物学会 (12/13/12)
  8. Yuki Usui, Kahori T. Ikeda, Motomu Matsui, Masaru Tomita and Akio Kanai, Evolutionary relationships between PB1 mRNA of Influenza A virus and host microRNAs among vertebrates, 第35回日本分子生物学会 (12/12/12)
  9. Motomu Matsui, Masaru Tomita and Akio Kanai, バクテリア界におけるCRP/FNRファミリー転写因子とターゲットモチーフの共進化, 第14回日本進化学会 (08/23/12)
  10. Motomu Matsui, Atsuko Shinhara, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Akio Kanai, 大腸菌のDiauxic Growthにおける新規anti-xylE RNAの発現解析, 第16回 山形分子生物学セミナー (12/18/08)
  11. Nozomu Yachie and Motomu MatsuiMedCD: PubMed Concept Dictionary, 第3回オープンバイオ研究会(人工知能学会 SIG-BMK) (03/10/06), *The first two authors contributed equally to this work.
Posters
[English]
  1. Motomu Matsui, Masaru Tomita and Akio Kanai, Stepwise co-evolution between bacterial CRP/FNR-type transcription factors and their transcriptional networks, RNA2013
  2. Yuki Usui, Kahori T. Ikeda, Motomu Matsui, Masaru Tomita and Akio Kanai, Evolutionary relationships between PB1 mRNA of Influenza A virus and host microRNAs among vertebrates, RNA2013
  3. Motomu Matsui, Atsuko Shinhara, Kiriko Aoyagi, Kenji Nakahigashi, Masaru Tomita, Akio Kanai, Transcriptome Analysis Revealed Novel sRNAs Related to Catabolite repression in Escherichia coli, RNA2010
  4. Atsuko Shinhara, Motomu Matsui, kiriko Hiraoka, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori, Akio Kanai, Deep Sequencing of Low Molecular Weight RNA reveals Over One Hundred Novel sRNAs in Escherichia coli, RNA2010
  5. Motomu Matsui, Atsuko Shinhara, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Akio Kanai, Possible role of psiE transcript as a xylE cis-antisense RNA promoting catabolite repression in Escherichia coli under glucose/xylose mixture, RNA2009
  6. Atsuko Shinhara, Motomu Matsui, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori, Akio Kanai, Deep Sequencing Analysis suggests the Expression of cis-antisense ncRNAs at the Ribosomal Binding Site in Escherichia coli, RNA2009
  7. Motomu Matsui, Atsuko Shinhara, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Akio Kanai, Analysis of Novel anti-xylE RNA Expression during Diauxic Growth in Escherichia coli, RNA2008
  8. Motomu Matsui, Atsuko Shinhara, Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Tomoharu Agata, Akiko Kashiwagi, Satoshi Harada, Tomoya Baba, Rintaro Saito, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori, Tetsuya Yomo and Akio Kanai, Analysis of Novel Non-coding and Antisense RNAs in Escherichia coli Transcriptome, RNA2007, *The first two authors contributed equally to this work.
  9. Rintaro Saito, Yosuke Ozawa, Shigeo Fujimori, Motomu Matsui, Shota Ushiama, Hisashi Kashima, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita, Comprehensive Analysis of Domain-Domain Interactions Using In VitroVirus, GIW2007
  10. Tomoko Kikuchi, Motomu Matsui, Mikiko Hattori, Rintaro Saito and Masaru Tomita, Comparative Analysis of RNA Editing Sites in Plant Mitochondrial Genomes, JSBi2007
  11. Motomu Matsui, Fumio Ando, Kosaku Shinoda, Naoyuki Sugiyama, Yuki Okada, Fumio Liu, Martin Robert, Rintaro Saito, Masaru Tomita, Uncharacterized Peptides Encoded by Small ORFs in Escherichia coli Genome: Computational Prediction and Experimental Verification, 20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress
  12. Motomu Matsui, Nozomu Yachie, Kosaku Shinoda, Naoyuki Sugiyama, Fumio Ando, Yuki Okada, Martin Robert, Rintaro Saito, Masaru Tomita, Genome-wide Analysis of novel small Peptide in Escherichia coli, CBI2006
  13. Yuki Okada, Motomu Matsui, Rintaro Saito and Masaru Tomita, Computational prediction and characterization of upstream Open Reading Frames in Mus Musculus and Homo Sapiens, RNA2005, *The first two authors contributed equally to this work.
[Japanese]
  1. Motomu Matsui and Wataru Iwasaki, Graph Splitting法: トワイライトゾーンを越える新たな系統解析アプローチ, BMB2015
  2. Motomu Matsui and Wataru Iwasaki, NGS時代の新たな系統解析アプローチ: Graph Splitting法, NGS Field 4th Meeting
  3. Motomu Matsui and Wataru Iwasaki, Graph Splitting法:遠縁な進化的関係の解明に資する新たな系統解析手法の開発と適用, BIO UT 2015
  4. Reina Fukuzawa, Motomu Matsui, Masaru Tomita and Mitsuhiro Itaya, 寄生性原虫トリパノソーマの進化的起源—多様な原核生物からの水平伝播遺伝子の探索第9回日本ゲノム微生物学会
  5. Motomu Matsui, Masaru Tomita and Akio Kanai, バクテリアにおける転写制御ネットワークの包括的進化解析, 第8回日本ゲノム微生物学会
  6. Reina Fukuzawa, Motomu Matsui, Masaru Tomita and Mitsuhiro Itaya, 大規模な比較ゲノム解析から見えるTrypanosomaとバクテリア間の水平伝播の考察第8回日本ゲノム微生物学会
  7. Motomu Matsui, Masaru Tomita and Akio Kanai, Phylogenetic network analysis of whole bacterial transcription factors, 第36回日本分子生物学会
  8. Reina Fukuzawa, Motomu Matsui, Masaru Tomita and Mitsuhiro Itaya, 大規模な比較ゲノム解析から見えるTrypanosomaとバクテリア間の水平伝播の考察第36回日本分子生物学会
  9. Yuki Usui, Kahori T. Ikeda, Motomu Matsui, Masaru Tomita and Akio Kanai, 宿主microRNAとA 型インフルエンザウイルスPB1 mRNA の相互作用は進化的に保存されていた第36回日本分子生物学会
  10. Junnosuke Imai, Motomu Matsui, Yoshiki Ikeda, Masaru Tomita and Akio Kanai, RNase DiCE : 新規リボヌクレアーゼ予測のための進化的に保存された識別配列, 第36回日本分子生物学会
  11. Gakuto Makino, Yoshiki Ikeda, Motomu Matsui, Masaru Tomita and Akio Kanai, シンテニー情報を利用したバクテリアsmall RNA の進化解析, 第36回日本分子生物学会
  12. Motomu Matsui, Yoshiki Ikeda, Gakuto Makino, Masaru Tomita, Akio Kanai and Kenji Nakahigashi, Deep Sequence Analysis of the Relationship between sRNA-related Factors and Dynamic Changes of sRNA Expression in Escherichia coli, JSBi2013 (2013年度・生命医薬情報学連合大会)
  13. Motomu Matsui, Masaru Tomita and Akio Kanai, Stepwise evolution of bacterial CRP/FNR-type transcription factors and their transcriptional networks, 第35回日本分子生物学会
  14. Yuki Usui, Kahori T. Ikeda, Motomu Matsui, Masaru Tomita and Akio Kanai, Evolutionary relationships between PB1 mRNA of Influenza A virus and host microRNAs among vertebrates, 第35回日本分子生物学会
  15. Motomu Matsui, Atsuko Shinhara, Kiriko Hiraoka, Kenji Nakahigashi, Masaru Tomita and Akio Kanai, Novel sRNAs Related to Catabolite Repression in Glucose/Xylose mixture media Revealed by RNA-seq Analysis in Escherichia coli, 第33回日本分子生物学会
  16. Motomu Matsui, Atsuko Shinhara, Kiriko Aoyagi, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita and Akio Kanai, Transcriptome analysis of Escherichia coli in Glucose/Xylose mixture using high-throughput sequencing, 第32回日本分子生物学会
  17. Motomu Matsui, Atsuko Shinhara, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Akio Kanai, Analysis of Gene Expression for Novel anti-xylE RNA in Escherichia coli during Diauxic Growth, 第31回日本分子生物学会
  18. Motomu Matsui, Atsuko Shinhara, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Akio Kanai, 大腸菌のDiauxic Growthにおける新規anti-xylE RNAの発現解析, 第30回日本分子生物学会
  19. Atsuko Shinhara, Motomu Matsui, Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Tomoharu Agata, Akiko Kashiwagi, Reiko Hirano, Satoshi Harada, Tomoya Baba, Rintaro Saito, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori, Tetsuya Yomo, Akio Kanai, Analysis of Novel Non-coding and Antisense RNAs in Escherichia coli Transcriptome Using Tiling Array, 第30回日本分子生物学会, *The first two authors contributed equally to this work.
  20. Rintaro Saito, Yosuke Ozawa, Shigeo Fujimori, Motomu Matsui, ShotaUshiama, HisashiKashima, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita, Construction of Domain-Domain Interaction Network Using In Vitro Virus and Its Application to Novel Protein Interaction Prediction, 第30回日本分子生物学会
  21. Motomu Matsui, Yuki Okada, Kosaku Shinoda, Naoyuki Sugiyama, Fumio Ando, Fumio Liu, Martin Robert, Rintaro Saito and Masaru Tomita, 大腸菌における small ORF より発現する未知ペプチドの情報学的予測,及び実験による検証, 第28回日本分子生物学会
  22. Fumio Liu, Motomu Matsui, Yuki Okada, Rintaro Saito, Shinichi Kikuchi and Masaru Tomita, Full-length cDNA データを用いたヒト疾患関連遺伝子周辺配列の特徴解析, 第28回日本分子生物学会
  23. Yuki Okada, Motomu Matsui, RIntaro Saito and Masaru Tomita, 多種間における情報学的手法を用いた uORF の解析, 第27回日本分子生物学会, *The first two authors contributed equally to this work.
Awards
  1. ポスター賞, 生物科学専攻リトリート2017
  2. 最優秀口頭発表賞,  JSBi 2015 (生命医薬情報学連合大会2015年大会), 2015 
  3. 研究奨励賞,  JSBi 2015 (生命医薬情報学連合大会2015年大会), 2015
  4. ポスター賞, BIO UT 2015 (第15回東京大学生命科学シンポジウム), 2015
  5. ポスター賞 (博士課程部門), 第8回日本ゲノム微生物学会2013
  6. SFC award, Faculty of Environment and Information Studies, Keio University, 2007