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Development of a bioinformatics method for genome-wide discovery of non-coding RNA genes

Research Project

Project/Area Number 18H04127
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 62:Applied informatics and related fields
Research InstitutionKeio University

Principal Investigator

Sakakibara Yasubumi  慶應義塾大学, 理工学部(矢上), 教授 (10287427)

Co-Investigator(Kenkyū-buntansha) 佐々木 えりか  公益財団法人実験動物中央研究所, マーモセット医学生物学研究部, 部長 (70390739)
星野 敦  基礎生物学研究所, 分野横断研究ユニット, 助教 (80312205)
Project Period (FY) 2018-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥43,810,000 (Direct Cost: ¥33,700,000、Indirect Cost: ¥10,110,000)
Fiscal Year 2022: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Fiscal Year 2021: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Fiscal Year 2020: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Fiscal Year 2019: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Fiscal Year 2018: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Keywords非コードRNA / バイオインフォマティクス / 深層学習 / 遺伝子発現 / マーモセット / アサガオ / 遺伝子発見 / 腸内細菌叢
Outline of Final Research Achievements

We developed a bioinformatics method based on a deep learning model for the analysis of non-coding RNA sequences in the genome, the blueprint of life that contains all genetic information. These sequences do not translate into proteins, but are transcribed to exert functions. This method achieved superior accuracy in sequence classification and clustering compared to the state-of-the-art methods. Moreover, we conducted a metatranscriptome analysis of the marmoset digestive tract, revealing the gene expression differences in the microbiome between the cecum, transverse colon, and feces. Furthermore, we constructed a gene expression database for petunia petals.

Academic Significance and Societal Importance of the Research Achievements

マイクロRNAを初めとする非コードRNA遺伝子の発見とその発現解析は,がんや発生などあらゆる分子生物学の課題で重要である.本研究で開発した手法は,ゲノム配列から非コードRNA遺伝子を網羅的かつ高精度に発見する課題の解決に向けて大きな前進となった.そして,生物医学分野の研究におけるモデル動物マーモセットおよびモデル植物のアサガオのトランスクリプトーム解析のための最適なプロトコルを構築した.

Report

(6 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (52 results)

All 2023 2022 2021 2020 2019 2018

All Journal Article (17 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 14 results,  Open Access: 13 results) Presentation (30 results) (of which Int'l Joint Research: 8 results,  Invited: 12 results) Book (5 results)

  • [Journal Article] Genome-Wide Analysis of Aquaporins in Japanese Morning Glory (Ipomoea nil)2023

    • Author(s)
      Inden Tamami、Hoshino Atsushi、Otagaki Shungo、Matsumoto Shogo、Shiratake Katsuhiro
    • Journal Title

      Plants

      Volume: 12 Issue: 7 Pages: 1511-1511

    • DOI

      10.3390/plants12071511

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine2022

    • Author(s)
      Uehara Mika、Inoue Takashi、Kominato Minori、Hase Sumitaka、Sasaki Erika、Toyoda Atsushi、Sakakibara Yasubumi
    • Journal Title

      mSystems

      Volume: 7 Issue: 5

    • DOI

      10.1128/msystems.00520-22

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome-wide analysis of R2R3-MYB transcription factors in Japanese morning glory2022

    • Author(s)
      Komatsuzaki Ayane、Hoshino Atsushi、Otagaki Shungo、Matsumoto Shogo、Shiratake Katsuhiro
    • Journal Title

      PLOS ONE

      Volume: 17 Issue: 10 Pages: e0271012-e0271012

    • DOI

      10.1371/journal.pone.0271012

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning2022

    • Author(s)
      Akiyama Manato、Sakakibara Yasubumi
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 4 Issue: 1

    • DOI

      10.1093/nargab/lqac012

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genomic style: yet another deep-learning approach to characterize bacterial genome sequences2021

    • Author(s)
      Yoshimura Yuka、Hamada Akifumi、Augey Yohann、Akiyama Manato、Sakakibara Yasubumi
    • Journal Title

      Bioinformatics Advances

      Volume: 1 Issue: 1

    • DOI

      10.1093/bioadv/vbab039

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset2021

    • Author(s)
      Jayakumar Vasanthan、Nishimura Osamu、Kadota Mitsutaka、Hirose Naoki、Sano Hiromi、Murakawa Yasuhiro、Yamamoto Yumiko、Nakaya Masataka、Tsukiyama Tomoyuki、Seita Yasunari、Nakamura Shinichiro、Kawai Jun、Sasaki Erika、Ema Masatsugu、Kuraku Shigehiro、Kawaji Hideya、Sakakibara Yasubumi
    • Journal Title

      Scientific Data

      Volume: 8 Issue: 1 Pages: 59-59

    • DOI

      10.1038/s41597-021-00935-6

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effectiveness of Create ML in microscopy image classifications: a simple and inexpensive deep learning pipeline for non-data scientists2021

    • Author(s)
      Nagaki Kiyotaka、Furuta Tomoyuki、Yamaji Naoki、Kuniyoshi Daichi、Ishihara Megumi、Kishima Yuji、Murata Minoru、Hoshino Atsushi、Takatsuka Hirotomo
    • Journal Title

      Chromosome Research

      Volume: 29 Issue: 3-4 Pages: 361-371

    • DOI

      10.1007/s10577-021-09676-z

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data2020

    • Author(s)
      Jayakumar Vasanthan、Ishii Hiromi、Seki Misato、Kumita Wakako、Inoue Takashi、Hase Sumitaka、Sato Kengo、Okano Hideyuki、Sasaki Erika、Sakakibara Yasubumi
    • Journal Title

      BMC Genomics

      Volume: 21 Issue: S3 Pages: 243-243

    • DOI

      10.1186/s12864-020-6657-2

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A conserved strategy of chalcone isomerase-like protein to rectify promiscuous chalcone synthase specificity2020

    • Author(s)
      T. Waki, A. Hoshino, et al.
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 870-870

    • DOI

      10.1038/s41467-020-14558-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Highly efficient induction of primate iPS cells by combining RNA transfection and chemical compounds2019

    • Author(s)
      Watanabe Toshiaki、Yamazaki Shun、Yoneda Nao、Shinohara Haruka、Tomioka Ikuo、Higuchi Yuichiro、Yagoto Mika、Ema Masatsugu、Suemizu Hiroshi、Kawai Kenji、Sasaki Erika
    • Journal Title

      Genes to Cells

      Volume: 24 Issue: 7 Pages: 473-484

    • DOI

      10.1111/gtc.12702

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Generation of Yellow Flowers of the Japanese Morning Glory by Engineering Its Flavonoid Biosynthetic Pathway toward Aurones2019

    • Author(s)
      Hoshino Atsushi、Mizuno Takayuki、Shimizu Keiichi、Mori Shoko、Fukada-Tanaka Sachiko、Furukawa Kazuhiko、Ishiguro Kanako、Tanaka Yoshikazu、Iida Shigeru
    • Journal Title

      Plant and Cell Physiology

      Volume: 60 Issue: 8 Pages: 1871-1879

    • DOI

      10.1093/pcp/pcz101

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] バイオテクノロジーで幻の黄色いアサガオを再現する2019

    • Author(s)
      星野敦
    • Journal Title

      B&I(バイオサイエンス&インダストリー)

      Volume: 77 Pages: 438-439

    • Related Report
      2019 Annual Research Report
  • [Journal Article] フラボノイド代謝工学で咲いた幻の黄色いアサガオ2019

    • Author(s)
      星野敦
    • Journal Title

      B&I(バイオサイエンス&インダストリー)

      Volume: 77 Pages: 464-465

    • Related Report
      2019 Annual Research Report
  • [Journal Article] アサガオの多様な変異体リソースと高精度ゲノム情報2019

    • Author(s)
      仁田坂英二,星野敦
    • Journal Title

      BSJ-Review

      Volume: 10 Issue: C Pages: 169-178

    • DOI

      10.24480/bsj-review.10c8.00168

    • ISSN
      2432-9819
    • Related Report
      2019 Annual Research Report
    • Open Access
  • [Journal Article] Anthocyanin mutants of Japanese and common morning glories exhibit normal proanthocyanidin accumulation in seed coats2018

    • Author(s)
      K.I. Park, E. Nitasaka and A. Hoshino
    • Journal Title

      Plant Biotechnology

      Volume: 35 Issue: 3 Pages: 259-266

    • DOI

      10.5511/plantbiotechnology.18.0613a

    • NAID

      130007495560

    • ISSN
      1342-4580, 1347-6114
    • Year and Date
      2018-09-25
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Convolutional neural networks for classification of alignments of non-coding RNA sequences2018

    • Author(s)
      Aoki Genta、Sakakibara Yasubumi
    • Journal Title

      Bioinformatics

      Volume: 34 Issue: 13 Pages: i237-i244

    • DOI

      10.1093/bioinformatics/bty228

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model2018

    • Author(s)
      Akiyama Manato、Sato Kengo、Sakakibara Yasubumi
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 16 Issue: 06 Pages: 1840025-1840025

    • DOI

      10.1142/s0219720018400255

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] NBRPアサガオの変異体リソースのゲノム情報整備2023

    • Author(s)
      星野敦、白澤健太、山田哲也、豊田敦、仁田坂英二
    • Organizer
      第43回日本植物生理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 大規模リシーケンスによるアサガオの遺伝子変異の解析I2022

    • Author(s)
      星野敦、仁田坂英二、白澤健太、山田哲也
    • Organizer
      第11回アサガオ研究集会
    • Related Report
      2022 Annual Research Report
  • [Presentation] アサガオ:ゲノム情報でキラリと光りはじめた日本独自のバイオリソース2022

    • Author(s)
      星野敦、白澤健太、仁田坂英二
    • Organizer
      日本植物生理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] アサガオの花弁周縁部に特異的な三重化した遺伝子のRNAサイレンシング2022

    • Author(s)
      中川颯也、朴慶一、森田裕将、飯田滋、星野敦
    • Organizer
      日本植物生理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Genomic style: a deep-learning approach to characterize bacterial genome sequences2021

    • Author(s)
      Yuka Yoshimura, Akifumi Hamada, Yohann Augey, Manato Akiyama and Yasubumi Sakakibara
    • Organizer
      2021年日本バイオインフォマティクス学会年会・ 第10回生命医薬情報学連合大会(IIBMP2021)
    • Related Report
      2021 Annual Research Report
  • [Presentation] アサガオの主要な変異原Tpnトランスポゾンの転移及び転移抑制機構2021

    • Author(s)
      水成友紀、白澤健太、星野敦、仁田坂英二
    • Organizer
      日本分子生物学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] リシーケンスによるアサガオ100系統の多型と遺伝子変異の解析2021

    • Author(s)
      星野敦、白澤健太、仁田坂英二
    • Organizer
      日本遺伝学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Development of meta-transcriptome analysis method and its application to meta-transcriptome map of common marmoset2019

    • Author(s)
      Uehara M, Kominato M, Hase S, Inoue T, Sasaki E, Toyoda A, Sakakibara Y
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB) / International Society for Computational Biology (ISCB) 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 慶應大学における医療へのAI活用の現状と動向について2019

    • Author(s)
      榊原康文
    • Organizer
      公益社団法人日本技術士会神奈川県支部 第80回CPD講座
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] アサガオのエピジェネティクスによる模様形成と経世代伝達2019

    • Author(s)
      星野敦
    • Organizer
      日本進化学会第21回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Regulation of DNA methylation during marmoset germ cell development2019

    • Author(s)
      渡部聡朗、藪上春香、井上貴史、峰重隆幸、圦本晃海、黒滝陽子、喜多善亮、下郡智美、川路英哉、蓑田亜希子、佐々木えりか
    • Organizer
      第42回日本分子生物学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] マーモセット胚の疑似着床後胚の培養法確立2019

    • Author(s)
      岸本恵子、Huaiyu Hu、佐々木えりか
    • Organizer
      第42回日本分子生物学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Editing the Non-Human Primate Genome2019

    • Author(s)
      Erika Sasaki
    • Organizer
      Soceity for the Study of Reproduction 52nd Annual Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Long-read sequence data improves the contiguity of Marmoset genome2019

    • Author(s)
      Vasanthan Jayakumar,Yasubumi Sakakibara
    • Organizer
      第8回日本マーモセット研究会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Development of Genetically Modified Non-Human Primate Disease Models2019

    • Author(s)
      Erika Sasaki
    • Organizer
      Keystone Symposia Conference/ Genome Engineering: From Mechanisms to Therapies
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Development Non-human Primate Disease models by Genetic Engineering2019

    • Author(s)
      Erika Sasaki
    • Organizer
      2nd Internatioal Primate Neuroscience Research Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] マーモセットにおける遺伝子改変モデルの展望2019

    • Author(s)
      佐々木えりか
    • Organizer
      第8回日本マーモセット研究会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Nonhuman Primate models for Translational Science2019

    • Author(s)
      佐々木えりか
    • Organizer
      Translational and Regulatory Sciences Symposium
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] アサガオの刷毛目絞を司るエピジェネティックな遺伝子発現御2019

    • Author(s)
      星野敦, 森田裕将, 長岐清孝
    • Organizer
      第60回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アサガオの刷毛目絞とエピゲノム解析2019

    • Author(s)
      星野敦, 森田裕将, 長岐清孝
    • Organizer
      第10回アサガオ研究集会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アサガオの葉における翼片形成に関わる遺伝子の解析22019

    • Author(s)
      岡本歩, 星野敦, 福多賢太郎, 野口英樹, 田中啓介, 乗越亮, 清水圭一, 仁田坂英二
    • Organizer
      第10回アサガオ研究集会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アサガオSCPL型アシル化酵素遺伝子とアントシアニン色素合成2019

    • Author(s)
      森田裕将, 三嶋麻友, 渡邊良介, 仁田坂英二, 飯田滋, 星野敦
    • Organizer
      第10回アサガオ研究集会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Creating neuronal disease models using genome editing2018

    • Author(s)
      Erika Sasaki
    • Organizer
      22nd Biennial Meeting of the International Society for Developmental Neuroscience
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Current state of marmoset population in Japan and exchange of the marmoset genome resources2018

    • Author(s)
      Erika Sasaki
    • Organizer
      ILAR roundtable “Care, Use and Welfare of Marmosets as Animal Models for Gene Editing-based Biomedical Research”
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Generating genetically modified model marmoset2018

    • Author(s)
      Erika Sasaki
    • Organizer
      ILAR roundtable “Care, Use and Welfare of Marmosets as Animal Models for Gene Editing-based Biomedical Research”
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 小型非ヒト霊長類マーモセットモデルと遺伝子改変技術2018

    • Author(s)
      佐々木えりか
    • Organizer
      関西実験動物研究会第139回研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Enhancer of Flavonoid Productionによるカルコン合成酵素の生成物特異性制御2018

    • Author(s)
      和氣駿之,大豆田亮,中野拓也,山田彩友美,寺下美穂,宇野海地,森田裕将,榊原圭子,星野敦,高橋征司,中山亨
    • Organizer
      日本農芸化学会2018年度北海道支部・東北支部合同支部大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アサガオの多様な変異体リソースと高精度ゲノム情報2018

    • Author(s)
      仁田坂英二,星野敦
    • Organizer
      植物学会第82回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アサガオにおける葉の翼片形成に関与する丸葉遺伝子の解析2018

    • Author(s)
      岡本歩,星野敦, 福多賢太郎, 野口英樹, 田中啓介, 乗越亮, 仁田坂 英二
    • Organizer
      三学会合同宮崎大会2018,日本動物学会九州支部(第71回),九州沖縄植物学会(第68回),日本生態学会九州地区(第63回)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Convolutional neural networks for classification of alignments of non-coding RNA sequences2018

    • Author(s)
      Genta Aoki and Yasubumi Sakakibara
    • Organizer
      The 26th International conference on Intelligent Systems for Molecular Biology (ISMB2018)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Book] 完全版 ゲノム編集実験スタンダード2019

    • Author(s)
      山本 卓、佐久間 哲史
    • Total Pages
      386
    • Publisher
      羊土社
    • ISBN
      9784758122443
    • Related Report
      2019 Annual Research Report
  • [Book] The 3-Dimensional Atlas of the Marmoset Brain: Reconstructible in Stereotaxic Coordinates (Brain Science)2018

    • Author(s)
      Atsushi Iriki, Hirotaka James Okano, Erika Sasaki, Hideyuki Okano(編集)
    • Total Pages
      388
    • Publisher
      Springer Japan社
    • ISBN
      9784431566106
    • Related Report
      2018 Annual Research Report
  • [Book] 医療応用をめざすゲノム編集 最新動向から技術・倫理的課題まで (DOJIN BIOSCIENCE SERIES). 11章:ゲノム編集による疾患モデルマーモセット(佐藤賢哉, 佐々木えりか著)2018

    • Author(s)
      真下 知士 (編集), 金田 安史 (編集)
    • Total Pages
      274
    • Publisher
      化学同人
    • ISBN
      9784759817294
    • Related Report
      2018 Annual Research Report
  • [Book] マーモセットラボマニュアル はじめての取扱いから研究最前線まで2018

    • Author(s)
      佐々木えりか監修、井上貴史・黒滝陽子・三木理雅編集
    • Total Pages
      207
    • Publisher
      アドスリー社
    • ISBN
      9784904419786
    • Related Report
      2018 Annual Research Report
  • [Book] The Common Marmoset in Captivity and Biomedical Research. Chapter 20:Creating Genetically Modified Marmosets.(Erika Sasaki著)2018

    • Author(s)
      Robert P. Marini (編集), Lynn M. Wachtman (編集), Suzette D. Tardif (編集), Keith Mansfield (編集), James G. Fox (編集)
    • Total Pages
      570
    • Publisher
      Academic Press
    • ISBN
      9780128118290
    • Related Report
      2018 Annual Research Report

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Published: 2018-04-23   Modified: 2024-01-30  

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