Fukunaga, Tsukasa

写真a

Affiliation

Faculty of Science and Technology, Department of Biosciences and Informatics (Yagami)

Position

Associate Professor
Page Top ▲

Profile Summary 【 Display / hide 】

  • シーケンス技術の進歩により、膨大な塩基配列データが次々と決定されています。しかし、それら塩基配列データが秘める「生命情報」の全貌は、その多くが謎に包まれたままです。 これらの未解明な生命情報を解き明かすには、大規模なデータを高速に処理するアルゴリズムや、機械学習に代表される高度なデータ解析手法の開発が不可欠です。また、それらの手法で得られた視点を基盤に、新たな生命科学を進めていく必要もあります。福永研究室では、RNA構造解析・遺伝子機能推定・ゲノム配列解析といったテーマを中心に、ソフトウェア開発からウェットラボ実験まで、 多角的なアプローチで研究を進めています。

Page Top ▲

Career 【 Display / hide 】

  • 2016.04
    -
    2017.09

    日本学術振興会, 特別研究員(PD)

  • 2016.04
    -
    2017.09

    Waseda University, Faculty of Science and Engineering, 特別研究員

  • 2017.10
    -
    2021.03

    Waseda University, Research Institute for Science and Engineering, 招聘研究員

  • 2017.10
    -
    2021.03

    The University of Tokyo, 情報理工学系研究科コンピュータ科学専攻, 助教

  • 2018.02
    -
    2019.03

    Osaka University, 医学系研究科, 招聘研究員

display all >>

Page Top ▲

Academic Background 【 Display / hide 】

  • 2007.04
    -
    2011.03

    The University of Tokyo, Faculty of Science, Undergraduate Program for Bioinformatics and Systems Biology

  • 2011.04
    -
    2016.03

    東京大学大学院, 新領域創成科学研究科, メディカル情報生命専攻

Page Top ▲

Academic Degrees 【 Display / hide 】

  • 博士(科学), The University of Tokyo, Coursework, 2016.03

    Bioinformatics for Understanding Animal Behavior

Page Top ▲
 

Research Areas 【 Display / hide 】

  • Life Science / Genome biology

  • Life Science / System genome science

  • Informatics / Life, health and medical informatics

Page Top ▲

Research Keywords 【 Display / hide 】

  • RNA二次構造

  • ゲノム進化

  • シアノバクテリア

  • データマイニング

  • バイオインフォマティクス

display all >>

Page Top ▲
 

Books 【 Display / hide 】

  • バイオインフォマティクスのための生命科学入門 (バイオインフォマティクスシリーズ 1)

    福永 津嵩(著), 岩切 淳一(著), 浜田 道昭(監修), コロナ社, 2022.07,  Page： 191

Page Top ▲

Papers 【 Display / hide 】

  • REPrise: de novo interspersed repeat detection using inexact seeding.

    Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga, Michiaki Hamada

    Mobile DNA 16 ( 1 ) 16 - 16 2025.04

    　View Summary

    BACKGROUND: Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have sufficient repeat detection performance. RESULTS: In this study, we developed REPrise, a de novo interspersed repeat detection software program based on a seed-and-extension method. Although the algorithm of REPrise is similar to that of RepeatScout, which is currently the de facto standard tool, we incorporated three unique techniques into REPrise: inexact seeding, affine gap scoring and loose masking. Analyses of rice and simulation genome datasets showed that REPrise outperformed RepeatScout in terms of sensitivity, especially when the repeat sequences contained many mutations. Furthermore, when applied to the complete human genome dataset T2T-CHM13, REPrise demonstrated the potential to detect novel repeat sequence families. CONCLUSION: REPrise can detect interspersed repeats with high sensitivity even in long genomes. Our software enhances repeat annotation in diverse genomic studies, contributing to a deeper understanding of genomic structures.

  • Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 6803.

    Tsukasa Fukunaga, Takako Ogawa, Wataru Iwasaki, Kintake Sonoike

    Plant & cell physiology  2024.07

    Lead author, Accepted

    　View Summary

    Phycobilisomes play a crucial role in the light-harvesting mechanisms of cyanobacteria, red algae, and glaucophytes, but the molecular mechanism of their regulation is largely unknown. In the cyanobacterium, Synechocystis sp. PCC 6803, we identified a gene, slr0244, as a phycobilisome-related gene using phylogenetic profiling analysis, a method to predict gene function based on comparative genomics. To investigate the physiological function of the slr0244 gene, we characterize the slr0244 mutants spectroscopically. The disruption of the slr0244 gene impaired state transition, a process by which the distribution of light energy absorbed by the phycobilisomes between two photosystems was regulated in response to the changes in light conditions. The Slr0244 protein seems to act somewhere at or downstream of the sensing step of the redox state of the plastoquinone pool in the process of state transition. These findings, together with the past report of the interaction of this gene product with thioredoxin or glutaredoxin, suggest that the slr0244 gene is a novel state-transition regulator that integrates the redox signal of plastoquinone pools with that of photosystem I-reducing side. The protein has two USP (universal stress protein) motifs in tandem. The second motif has two conserved cysteine residues found in USPs of other cyanobacteria and land plants. These redox-type USPs with conserved cysteines may function as redox regulators in various photosynthetic organisms. Our study also showed the efficacy of the phylogenetic profiling analysis in predicting the function of cyanobacterial genes that have not been annotated so far.

  • DeepRaccess: high-speed RNA accessibility prediction using deep learning

    Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga, Michiaki Hamada

    Frontiers in Bioinformatics (Frontiers Media SA)  3 2023.10

    Corresponding author, Accepted

    　View Summary

    RNA accessibility is a useful RNA secondary structural feature for predicting RNA-RNA interactions and translation efficiency in prokaryotes. However, conventional accessibility calculation tools, such as Raccess, are computationally expensive and require considerable computational time to perform transcriptome-scale analysis. In this study, we developed DeepRaccess, which predicts RNA accessibility based on deep learning methods. DeepRaccess was trained to take artificial RNA sequences as input and to predict the accessibility of these sequences as calculated by Raccess. Simulation and empirical dataset analyses showed that the accessibility predicted by DeepRaccess was highly correlated with the accessibility calculated by Raccess. In addition, we confirmed that DeepRaccess could predict protein abundance in E.coli with moderate accuracy from the sequences around the start codon. We also demonstrated that DeepRaccess achieved tens to hundreds of times software speed-up in a GPU environment. The source codes and the trained models of DeepRaccess are freely available at https://github.com/hmdlab/DeepRaccess.

  • Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury

    Motoyo Maruyama, Atsushi Sakai, Tsukasa Fukunaga, Yoshitaka Miyagawa, Takashi Okada, Michiaki Hamada, Hidenori Suzuki

    Frontiers in Immunology (Frontiers Media SA)  14 2023.08

    Accepted

    　View Summary

    Primary sensory neurons regulate inflammatory processes in innervated regions through neuro-immune communication. However, how their immune-modulating functions are regulated in concert remains largely unknown. Here, we show that Neat1 long non-coding RNA (lncRNA) organizes the proinflammatory gene expressions in the dorsal root ganglion (DRG) in chronic intractable neuropathic pain in rats. Neat1 was abundantly expressed in the DRG and was upregulated after peripheral nerve injury. Neat1 overexpression in primary sensory neurons caused mechanical and thermal hypersensitivity, whereas its knockdown alleviated neuropathic pain. Bioinformatics analysis of comprehensive transcriptome changes indicated the inflammatory response was the most relevant function of genes upregulated through Neat1. Consistent with this, upregulation of proinflammatory genes in the DRG following nerve injury was suppressed by Neat1 knockdown. Expression changes of these proinflammatory genes were regulated through Neat1-mRNA interaction-dependent and -independent mechanisms. Notably, Neat1 increased proinflammatory genes by stabilizing its interacting mRNAs in neuropathic pain. Finally, Neat1 in primary sensory neurons contributed to spinal inflammatory processes that mediated peripheral neuropathic pain. These findings demonstrate that Neat1 lncRNA is a key regulator of neuro-immune communication in neuropathic pain.

  • Bioinformatics approaches for unveiling virus-host interactions.

    Hitoshi Iuchi, Junna Kawasaki, Kento Kubo, Tsukasa Fukunaga, Koki Hokao, Gentaro Yokoyama, Akiko Ichinose, Kanta Suga, Michiaki Hamada

    Computational and structural biotechnology journal 21   1774 - 1784 2023

    Accepted

    　View Summary

    The coronavirus disease-2019 (COVID-19) pandemic has elucidated major limitations in the capacity of medical and research institutions to appropriately manage emerging infectious diseases. We can improve our understanding of infectious diseases by unveiling virus-host interactions through host range prediction and protein-protein interaction prediction. Although many algorithms have been developed to predict virus-host interactions, numerous issues remain to be solved, and the entire network remains veiled. In this review, we comprehensively surveyed algorithms used to predict virus-host interactions. We also discuss the current challenges, such as dataset biases toward highly pathogenic viruses, and the potential solutions. The complete prediction of virus-host interactions remains difficult; however, bioinformatics can contribute to progress in research on infectious diseases and human health.

display all >>

Page Top ▲

Research Projects of Competitive Funds, etc. 【 Display / hide 】

  • 深層学習を用いたRNA二次構造情報解析の高速化

    2023.04
    -
    2026.03

    日本学術振興会, 科学研究費助成事業, 若手研究, No Setting

  • 大規模メタゲノムデータを用いた高精度機能未知遺伝子推定手法の開発

    2022.04
    -
    2024.03

    日本学術振興会, 科学研究費助成事業 新学術領域研究(研究領域提案型), 新学術領域研究(研究領域提案型), No Setting

  • リピート要素のde novo発見に基づく長鎖ノンコーディングRNAの機能の解明

    2020.04
    -
    2023.03

    日本学術振興会, 科学研究費助成事業 基盤研究(A), 基盤研究(A), No Setting

  • 逆イジングモデル法に基づく機能未知な微生物遺伝子の機能推定

    2020.04
    -
    2022.03

    Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), No Setting

  • 統計的論理関係解析法に基づく機能未知遺伝子の機能推定

    2019.04
    -
    2022.03

    Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists, Grant-in-Aid for Early-Career Scientists, No Setting

display all >>

Page Top ▲

Awards 【 Display / hide 】

  • 優秀プレゼンテーション賞

    2024.11, 情報処理学会第80回バイオ情報学研究会, CapR-G4:G4構造を考慮したRNA二次構造の構造プロファイル計算

  • Oxford journals-JSBi Prize

    2024.08, 日本バイオインフォマティクス学会, Function estimation of the function-unknown genes through RNA structural analysis and comparative genomic analysis

  • 優秀口頭発表賞

    福永津嵩, 岩崎渉, 2021, 第十回生命医薬情報学連合大会, The inverse Potts model improves accuracy of phylogenetic profiling

  • ポスター賞

    毛利公一, 尾崎遼, 福永津嵩, 2020, 第九回生命医薬情報学連合大会, 統計的有意性を担保可能な系列パターンマイニングに基づく配列モチーフ検出ソフトウェアの開発

  • ポスター賞

    福永津嵩, 浜田道昭, 2016, 第五回生命医薬情報学連合大会, RIblast: A high-speed RNA-RNA interaction prediction system for comprehensive lncRNA interactome analysis.

Page Top ▲
 

Courses Taught 【 Display / hide 】

  • TOPICS IN BIOSCIENCES AND INFORMATICS 1

    2025

  • SEMINAR IN BIOSCIENCES AND INFORMATICS

    2025

  • INTRODUCTION TO BIOLOGY TODAY

    2025

  • INTRODUCTION TO ALGORITHMS

    2025

  • INDEPENDENT STUDY ON FUNDAMENTAL SCIENCE AND TECHNOLOGY

    2025

display all >>

Page Top ▲
 

Committee Experiences 【 Display / hide 】

  • 2024.04
    -
    Present

    編集委員, IPSJ Transactions on Bioinformatics

  • 2024.04
    -
    Present

    理事, 日本バイオインフォマティクス学会

  • 2024.04
    -
    Present

    幹事, 日本バイオインフォマティクス学会

  • 2023.07
    -
    Present

    Review Editor, Frontiers in Bioinformatics

  • 2023.04
    -
    Present

    バイオ情報学研究会運営委員, 情報処理学会

display all >>

Page Top ▲