KEIO RESEARCHERS INFORMATION SYSTEM

Profile Summary 【 Display / hide 】

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。

Career 【 Display / hide 】

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

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Academic Background 【 Display / hide 】

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

Academic Degrees 【 Display / hide 】

Academic Degrees 【 Display / hide 】

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

  Bioinformatics for Understanding Animal Behavior

Research Areas 【 Display / hide 】

Research Areas 【 Display / hide 】

• Life Science / Genome biology

• Life Science / System genome science

• Informatics / Life, health and medical informatics

Research Keywords 【 Display / hide 】

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

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Books 【 Display / hide 】

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

  • CiNii Research

Papers 【 Display / hide 】

Papers 【 Display / hide 】

• MitoNGS: an online platform to analyze fish metabarcoding data in high resolution

  Tao Zhu, Yukuto Sato, Tsukasa Fukunaga, Masaki Miya, Wataru Iwasaki, Susumu Yoshizawa

  Molecular Biology and Evolution (Oxford University Press (OUP))  43 ( 3 )  2026.03

  ISSN  07374038

  　View Summary

  Abstract
  
  Environmental DNA (eDNA) metabarcoding has become a powerful tool for assessing fish biodiversity in aquatic ecosystems. However, accurate species-level identification remains challenging due to incomplete and contaminated reference databases, as well as ambiguous taxa sharing identical barcode sequences. Here, we present MitoNGS, a next-generation platform that succeeds the widely used MiFish pipeline, designed for high-resolution analysis of fish metabarcoding data. MitoNGS addresses these challenges by incorporating more comprehensive references including non-fish species and detailed annotations of heterospecific regions. Additionally, it introduces the “species complex” strategy in conjunction with environmental habitat and geographic occurrence data to resolve ambiguous taxa. Furthermore, MitoNGS expands the functionalities of the legacy MiFish pipeline. It can analyze data from any mitochondrial markers and from Nanopore sequencing platforms. MitoNGS demonstrated excellent performance on our testing datasets from diverse locations, markers, and sequencing platforms. MitoNGS offers a user-friendly, web-based solution for fish detection, biodiversity monitoring, conservation research, and bioresource management. MitoNGS is freely available via https://mitofish.aori.u-tokyo.ac.jp/mito-ngs.

  • Access to Document (DOI)

• Selection of Short 5'-UTR of Chemically Synthesized mRNA to Improve Translation Efficiency.

  Sana Ohashi, Sumie Ishiguro, Tsukasa Fukunaga, Akinobu Matsumoto, Mina Hirata, Masahito Inagaki, Naoko Abe, Fumitaka Hashiya, Hiroshi Abe

  Chemical & pharmaceutical bulletin 73 ( 5 ) 449 - 456 2025.05

  ISSN  00092363

  　View Summary

  The advent of mRNA medicine, initially implemented as a vaccine during the coronavirus disease 2019 (COVID-19) pandemic, has attracted interest in diverse therapeutic applications, including cancer vaccines and protein replacement therapies. Our group recently established a method for the complete chemical synthesis of mRNA. Although this approach has some advantages, chemically synthesized mRNA is limited to approximately 150 nucleotides in length and necessitates optimized designs for untranslated regions (UTRs) and coding sequences. To address this challenge, we investigated whether the non-reporter-based selection methods, including ribosome profiling and polysome profiling, which were often used for UTR optimization in long mRNA, could be adapted for short mRNA to identify highly translated UTR sequences. Using these methods, we collected mRNAs that interacted with ribosomes and analyzed their 5'-UTR sequences. We successfully identified a 9-nucleotide 5'-UTR that demonstrated approximately double the translation efficiency of the Kozak sequence, a widely used positive control. This work highlights the adaptability of ribosome-focused selection techniques for short, chemically synthesized mRNA and provides a foundation for effective sequence design. These findings advance the development of chemically synthesized mRNA as a viable alternative to in vitro-transcribed mRNA, paving the way for innovative therapeutic applications.

  • Access to Document (DOI)

• 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

  Accepted

  　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.

  • Access to Document (DOI)

• 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 65 ( 9 ) 1450 - 1460 2024.07

  Lead author, Accepted,  ISSN  00320781

  　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.

  • Access to Document (DOI)

• 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.

  • Access to Document (DOI)

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

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

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  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

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  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

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  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

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  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

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Awards 【 Display / hide 】

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.

Courses Taught 【 Display / hide 】

Courses Taught 【 Display / hide 】

• ADVANCED LABORATORY COURSE IN BIOSCIENCES AND INFORMATICS A

  2025

• ADVANCED LABORATORY COURSE IN BIOSCIENCES AND INFORMATICS B

  2025

• TOPICS IN BIOSCIENCES AND INFORMATICS 1

  2025

• SEMINAR IN BIOSCIENCES AND INFORMATICS

  2025

• INTRODUCTION TO BIOLOGY TODAY

  2025

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Committee Experiences 【 Display / hide 】

Committee Experiences 【 Display / hide 】

• 2024.04

  -

  Present

  編集委員, IPSJ Transactions on Bioinformatics

• 2024.04

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  Present

  理事, 日本バイオインフォマティクス学会

• 2024.04

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  Present

  幹事, 日本バイオインフォマティクス学会

• 2023.07

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  Present

  Review Editor, Frontiers in Bioinformatics

• 2023.04

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  Present

  バイオ情報学研究会運営委員, 情報処理学会

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