FUKUNAGA Tsukasa 福永津嵩

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Fukunaga Tsukasa 福永津嵩

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Researcher Number	80791433
Other IDs
Affiliation (Current)	2026: 慶應義塾大学, 理工学部(矢上), 准教授
Affiliation (based on the past Project Information) *help	2022 – 2024: 早稲田大学, 高等研究所, 准教授(任期付) 2020 – 2022: 早稲田大学, 高等研究所, 講師(任期付) 2017 – 2020: 東京大学, 大学院情報理工学系研究科, 助教
Review Section/Research Field	Principal Investigator Complex systems / Basic Section 62010:Life, health and medical informatics-related / Biological Sciences Except Principal Investigator Medium-sized Section 62:Applied informatics and related fields
Keywords	Principal Investigator アルゴリズム / 遺伝子機能推定 / 高速化 / メタゲノム / 機械学習 / 系統プロファイル法 / 機能未知遺伝子 / 確率モデル / lncRNA / 比較ゲノム … More / 融合遺伝子 / 深層学習 / RNA二次構造 / 進化 / ゲノム進化 / 論理関係 / 多重検定補正 / ゲノム解析 / データベース … More Except Principal Investigator 散在的リピート / BERT / 長鎖ノンコーディングRNA / 難溶性RNA / RNA結合タンパク質 / lncRNA / アルゴリズム / トランスポゾン / リピート要素 Less

深層学習を用いたRNA二次構造情報解析の高速化Principal Investigator
- Principal Investigator
  
  福永津嵩
- Project Period (FY)
  2023 – 2025
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Waseda University
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Principal Investigator
- Principal Investigator
  
  福永津嵩
- Project Period (FY)
  2022 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Waseda University
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Principal Investigator
- Principal Investigator
  
  福永津嵩
- Project Period (FY)
  2020 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Waseda University
Elucidation of the function of long non-coding RNAs based on de novo discovery of repeat elements
- Principal Investigator
  
  Hamada Michiaki
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  Waseda University
Function estimation of functional-unknown genes using statistical logical relationship analysisPrincipal Investigator
- Principal Investigator
  
  Fukunaga Tsukasa
- Project Period (FY)
  2019 – 2022
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Waseda University
  The University of Tokyo
lncRNA-mRNAの相互作用ネットワークに基づくlncRNAの機能推定Principal Investigator
- Principal Investigator
  
  福永津嵩
- Project Period (FY)
  2017 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Biological Sciences
- Research Institution
  The University of Tokyo

All 2025 2024 2023 2022 2021 2020 2019 2018 2017

All Journal Article Presentation

[Journal Article] REPrise: de novo interspersed repeat detection using inexact seeding2025
- Author(s)
  Takeda Atsushi、Nonaka Daisuke、Imazu Yuta、Fukunaga Tsukasa、Hamada Michiaki
- Journal Title
  
  Mobile DNA
  
  Volume: 16 Issue: 1 Pages: 16-16
- DOI
  10.1186/s13100-025-00353-0
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K16997, KAKENHI-PROJECT-23KJ2044
[Journal Article] Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 68032024
- Author(s)
  Tsukasa Fukunaga , Takako Ogawa , Wataru Iwasaki , Kintake Sonoike
- Journal Title
  
  Plant and Cell Physiology
  
  Volume: 65 Issue: 9 Pages: 1450-1460
- DOI
  10.1093/pcp/pcae083
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-22H04891, KAKENHI-PLANNED-23H04961, KAKENHI-PROJECT-23K23914
[Journal Article] REPrise: De novo repeat detection using inexact seeding2024
- Author(s)
  Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga, Michiaki Hamada
- Journal Title
  
  biorxiv
  
  Volume: -
- DOI
  10.1101/2024.01.21.576581
- Open Access
- Data Source
  KAKENHI-PROJECT-23KJ2044, KAKENHI-PROJECT-20H00624
[Journal Article] DeepRaccess: high-speed RNA accessibility prediction using deep learning2023
- Author(s)
  Hara Kaisei、Iwano Natsuki、Fukunaga Tsukasa、Hamada Michiaki
- Journal Title
  
  Frontiers in Bioinformatics
  
  Volume: 3 Pages: 1275787-1275787
- DOI
  10.3389/fbinf.2023.1275787
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K16997, KAKENHI-PUBLICLY-22H04891, KAKENHI-PROJECT-20H00624, KAKENHI-PROJECT-22H04925
[Journal Article] Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families2022
- Author(s)
  Tsukasa Fukunaga、Wataru Iwasaki
- Journal Title
  
  Bioinformatics
  
  Volume: 38 Issue: 16 Pages: 4039-4041
- DOI
  10.1093/bioinformatics/btac433
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-19K20395, KAKENHI-PLANNED-19H05688, KAKENHI-PUBLICLY-20H05582
[Journal Article] Inverse Potts model improves accuracy of phylogenetic profiling2022
- Author(s)
  Fukunaga Tsukasa、Iwasaki Wataru
- Journal Title
  
  Bioinformatics
  
  Volume: 38 Issue: 7 Pages: 1794-1800
- DOI
  10.1093/bioinformatics/btac034
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K20395, KAKENHI-PLANNED-19H05688, KAKENHI-PUBLICLY-20H05582
[Journal Article] LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods2022
- Author(s)
  Tsukasa Fukunaga、Michiaki Hamada
- Journal Title
  
  Bioinformatics Advances
  
  Volume: 2 Issue: 1
- DOI
  10.1093/bioadv/vbac078
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22H04925, KAKENHI-PUBLICLY-20H05582
[Journal Article] Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families2021
- Author(s)
  Fukunaga Tsukasa、Iwasaki Wataru
- Journal Title
  
  Bioinformatics Advances
  
  Volume: 1 Issue: 1
- DOI
  10.1093/bioadv/vbab014
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-19H05688, KAKENHI-PROJECT-19K20395, KAKENHI-PROJECT-16H06279, KAKENHI-PUBLICLY-20H05582
[Journal Article] Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with Tretinoin increases the Sunitnib sensitivity to better suppress the RCC progression2020
- Author(s)
  Hangchuan Shi, Yin Sun, Miao He, Xiong Yang, Michiaki Hamada, Tsukasa Fukunaga, Xiaoping Zhang and Chawnshang Chang.
- Journal Title
  
  Oncogene
  
  Volume: 39 Issue: 3 Pages: 530-545
- DOI
  10.1038/s41388-019-0962-8
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879
[Journal Article] Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data2020
- Author(s)
  Fukunaga Tsukasa、Iwasaki Wataru
- Journal Title
  
  PLOS ONE
  
  Volume: 15 Issue: 5 Pages: e0232106-e0232106
- DOI
  10.1371/journal.pone.0232106
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K20395
[Journal Article] LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data2019
- Author(s)
  Tsukasa Fukunaga, Junichi Iwakiri, Yukiteru Ono and Michiaki Hamada
- Journal Title
  
  Front. Genet.
  
  Volume: - Pages: 462-462
- DOI
  10.3389/fgene.2019.00462
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17K20032, KAKENHI-PROJECT-16K16143, KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06279
[Journal Article] A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs2018
- Author(s)
  Fukunaga Tsukasa、Hamada Michiaki
- Journal Title
  
  Journal of Computational Biology
  
  Volume: 25 Issue: 9 Pages: 976-986
- DOI
  10.1089/cmb.2017.0260
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-16H01318, KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879
[Presentation] 転写因子RpaBのDNA結合活性のレドックス制御に関わる因子の同定2024
- Author(s)
  河原崎康介, 岩田和宜, 福永津嵩, 園池公毅, 日原由香子.
- Organizer
  藍藻の分子生物学2024
- Data Source
  KAKENHI-PUBLICLY-22H04891
[Presentation] Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Gene Encoding Novel State-Transition Regulator in Synechocystis sp. PCC 6803.2024
- Author(s)
  Tsukasa Fukunaga, Takako Ogawa, Wataru Iwasaki, Kintake Sonoike.
- Organizer
  European workshop on the biology of cyanobacteria 2024
- Data Source
  KAKENHI-PUBLICLY-22H04891
[Presentation] De novo interspersed repeat detection using inexact seed2024
- Author(s)
  Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga, Michiaki Hamada
- Organizer
  ISMB2024
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] Redox-type USP protein: a novel regulator of photosynthesis.2024
- Author(s)
  Tsukasa Fukunaga, Takako Ogawa, Kintake Sonoike
- Organizer
  2nd Asia-Oceania International Congress on Photosynthesis
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H04891
[Presentation] Deep Learning-based ncRNA Detection: Surpassing RNAz with Advanced MSA Transformer Models.2024
- Author(s)
  Ibuki Kaburagi, Tsukasa Fukunaga, Michiaki Hamada
- Organizer
  1st Asia & Pacific Bioinformatics Joint Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] 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2024
- Author(s)
  福永津嵩, 浜田道昭.
- Organizer
  第80回バイオ情報学(SIGBIO)研究会
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] 相同配列情報を活用した高速なRNA二次構造予測手法の開発.2024
- Author(s)
  西村友宏, 久保顕登, 福永津嵩, 浜田道昭.
- Organizer
  情報処理学会第77回バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] De novo interspersed repeat detection using inexact seeding.2024
- Author(s)
  Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga, Hamada Michiaki.
- Organizer
  1st Asia & Pacific Bioinformatics Joint Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] A fast RNA secondary structure prediction method using homologous sequence information.2024
- Author(s)
  Tomohiro Nishimura, Kento Kubo, Tsukasa Fukunaga, Michiaki Hamada.
- Organizer
  1st Asia & Pacific Bioinformatics Joint Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] 比較ゲノム解析により明らかとなった, Synechocystis sp. PCC 6803におけるユニバーサルストレスタンパク質のステート遷移制御機能2023
- Author(s)
  福永津嵩, 小川敬子, 岩崎渉, 園池公毅.
- Organizer
  第65回植物生理学会年会
- Data Source
  KAKENHI-PUBLICLY-22H04891
[Presentation] DeepRaccess: 深層学習を用いた高速なRNAアクセシビリティ予測2023
- Author(s)
  原快成、岩野夏樹、福永津嵩、浜田道昭.
- Organizer
  第76回バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-23K16997
[Presentation] DeepRaccess: 深層学習を用いた高速なRNAアクセシビリティ予測2023
- Author(s)
  原快成、岩野夏樹、福永津嵩、浜田道昭.
- Organizer
  第76回バイオ情報学研究会
- Data Source
  KAKENHI-PUBLICLY-22H04891
[Presentation] Mirage: A phylogenetic mixture model to reconstruct gene content evolutionary history using a realistic evolutionary rate model2020
- Author(s)
  福永津嵩、岩崎渉
- Organizer
  第9回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-19K20395
[Presentation] MotiMul: A significant discriminative sequence motif discovery algorithm with multiple testing correction.2020
- Author(s)
  Koichi Mori, Haruka Ozaki and Tsukasa Fukunaga
- Organizer
  IEEE BIBM 2020
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K20395
[Presentation] 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2020
- Author(s)
  Koichi Mori, Haruka Ozaki and Tsukasa Fukunaga
- Organizer
  第9回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-19K20395
[Presentation] RNA相互作用解析のためのバイオインフォマティクスソフトウェア開発2019
- Author(s)
  福永津嵩
- Organizer
  RNAフロンティアミーティング2019
- Data Source
  KAKENHI-PUBLICLY-17H05605
[Presentation] Tarone法を用いた系列パターンマイニングの多重検定補正2019
- Author(s)
  毛利公一、福永津嵩
- Organizer
  日本バイオインフォマティクス学会2019年年会
- Data Source
  KAKENHI-PROJECT-19K20395
[Presentation] Tarone法を用いた頻出部分文字列マイニングの多重検定補正2019
- Author(s)
  毛利公一、福永津嵩
- Organizer
  IBIS2019
- Data Source
  KAKENHI-PROJECT-19K20395
[Presentation] ヒトlncRNA-RNAの網羅的相互作用予測及びデータベースの構築2017
- Author(s)
  福永津嵩、岩切淳一、小野幸輝、浜田道昭
- Organizer
  第五回NGS現場の会
- Data Source
  KAKENHI-PUBLICLY-17H05605
[Presentation] lncRNA-mRNAの網羅的相互作用予測へ向けた高速なRNA-RNA相互作用予測ソフトウェアRIblastの開発2017
- Author(s)
  福永津嵩、浜田道昭
- Organizer
  第19回日本RNA学会年会
- Data Source
  KAKENHI-PUBLICLY-17H05605
[Presentation] RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.2017
- Author(s)
  福永津嵩、浜田道昭
- Organizer
  第６回生命医薬情報学連合大会
- Data Source
  KAKENHI-PUBLICLY-17H05605

1. Hamada Michiaki (00596538)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
2. 足達俊吾 (90783803)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. 小野口真広 (30645297)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. IWASAKI Wataru

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
5. 岩切淳一

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

FUKUNAGA Tsukasa 福永 津嵩

Fukunaga Tsukasa 福永 津嵩

Research Projects

Research Products

Co-Researchers

深層学習を用いたRNA二次構造情報解析の高速化Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

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Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

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Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Elucidation of the function of long non-coding RNAs based on de novo discovery of repeat elements

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Function estimation of functional-unknown genes using statistical logical relationship analysisPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

lncRNA-mRNAの相互作用ネットワークに基づくlncRNAの機能推定Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] REPrise: de novo interspersed repeat detection using inexact seeding2025

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 68032024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] REPrise: De novo repeat detection using inexact seeding2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] DeepRaccess: high-speed RNA accessibility prediction using deep learning2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Inverse Potts model improves accuracy of phylogenetic profiling2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families2021

Author(s)

Journal Title

DOI

FUKUNAGA Tsukasa 福永津嵩

Fukunaga Tsukasa 福永津嵩