1.
Shun Yamanouchi*, Tsukasa Fukunaga and Wataru Iwasaki*.
CoLaML: Inferring latent evolutionary modes from heterogeneous gene content. [preprint]
2.
XX XX, Tsukasa Fukunaga, XX XX.
3.
Tao Zhu, Yukuto Sato, Tsukasa Fukunaga, Masaki Miya, Wataru Iwasaki, Susumu Yoshizawa*.
MitoNGS: an online platform to analyze fish metabarcoding data in high-resolution. [preprint]
1.
福永 津嵩(共著)、岩切淳一(共著)、浜田道昭(監修)
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)
コロナ社 (2022/7/14)
2.
Michiaki Hamada (Editor), Tsukasa Fukunaga (Editor), Chao Zeng (Editor)
RNA-RNA and RNA-DNA Interactions. (Methods in Molecular Biology vol. 2949)
Springer Nature (2025/11/1)
(first and/or corresponding author: 15)
29.
Sana Ohashi, Sumie Ishiguro, Tsukasa Fukunaga, Akinobu Matsumoto, Mina Hirata, Masahito Inagaki, Naoko Abe, Fumitaka Hashiya, Hiroshi Abe*.
Selection of Short 5′-UTR of Chemically Synthesized mRNA to Improve Translation Efficiency.
Chemical and Pharmaceutical Bulletin, 73, 5, (2025) [Pubmed]
28.
Atsuhi Takeda#, Daisuke Nonaka#, Yuta Imazu, Tsukasa Fukunaga* and Michiaki Hamada*.
REPrise: de novo interspersed repeat detection using inexact seeding. [preprint]
Mobile DNA, 16, 16, (2025) [Pubmed]
27.
Tsukasa Fukunaga, Takako Ogawa, Wataru Iwasaki and Kintake Sonoike*.
Plant and Cell Physiology, 9, 1450-1460, (2024) [Pubmed]
26.
Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga* and Michiaki Hamada*.
DeepRaccess: High-speed RNA accessibility prediction using deep learning. [preprint]
Frontiers in Bioinformatics, 3, 1275787, (2023) [Pubmed]
25.
Motoyo Maruyama, Atushi Sakai*, Tsukasa Fukunaga, Yoshitaka Miyagawa, Takashi Okada, Michiaki Hamada and Hidenori Suzuki.
Frontiers in Immunology, 14, 1185322, (2023) [Pubmed]
24.
Tsukasa Fukunaga* and Michiaki Hamada.
LinAliFold and CentroidLinAliFold: Fast RNA consensus secondary structure prediction for aligned sequences using beam search methods. [preprint]
Bioinformatics Advances, 2, vbac078, (2022) [Pubmed]
23.
Tsukasa Fukunaga* and Wataru Iwasaki.
Bioinformatics, 38, 4039-4041 (2022) [Pubmed]
22.
Tsukasa Fukunaga* and Wataru Iwasaki.
Inverse Potts model improves accuracy of phylogenetic profiling. [preprint]
Bioinformatics, 38, 1794-1800, (2022) [Pubmed]
21.
Tsukasa Fukunaga* and Wataru Iwasaki*.
Mirage: Estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families. [preprint]
Bioinformatics Advances, 1, vbab014, (2021) [Pubmed]
20.
Shion Hosoda*, Tsukasa Fukunaga and Michiaki Hamada*.
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. [preprint]
Bioinformatics, 37, i16-i24, (2021) [PubMed]
19.
Hirotaka Matsumoto*, Takahiro Mimori and Tsukasa Fukunaga.
Novel metric for hyperbolic phylogenetic tree embeddings. [preprint]
Biology Methods & Protocols, 6, bpab006, (2021) [PubMed]
18.
Koichi Mori, Haruka Ozaki and Tsukasa Fukunaga*.
MotiMul: A significant discriminative sequence motif discovery algorithm with multiple testing correction. [preprint]
IEEE BIBM, 186-193, (2020)
17.
Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori and Michiaki Hamada*.
Microbiome, 8, 95, (2020) [PubMed]
16.
Tsukasa Fukunaga* and Wataru Iwasaki.
PLoS One, 15, e0232106, (2020) [PubMed]
15.
Hangchuan Shi, Yin Sun, Miao He, Xiong Yang, Michiaki Hamada, Tsukasa Fukunaga, Xiaoping Zhang* and Chawnshang Chang*.
Oncogene, 39, 530-545, (2020) [PubMed]
14.
Tsukasa Fukunaga#, Junichi Iwakiri#, Yukiteru Ono and Michiaki Hamada*.
Frontiers in Genetics, 10, 462, (2019) [PubMed]
13.
Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga and Michiaki Hamada*.
Bioinformatics, 35, 4543-4552. (2019) [PubMed]
12.
Tsukasa Fukunaga* and Michiaki Hamada*.
Journal of Computational Biology, 25, 976-986. (2018) [PubMed]
11.
Chao Zeng, Tsukasa Fukunaga and Michiaki Hamada*.
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data.
BMC Genomics, 19, 414. (2018) [PubMed]
10.
Yukuto Sato*, Masaki Miya, Tsukasa Fukunaga, Tetsuya Sado, and Wataru Iwasaki*.
Molecular Biology and Evolution, 35, 1553-1555., (2018) [PubMed]
9.
Yohei Kumagai, Susumu Yoshizawa*, Yu Nakajima, Mai Watanabe, Tsukasa Fukunaga, Yoshitoshi Ogura, Tetsuya Hayashi, Kenshiro Oshima, Masahira Hattori, Masahiko Ikeuchi, Kazuhiro Kogure, Edward F. Delong, and Wataru Iwasaki*.
The ISME journal, 12, 1329-1343., (2018) [PubMed]
8.
Tsukasa Fukunaga* and Michiaki Hamada*.
RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.
Bioinformatics, 33, 2666-2674., (2017) [PubMed] [preprint]
7.
Tsukasa Fukunaga*and Wataru Iwasaki*.
BMC Bioinformatics, 18, 46. (2017) [PubMed]
6.
Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, and Kiyoshi Asai*.
Rtools: a web server for various secondary structural analyses on single RNA sequences.
Nucleic Acids Research, 44, W302-W307. (2016) [PubMed]
5.
Masaki Miya*, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Yde Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondo, and Wataru Iwasaki.
Royal Society Open Science, 2, 150088. (2015) [PubMed]
4.
Tsukasa Fukunaga*, Shoko Kubota, Shoji Oda, and Wataru Iwasaki*.
GroupTracker: Video Tracking System for Multiple Animals under Severe Occlusion.
Computational Biology and Chemistry, 57, 39-45. (2015) [PubMed]
3.
Tsukasa Fukunaga*, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, and Hisanori Kiryu.
Genome Biology, 15, R16. (2014) [PubMed]
2.
Wataru Iwasaki*, Tsukasa Fukunaga, Ryota Isagozawa, Koichiro Yamada, Yasunobu Maeda, Takashi P. Satoh, Tetsuya Sado, Kohji Mabuchi, Hirohiko Takeshima, Masaki Miya, and Mutsumi Nishida*.
Molecular Biology and Evolution, 30, 2531-2540. (2013) [PubMed]
1.
Masaki Miya*, Matt Friedman, Takashi P. Satoh, Hirohiko Takeshima, Tetsuya Sado, Wataru Iwasaki, Yusuke Yamanoue, Masanori Nakatani, Kohji Mabuchi, Jun G. Inoue, Jan Yde Poulsen, Tsukasa Fukunaga, Yukuto Sato, and Mutsumi Nishida.
Plos one, 8, e73535. (2013) [PubMed]
14.
福永津嵩.
生物配列解析.
巌佐庸・大槻久・佐竹暁子・望月敦史 (編)『理論生物学事典』pp. 432–433, 朝倉書店 (2025)
13.
Tsukasa Fukunaga*.
Machine Learning Approaches for Predicting RNA–RNA/DNA Interactions.
Methods in Molecular Biology, 2949, 229-237. (2025) [PubMed]
12.
福永津嵩.
5分で分かる!? 有名論文ナナメ読み：Kazutaka Kato et al. : MAFFT : A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform.
情報処理, 65.7, 376-377. (2024)
11.
由良敬，松永浩子，細川正人，和泉自泰，村松知成，福永津嵩，浜田道昭，馬場健史，竹山春子.
シングルセル/微小組織マルチオミクス解析.
実験医学増刊号, 42.2, 1章4節. (2024)
10.
Hitoshi Iuchi*, Junna Kawasaki, Kento Kubo, Tsukasa Fukunaga, Koki Hokao, Gentaro Yokoyama, Akiko Ichinose, Kanta Suga and Michiaki Hamada*.
Bioinformatics approaches for unveiling virus–host interactions.
Computational and Structural Biotechnology Journal, 21, 1774-1784. (2023) [PubMed]
9.
Tsukasa Fukunaga, Junichi Iwakiri and Michiaki Hamada*.
Web services for RNA-RNA interaction prediction.
Methods in Molecular Biology, 2586, 175-195. (2023) [PubMed]
8.
Tsukasa Fukunaga* and Michiaki Hamada.
Methods in Molecular Biology, 2586, 163-173. (2023) [PubMed]
7.
Chao Zeng*, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga and Michiaki Hamada*.
Methods in Molecular Biology, 2509, 315-340. (2022) [PubMed] [preprint]
6.
Hitoshi Iuchi*, Taro Matsutani, Keisuke Yamada, Shunsuke Sumi, Shion Hosoda, Shitao Zhao, Tsukasa Fukunaga and Michiaki Hamada*.
Representation learning applications in biological sequence analysis.
Computational and Structural Biotechnology Journal, 19, 3198-3208. (2021) [PubMed] [preprint]
5.
尾崎遼、福永 津嵩 、松本拡高.
ENCODE3勉強会.
実験医学, 39, 467-472. (2021)
4.
福永 津嵩.
JSBi Bioinformatics Review, 1, 3-11. (2020)
3.
Tsukasa Fukunaga and Michiaki Hamada*.
Computational Approaches for Alternative and Transient Secondary Structures for Ribonucleic Acids.
Briefings in Functional Genomics, 18, 182-191. (2019) [PubMed]
2.
福永 津嵩、浜田 道昭.
バイオイメージインフォマティクスにおける機械学習技術の活用.
日本画像学会誌, 56, 163-167. (2017)
1.
福永 津嵩、岩崎 渉.
Computational Ethology: バイオインフォマティクスと動物行動学の融合.
領域融合レビュー, 4, e003. (2015)