Wataru Iwasaki

ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 51

Top Venues

Communications biology

Nature communications

Nucleic acids research

Molecular biology and evolution

The University of Tokyo

The University of Tokyo (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

The University of Tokyo

Japan

Associate Professor :: Department of Biological Sciences

The University of Tokyo

Japan

Assistant Professor (Tenured) :: Atmosphere and Ocean Research Institute

The University of Tokyo

Japan

Assistant Professor :: Department of Computational Biology

Education History

The University of Tokyo

Japan

PHD :: Department of Computational Biology

The University of Tokyo

Japan

MSC :: Department of Computational Biology

The University of Tokyo

Japan

BSC :: Department of Biophysics and Biochemistry

Publications

Salvatore Cosentino, Sira Sriswasdi, Wataru Iwasaki
SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models. Genome biology 25 (1) (2024)
Sachiko Masuda, Pamela Gan, Yuya Kiguchi, Mizue Anda, Kazuhiro Sasaki, Arisa Shibata, Wataru Iwasaki, Wataru Suda, Ken Shirasu
Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing. Communications biology 7 (1) (2024)
Tsukasa Fukunaga, Takako Ogawa, Wataru Iwasaki, Kintake Sonoike
Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 6803. Plant & cell physiology (2024)
Salvatore Cosentino, Sira Sriswasdi, Wataru Iwasaki
SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models. Genome biology 25 (1) (2024)
Yuhei Chadani, Shun Yamanouchi, Eri Uemura, Kohei Yamasaki, Tatsuya Niwa, Toma Ikeda, Miku Kurihara, Wataru Iwasaki, Hideki Taguchi
The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic acids research 52 (10) (2024)
Yuhei Chadani, Shun Yamanouchi, Eri Uemura, Kohei Yamasaki, Tatsuya Niwa, Toma Ikeda, Miku Kurihara, Wataru Iwasaki, Hideki Taguchi
The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic acids research 52 (10) (2024)
Sachiko Masuda, Pamela Gan, Yuya Kiguchi, Mizue Anda, Kazuhiro Sasaki, Arisa Shibata, Wataru Iwasaki, Wataru Suda, Ken Shirasu
Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing. Communications biology 7 (1) (2024)
Yuhei Chadani, Shun Yamanouchi, Eri Uemura, Kohei Yamasaki, Tatsuya Niwa, Toma Ikeda, Miku Kurihara, Wataru Iwasaki, Hideki Taguchi
The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic acids research 52 (10) (2024)
Kento Tominaga, Shogo Ozaki, Shohei Sato, Tsutomu Katayama, Yuki Nishimura, Kimiho Omae, Wataru Iwasaki
Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae . Proceedings of the National Academy of Sciences of the United States of America 121 (19) (2024)
Sachiko Masuda, Pamela Gan, Yuya Kiguchi, Mizue Anda, Kazuhiro Sasaki, Arisa Shibata, Wataru Iwasaki, Wataru Suda, Ken Shirasu
Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing. Communications biology 7 (1) (2024)
Naoki Konno, Shintaro Maeno, Yasuhiro Tanizawa, Masanori Arita, Akihito Endo, Wataru Iwasaki
Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments. Communications biology 7 (1) (2024)
Kento Tominaga, Shogo Ozaki, Shohei Sato, Tsutomu Katayama, Yuki Nishimura, Kimiho Omae, Wataru Iwasaki
Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae . Proceedings of the National Academy of Sciences of the United States of America 121 (19) (2024)
Yuhei Chadani, Shun Yamanouchi, Eri Uemura, Kohei Yamasaki, Tatsuya Niwa, Toma Ikeda, Miku Kurihara, Wataru Iwasaki, Hideki Taguchi
The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic acids research (2024)
Naoki Konno, Shintaro Maeno, Yasuhiro Tanizawa, Masanori Arita, Akihito Endo, Wataru Iwasaki
Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments. Communications biology 7 (1) (2024)
Kento Tominaga, Shogo Ozaki, Shohei Sato, Tsutomu Katayama, Yuki Nishimura, Kimiho Omae, Wataru Iwasaki
Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae . Proceedings of the National Academy of Sciences of the United States of America 121 (19) (2024)
Naoki Konno, Wataru Iwasaki
Machine learning enables prediction of metabolic system evolution in bacteria. Science advances 9 (2) (2023)
Naoki Konno, Wataru Iwasaki
Machine learning enables prediction of metabolic system evolution in bacteria. Science advances 9 (2) (2023)
Chunlai Tam, Wataru Iwasaki
AlphaCutter: Efficient removal of non-globular regions from predicted protein structures. Proteomics (2023)
Tao Zhu, Yukuto Sato, Tetsuya Sado, Masaki Miya, Wataru Iwasaki
MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years. Molecular biology and evolution 40 (3) (2023)
Mizue Anda, Shun Yamanouchi, Salvatore Cosentino, Mitsuo Sakamoto, Moriya Ohkuma, Masako Takashima, Atsushi Toyoda, Wataru Iwasaki
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years. Nature communications 14 (1) (2023)
Kei Hiruma, Seishiro Aoki, Junya Takino, Takeshi Higa, Yuniar Devi Utami, Akito Shiina, Masanori Okamoto, Masami Nakamura, Nanami Kawamura, Yoshihiro Ohmori, Ryohei Sugita, Keitaro Tanoi, Toyozo Sato, Hideaki Oikawa, Atsushi Minami, Wataru Iwasaki, Yusuke Saijo
A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae. Nature communications 14 (1) (2023)
Kazuki Miyata, Wataru Iwasaki
Seq2Phase: language model-based accurate prediction of client proteins in liquid-liquid phase separation. Bioinformatics advances 4 (1) (2023)
Naoki Konno, Wataru Iwasaki
Machine learning enables prediction of metabolic system evolution in bacteria. Science advances 9 (2) (2023)
Kazuki Miyata, Wataru Iwasaki
Seq2Phase: language model-based accurate prediction of client proteins in liquid-liquid phase separation. Bioinformatics advances 4 (1) (2023)
Tao Zhu, Yukuto Sato, Tetsuya Sado, Masaki Miya, Wataru Iwasaki
MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in ten years. Molecular biology and evolution (2023)
Tao Zhu, Yukuto Sato, Tetsuya Sado, Masaki Miya, Wataru Iwasaki
MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years. Molecular biology and evolution 40 (3) (2023)
Naoki Konno, Wataru Iwasaki
Machine learning enables prediction of metabolic system evolution in bacteria. Science advances 9 (2) (2023)
Kazumori Mise, Wataru Iwasaki
Unexpected absence of ribosomal protein genes from metagenome-assembled genomes. ISME communications 2 (1) (2022)
Asano Ishikawa, Shun Yamanouchi, Wataru Iwasaki, Jun Kitano
Convergent copy number increase of genes associated with freshwater colonization in fishes. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 377 (1855) (2022)
Tsukasa Fukunaga, Wataru Iwasaki
Inverse Potts model improves accuracy of phylogenetic profiling. Bioinformatics (Oxford, England) 38 (7) (2022)
Yannis Nevers, Tamsin E M Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, null null, Wataru Iwasaki, Odile Lecompte, Erik L L Sonnhammer, David S Roos, Toni Gabaldón, David Thybert, Paul D Thomas, Yanhui Hu, David M Emms, Elspeth A Bruford, Salvador Capella, Maria J Martin, Christophe Dessimoz, Adrian Altenhoff
The Quest for Orthologs orthology benchmark service in 2022. Nucleic acids research (2022)
Arnon Plianchaisuk, Kazuya Kusama, Kiyoko Kato, Sira Sriswasdi, Kazuhiro Tamura, Wataru Iwasaki
Origination of LTR Retroelement-Derived NYNRIN Coincides with Therian Placental Emergence. Molecular biology and evolution 39 (9) (2022)
Joel H Nitta, Brent D Mishler, Wataru Iwasaki, Atsushi Ebihara
Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation. American journal of botany 109 (5) (2022)
Tsukasa Fukunaga, Wataru Iwasaki
Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families. Bioinformatics (Oxford, England) 38 (16) (2022)
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, Nozomu Yachie
Deep distributed computing to reconstruct extremely large lineage trees. Nature biotechnology 40 (4) (2022)
Masako Nishikawa, Hiroshi Kanno, Yuqi Zhou, Ting-Hui Xiao, Takuma Suzuki, Yuma Ibayashi, Jeffrey Harmon, Shigekazu Takizawa, Kotaro Hiramatsu, Nao Nitta, Risako Kameyama, Walker Peterson, Jun Takiguchi, Mohammad Shifat-E-Rabbi, Yan Zhuang, Xuwang Yin, Abu Hasnat Mohammad Rubaiyat, Yunjie Deng, Hongqian Zhang, Shigeki Miyata, Gustavo K Rohde, Wataru Iwasaki, Yutaka Yatomi, Keisuke Goda
Massive image-based single-cell profiling reveals high levels of circulating platelet aggregates in patients with COVID-19. Nature communications 12 (1) (2021)
Tsukasa Fukunaga, Wataru Iwasaki
Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families. Bioinformatics advances 1 (1) (2021)
Tsukasa Fukunaga, Wataru Iwasaki
Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families. Bioinformatics advances 1 (1) (2021)
Yuka W Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, Haruhiko Siomi
Piwi-piRNA complexes induce stepwise changes in nuclear architecture at target loci. The EMBO journal 40 (18) (2021)
Gökalp Yildirir, Jana Sperschneider, Mathu Malar C, Eric C H Chen, Wataru Iwasaki, Calvin Cornell, Nicolas Corradi
Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. The New phytologist (2021)
Kaori Motoki, Tomo-O Watsuji, Yoshihiro Takaki, Ken Takai, Wataru Iwasaki
Metatranscriptomics by In Situ RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters. mSystems 5 (5) (2020)
Satoshi Hiraoka, Yusuke Okazaki, Mizue Anda, Atsushi Toyoda, Shin-Ichi Nakano, Wataru Iwasaki
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nature communications 10 (1) (2019)
David M Needham, Susumu Yoshizawa, Toshiaki Hosaka, Camille Poirier, Chang Jae Choi, Elisabeth Hehenberger, Nicholas A T Irwin, Susanne Wilken, Cheuk-Man Yung, Charles Bachy, Rika Kurihara, Yu Nakajima, Keiichi Kojima, Tomomi Kimura-Someya, Guy Leonard, Rex R Malmstrom, Daniel R Mende, Daniel K Olson, Yuki Sudo, Sebastian Sudek, Thomas A Richards, Edward F DeLong, Patrick J Keeling, Alyson E Santoro, Mikako Shirouzu, Wataru Iwasaki, Alexandra Z Worden
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences of the United States of America 116 (41) (2019)
Hikari Yoshitane, Yoshimasa Asano, Aya Sagami, Seinosuke Sakai, Yutaka Suzuki, Hitoshi Okamura, Wataru Iwasaki, Haruka Ozaki, Yoshitaka Fukada
Functional D-box sequences reset the circadian clock and drive mRNA rhythms. Communications biology 2 (2019)
Sira Sriswasdi, Masako Takashima, Ri-Ichiroh Manabe, Moriya Ohkuma, Wataru Iwasaki
Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. Communications biology 2 (2019)
Masayuki Ushio, Koichi Murata, Tetsuya Sado, Isao Nishiumi, Masamichi Takeshita, Wataru Iwasaki, Masaki Miya
Demonstration of the potential of environmental DNA as a tool for the detection of avian species. Scientific reports 8 (1) (2018)
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, Wataru Iwasaki
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. The ISME journal 12 (5) (2018)
Daniel K Olson, Susumu Yoshizawa, Dominique Boeuf, Wataru Iwasaki, Edward F DeLong
Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre. The ISME journal 12 (4) (2018)
Masako Takashima, Sira Sriswasdi, Ri-Ichiroh Manabe, Moriya Ohkuma, Takashi Sugita, Wataru Iwasaki
A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes. Yeast (Chichester, England) 35 (1) (2017)
Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Kobayashi Makoto, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, Masaki Miya
Environmental DNA enables detection of terrestrial mammals from forest pond water. Molecular ecology resources 17 (6) (2017)
Sira Sriswasdi, Ching-Chia Yang, Wataru Iwasaki
Generalist species drive microbial dispersion and evolution. Nature communications 8 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Wataru Iwasaki