Researcher Information
researchmap URL
Research Interests
Research Areas
Research History
- Apr. 2026 - Present
Japan Agency for Marine-Earth Science and Technology, Science and Technology Avant-garde Research of Life (X-star), Researcher - Apr. 2024 - Mar. 2026
Japan Agency for Marine-Earth Science and Technology, CeBN, Researcher - Apr. 2022 - Mar. 2024
Japan Agency for Marine-Earth Science and Technology, Research Center for Bioscience and Nanoscience, Project Researcher
Research activity information
Papers
- Yusuke Tsuda; Yasuhiro Tanizawa; Thi My Hanh Vu; Yosuke Nishimura; Masaki Shintani; Haruka Abe; Futoshi Hasebe; Ikuro Kasuga; Miki Nagao; Masato Suzuki
VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance
bioRxiv, 01 Apr. 2026 - Yosuke Nishimura; Kensei Kaneko; Tatsuya Kamijo; Nanako Isogai; Maho Tokuda; Hui Xie; Yusuke Tsuda; Aki Hirabayashi; Ryota Moriuchi; Hideo Dohra; Kazuhide Kimbara; Chiho Suzuki-Minakuchi; Hideaki Nojiri; Haruo Suzuki; Masato Suzuki; Masaki Shintani
A replication-centered phylogeny illuminates the evolutionary landscape of bacterial plasmids
bioRxiv, 30 Mar. 2026
Lead, Corresponding - Masato Suzuki; Haruo Suzuki; Yosuke Nishimura; Hideaki Nojiri; Masaki Shintani
Enhancing plasmid typing with MOB-typer: resolving IncP and other incompatibility group misclassifications in Pseudomonas.
Microbial genomics, 09 Sep. 2025
11, 9
Corresponding - Takayoshi Fujiwara; Toshiaki Hosaka; Masumi Hasegawa-Takano; Yosuke Nishimura; Kento Tominaga; Kaho Mori; Satoshi Nishino; Yuno Takahashi; Tomomi Uchikubo-Kamo; Kazuharu Hanada; Takashi Maoka; Shinichi Takaichi; Keiichi Inoue; Mikako Shirouzu; Susumu Yoshizawa
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota
Nature Microbiology, 04 Sep. 2025 - Syun-ichi Urayama; Akihito Fukudome; Pascal Mutz; Yosuke Matsushita; Yoshihiro Takaki; Yosuke Nishimura; Sofia Medvedeva; Mart Krupovic; Eugene V. Koonin; Takuro Nunoura
Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily
bioRxiv, 03 Sep. 2025 - Mitsuhiro Yoshida; Sofia Medvedeva; Akihito Fukudome; Yuri I Wolf; Syun-ichi Urayama; Yosuke Nishimura; Yoshihiro Takaki; Eugene V Koonin; Mart Krupovic; Takuro Nunoura
“Paraxenoviridae”, a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes
The ISME Journal, 04 Jul. 2025
[Reviewed] - Wenwen Liu; Komei Nagasaka; Junyi Wu; Hiroki Ban; Ethan Mimick; Lingjie Meng; Russell Y. Neches; Mohammad Moniruzzaman; Takashi Yoshida; Yosuke Nishimura; Hisashi Endo; Yusuke Okazaki; Hiroyuki Ogata
Giant viruses specific to deep oceans show persistent presence and activity
mSystems, 24 Jun. 2025
10, 12, e00932-25
[Reviewed] - Yuya Nagata; Norio Miyamoto; Keita Sato; Yosuke Nishimura; Yuki Tanioka; Yuji Yamanaka; Susumu Yoshizawa; Kuto Takahashi; Kohei Obayashi; Hisao Tsukamoto; Ken Takai; Hideyo Ohuchi; Takahiro Yamashita; Yuki Sudo; Keiichi Kojima
A repertoire of visible light-sensitive opsins in the deep-sea hydrothermal vent shrimp Rimicaris hybisae
Journal of Biological Chemistry, 25 May 2025
301, 7, 110291, 110291 - Yosuke Nishimura; Kensei Kaneko; Tatsuya Kamijo; Nanako Isogai; Maho Tokuda; Hui Xie; Yusuke Tsuda; Aki Hirabayashi; Ryota Moriuchi; Hideo Dohra; Kazuhide Kimbara; Chiho Suzuki-Minakuchi; Hideaki Nojiri; Haruo Suzuki; Masato Suzuki; Masaki Shintani
A large-scale phylogeny of replication initiation proteins illuminates plasmid macroevolutionary landscape
bioRxiv, 24 Apr. 2025 - Mitsuhiro Yoshida; Sofia Medvedeva; Akihito Fukudome; Yuri I. Wolf; Syun-ichi Urayama; Yosuke Nishimura; Yoshihiro Takaki; Eugene V. Koonin; Mart Krupovic; Takuro Nunoura
“Paraxenoviridae”, a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes
bioRxiv, 27 Feb. 2025 - Takayoshi Fujiwara; Toshiaki Hosaka; Masumi Hasegawa-Takano; Yosuke Nishimura; Kento Tominaga; Kaho Mori; Satoshi Nishino; Yuno Takahashi; Tomomi Uchikubo-Kamo; Kazuharu Hanada; Takashi Maoka; Shinichi Takaichi; Keiichi Inoue; Mikako Shirouzu; Susumu Yoshizawa
Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating
bioRxiv, 09 Nov. 2024 - Masumi Hasegawa-Takano; Toshiaki Hosaka; Keiichi Kojima; Yosuke Nishimura; Marie Kurihara; Yu Nakajima; Yoshiko Ishizuka-Katsura; Tomomi Kimura-Someya; Mikako Shirouzu; Yuki Sudo; Susumu Yoshizawa
Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria
The ISME Journal, 01 Nov. 2024
18, 1
[Reviewed] - Yosuke Nishimura; Kensei Kaneko; Tatsuya Kamijo; Nanako Isogai; Maho Tokuda; Hui Xie; Yusuke Tsuda; Aki Hirabayashi; Ryota Moriuchi; Hideo Dohra; Kazuhide Kimbara; Chiho Suzuki-Minakuchi; Hideaki Nojiri; Haruo Suzuki; Masato Suzuki; Masaki Shintani
Incompatibility groups of Pseudomonas plasmids revisited: comprehensive analysis of R-factors and their replicons
bioRxiv, 03 Sep. 2024
Lead - Justine Charon; Ingrida Olendraite; Marco Forgia; Li Chuin Chong; Luke S. Hillary; Simon Roux; Anne Kupczok; Humberto Debat; Shoichi Sakaguchi; Rachid Tahzima; So Nakagawa; Artem Babaian; Aare Abroi; Nicolas Bejerman; Karima Ben Mansour; Katherine Brown; Anamarija Butkovic; Amelia Cervera; Florian Charriat; Guowei Chen; Yuto Chiba; Lander De Coninck; Tatiana Demina; Guillermo Dominguez-Huerta; Jeremy Dubrulle; Serafin Gutierrez; Erin Harvey; Fhilmar Raj Jayaraj Mallika; Dimitris Karapliafis; Shen Jean Lim; Sunitha Manjari Kasibhatla; Jonathon C. O. Mifsud; Yosuke Nishimura; Ayda Susana Ortiz-Baez; Milica Raco; Ricardo Rivero; Sabrina Sadiq; Shahram Saghaei; James Emmanuel San; Hisham Mohammed Shaikh; Ella Tali Sieradzki; Matthew B. Sullivan; Yanni Sun; Michelle Wille; Yuri I. Wolf; Nikita Zrelovs; Uri Neri
〔Major achievements〕Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities
Frontiers in Virology, 04 Apr. 2024
4
[Reviewed] - Yosuke Nishimura; Kohei Yamada; Yusuke Okazaki; Hiroyuki Ogata
〔Major achievements〕DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics
Microbes and Environments, 20 Mar. 2024
39, 1, ME23061
[Reviewed]
Lead, Corresponding - Mako Takada; Chunqi Jiang; Youta Sugai; Masumi Hasegawa-Takano; Takayoshi Fujiwara; Yuya Tsukamoto; Yu Nakajima; Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕Draft genome sequences of three rhodopsin possessing Croceitalea sp. strains, isolated from the sea surface microlayer in Japan.
Microbiology resource announcements, 16 Feb. 2024
e0003824
[Reviewed] - Syun-ichi Urayama; Akihito Fukudome; Miho Hirai; Tomoyo Okumura; Yosuke Nishimura; Yoshihiro Takaki; Norio Kurosawa; Eugene V. Koonin; Mart Krupovic; Takuro Nunoura
〔Major achievements〕Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan
Nature Microbiology, 17 Jan. 2024
9, 2, 514, 523
[Reviewed] - Syun-ichi Urayama; Akihito Fukudome; Miho Hirai; Tomoyo Okumura; Yosuke Nishimura; Yoshihiro Takaki; Norio Kurosawa; Eugene V. Koonin; Mart Krupovic; Takuro Nunoura
Distinct groups of RNA viruses associated with thermoacidophilic bacteria
bioRxiv, 03 Jul. 2023 - Susumu Yoshizawa; Tomonori Azuma; Keiichi Kojima; Keisuke Inomura; Masumi Hasegawa; Yosuke Nishimura; Masuzu Kikuchi; Gabrielle Armin; Yuya Tsukamoto; Hideaki Miyashita; Kentaro Ifuku; Takashi Yamano; Adrian Marchetti; Hideya Fukuzawa; Yuki Sudo; Ryoma Kamikawa
〔Major achievements〕Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms
Microbes and Environments, 20 Jun. 2023
38, 2, ME23015
[Reviewed] - Shiozaki Takuhei; Yosuke Nishimura; Susumu Yoshizawa; Hideto Takami; Koji Hamasaki; Amane Fujiwara; Shigeto Nishino; Naomi Harada
〔Major achievements〕Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean.
The ISME journal, 23 May 2023
[Reviewed]
Lead - Keiichi Kojima; Shiho Kawanishi; Yosuke Nishimura; Masumi Hasegawa; Shin Nakao; Yuya Nagata; Susumu Yoshizawa; Yuki Sudo
〔Major achievements〕A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis
Scientific Reports, 28 Apr. 2023
13, 1, 6974, 6974
[Reviewed] - Kento Tominaga; Nana Ogawa-Haruki; Yosuke Nishimura; Hiroyasu Watai; Keigo Yamamoto; Hiroyuki Ogata; Takashi Yoshida
〔Major achievements〕Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis.
mSystems, 23 Feb. 2023
8, 1, e0093122
[Reviewed] - Takuhei Shiozaki; Yosuke Nishimura; Susumu Yoshizawa; Hideto Takami; Koji Hamasaki; Amane Fujiwara; Shigeto Nishino; Naomi Harada
Distribution and survival strategies of diazotrophs in the Arctic Ocean revealed by global-scale metagenomic analysis
bioRxiv, 30 Oct. 2022
Lead - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments.
Scientific data, 17 Jun. 2022
9, 1, 305, 305
[Reviewed]
Lead, Corresponding - Susumu YOSHIZAWA; Masumi HASEGAWA; Yosuke NISHIMURA
シアノバクテリアの光合成とは異なる光エネルギー利用機構
KAGAKU TO SEIBUTSU, 01 Apr. 2022
60, 4, 165, 167 - Susumu Yoshizawa; Tomonori Azuma; Keiichi Kojima; Keisuke Inomura; Masumi Hasegawa; Yosuke Nishimura; Masuzu Kikuchi; Gabrielle Armin; Hideaki Miyashita; Kentaro Ifuku; Takashi Yamano; Adrian Marchetti; Hideya Fukuzawa; Yuki Sudo; Ryoma Kamikawa
Proton-pumping rhodopsins in marine diatoms
bioRxiv, 20 Jan. 2022 - Kento Tominaga; Nana Ogawa-Haruki; Yosuke Nishimura; Hiroyasu Watai; Keigo Yamamoto; Hiroyuki Ogata; Takashi Yoshida
Prevalence of viral frequency-dependent infection in coastal marine prokaryotes revealed using monthly time series virome analysis
bioRxiv, 23 Sep. 2021
8, 1, e0093122 - Yosuke Nishimura; Susumu Yoshizawa
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments
bioRxiv, 18 Aug. 2021
9, 1, 305, 305
Lead, Corresponding - Masumi Hasegawa; Toshiaki Hosaka; Keiichi Kojima; Yosuke Nishimura; Yu Nakajima; Tomomi Kimura-Someya; Mikako Shirouzu; Yuki Sudo; Susumu Yoshizawa
A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.
Scientific reports, 07 Oct. 2020
10, 1, 16752, 16752
[Reviewed] - Hasegawa Masumi; Hosaka Toshiaki; Kojima Keiichi; Nishimura Yosuke; Nakajima Yu; Kimura―Someya Tomomi; Shirouzu Mikako; Sudo Yuki; Yoshizawa Susumu
The light-utilization mechanisms different from photosynthesis in cyanobacteria: The discovering of cyanorhodopsin.
Abstracts of Annual Meeting of the Geochemical Society of Japan, 2020
67, 186, 186 - Kento Tominaga; Daichi Morimoto; Yosuke Nishimura; Hiroyuki Ogata; Takashi Yoshida
In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes.
Frontiers in microbiology, 2020
11, 738, 738
[Reviewed] - Yusuke Okazaki; Yosuke Nishimura; Takashi Yoshida; Hiroyuki Ogata; Shin‐ichi Nakano
Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
Environmental Microbiology, Dec. 2019
21, 12, 4740, 4754
[Reviewed] - Daichi Morimoto; Kento Tominaga; Yosuke Nishimura; Naohiro Yoshida; Shigeko Kimura; Yoshihiko Sako; Takashi Yoshida
Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa.
Applied and environmental microbiology, 15 Sep. 2019
85, 18
[Reviewed] - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; Kiyoko F. Aoki-Kinoshita; Kazuharu Arakawa; Masaki Banno; Joachim Baran; Jerven T. Bolleman; Raoul J.P. Bonnal; Hidemasa Bono; Jesualdo T. Fernández-Breis; Robert Buels; Matthew P. Campbell; Hirokazu Chiba; Peter J.A. Cock; Kevin B. Cohen; Michel Dumontier; Takatomo Fujisawa; Toyofumi Fujiwara; Leyla Garcia; Pascale Gaudet; Emi Hattori; Robert Hoehndorf; Kotone Itaya; Maori Ito; Daniel Jamieson; Simon Jupp; Nick Juty; Alex Kalderimis; Fumihiro Kato; Hideya Kawaji; Takeshi Kawashima; Akira R. Kinjo; Yusuke Komiyama; Masaaki Kotera; Tatsuya Kushida; James Malone; Masaaki Matsubara; Satoshi Mizuno; Sayaka Mizutani; Hiroshi Mori; Yuki Moriya; Katsuhiko Murakami; Takeru Nakazato; Hiroyo Nishide; Yosuke Nishimura; Soichi Ogishima; Tazro Ohta; Shujiro Okuda; Hiromasa Ono; Yasset Perez-Riverol; Daisuke Shinmachi; Andrea Splendiani; Francesco Strozzi; Shinya Suzuki; Junichi Takehara; Mark Thompson; Toshiaki Tokimatsu; Ikuo Uchiyama; Karin Verspoor; Mark D. Wilkinson; Sarala Wimalaratne; Issaku Yamada; Nozomi Yamamoto; Masayuki Yarimizu; Shoko Kawamoto; Toshihisa Takagi
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
F1000Research, Sep. 2019
8
[Reviewed] - Atsushi Shibukawa; Keiichi Kojima; Yu Nakajima; Yosuke Nishimura; Susumu Yoshizawa; Yuki Sudo
Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12.
Biochemistry, 02 Jul. 2019
58, 26, 2934, 2943
[Reviewed] - Takashi Yoshida; Yosuke Nishimura; Hiroyasu Watai; Nana Haruki; Daichi Morimoto; Hiroto Kaneko; Takashi Honda; Keigo Yamamoto; Pascal Hingamp; Yoshihiko Sako; Susumu Goto; Hiroyuki Ogata
〔Major achievements〕Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan
The ISME Journal, May 2018
12, 5, 1287, 1295
[Reviewed]
Lead - Yosuke Nishimura; Takashi Yoshida; Megumi Kuronishi; Hideya Uehara; Hiroyuki Ogata; Susumu Goto
〔Major achievements〕ViPTree: the viral proteomic tree server.
Bioinformatics (Oxford, England), 01 Aug. 2017
33, 15, 2379, 2380
[Reviewed]
Lead - Yosuke Nishimura; Hiroyasu Watai; Takashi Honda; Tomoko Mihara; Kimiho Omae; Simon Roux; Romain Blanc-Mathieu; Keigo Yamamoto; Pascal Hingamp; Yoshihiko Sako; Matthew B. Sullivan; Susumu Goto; Hiroyuki Ogata; Takashi Yoshida
〔Major achievements〕Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean
mSphere, Mar. 2017
2, 2, e00359-16
[Reviewed]
Lead - Anjana Bhunchoth; Romain Blanc-Mathieu; Tomoko Mihara; Yosuke Nishimura; Ahmed Askora; Namthip Phironrit; Chalida Leksomboon; Orawan Chatchawankanphanich; Takeru Kawasaki; Miyako Nakano; Makoto Fujie; Hiroyuki Ogata; Takashi Yamada
Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages
Virology, Jul. 2016
494, 56, 66
[Reviewed] - Tomoko Mihara; Yosuke Nishimura; Yugo Shimizu; Hiroki Nishiyama; Genki Yoshikawa; Hideya Uehara; Pascal Hingamp; Susumu Goto; Hiroyuki Ogata
Linking Virus Genomes with Host Taxonomy
Viruses, 01 Mar. 2016
8, 3, 66, 66
[Reviewed] - Masaaki Kotera; Yosuke Nishimura; Zen-Ichi Nakagawa; Ai Muto; Yuki Moriya; Shinobu Okamoto; Shuichi Kawashima; Toshiaki Katayama; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto
PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, Dec. 2014
12, 6
[Reviewed]
Lead - Katayama T; Wilkinson MD; Aoki-Kinoshita KF; Kawashima S; Yamamoto Y; Yamaguchi A; Okamoto S; Kawano S; Kim JD; Wang Y; Wu H; Kano Y; Ono H; Bono H; Kocbek S; Aerts J; Akune Y; Antezana E; Arakawa K; Takagi T
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Journal of Biomedical Semantics, 2014
[Reviewed] - Masataka Takarabe; Masaaki Kotera; Yosuke Nishimura; Susumu Goto; Yoshihiro Yamanishi
Drug target prediction using adverse event report systems: a pharmacogenomic approach
BIOINFORMATICS, Sep. 2012
28, 18, I611, I618
[Reviewed] - Yosuke Nishimura
GENOME-WIDE ANALYSIS OF PLANT UGT FAMILY BASED ON SEQUENCE AND SUBSTRATE INFORMATION
Genome Informatics 2010, Jul. 2010
[Reviewed]
Misc.
- 富永賢人; 晴気七菜; 藤原健太郎; 西村陽介; 西村陽介; 山本圭吾; 綿井博康; 左子芳彦; 緒方博之; 吉田天士
大阪湾における海洋微生物・ウイルスの群集ダイナミクスと生態学的相互作用解析
日本ゲノム微生物学会年会要旨集, 2019
13th - 緒方博之; BLANC‐MATHIEU Romain; HINGAMP Pascal; 西村陽介; 李岩沢; 吉田天士
マルチオミクス解析が明らかにする海洋ウイルスの多様性と存在意義
日本進化学会大会プログラム・講演要旨集(Web), 24 Aug. 2017
19th, 59 (WEB ONLY) - 綿井博康; 本田貴史; 山本圭吾; 西村陽介; 五斗進; 緒方博之; 左子芳彦; 吉田天士
完全長ゲノムに基づく海洋ウイルスの定量的動態解析とその宿主微生物の推定
日本水産学会大会講演要旨集, 26 Mar. 2016
2016, 90 - 綿井博康; 西村陽介; 山本圭吾; 五斗進; 緒方博之; 左子芳彦; 吉田天士
genomic‐OTUを用いたメタゲノム解析による海洋ウイルスの季節変動
日本微生物生態学会大会(Web), 2016
31st, 320 (WEB ONLY) - 西村陽介; 小寺正明; 時松敏明; 五斗進
後生動物10生物種におけるイントラジェニックmiRNAとホスト遺伝子の機能関連解析
日本分子生物学会年会プログラム・要旨集(Web), 2012
35th, WEB ONLY 1LBA-0755
Presentations
- 西村陽介
メタゲノムビッグデータで 環境微生物の生合成ポテンシャルを理解する
日本農芸化学会2025年度大会, 12 Mar. 2026 - 西村陽介
微⽣物の⽣合成遺伝⼦群と その環境特性を理解する
第 20 回日本ゲノム微生物学会年会, 06 Mar. 2026 - 西村陽介
全球規模のメタゲノムデータを活用した研究と 比較ゲノム解析ツールの紹介
微生物生態学会 環境ウイルス研究部会 拡大研究交流会, 02 Mar. 2026, [Invited] - 西村陽介
微生物進化を駆動する可動遺伝因子― メタゲノムデータと配列解析でその実像に迫る
第48回日本分子生物学会, 04 Dec. 2025, [Invited] - 西村陽介
複製開始因⼦のビッグデータ解析で プラスミドの進化史を理解する
日本遺伝学会第97回大会, 12 Sep. 2025, [Invited] - 西村陽介
RIP大系統樹で理解するプラスミドスフィア
第３回プラスミド研究会, 25 Aug. 2025, [Invited] - 西村陽介
必須遺伝子を捉えてモビロームの進化を解明する
日本微生物生態学会 第37回大会, 29 Oct. 2024, [Invited] - Yosuke Nishimura; Kensei Kaneko; Tatsuya Kamijo; Ryota Moriuchi; Hideo Dora; Kazuhide Kimbara; Chiho Minakuchi; Hideaki Nojiri; Haruo Suzuki; Masato Suzuki; Masaki Shintani
Reassessment of Pseudomonas plasmid incompatibility groups based on complete sequence information and molecular experiments
ISPB (International Society for Plasmid Biology) 2024, 04 Sep. 2024 - 西村陽介
公共メタゲノムビッグデータから見る抗生物質耐性遺伝子の分布と多様性
第97回日本細菌学会総会, 09 Aug. 2024, [Invited] - 千葉 悠斗; ◯西村 陽介
RNAウイルスのゲノム複製を担う酵素RdRpの「特異な」進化
第18回日本ゲノム微生物学会年会, 13 Mar. 2024 - 西村陽介
データベースのMAG、信頼できますか？
日本微生物生態学会 第36回大会, 30 Nov. 2023, [Invited] - Yuto Chiba; Yosuke Nishimura
How to report the divided RdRps
The First RdRp Summit, 22 May 2023 - 西村陽介
.
ESJ70, 13 Mar. 2023, [Invited] - Yosuke Nishimura
Uncovering viral ‘dark matter’ in various Earth environments by leveraging public metagenome big data analysis
第45回日本分子生物学会年会, 01 Dec. 2022, [Invited] - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕The OceanDNA MAG catalog: an unprecedented-scale genome resource of marine prokaryotes
ASME12 (Asian Symposium on Microbial Ecology), 18 Apr. 2022, [Invited] - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕網羅的ゲノム解析で解明する海洋好気性光合成細菌の実像
SGMJ 16, 02 Mar. 2022 - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕データ解析で明らかにする海洋性0.2マイクロメートル透過性微生物の実態
JSME 34, 31 Oct. 2021 - Masumi Hasegawa; Keiichi Kojima; Shin Nakao; Yosuke Nishimura; Yuki Sudo; Susumu Yoshizawa
褐虫藻の光利用:Symbiodiniaceae 科褐虫藻ロドプシンの探索と機能解析
JSME 34, 30 Oct. 2021 - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕The OceanDNA MAG catalog: 50,000 prokaryotic genomes originated from oceans
IIBMP2021, 28 Sep. 2021 - Kento Tominaga; Nana Haruki; Yosuke Nishimura; Hiroyasu Watai; Keigo Yamamoto; Hiroyuki Ogata; Takashi Yoshida
Monthly virome analysis in Osaka bay revealed prevalence of viral frequency dependent infection
Aquatic Virus Wrokshop (AVW) 10, 01 Jul. 2021 - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕オープン・ビッグデータ × メタゲノム解析 ―5万ゲノムの海洋微生物カタログ―
第21回マリンバイオテクノロジー学会, 15 May 2021, [Invited] - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕網羅的メタゲノム解析で構築する海洋微生物ゲノムカタログ
SGMJ 15, 04 Mar. 2021 - Masumi Hasegawa; Yosuke Nishimura; Susumu Yoshizawa
シアノバクテリアの光合成とは異なる光利用：シアノロドプシンの発見
日本地球化学会 第67回オンライン大会, 19 Nov. 2020 - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕メタゲノム由来ゲノムにより解き明かす海洋微生物の多様性
SGMJ 14, Mar. 2020 - Kyoji Horie; Hitomi Watanabe; Yosuke Nishimura; Hikaru Watanabe; Masahide Seki; Akio Seita; Kagayaki Kato; Yuichi Wakamoto; Jun Sese; Yutaka Suzuki; Takuji Yamada; Gen Kondoh; Junko Yoshida
Identifying the heterogeneity of ground state pluripotency in mouse embryonic stem cells and elucidating its regulatory mechanism
MBSJ 42, 04 Dec. 2019 - Masumi Hasegawa; Yosuke Nishimura; Susumu Yoshizawa
褐虫藻Symbiodinium minutum 由来の ロドプシン遺伝子の探索と機能解析
2019年日本ベントス学会・日本プランクトン学会合同大会, 20 Sep. 2019 - Susumu Yoshizawa; Yosuke Nishimura; Wataru Iwasaki
メタゲノム中のダークマター機能性遺伝子の解析
JSME 33, 13 Sep. 2019 - Masumi Hasegawa; Yosuke Nishimura; Susumu Yoshizawa
ロドプシンから探るシアノバクテリアの多様な光利用
JSME 33, 11 Sep. 2019 - Yusuke Okazaki; Yosuke Nishimura; Takashi Yoshida; Hiroyuki Ogata; Shinichi Nakano
メタゲノム解析でひも解く淡水湖のファージの多様性と生態
JSME 33, 11 Sep. 2019 - Yosuke Nishimura; Susumu Yoshizawa
〔Major achievements〕網羅的なロドプシン系統解析から理解する微生物の進化と生態
JSME 33, 11 Sep. 2019 - Yosuke Nishimura; Wataru Iwasaki; Susumu Yoshizawa
〔Major achievements〕環境間メタゲノム比較による新規光受容体遺伝子の探索
IIBMP2019, 09 Sep. 2019 - Kento Tominaga; Yosuke Nishimura; Keigo Yamamoto; Hiroyuki Ogata; Yoshihiko Sako; Takashi Yoshida
大阪湾の海洋微生物・ウイルスの生態学的相互作用解析
The 2019 Spring meeting of JSFS, 27 Mar. 2019 - Yosuke Nishimura; Takashi Yoshida; Susumu Goto; Hiroyuki Ogata
〔Major achievements〕海洋におけるウイルス生態系の理解へ向けて
IIBMP2018, 20 Sep. 2018 - Yosuke Nishimura
〔Major achievements〕A multi-omics approach to elucidate marine virus ecology
RinkaiHackathon 2018 Symposium, 10 Jun. 2018, [Invited] - Yosuke Nishimura
環境ゲノムに基づく海洋ウイルス研究の新展開
東京大学医科学研究所共同研究拠点事業 平成29年度 若手シンポジウム, 13 Nov. 2017, [Invited] - Yosuke Nishimura; Takashi Yoshida; Hiroyuki Ogata; Susumu Goto
あなたのウイルスゲノムを分類します
JSME 31, 23 Oct. 2016 - Yosuke Nishimura; Takashi Yoshida; Hiroyuki Ogata; Susumu Goto
環境ウイルスゲノムの自動分類法
2016年 ファージ・環境ウイルス研究合同シンポジウム, 22 Oct. 2016 - Hiryoyasu Watai; Yosuke Nishimura; Keigo Yamamoto; Susumu Goto; Hiroyuki Ogata; Yoshihiko Sako; Takashi Yoshida
Seasonal dynamics of marine viral communities in Japanese coastal area revealed by genomic OTUs analysis
東京大学大気海洋研究所共同利用研究集会 水圏微生物研究フォーラム 2016, 09 Aug. 2016 - Yosuke Nishimura; Hiroyasu Watai; Takashi Honda; Tomoko Mihara; Kimiho Omae; Romain Blanc-Mathieu; Keigo Yamamoto; Yoshihiko Sako; Susumu Goto; Hiroyuki Ogata; Takashi Yoshida
完全ゲノムから定量化した海洋ウイルスの多様性とその宿主予測
東京大学大気海洋研究所共同利用研究集会 水圏微生物研究フォーラム 2016, 09 Aug. 2016 - Yosuke Nishimura; Hiroyasu Watai; Simon Roux; Pascal Hingamp; Yoshihiko Sako; Matthew B Sullivan; Susumu Goto; Hiroyuki Ogata; Takashi Yoshida
〔Major achievements〕Metagenomic whole genomes of marine DNA viruses
8th Aquatic Virus Wrokshop (AVW), 13 Jul. 2016 - Takashi Yoshida; Yosuke Nishimura; Watai Hiroyasu; Susumu Goto; Sako Yoshihiko; Hiroyuki Ogata
DIURNAL DYNAMICS OF NOVEL VIRUSES AND THEIR TRANSCRIPTION IN A JAPANESE COASTAL SEA BY READ MAPPING ANALYSES
8th Aquatic Virus Wrokshop (AVW), 12 Jul. 2016 - Yosuke Nishimura; Hiroyasu Watai; Takashi Honda; Kimiho Omae; Tomoko Mihara; Pascal Hingamp; Keigo Yamamoto; Yoshihiko Sako; Takashi Yoshida; Susumu Goto; Hiroyuki Ogata
Revealing complete genomes from metagenomes: a case study for viruses in the ocean
IIBMP2015, 30 Oct. 2015 - Yosuke Nishimura; Tomoko Mihara; Takashi Yoshida; Pascal Hingamp; Hiroyuki Ogata; Susumu Goto
A viral proteomic tree server and its application to a marine metagenomic study
JSME 30, 18 Oct. 2015 - Yosuke Nishimura; Hiroyasu Watai; Takashi Honda; Tomoko Mihara; Keigo Yamamoto; Sako Yoshihiko; Takashi Yoshida; Susumu Goto; Hiroyuki Ogata
メタオミクスによる海洋ウイルスと微生物群集の経時的観測
NGS現場の会第四回研究会, 01 Jul. 2015
Professional Memberships
Works
Media Coverage
- 微生物ダークマターに迫る（ぶらっとラボ）
朝日新聞, 夕刊3面, 25 Jul. 2022, Paper
