Yosuke Nishimura
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ViPTree: the viral proteomic tree server
Y Nishimura, T Yoshida, M Kuronishi, H Uehara, H Ogata, S Goto
Bioinformatics 33 (15), 2379-2380, 2017
Linking virus genomes with host taxonomy
T Mihara, Y Nishimura, Y Shimizu, H Nishiyama, G Yoshikawa, H Uehara, ...
Viruses 8 (3), 66, 2016
Drug target prediction using adverse event report systems: a pharmacogenomic approach
M Takarabe, M Kotera, Y Nishimura, S Goto, Y Yamanishi
Bioinformatics 28 (18), i611-i618, 2012
Environmental viral genomes shed new light on virus-host interactions in the ocean
Y Nishimura, H Watai, T Honda, T Mihara, K Omae, S Roux, ...
mSphere 2 (2), e00359-16, 2017
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
T Katayama, MD Wilkinson, KF Aoki-Kinoshita, S Kawashima, ...
Journal of biomedical semantics 5, 1-13, 2014
Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages
A Bhunchoth, R Blanc-Mathieu, T Mihara, Y Nishimura, A Askora, ...
Virology 494, 56-66, 2016
Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
Y Okazaki, Y Nishimura, T Yoshida, H Ogata, S Nakano
Environmental microbiology 21 (12), 4740-4754, 2019
Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan
T Yoshida#, Y Nishimura#, H Watai, N Haruki, D Morimoto, H Kaneko, ...
The ISME Journal 12 (5), 1287-1295, 2018
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments
Y Nishimura, S Yoshizawa
Scientific Data 9, 305, 2022
Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with …
A Shibukawa, K Kojima, Y Nakajima, Y Nishimura, S Yoshizawa, Y Sudo
Biochemistry 58 (26), 2934-2943, 2019
In silico prediction of virus-host interactions for marine bacteroidetes with the use of metagenome-assembled genomes
K Tominaga, D Morimoto, Y Nishimura, H Ogata, T Yoshida
Frontiers in Microbiology 11, 534673, 2020
A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage
M Hasegawa, T Hosaka, K Kojima, Y Nishimura, Y Nakajima, ...
Scientific reports 10 (1), 16752, 2020
Cooccurrence of broad-and narrow-host-range viruses infecting the bloom-forming toxic cyanobacterium Microcystis aeruginosa
D Morimoto, K Tominaga, Y Nishimura, N Yoshida, S Kimura, Y Sako, ...
Applied and environmental microbiology 85 (18), e01170-19, 2019
PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list
M Kotera#, Y Nishimura#, ZI Nakagawa, A Muto, Y Moriya, S Okamoto, ...
Journal of bioinformatics and computational biology 12 (06), 1442001, 2014
Prevalence of viral frequency-dependent infection in coastal marine prokaryotes revealed using monthly time series virome analysis
K Tominaga, N Ogawa-Haruki, Y Nishimura, H Watai, K Yamamoto, ...
Msystems 8 (1), e00931-22, 2023
Light-driven proton pumps as a potential regulator for carbon fixation in marine diatoms
S Yoshizawa, T Azuma, K Kojima, K Inomura, M Hasegawa, Y Nishimura, ...
Microbes and Environments 38 (2), ME23015, 2023
Genome-wide analysis of plant UGT family based on sequence and substrate information
Y Nishimura, T Tokimatsu, M Kotera, S Goto, M Kanehisa
Genome Informatics 2010: Genome Informatics Series Vol. 24, 127-138, 2010
Proton-pumping rhodopsins in marine diatoms
S Yoshizawa, T Azuma, K Kojima, K Inomura, M Hasegawa, Y Nishimura, ...
bioRxiv, 2022.01. 18.476826, 2022
Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean
T Shiozaki#, Y Nishimura#, S Yoshizawa, H Takami, K Hamasaki, ...
The ISME Journal 17 (8), 1340-1350, 2023
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan
S Urayama, A Fukudome, M Hirai, T Okumura, Y Nishimura, Y Takaki, ...
Nature Microbiology, 1-10, 2024
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Articles 1–20