All Stories

  1. “Paraxenoviridae”, a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes

    Article • February 2025, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  2. Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating

    Article • November 2024, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  3. A large-scale phylogeny of replication initiation proteins illuminates plasmid macroevolutionary landscape

    Article • September 2024, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  4. Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities

    Article • Frontiers in Virology, April 2024, Frontiers

    Yosuke Nishimura

  5. Draft genome sequences of three rhodopsin possessing Croceitalea sp. strains, isolated from the sea surface microlayer in Japan

    Article • Microbiology Resource Announcements, March 2024, ASM Journals

    Yosuke Nishimura

  6. Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan

    Article • Nature Microbiology, January 2024, Springer Science + Business Media

    Yosuke Nishimura

  7. DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics

    Article • Microbes and Environments, January 2024, Japanese Society of Microbial Ecology

    Yosuke Nishimura

  8. Distinct groups of RNA viruses associated with thermoacidophilic bacteria

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  9. Correction: Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean

    Article • The ISME Journal, June 2023, Oxford University Press (OUP)

    Yosuke Nishimura

  10. Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean

    Article • The ISME Journal, May 2023, Oxford University Press (OUP)

    Yosuke Nishimura

  11. Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis

    Article • mSystems, February 2023, ASM Journals

    Yosuke Nishimura

  12. Distribution and survival strategies of diazotrophs in the Arctic Ocean revealed by global-scale metagenomic analysis

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  13. The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

    Article • Scientific Data, June 2022, Springer Science + Business Media

    Yosuke Nishimura

  14. Proton-pumping rhodopsins in marine diatoms

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  15. Prevalence of viral frequency-dependent infection in coastal marine prokaryotes revealed using monthly time series virome analysis

    Article • September 2021, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  16. The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  17. Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

    Article • Environmental Microbiology, November 2019, Wiley

    Yosuke Nishimura

  18. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

    Article • F1000Research, September 2019, Faculty of 1000, Ltd.

    Dr. Yasset Perez-Riverol, Dr Kevin Bretonnel Cohen, Robert Hoehndorf, Karin M Verspoor, Yusuke Komiyama, Dr. Hidemasa Bono, Katsuhiko Murakami, Hiromasa Ono, Shin Kawano, Shuichi Kawashima, Tatsuya Kushida, Yosuke Nishimura, Kazuharu Arakawa, hongyan Wu

  19. Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa

    Article • Applied and Environmental Microbiology, September 2019, ASM Journals

    Yosuke Nishimura

  20. Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12

    Article • Biochemistry, May 2019, American Chemical Society (ACS)

    Yosuke Nishimura

  21. Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Yosuke Nishimura

  22. Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan

    Article • The ISME Journal, January 2018, Springer Science + Business Media

    Yosuke Nishimura

  23. ViPTree: the viral proteomic tree server

    Article • Bioinformatics, March 2017, Oxford University Press (OUP)

    Yosuke Nishimura

  24. 600 new genera for marine viruses

    Article • mSphere, March 2017, ASM Journals

    Dr. Hiroyuki Ogata, Yosuke Nishimura

  25. Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages

    Article • Virology, July 2016, Elsevier

    Yosuke Nishimura

  26. Linking Virus Genomes with Host Taxonomy

    Article • Viruses, March 2016, MDPI AG

    Yosuke Nishimura

  27. PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list

    Article • Journal of Bioinformatics and Computational Biology, December 2014, World Scientific Pub Co Pte Lt

    Yosuke Nishimura

  28. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

    Article • Journal of Biomedical Semantics, January 2014, Springer Science + Business Media

    Matúš Kalaš, Yosuke Nishimura

  29. Drug target prediction using adverse event report systems: a pharmacogenomic approach

    Article • Bioinformatics, September 2012, Oxford University Press (OUP)

    Yosuke Nishimura

  30. GENOME-WIDE ANALYSIS OF PLANT UGT FAMILY BASED ON SEQUENCE AND SUBSTRATE INFORMATION

    Article • July 2010, World Scientific Pub Co Pte Lt

    Yosuke Nishimura