Author

Ryo Shimizu

Joint Research Center for Human Retrovirus Infection, Kumamoto UniversityPrimary ORCID profile (0009-0001-5962-1106 · 2 papers)Unclaimed ORCID profile · follow to get notified of new preprints

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Same name, identified by ORCID

Ryo ShimizuiD2 papers · Kyoto University

Biology Disciplines

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Microbiology· 3

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Research Focus:host-pathogen & immune response· 2 Organism:human· 2 Assay:proteomics· 2 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:variant effect prediction· 1 Organism:virus· 1

Frequent Co-Authors

Akatsuki SaitoiD· 3 shared Michael Jonathan· 3 shared Terumasa IkedaiD· 3 shared Alfredo A. HinayiD· 2 shared Arnon PlianchaisukiD· 2 shared Ayaka SakamotoiD· 2 shared Chihiro MotozonoiD· 2 shared Hayato ItoiD· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersMicrobiology

Akatsuki SaitoORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

APOBEC3 antagonism fully explains HIV-1 Vif essentiality under interferon and differentiation conditions

Ryo Shimizu, Michael Jonathan, Hiromi Terasawa, Akatsuki Saito, Kazuaki Monde, Terumasa Ikeda

This study shows that HIV-1 Vif's essential role in infectivity under interferon and differentiation conditions is fully explained by its antagonism of APOBEC3 proteins, not other targets.

bioRxiv · Apr 17, 2026 · PreprintMicrobiology

A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity

Shuhei Tsujino, Masumi Tsuda, Sayaka Deguchi, Jumpei Ito, Taha Y. Taha, Hesham Nasser, Lei Wang, Julia Rosecrans, Rigel Suzuki, Saori Suzuki, Kumiko Yoshimatsu, Mélanie Ott, Terumasa Ikeda, Kei Sato, Kazuo Takayama, , Miki Kawano

This study identifies the non-spike R204P mutation in the SARS-CoV-2 Omicron XEC variant as a driver of increased inflammation and pathogenicity through NF-κB activation.

Nature Communications · Dec 14, 2025Peer-reviewedMicrobiology

A Protein Language Model for Exploring Viral Fitness Landscapes

Jumpei Ito, Adam Patrick Strange, Wei Liu, Gustav Joas, Spyros Lytras, Keita Matsuno, Naganori Nao, Hirofumi Sawa, Keita Mizuma, Isshu Kojima, Jingshu Li, Tomoya Tsubo, Shinya Tanaka, Masumi Tsuda, Lei Wang, , Kei Sato

This paper introduces CoVFit, a protein language model that predicts SARS-CoV-2 variant fitness using spike protein sequences, identifying fitness-enhancing mutations and predicting emerging variants.

Nature Communications · May 13, 2025Peer-reviewedMicrobiology