Author

Yukari Nakajima

Kyoto UniversityORCID 0000-0002-6401-8678Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Organism:bacteria (other)· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1

Frequent Co-Authors

Akatsuki SaitoiD· 2 shared Alfredo A. HinayiD· 2 shared Arnon PlianchaisukiD· 2 shared Ayaka SakamotoiD· 2 shared Chihiro MotozonoiD· 2 shared Hayato ItoiD· 2 shared Hirofumi SawaiD· 2 shared Hiroki Futatsusako· 2 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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Curved chords = mutual co-authorship

2 shared papersMicrobiology

Akatsuki SaitoORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

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

The N-terminal extension region of BamE coordinates interaction between the β-barrel domain of BamA and BamD for efficient assembly

Yuki Maruno, Edward M. Germany, Yukari Nakajima, Rei Ohyama, Yukihiko Masumura, Takuya Shiota

This study identifies the N-terminal extension of BamE as critical for coordinating BamA and BamD interactions during β-barrel protein assembly in Gram-negative bacteria.

bioRxiv · Oct 31, 2024 · PreprintBiochemistry