Author

Yutaro Kumagai

Cellular and Molecular Biotechnology Research InstituteORCID 0000-0002-5039-3979Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Genomics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Kenta NakaiiD· 2 shared Akio TsuruiD· 1 shared Alexis VandenboniD· 1 shared Daisuke OriiD· 1 shared Haruna Okude· 1 shared Hideyuki NakashimaiD· 1 shared Ken J. IshiiiD· 1 shared Kenji KohnoiD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersBioinformatics

Kenta NakaiORCID

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Author profile →

4 papers

Recent·Most cited

Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis

Daisuke Ori, Haruna Okude, Riko Konishi, Motoya Murase, Shuya Hiroki, Saki Takahara, Towa Tanaka, Rina Toyodome, Norisuke Kano, Takumi Kawasaki, Ken J. Ishii, Kouji Kobiyama, Hideyuki Nakashima, Kinichi Nakashima, Miwa Sasai, , Taro Kawai

This study identifies Gelsolin as a regulator of ER stress in psoriasis-like dermatitis, showing it counteracts inflammatory circuits driven by IMQ-induced organelle stress.

bioRxiv · Nov 20, 2025 · PreprintImmunology

BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks.

Yutaro Kumagai

BootCellNet identifies cell populations and infers gene regulatory networks from scRNA-seq data, enabling robust and explainable cell-type discovery.

PLoS Computational Biology · Sep 30, 2024Peer-reviewedBioinformatics

Multi-omics computational analysis unveils the in-volvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization

Yubo Zhang, Wenbo Yang, Yutaro Kumagai, Martin Loza, Weihang Zhang, Sung‐Joon Park, Kenta Nakai

This study identifies hysteresis genes in macrophage polarization and shows that AP-1 and CTCF regulate chromatin state changes during de/repolarization.

Frontiers in Immunology · Dec 20, 2023Peer-reviewedBioinformatics

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki, Kenta Nakai

The paper examines the temporal dynamics of histone modifications in mouse dendritic cells after LPS stimulation, revealing distinct patterns and links to transcription factor activity.

Genome biology · Sep 19, 2018Peer-reviewedGenomics