Author

Shun‐Ichiro Kageyama

National Cancer Center Exploratory Oncology Research & Clinical Trial CenterORCID 0000-0002-6072-0144Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Cancer Biology· 2 Genomics· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Organism:human· 6 Research Focus:cell type annotation· 5 Assay:spatial transcriptomics· 4 Approach:statistical model· 4 Research Focus:spatial domain detection· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Assay:metagenomics· 2

Frequent Co-Authors

Katsuya TsuchiharaiD· 5 shared Shunsuke A. SakaiiD· 5 shared Riu YamashitaiD· 4 shared Ayako SuzukiiD· 3 shared Hideaki BandoiD· 3 shared Ryosuke NomuraiD· 3 shared Takao FujisawaiD· 3 shared Kyoko KuriharaiD· 2 shared

Activity by Year

2024-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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5 shared papersCancer Biology

Katsuya TsuchiharaORCID

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

SPATNIC enables H&E-grounded cancer-cell identification across spatial and single-cell transcriptomic modalities in colorectal cancer

Shunsuke A. Sakai, Ryosuke Nomura, Masaki Ohira, Kyoko Kurihara, SungGi Chi, Yuki Matsubara, Yukiko Morinaga, Takeshi Kato, Naoko Takeda-Miyata, Motohiro Kojima, Shingo Sakashita, Hiromichi Ebi, Rui Yamaguchi, Eiji Oki, Takao Fujisawa, , Riu Yamashita

SPATNIC is a variational autoencoder that identifies cancer cells from spatial and single-cell transcriptomic data in colorectal cancer, outperforming existing tools and identifying a rare cancer stem cell population.

bioRxiv · Oct 22, 2026 · PreprintCancer Biology

Catalog of gut microbiota alterations associated with anticancer therapies across multiple cancer types

Kyoko Kurihara, Shunsuke A. Sakai, Kentaro Sawada, Naoko Iida, Satoshi Horasawa, Takao Fujisawa, Yoshiaki Nakamura, Shun‐Ichiro Kageyama, Hideaki Bando, Takayuki Yoshino, Katsuya Tsuchihara, Riu Yamashita

The paper analyzes gut microbiota changes across 264 cancer patients treated with 22 anticancer drugs, finding drug-specific and treatment-related microbiota alterations.

bioRxiv · May 9, 2026 · PreprintMicrobiology

Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer

Shunsuke A. Sakai, Masayuki Okumura, Y Morinaga, Ken Kato, Motohiro Kojima, Falko Hofmann, Brian Reichholf, Pablo Augusto Vieyra-Garcia, Yuka Nakamura, Shingo Sakashita, Masaki Nakamura, Hidehiro Hojo, Yuichiro Tsukada, Masaaki Ito, Kohei Shitara, , Shun‐Ichiro Kageyama

The paper identifies POSTN-expressing cancer-associated fibroblasts (CAFs) linked to chemoradiotherapy resistance in rectal cancer using spatial multi-omics data.

bioRxiv · May 5, 2026 · PreprintCancer Biology

SpatialCompassV (SCOMV): De novo cell and gene spatial pattern classification and spatially differential gene identification

Ryosuke Nomura, Shunsuke A. Sakai, Shun‐Ichiro Kageyama, Katsuya Tsuchihara, Riu Yamashita

SCOMV classifies cell and gene spatial patterns and identifies spatially differential genes in spatial transcriptomic data without prior knowledge.

bioRxiv · Feb 28, 2026 · PreprintBioinformatics

Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome

Yuya Kiguchi, Nagisa Hamamoto, Yukie Kashima, Lucky Ronald Runtuwene, Aya Ishizaka, Yuta Kuze, Tomohiro Enokida, Nobukazu Tanaka, Makoto Tahara, Shun‐Ichiro Kageyama, Takao Fujisawa, Riu Yamashita, Akinori Kanai, Josef S. B. Tuda, Taketoshi Mizutani, Yutaka Suzuki

The paper identifies a novel giant extrachromosomal element, Inocles, prevalent in the human oral microbiome that contributes to bacterial stress tolerance and may serve as a biomarker for gastrointestinal cancers.

Nature Communications · Aug 11, 2025Peer-reviewedGenomics

Spatial domain analysis to estimate spatiotemporal pathological mechanisms in microenvironment with single-cell spatial omics data

Shunsuke A. Sakai, Ryosuke Nomura, Satoi Nagasawa, SungGi Chi, Ayako Suzuki, Yutaka Suzuki, Shumpei Ishikawa, Katsuya Tsuchihara, Shun‐Ichiro Kageyama, Riu Yamashita

The paper introduces SpatialKNife, a toolkit for analyzing single-cell spatial omics data to estimate spatiotemporal pathological mechanisms in microenvironments.

bioRxiv · Jun 18, 2024 · PreprintBioinformatics