Author

Masato Ishikawa

Kyoto University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Biology Disciplines

Click to filter author papers

Bioinformatics· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:cell-cell communication· 2 Research Focus:clustering· 2 Assay:spatial transcriptomics· 2 Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Organism:mouse· 1

Frequent Co-Authors

Haruka HiroseiD· 2 shared Shuto HayashiiD· 2 shared Yasuhiro KojimaiD· 2 shared Atsushi EnomotoiD· 1 shared Fumiko ChiwakiiD· 1 shared Hiroyuki ManoiD· 1 shared Kazuya Nishimura· 1 shared Kota ItahashiiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBioinformatics

Haruka HiroseORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Probabilistic coupling of cellular and microenvironmental heterogeneity by masked self-supervised learning

Yasuhiro Kojima, Yosuke Tanaka, Haruka Hirose, Fumiko Chiwaki, Kazuya Nishimura, Shuto Hayashi, Kota Itahashi, Masato Ishikawa, Teppei Shimamura, Hiroyuki Mano

Mievformer uses masked self-supervised learning to model microenvironmental and cellular heterogeneity in spatial transcriptomics data, outperforming existing methods in niche clustering and real dataset analysis.

bioRxiv · Apr 24, 2026 · PreprintBioinformatics

Single-cell colocalization analysis using a deep generative model

Yasuhiro Kojima, Shinji Mii, Shuto Hayashi, Haruka Hirose, Masato Ishikawa, Masashi Akiyama, Atsushi Enomoto, Teppei Shimamura

DeepCOLOR identifies cell-cell interactions by reconstructing spatial colocalization maps from single-cell and spatial transcriptomes in various tissues.

Cell Systems · Feb 1, 2024Peer-reviewedBioinformatics