CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. - Jing Huang 024; Wen Wei; Joyce Chen; Jane Zhang; Guoying Liu; Xiaojun Di; Rui Mei; Shumpei Ishikawa; Hiroyuki Aburatani; Keith W. Jones; Michael H. Shapero (BMC Bioinform., 2006)

Noise Reduction from Genotyping Microarrays Using Probe Level Information. - Daisuke Komura; Kunihiro Nishimura; Shumpei Ishikawa; Binaya Panda; Jing Huang 024; Hiroshi Nakamura; Sigeo Ihara; Michitaka Hirose; Keith W. Jones; Hiroyuki Aburatani (Silico Biol., 2006)

Machine learning methods for histopathological image analysis. - Daisuke Komura; Shumpei Ishikawa (CoRR, 2017)

A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays. - Ching-Wei Wang; Yu-Ching Lee; Evelyne Calista; Fan Zhou 003; Hongtu Zhu; Ryohei Suzuki; Daisuke Komura; Shumpei Ishikawa; Shih-Ping Cheng (Bioinform., 2018)

Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. - Hiroki Konishi; Daisuke Komura; Hiroto Katoh; Shinichiro Atsumi; Hirotomo Koda; Asami Yamamoto; Yasuyuki Seto; Masashi Fukayama; Rui Yamaguchi; Seiya Imoto; Shumpei Ishikawa (BMC Bioinform., 2019)

Viola: a structural variant signature extractor with user-defined classifications. - Itsuki Sugita; Shohei Matsuyama; Hiroki Dobashi; Daisuke Komura; Shumpei Ishikawa (Bioinform., 2022)

Restaining-based annotation for cancer histology segmentation to overcome annotation-related limitations among pathologists. - Daisuke Komura; Takumi Onoyama; Koki Shinbo; Hiroto Odaka; Minako Hayakawa; Mieko Ochi; Ranny Rahaningrum Herdiantoputri; Haruya Endo; Hiroto Katoh; Tohru Ikeda; Tetsuo Ushiku; Shumpei Ishikawa (Patterns, 2023)

Meet the authors: Daisuke Komura and Shumpei Ishikawa. - Daisuke Komura; Shumpei Ishikawa (Patterns, 2023)

Enhanced Interpretability in Histopathological Images via Combined Tissue and Cell-Level Graph Analysis. - Mieko Ochi; Daisuke Komura; Tetsuo Ushiku; Yasushi Rino; Shumpei Ishikawa (AMAI@MICCAI, 2024)

SegRep: Mask-Supervised Learning for Segment Representation in Pathology Images. - Chichun Yang; Daisuke Komura; Mieko Ochi; Miwako Kakiuchi; Hiroto Katoh; Tetsuo Ushiku; Shumpei Ishikawa (IEEE Access, 2024)

Pathology Foundation Models. - Mieko Ochi; Daisuke Komura; Shumpei Ishikawa (CoRR, 2024)

Multimodal Whole Slide Foundation Model for Pathology. - Tong Ding; Sophia J. Wagner; Andrew H. Song; Richard J. Chen; Ming Y. Lu; Andrew Zhang; Anurag J. Vaidya; Guillaume Jaume; Muhammad Shaban; Ahrong Kim; Drew F. K. Williamson; Bowen Chen; et al. (CoRR, 2024)

SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data. - Shunsuke A. Sakai; Ryosuke Nomura; Satoi Nagasawa; Sunggi Chi; Ayako Suzuki; Yutaka Suzuki; Mitsuho Imai; Yoshiaki Nakamura; Takayuki Yoshino; Shumpei Ishikawa; Katsuya Tsuchihara; Shun-Ichiro Kageyama; et al. (PLoS Comput. Biol., 2025)

Comprehensive Pathological Image Segmentation via Teacher Aggregation for Tumor Microenvironment Analysis. - Daisuke Komura; Maki Takao; Mieko Ochi; Takumi Onoyama; Hiroto Katoh; Hiroyuki Abe; Hiroyuki Sano; Teppei Konishi; Toshio Kumasaka; Tomoyuki Yokose; Yohei Miyagi; Tetsuo Ushiku; et al. (CoRR, 2025)