業績

2021年

Sugita, I., Matsuyama, S., Dobashi, H., Komura, D., Ishikawa, S., 2021. Viola: a structural variant signature extractor with user-defined classifications. Bioinformatics.
Ishigami, D., Miyawaki, S., Nakatomi, H., Takayanagi, S., Teranishi, Y., Ohara, K., Hongo, H., Dofuku, S., Kin, T., Abe, H., Mitsui, J., Komura, D., Katoh, H., Ishikawa, S., Saito, N., 2021. Brainstem intraparenchymal schwannoma with genetic analysis: a case report and literature review. BMC Med Genomics 14, 205.
Zhang, M., Sugita, I., Komura, D., Katoh, H., Shimada, S., Inazawa, J., Tanaka, S., Ishikawa, S., 2021. Genomic landscape of a mouse model of diffuse-type gastric adenocarcinoma. Gastric Cancer.
Komura, D., Ishikawa, S., 2021. Advanced deep learning applications in diagnostic pathology. Translational and Regulatory Sciences 3, 36–42.
Katoh, H., Ishikawa, S., 2021. Lifestyles, genetics, and future perspectives on gastric cancer in east Asian populations. J Hum Genet 66, 887–899.
Imai, S., Ooki, T., Murata-Kamiya, N., Komura, D., Tahmina, K., Wu, W., Takahashi-Kanemitsu, A., Knight, C.T., Kunita, A., Suzuki, N., Del Valle, A.A., Tsuboi, M., Hata, M., Hayakawa, Y., Ohnishi, N., Ueda, K., Fukayama, M., Ushiku, T., Ishikawa, S., Hatakeyama, M., 2021. Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis. Cell Host Microbe 29, 941-958.e10.
Ohkuma, R., Yada, E., Ishikawa, S., Komura, D., Kubota, Y., Hamada, K., Horiike, A., Ishiguro, T., Hirasawa, Y., Ariizumi, H., Shida, M., Watanabe, M., Onoue, R., Ando, K., Tsurutani, J., Yoshimura, K., Sasada, T., Aoki, T., Murakami, M., Norose, T., Ohike, N., Takimoto, M., Kobayashi, S., Tsunoda, T., Wada, S., 2021. High levels of human epididymis protein 4 mRNA and protein expression are associated with chemoresistance and a poor prognosis in pancreatic cancer. Int J Oncol 58, 57–69.

2020年

Koyama, K., Maeda, D., Kito, M., Tamura, D., Kudo-Asabe, Y., Katoh, H., Ishikawa, S., Nanjo, H., Terada, Y., Goto, A., 2020. Clinicopathological and molecular analyses of linearly expanded epithelial cells with β-catenin alterations, “β-catenin signature”, in the normal fallopian tube. Histopathology 77, 880–889.
Atsumi, S., Katoh, H., Komura, D., Hashimoto, I., Furuya, G., Koda, H., Konishi, H., Suzuki, R., Yamamoto, A., Yuba, S., Abe, H., Rino, Y., Oshima, T., Ushiku, T., Fukayama, M., Seto, Y., Ishikawa, S., 2020. Focal adhesion ribonucleoprotein complex proteins are major humoral cancer antigens and targets in autoimmune diseases. Communications Biology 3, 1–15.
Bailey, M.H., Meyerson, W.U., Dursi, L.J., Wang, L.-B., Dong, G., Liang, W.-W., Weerasinghe, A., Li, S., Kelso, S., MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena, G., Ellrott, K., Wendl, M.C., Wheeler, D.A., Getz, G., Simpson, J.T., Gerstein, M.B., Ding, L., PCAWG Consortium, 2020. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11, 4748.
Midorikawa, Y., Yamamoto, S., Tatsuno, K., Renard-Guillet, C., Tsuji, S., Hayashi, A., Ueda, H., Fukuda, S., Fujita, T., Katoh, H., Ishikawa, S., Covington, K.R., Creighton, C.J., Sugitani, M., Wheeler, D.A., Shibata, T., Nagae, G., Takayama, T., Aburatani, H., 2020. Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression. Cancer Res 80, 3810–3819.
Shinozaki-Ushiku, A., Ishikawa, S., Komura, D., Seto, Y., Aburatani, H., Ushiku, T., 2020. The first case of gastric carcinoma with NTRK rearrangement: identification of a novel ATP1B-NTRK1 fusion. Gastric Cancer 23, 944–947.
Li, C.H., Prokopec, S.D., Sun, R.X., Yousif, F., Schmitz, N., PCAWG Tumour Subtypes and Clinical Translation, Boutros, P.C., PCAWG Consortium, 2020. Sex differences in oncogenic mutational processes. Nat Commun 11, 4330.
Ikeda, H., Muroi, M., Kondoh, Y., Ishikawa, S., Kakeya, H., Osada, H., Imoto, M., 2020. Miclxin, a Novel MIC60 Inhibitor, Induces Apoptosis via Mitochondrial Stress in β-Catenin Mutant Tumor Cells. ACS Chem Biol 15, 2195–2204.
Komura, D., Kawabe, A., Fukuta, K., Sano, K., Umezaki, T., Koda, H., Suzuki, R., Tominaga, K., Konishi, H., Nishida, S., Furuya, G., Katoh, H., Ushiku, T., Fukayama, M., Ishikawa, S., 2020. Deep Texture Representations as a Universal Encoder for Pan-cancer Histology. bioRxiv 2020.07.28.224253.
Sano, K., Matsuda, S., Tohyama, S., Komura, D., Shimizu, E., Sutoh, C., 2020. Deep learning-based classification of the mouse estrous cycle stages. Scientific Reports 10, 11714.
Ohkuma, R., Yada, E., Ishikawa, S., Komura, D., Kubota, Y., Hamada, K., Horiike, A., Ishiguro, T., Hirasawa, Y., Ariizumi, H., Shida, M., Watanabe, M., Onoue, R., Ando, K., Tsurutani, J., Yoshimura, K., Sasada, T., Aoki, T., Murakami, M., Norose, T., Ohike, N., Takimoto, M., Kobayashi, S., Tsunoda, T., Wada, S., 2020. High expression levels of polymeric immunoglobulin receptor are correlated with chemoresistance and poor prognosis in pancreatic cancer. Oncol Rep 44, 252–262.
Matsubara, D., Yoshimoto, T., Soda, M., Amano, Y., Kihara, A., Funaki, T., Ito, T., Sakuma, Y., Shibano, T., Endo, S., Hagiwara, K., Ishikawa, S., Fukayama, M., Murakami, Y., Mano, H., Niki, T., 2020. Reciprocal expression of trefoil factor-1 and thyroid transcription factor-1 in lung adenocarcinomas. Cancer Sci 111, 2183–2195.
Suzuki, A., Katoh, H., Komura, D., Kakiuchi, M., Tagashira, A., Yamamoto, S., Tatsuno, K., Ueda, H., Nagae, G., Fukuda, S., Umeda, T., Totoki, Y., Abe, H., Ushiku, T., Matsuura, T., Sakai, E., Ohshima, T., Nomura, S., Seto, Y., Shibata, T., Rino, Y., Nakajima, A., Fukayama, M., Ishikawa, S., Aburatani, H., 2020. Defined lifestyle and germline factors predispose Asian populations to gastric cancer. Science Advances 6, eaav9778.
Watabe, S., Kikuchi, Y., Morita, S., Komura, D., Numakura, S., Kumagai-Togashi, A., Watanabe, M., Matsutani, N., Kawamura, M., Yasuda, M., Uozaki, H., 2020. Clinicopathological significance of microRNA-21 in extracellular vesicles of pleural lavage fluid of lung adenocarcinoma and its functions inducing the mesothelial to mesenchymal transition. Cancer Med 9, 2879–2890.
Takai, E., Maeda, D., Li, Z., Kudo-Asabe, Y., Totoki, Y., Nakamura, H., Nakamura, A., Nakamura, R., Kirikawa, M., Ito, Y., Yoshida, M., Inoue, T., Habuchi, T., Ikoma, S., Katoh, H., Kato, M., Shibata, T., Ishikawa, S., Yachida, S., Goto, A., 2020. Post-mortem Plasma Cell-Free DNA Sequencing: Proof-of-Concept Study for the “Liquid Autopsy.” Scientific Reports 10, 1–10.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, 2020. Pan-cancer analysis of whole genomes. Nature 578, 82–93.
Hiroshima, Y., Kasajima, R., Kimura, Y., Komura, D., Ishikawa, S., Ichikawa, Y., Bouvet, M., Yamamoto, N., Oshima, T., Morinaga, S., Singh, S.R., Hoffman, R.M., Endo, I., Miyagi, Y., 2020. Novel targets identified by integrated cancer-stromal interactome analysis of pancreatic adenocarcinoma. Cancer Lett. 469, 217–227.
Ohkuma, R., Yada, E., Ishikawa, S., Komura, D., Ishizaki, H., Tamada, K., Kubota, Y., Hamada, K., Ishida, H., Hirasawa, Y., Ariizumi, H., Satoh, E., Shida, M., Watanabe, M., Onoue, R., Ando, K., Tsurutani, J., Yoshimura, K., Yokobori, T., Sasada, T., Aoki, T., Murakami, M., Norose, T., Ohike, N., Takimoto, M., Izumizaki, M., Kobayashi, S., Tsunoda, T., Wada, S., 2020. High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer. PLoS ONE 15, e0226707.

2019年

Nishizawa, T., Nakano, K., Fujii, E., Komura, D., Kuroiwa, Y., Ishimaru, C., Monnai, M., Aburatani, H., Ishikawa, S., Suzuki, M., 2019. In vivo effects of mutant RHOA on tumor formation in an orthotopic inoculation model. Oncology Reports 42, 1745–1754.
Suga, H., Oka, T., Sugaya, M., Sato, Y., Ishii, T., Nishida, H., Ishikawa, S., Fukayama, M., Sato, S., 2019. Keratinocyte Proline-Rich Protein Deficiency in Atopic Dermatitis Leads to Barrier Disruption. Journal of Investigative Dermatology 139, 1867-1875.e7.
Komura, D., Ishikawa, S., 2019. Machine learning approaches for pathologic diagnosis. Virchows Arch 475, 131–138.
Konishi, H., Komura, D., Katoh, H., Atsumi, S., Koda, H., Yamamoto, A., Seto, Y., Fukayama, M., Yamaguchi, R., Imoto, S., Ishikawa, S., 2019. Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. BMC Bioinformatics 20, 267.
Krishnan, N.M., Katoh, H., Palve, V., Pareek, M., Sato, R., Ishikawa, S., Panda, B., 2019. Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma. PeerJ 7, e6464.
Okamoto, H., Yoshimatsu, Y., Tomizawa, T., Kunita, A., Takayama, R., Morikawa, T., Komura, D., Takahashi, K., Oshima, T., Sato, M., Komai, M., Podyma-Inoue, K.A., Uchida, H., Hamada, H., Fujiu, K., Ishikawa, S., Fukayama, M., Fukuhara, T., Watabe, T., 2019. Interleukin-13 receptor α2 is a novel marker and potential therapeutic target for human melanoma. Scientific Reports 9, 1281.
Bándi, P., Geessink, O., Manson, Q., Van Dijk, M., Balkenhol, M., Hermsen, M., Ehteshami Bejnordi, B., Lee, B., Paeng, K., Zhong, A., Li, Q., Zanjani, F.G., Zinger, S., Fukuta, K., Komura, D., Ovtcharov, V., Cheng, S., Zeng, S., Thagaard, J., Dahl, A.B., Lin, H., Chen, H., Jacobsson, L., Hedlund, M., Çetin, M., Halıcı, E., Jackson, H., Chen, R., Both, F., Franke, J., Küsters-Vandevelde, H., Vreuls, W., Bult, P., van Ginneken, B., van der Laak, J., Litjens, G., 2019. From Detection of Individual Metastases to Classification of Lymph Node Status at the Patient Level: The CAMELYON17 Challenge. IEEE Transactions on Medical Imaging 38, 550–560.
Nakayama, A., Abe, H., Kunita, A., Saito, R., Kanda, T., Yamashita, H., Seto, Y., Ishikawa, S., Fukayama, M., 2019. Viral loads correlate with upregulation of PD-L1 and worse patient prognosis in Epstein–Barr Virus-associated gastric carcinoma. PLOS ONE 14, e0211358.
Akiyama, Y., Maeda, D., Katoh, H., Morikawa, T., Niimi, A., Nomiya, A., Sato, Y., Kawai, T., Goto, A., Fujimura, T., Fukuhara, H., Nakagawa, T., Igawa, Y., Ishikawa, S., Fukayama, M., Kume, H., Homma, Y., 2019. Molecular Taxonomy of Interstitial Cystitis/Bladder Pain Syndrome Based on Whole Transcriptome Profiling by Next-Generation RNA Sequencing of Bladder Mucosal Biopsies. J. Urol. 202, 290–300.

2018年

Funahashi, S.-I., Kawai, S., Fujii, E., Taniguchi, K., Nakano, K., Ishikawa, S., Aburatani, H., Suzuki, M., 2018. Generation of an anti-desmoglein 3 antibody without pathogenic activity of pemphigus vulgaris for therapeutic application to squamous cell carcinoma. J. Biochem. 164, 471–481.
Nakano, K., Nishizawa, T., Komura, D., Fujii, E., Monnai, M., Kato, A., Funahashi, S.-I., Ishikawa, S., Suzuki, M., 2018. Difference in morphology and interactome profiles between orthotopic and subcutaneous gastric cancer xenograft models. J Toxicol Pathol 31, 293–300.
Hosonaga, M., Arima, Y., Sampetrean, O., Komura, D., Koya, I., Sasaki, T., Sato, E., Okano, H., Kudoh, J., Ishikawa, S., Saya, H., Ishikawa, T., 2018. HER2 Heterogeneity Is Associated with Poor Survival in HER2-Positive Breast Cancer. Int J Mol Sci 19.
Tanaka, A., Ishikawa, S., Ushiku, T., Yamazawa, S., Katoh, H., Hayashi, A., Kunita, A., Fukayama, M., 2018. Frequent CLDN18-ARHGAP fusion in highly metastatic diffuse-type gastric cancer with relatively early onset. Oncotarget 9, 29336–29350.
Wang, C.-W., Lee, Y.-C., Calista, E., Zhou, F., Zhu, H., Suzuki, R., Komura, D., Ishikawa, S., Cheng, S.-P., 2018. A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays. Bioinformatics 34, 1767–1773.
Nishizawa, T., Nakano, K., Harada, A., Kakiuchi, M., Funahashi, S.-I., Suzuki, M., Ishikawa, S., Aburatani, H., 2018. DGC-specific RHOA mutations maintained cancer cell survival and promoted cell migration via ROCK inactivation. Oncotarget 9, 23198–23207.
Komura, D., Ishikawa, S., 2018. Machine Learning Methods for Histopathological Image Analysis. Comput Struct Biotechnol J 16, 34–42.