Publication List of Seiya Imoto

1. Peer reviewed papers

1. Pérez-Saldívar M, Nakamura Y, Kiyotani K, Imoto S, Katayama K, Yamaguchi R, Miyano S, Martínez-Barnetche J, Godoy-Lozano EE, Ordoñez G, Sotelo J, González-Conchillos H, Martínez-Palomo A, Flores-Rivera J, Santos-Argumedo L, Sánchez-Salguero ES, Espinosa-Cantellano M. Comparative analysis of the B cell receptor repertoire during relapse and remission in patients with multiple sclerosis. Clin Immunol. 2024 Nov 15:110398. doi: 10.1016/j.clim.2024.110398. Online ahead of print.
2. Maeda-Minami A, Yoshino T, Katayama K, Horiba Y, Hikiami H, Shimada Y, Namiki T, Tahara E, Minamizawa K, Muramatsu SI, Yamaguchi R, Imoto S, Miyano S, Mima H, Uneda K, Nogami T, Fukunaga K, Watanabe K. Machine learning model for predicting the cold-heat pattern in Kampo medicine: a multicenter prospective observational study. Front Pharmacol. 2024 Oct 25;15:1412593. doi: 10.3389/fphar.2024.1412593. eCollection 2024.
3. Kawataki S, Kubota Y, Katayama K, Imoto S, Takekawa M. GADD45β-MTK1 signaling axis mediates oncogenic stress-induced activation of the p38 and JNK pathways. Cancer Sci. 2024 Nov 11. doi: 10.1111/cas.16389. Online ahead of print.
4. Tanaka H, Toya E, Chubachi S, Namkoong H, Asakura T, Azekawa S, Otake S, Nakagawara K, Fukushima T, Watase M, Sakurai K, Masaki K, Kamata H, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Combined use of serum ferritin and KL-6 levels as biomarkers for predicting COVID-19 severity. Respir Investig. 2024 Oct 3;62(6):1132-1136. doi: 10.1016/j.resinv.2024.09.011. Online ahead of print.
5. Wang QS, Hasegawa T, Namkoong H, Saiki R, Edahiro R, Sonehara K, Tanaka H, Azekawa S, Chubachi S, Takahashi Y, Sakaue S, Namba S, Yamamoto K, Shiraishi Y, Chiba K, Tanaka H, Makishima H, Nannya Y, Zhang Z, Tsujikawa R, Koike R, Takano T, Ishii M, Kimura A, Inoue F, Kanai T, Fukunaga K, Ogawa S, Imoto S, Miyano S, Okada Y; Japan COVID-19 Task Force. Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance. Nature Genet. 2024 Sep 24. doi: 10.1038/s41588-024-01896-3. Online ahead of print.
6. Wang X, Li F, Zhang Y, Imoto S, Shen HH, Li S, Guo Y, Yang J, Song J. Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. Brief Bioinform. 2024 Jul 25;25(5):bbae446. doi: 10.1093/bib/bbae446.
7. Meguro S, Johmura Y, Wang TW, Kawakami S, Tanimoto S, Omori S, Okamura YT, Hoshi S, Kayama E, Yamaguchi K, Hatakeyama S, Yamazaki S, Shimizu E, Imoto S, Furukawa Y, Kojima Y, Nakanishi M. Preexisting senescent fibroblasts in the aged bladder create a tumor-permissive niche through CXCL12 secretion. Nature Aging. 2024 Sep 9. doi: 10.1038/s43587-024-00704-1. Online ahead of print.
8. Sato A, Yusa N, Takamori H, Shimizu E, Yokoyama K, Ichikawa S, Yokoyama H, Kasahara Y, Enda K, Fujishima F, Ichinohasama R, Ota Y, Imoto S, Nannya Y. Common progenitor origin for Rosai-Dorfman disease and clear cell sarcoma. J Pathol. 2024 Sep 3. doi: 10.1002/path.6345. Online ahead of print.
9. Kimura Y, Ono Y, Katayama K, Imoto S. IVEA: an integrative variational Bayesian inference method for predicting enhancer-gene regulatory interactions. Bioinform Adv. 2024 Aug 20;4(1):vbae118. doi: 10.1093/bioadv/vbae118.
10. Fujimoto K, Hayashi T, Yamamoto M, Sato N, Shimohigoshi M, Miyaoka D, Yokota C, Watanabe M, Hisaki Y, Kamei Y, Yokoyama Y, Yabuno T, Hirose A, Nakamae M, Nakamae H, Uematsu M, Sato S, Yamaguchi K, Furukawa Y, Akeda Y, Hino M, Imoto S*, Uematsu S*. An enterococcal phage-derived enzyme suppresses graft-versus-host disease. Nature. 2024 Jul 10. https://doi.org/10.1038/s41586-024-07667-8
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00290.html
11. Wang Z, Ma J, Gao Q, Bain C, Imoto S, Liò P, Cai H, Chen H, Song J. Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. Med Image Anal. 2024 Jun 26;97:103252. doi: 10.1016/j.media.2024.103252. Online ahead of print.
12. Sato N, Zhang YZ, Gu Z, Imoto S. Biotextgraph: graphical summarization of functional similarities from textual information. Bioinformatics. 2024 Jun 8:btae357. doi: 10.1093/bioinformatics/btae357. Online ahead of print.
13. Tanaka H, Chubachi S, Asakura T, Namkoong H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Lee H, Watase M, Sakurai K, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Prognostic significance of chronic kidney disease and impaired renal function in Japanese patients with COVID-19. BMC Infect Dis. 2024 May 25;24(1):527. doi: 10.1186/s12879-024-09414-w.
14. Murakami K, Tago SI, Takishita S, Morikawa H, Kojima R, Yokoyama K, Ogawa M, Fukushima H, Takamori H, Nannya Y, Imoto S, Fuji M. Pathogenicity prediction of gene fusion in structural variations: a knowledge graph-infused explainable artificial intelligence (XAI) framework. Cancers (Basel). 2024 May 17;16(10):1915. doi: 10.3390/cancers16101915.
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00285.html
15. Otake S, Shiraishi Y, Chubachi S, Tanabe N, Maetani T, Asakura T, Namkoong H, Shimada T, Azekawa S, Nakagawara K, Tanaka H, Fukushima T, Watase M, Terai H, Sasaki M, Ueda S, Kato Y, Harada N, Suzuki S, Yoshida S, Tateno H, Yamada Y, Jinzaki M, Hirai T, Okada Y, Koike R, Ishii M, Hasegawa N, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Lung volume measurement using chest CT in COVID-19 patients: a cohort study in Japan. BMJ Open Respir Res. 2024 Apr 24;11(1):e002234. doi: 10.1136/bmjresp-2023-002234.
16. Zeng X, Wang TW, Yamaguchi K, Hatakeyama S, Yamazaki S, Shimizu E, Imoto S, Furukawa Y, Johmura Y, Nakanishi M. M2 macrophage-derived TGF-β induces age-associated loss of adipogenesis through progenitor cell senescence. Mol Metab. 2024 Apr 23:101943. doi: 10.1016/j.molmet.2024.101943. Online ahead of print.
17. Watanabe M, Uematsu M, Fujimoto K, Hara T, Yamamoto M, Miyaoka D, Yokota C, Kamei Y, Sugimoto A, Kawasaki N, Yabuno T, Sato N, Sato S, Yamaguchi K, Furukawa Y, Tsuruta D, Okada F, Imoto S*, Uematsu S*. Targeted lysis of Staphylococcus hominis linked to axillary osmidrosis using bacteriophage-derived endolysin. J Invest Dermatol. 2024 Apr 18:S0022-202X(24)00294-X. doi: 10.1016/j.jid.2024.03.039. Online ahead of print.
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00281.html
18. Azekawa S, Maetani T, Chubachi S, Asakura T, Tanabe N, Shiraishi Y, Namkoong H, Tanaka H, Shimada T, Fukushima T, Otake S, Nakagawara K, Watase M, Terai H, Sasaki M, Ueda S, Kato Y, Harada N, Suzuki S, Yoshida S, Tateno H, Yamada Y, Jinzaki M, Hirai T, Okada Y, Koike R, Ishii M, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. CT-derived vertebral bone mineral density is a useful biomarker to predict COVID-19 outcome. Bone. 2024 Apr 8:117095. doi: 10.1016/j.bone.2024.117095.
19. Nakagawara K, Shiraishi Y, Chubachi S, Tanabe N, Maetani T, Asakura T, Namkoong H, Tanaka H, Shimada T, Azekawa S, Otake S, Fukushima T, Watase M, Terai H, Sasaki M, Ueda S, Kato Y, Harada N, Suzuki S, Yoshida S, Tateno H, Yamada Y, Jinzaki M, Hirai T, Okada Y, Koike R, Ishii M, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Integrated assessment of computed tomography density in pectoralis and erector spinae muscles as a prognostic biomarker for coronavirus disease 2019. Clin Nutr. 2024 Feb 5;43(3):815-824. doi: 10.1016/j.clnu.2024.02.004. Online ahead of print.
20. Kuwatsuka Y, Kasajima R, Yamaguchi R, Uchida N, Konuma T, Tanaka M, Shingai N, Miyakoshi S, Kozai Y, Uehara Y, Eto T, Toyosaki M, Nishida T, Ishimaru F, Kato K, Fukuda T, Imoto S, Atsuta Y, Takahashi S. Machine learning prediction model for neutrophil recovery after unrelated cord blood transplantation. Transplant Cell Ther. 2024 Feb 7:S2666-6367(24)00182-9. doi: 10.1016/j.jtct.2024.02.001. Online ahead of print.
21. Matsubara Y, Kiyohara H, Mikami Y, Nanki K, Namkoong H, Chubachi S, Tanaka H, Azekawa S, Sugimoto S, Yoshimatsu Y, Sujino T, Takabayashi K, Hosoe N, Sato T, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Fukunaga K, Kanai T; Japan COVID-19 Task Force. Gastrointestinal symptoms in COVID-19 and disease severity: a Japanese registry-based retrospective cohort study. J Gastroenterol. 2024 Jan 25. doi: 10.1007/s00535-023-02071-x. Online ahead of print.
22. Heryanto YD, Zhang YZ, Imoto S. Predicting cell types with supervised contrastive learning on cells and their types. Sci Rep. 2024 Jan 3;14(1):430. doi: 10.1038/s41598-023-50185-2.
23. Murakami M, Fujii K, Naito W, Kamo M, Kitajima M, Yasutaka T, Imoto S. COVID-19 infection risk assessment and management at the Tokyo 2020 Olympic and Paralympic Games: A scoping review. Journal of Infection and Public Health, 2024 Apr;17 Suppl 1:18-26. doi: 10.1016/j.jiph.2023.03.025.
24. Kusumoto T, Chubachi S, Namkoong H, Tanaka H, Lee H, Otake S, Nakagawara K, Fukushima T, Morita A, Watase M, Asakura T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Edahiro R, Murakami K, Sato Y, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Characteristics of patients with COVID-19 who have deteriorating chest X-ray findings within 48 h: a retrospective cohort study. Sci Rep. 2023 Dec 12;13(1):22054. doi: 10.1038/s41598-023-49340-6.
25. Khor AHP, Koguchi T, Liu H, Kakuta M, Matsubara D, Wen R, Sagiya Y, Imoto S, Nakagawa H, Matsuda K, Tanikawa C. Regulation of the innate immune response and gut microbiome by p53. Cancer Sci. 2024 Jan;115(1):184-196. doi: 10.1111/cas.15991.
26. Seki M, Zhang Y-Z, Imoto S. Imputing time-series microbiome abundance profiles with diffusion model. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2023, 914-919. doi: 10.1109/BIBM58861.2023.10385703.
27. Saito H, Yoshimura H, Yoshida M, Tani Y, Kawashima M, Uchiyama T, Zhao T, Yamamoto C, Kobashi Y, Sawano T, Imoto S, Park H, Nakamura N, Iwami S, Kaneko Y, Nakayama A, Kodama T, Wakui M, Kawamura T, Tsubokura M. Antibody profiling of microbial antigens in the blood of COVID-19 mRNA vaccine recipients using microbial protein microarrays. Vaccines (Basel). 2023 Nov 7;11(11):1694. doi: 10.3390/vaccines11111694.
28. Sato N, Shiraki A, Mori KP, Sakai K, Takemura Y, Yanagita M, Imoto S, Tanabe K, Shiraki K. Preemptive intravenous human immunoglobulin G suppresses BK polyomavirus replication and spread of infection in vitro. Am J Transplant. 2024 May;24(5):765-773. doi: 10.1016/j.ajt.2023.11.007.
29. Sakurai K, Chubachi S, Asakura T, Namkoong H, Tanaka H, Azekawa S, Shimada T, Otake S, Nakagawara K, Fukushima T, Lee H, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Prognostic significance of hypertension history and blood pressure on admission in Japanese patients with coronavirus disease 2019: integrative analysis from the Japan COVID-19 Task Force. Hypertens Res. 2024 Mar;47(3):639-648. doi: 10.1038/s41440-023-01490-w.
30. Fukushima T, Maetani T, Chubachi S, Tanabe N, Asakura T, Namkoong H, Tanaka H, Shimada T, Azekawa S, Otake S, Nakagawara K, Watase M, Shiraishi Y, Terai H, Sasaki M, Ueda S, Kato Y, Harada N, Suzuki S, Yoshida S, Tateno H, Yamada Y, Jinzaki M, Hirai T, Okada Y, Koike R, Ishii M, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Epicardial adipose tissue measured from analysis of adipose tissue area using chest CT imaging is the best potential predictor of COVID-19 severity. Metabolism. 2024 Jan;150:155715. doi: 10.1016/j.metabol.2023.155715.
31. Wang QS, Edahiro R, Namkoong H, Hasegawa T, Shirai Y, Sonehara K; Japan COVID-19 Task Force; Kumanogoh A, Ishii M, Koike R, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K, Okada Y. Estimating gene-level false discovery probability improves eQTL statistical fine-mapping precision. NAR Genom Bioinform. 2023 Oct 30;5(4):lqad090. doi: 10.1093/nargab/lqad090.
32. Heryanto YD, Imoto S. The transcriptome signature analysis of the epithelial-mesenchymal transition and immune cell infiltration in colon adenocarcinoma. Sci Rep. 2023 Oct 26;13(1):18383. doi: 10.1038/s41598-023-45792-y.
33. Sato N, Uematsu M, Fujimoto K, Uematsu S, Imoto S. ggkegg: analysis and visualization of KEGG data utilizing grammar of graphics. Bioinformatics. 2023 Oct 3;39(10):btad622. doi: 10.1093/bioinformatics/btad622.
34. Zhang YZ, Bai Z, Imoto S. Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings. Bioinformatics. 2023 Oct 10:btad617. doi: 10.1093/bioinformatics/btad617. Online ahead of print.
35. Tanaka H, Maetani T, Chubachi S, Tanabe N, Shiraishi Y, Asakura T, Namkoong H, Shimada T, Azekawa S, Otake S, Nakagawara K, Fukushima T, Watase M, Terai H, Sasaki M, Ueda S, Kato Y, Harada N, Suzuki S, Yoshida S, Tateno H, Yamada Y, Jinzaki M, Hirai T, Okada Y, Koike R, Ishii M, Hasegawa N, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Clinical utilization of artificial intelligence-based COVID-19 pneumonia quantification using chest computed tomography - a multicenter retrospective cohort study in Japan. Respir Res. 2023 Oct 5;24(1):241. doi: 10.1186/s12931-023-02530-2.
36. Suzuki M, Kasajima R, Yokose T, Shimizu E, Hatakeyama S, Yamaguchi K, Yokoyama K, Katayama K, Yamaguchi R, Furukawa Y, Miyano S, Imoto S, Shinozaki-Ushiku A, Ushiku T, Miyagi Y. KMT2C expression and DNA homologous recombination repair factors in lung cancers with a high-grade fetal adenocarcinoma component. Transl Lung Cancer Res. 2023 Aug 30;12(8):1738-1751. doi: 10.21037/tlcr-23-137. Epub 2023 Aug 16.
37. COVID-19 Host Genetics Initiative. A second update on mapping the human genetic architecture of COVID-19. Nature. 2023 Sep;621(7977):E7-E26. doi: 10.1038/s41586-023-06355-3. Epub 2023 Sep 6.
38. Kawachi K, Tang X, Kasajima R, Yamanaka T, Shimizu E, Katayama K, Yamaguchi R, Yokoyama K, Yamaguchi K, Furukawa Y, Miyano S, Imoto S, Yoshioka E, Washimi K, Okubo Y, Sato S, Yokose T, Miyagi Y. Genetic analysis of low-grade adenosquamous carcinoma of the breast progressing to high-grade metaplastic carcinoma. Breast Cancer Res Treat. 2023 Aug 31. doi: 10.1007/s10549-023-07078-9.
39. Park H, Imoto S, Miyano S. Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification. PLoS One, 2023 Aug 23;18(8):e0286044. doi: 10.1371/journal.pone.0286044.
40. Liu Y, Zhang YZ, Imoto S. Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases. PLoS One, 2023 Aug 21;18(8):e0290307. doi: 10.1371/journal.pone.0290307.
41. Kusumoto T, Chubachi S, Namkoong H, Tanaka H, Lee H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Morita A, Watase M, Sakurai K, Asakura T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Edahiro R, Sano H, Sato Y, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Association between ABO blood group/genotype and COVID-19 in a Japanese population. Ann Hematol, 2023 Aug 15. doi: 10.1007/s00277-023-05407-y. Online ahead of print.
42. Wang Z, Gao Q, Yi X, Zhang X, Zhang Y, Zhang D, Liò P, Bain C, Bassed R, Li S, Guo Y, Imoto S, Yao J, Daly RJ, Song J. Surformer: an interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. Comput Methods Programs Biomed, 2023 Jul 28;241:107733. doi: 10.1016/j.cmpb.2023.107733. Online ahead of print.
43. Tanaka H, Namkoong H, Chubachi S, Irie S, Uwamino Y, Lee H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Okada Y, Takano T, Imoto S, Koike R, Kimura A, Miyano S, Ogawa S, Kanai T, Sato TA, Fukunaga K; Japan COVID-19 Task Force. Clinical characteristics of patients with COVID-19 harboring detectable intracellular SARS-CoV-2 RNA in peripheral blood cells. Int J Infect Dis, 2023 Aug 2:S1201-9712(23)00680-X. doi: 10.1016/j.ijid.2023.07.030. Online ahead of print.
44. Zhang YZ, Liu Y, Bai Z, Fujimoto K, Uematsu S, Imoto S. Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning. Brief Bioinform, 2023 Jul 18:bbad239. doi: 10.1093/bib/bbad239. Online ahead of print.
45. Tanaka H, Chubachi S, Namkoong H, Sato Y, Asakura T, Lee H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Watase M, Sakurai K, Kusumoto T, Kondo Y, Masaki K, Kamata H, Ishii M, Kaneko Y, Hasegawa N, Ueda S, Sasaki M, Izumo T, Inomata M, Miyazawa N, Kimura Y, Suzuki Y, Harada N, Ichikawa M, Takata T, Ishikura H, Yoshiyama T, Kokuto H, Murakami K, Sano H, Ueda T, Kuwahara N, Fujiwara A, Ogura T, Inoue T, Asami T, Mutoh Y, Nakachi I, Baba R, Nishi K, Tani M, Kagyo J, Hashiguchi M, Oguma T, Asano K, Nishikawa M, Watanabe H, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Propensity-score matched analysis of the effectiveness of baricitinib in patients with coronavirus disease 2019 (COVID-19) using nationwide real-world data: an observational matched cohort study from the Japan COVID-19 Task Force. Open Forum Infect Dis. 2023 Jun 8;10(7):ofad311. doi: 10.1093/ofid/ofad311.
46. Takeshita JI, Murakami M, Kamo M, Naito W, Yasutaka T, Imoto S. Quantifying the effect of isolation and negative certification on COVID-19 transmission. Sci Rep. 2023 Jul 12;13(1):11264. doi: 10.1038/s41598-023-37872-w.
47. Yamauchi T, Koyama N, Hirai A, Suganuma H, Suzuki S, Murashita K, Mikami T, Tamada Y, Sato N, Imoto S, Itoh K, Nakaji S. Definition of a dietary pattern expressing the intake of vegetables and fruits and its association with intestinal microbiota. Nutrients, 2023 Apr 27;15(9):2104. doi: 10.3390/nu15092104.
48. Xu J, Li F, Li C, Guo X, Landersdorfer C, Shen HH, Peleg AY, Li J, Imoto S, Yao J, Akutsu T, Song J. iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Brief Bioinform, 2023 Jun 27:bbad240. doi: 10.1093/bib/bbad240.
49. Sato A, Kobayashi M, Yusa N, Ogawa M, Shimizu E, Kawamata T, Yokoyama K, Ota Y, Ichinohe T, Ohno H, Mori Y, Sakaida E, Kondo T, Imoto S, Nannya Y, Mitani K, Tojo A. Clinical and prognostic features of Langerhans cell histiocytosis in adults. Cancer Sci, 2023 Jun 26. doi: 10.1111/cas.15879.
50. Azekawa S, Chubachi S, Asakura T, Namkoong H, Sato Y, Edahiro R, Lee H, Tanaka H, Otake S, Nakagawara K, Fukushima T, Watase M, Sakurai K, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Serum KL-6 levels predict clinical outcomes and are associated with MUC1 polymorphism in Japanese patients with COVID-19. BMJ Open Respir Res, 2023 May;10(1):e001625. doi: 10.1136/bmjresp-2023-001625.
51. Washimi K, Kasajima R, Shimizu E, Sato S, Okubo Y, Yoshioka E, Narimatsu H, Hiruma T, Katayama K, Yamaguchi R, Yamaguchi K, Furukawa Y, Miyano S, Imoto S, Yokose T, Miyagi Y. Histological markers, sickle-shaped blood vessels, myxoid area, and infiltrating growth pattern help stratify the prognosis of patients with myxofibrosarcoma/undifferentiated sarcoma. Sci Rep, 2023 Apr 25;13(1):6744. doi: 10.1038/s41598-023-34026-w.
52. Jikuya R, Johnson TA, Maejima K, An J, Ju YS, Lee H, Ha K, Song W, Kim Y, Okawa Y, Sasagawa S, Kanazashi Y, Fujita M, Imoto S, Mitome T, Ohtake S, Noguchi G, Kawaura S, Iribe Y, Aomori K, Tatenuma T, Komeya M, Ito H, Ito Y, Muraoka K, Furuya M, Kato I, Fujii S, Hamanoue H, Tamura T, Baba M, Suda T, Kodama T, Makiyama K, Yao M, Shuch BM, Ricketts CJ, Schmidt LS, Linehan WM, Nakagawa H, Hasumi H. Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma. EBioMedicine, 2023 May 12;92:104596. doi: 10.1016/j.ebiom.2023.104596. Online ahead of print.
53. Yamaguchi K, Nakagawa S, Saku A, Isobe Y, Yamaguchi R, Sheridan P, Takane K, Ikenoue T, Zhu C, Miura M, Okawara Y, Nagatoishi S, Kozuka-Hata H, Oyama M, Aikou S, Ahiko Y, Shida D, Tsumoto K, Miyano S, Imoto S, Furukawa Y. Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex. iScience, 2023 Apr 1;26(4):106563. doi: 10.1016/j.isci.2023.106563. eCollection 2023 Apr 21.
54. Ozawa T, Asakura T, Chubachi S, Namkoong H, Tanaka H, Lee K, Fukushima T, Otake S, Nakagawara K, Watase M, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Edahiro R, Murakami K, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Use of the neutrophil-to-lymphocyte ratio and an oxygen requirement to predict disease severity in patients with COVID-19. Respir Investig, 2023 Apr 19;61(4):454-459. doi: 10.1016/j.resinv.2023.03.007.
55. Iwamoto R, Yamaguchi K, Katayama K, Ando H, Setsukinai KI, Kobayashi H, Okabe S, Imoto S, Kitajima M. Identification of SARS-CoV-2 variants in wastewater using targeted amplicon sequencing during a low COVID-19 prevalence period in Japan. Science of the Total Environment, 2023 Apr 25:163706. doi: 10.1016/j.scitotenv.2023.163706. Online ahead of print.
56. Nakagawara K, Kamata H, Chubachi S, Namkoong H, Tanaka H, Lee H, Otake S, Fukushima T, Kusumoto T, Morita A, Azekawa S, Watase M, Asakura T, Masaki K, Ishii M, Endo A, Koike R, Ishikura H, Takata T, Matsushita Y, Harada N, Kokutou H, Yoshiyama T, Kataoka K, Mutoh Y, Miyawaki M, Ueda S, Ono H, Ono T, Shoko T, Muranaka H, Kawamura K, Mori N, Mochimaru T, Fukui M, Chihara Y, Nagasaki Y, Okamoto M, Amishima M, Odani T, Tani M, Nishi K, Shirai Y, Edahiro R, Ando A, Hashimoto N, Ogura S, Kitagawa Y, Kita T, Kagaya T, Kimura Y, Miyazawa N, Tsuchida T, Fujitani S, Murakami K, Sano H, Sato Y, Tanino Y, Otsuki R, Mashimo S, Kuramochi M, Hosoda Y, Hasegawa Y, Ueda T, Takaku Y, Ishiguro T, Fujiwara A, Kuwahara N, Kitamura H, Hagiwara E, Nakamori Y, Saito F, Kono Y, Abe S, Ishii T, Ohba T, Kusaka Y, Watanabe H, Masuda M, Watanabe H, Kimizuka Y, Kawana A, Kasamatsu Y, Hashimoto S, Okada Y, Takano T, Katayama K, Ai M, Kumanogoh A, Sato T, Tokunaga K, Imoto S, Kitagawa Y, Kimura A, Miyano S, Hasegawa N, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study. BMC Pulm Med. 2023 Apr 26;23(1):146. doi: 10.1186/s12890-023-02418-3.
57. Takaori A, Hashimoto D, Ikeura T, Ito T, Nakamaru K, Masuda M, Nakayama S, Yamaki S, Yamamoto T, Fujimoto K, Matsuo Y, Akagawa S, Ishida M, Yamaguchi K, Imoto S, Hirota K, Uematsu S, Satoi S, Sekimoto M, Naganuma M. Impact of neoadjuvant therapy on gut microbiome in patients with resectable/borderline resectable pancreatic ductal adenocarcinoma. Pancreatology, 2023 Apr 5:S1424-3903(23)00074-1. doi: 10.1016/j.pan.2023.04.001. Online ahead of print.
58. Tanaka H, Chubachi S, Asakura T, Namkoong H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Lee H, Watase M, Sakurai K, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Characteristics and Clinical Effectiveness of COVID-19 Vaccination in Hospitalized Patients in Omicron-dominated Epidemic Wave - A Nationwide Study in Japan. Int J Infect Dis, 2023 Apr 20:S1201-9712(23)00529-5. doi: 10.1016/j.ijid.2023.04.399. Online ahead of print.
59. Heryanto YD, Imoto S. Identifying key regulators of keratinization in lung squamous cell cancer using integrated TCGA analysis. Cancers, 2023, 15(7), 2066. doi: 10.3390/cancers15072066.
60. Wang Z, Bi Y, Pan T, Wang X, Bain C, Bassed R, Imoto S, Yao J, Daly RJ, Song J. Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. Bioinformatics, 2023 Mar 2:btad114. doi: 10.1093/bioinformatics/btad114.
61. Abe S, Tago S, Yokoyama K, Ogawa M, Takei T, Imoto S, Fuji M. Explainable AI for estimating pathogenicity of genetic variants using large-scale knowledge graphs. Cancers (Basel). 2023 Feb 9;15(4):1118. doi: 10.3390/cancers15041118.
62. Pan T, Li C, Bi Y, Wang Z, Gasser RB, Purcell AW, Akutsu T, *Webb GI, *Imoto S, *Song J. PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinformatics, 2023 Feb 16:btad094. doi: 10.1093/bioinformatics/btad094. Online ahead of print.
63. Murakami M, Sato H, Irie T, Kamo M, Naito W, Yasutaka T, Imoto S. Sensitivity of rapid antigen tests for COVID-19 during the Omicron variant outbreak among players and staff members of the Japan Professional Football League and clubs: a retrospective observational study. BMJ Open. 2023 Jan 30;13(1):e067591. doi: 10.1136/bmjopen-2022-067591.
    Press Release:
    https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00215.html
64. Nakagawara K, Kamata H, Chubachi S, Namkoong H, Tanaka H, Lee H, Otake S, Fukushima T, Kusumoto T, Morita A, Azekawa S, Watase M, Asakura T, Masaki K, Ishii M, Endo A, Koike R, Ishikura H, Takata T, Matsushita Y, Harada N, Kokutou H, Yoshiyama T, Kataoka K, Mutoh Y, Miyawaki M, Ueda S, Ono H, Ono T, Shoko T, Muranaka H, Kawamura K, Mori N, Mochimaru T, Fukui M, Chihara Y, Nagasaki Y, Okamoto M, Amishima M, Odani T, Tani M, Nishi K, Shirai Y, Edahiro R, Ando A, Hashimoto N, Ogura S, Kitagawa Y, Kita T, Kagaya T, Kimura Y, Miyazawa N, Tsuchida T, Fujitani S, Murakami K, Sano H, Sato Y, Tanino Y, Otsuki R, Mashimo S, Kuramochi M, Hosoda Y, Hasegawa Y, Ueda T, Takaku Y, Ishiguro T, Fujiwara A, Kuwahara N, Kitamura H, Hagiwara E, Nakamori Y, Saito F, Kono Y, Abe S, Ishii T, Ohba T, Kusaka Y, Watanabe H, Masuda M, Watanabe H, Kimizuka Y, Kawana A, Kasamatsu Y, Hashimoto S, Okada Y, Takano T, Katayama K, Ai M, Kumanogoh A, Sato T, Tokunaga K, Imoto S, Kitagawa Y, Kimura A, Miyano S, Hasegawa N, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Diagnostic significance of secondary bacteremia in patients with COVID-19. J Infect Chemother, 2023 Jan 19:S1341-321X(23)00014-4. doi: 10.1016/j.jiac.2023.01.006. Online ahead of print.
65. Watase M, Masaki K, Chubachi S, Namkoong H, Tanaka H, Lee H, Fukushima T, Otake S, Nakagawara K, Kusumoto T, Asakura T, Kamata H, Ishii M, Hasegawa N, Oyamada Y, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Edahiro R, Sano H, Sato Y, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Impact of accumulative smoking exposure and chronic obstructive pulmonary disease on COVID-19 outcomes: Report based on findings from the Japan COVID-19 Task Force. Int J Infect Dis. 2023 Mar:128:121-127. doi: 10.1016/j.ijid.2022.12.019.
66. Shingaki S, Koya J, Yuasa M, Saito Y, Tabata M, McClure MB, Ogawa S, Katayama K, Togashi Y, Imoto S, Kogure Y, Kataoka K. Tumor-promoting function and regulatory landscape of PD-L2 in B-cell lymphoma. Leukemia, 2023 Feb;37(2):492-496. doi: 10.1038/s41375-022-01772-1.
67. Arimura S, Inoue-Yamauchi A, Katayama K, Kanno T, Jozawa H, Imoto S, Yamanashi Y. Loss of Dok-3 in non-tumor cells induces malignant transformation of benign epithelial tumor cells of the intestine. Cancer Res Commun, 2022 Dec 8;2(12):1590-1600. doi: 10.1158/2767-9764.CRC-22-0347.
68. Fukushima T, Chubachi S, Namkoong H, Asakura T, Tanaka H, Lee H, Azekawa S, Okada Y, Koike R, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Clinical significance of prediabetes, undiagnosed diabetes, and diagnosed diabetes on clinical outcomes in COVID-19: Integrative analysis from the Japan COVID-19 Task Force. Diabetes Obes Metab. 2023 Jan;25(1):144-155. doi: 10.1111/dom.14857.
69. Park H, Imoto S, Miyano S. Gene regulatory network-classifier: gene regulatory network-based classifier and its applications to gastric cancer drug (5-fluorouracil) marker identification. J Comput Biol. 2023 Feb;30(2):223-243. doi: 10.1089/cmb.2022.0181.
70. Lee H, Chubachi S, Namkoong H, Asakura T, Tanaka H, Otake S, Nakagawara K, Morita A, Fukushima T, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Murakami K, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Characteristics of hospitalized patients with COVID-19 during the first to fifth waves of infection: a report from the Japan COVID-19 Task Force. BMC Infect Dis. 2022 Dec 12;22(1):935. doi: 10.1186/s12879-022-07927-w.
71. Nakagawara K, Chubachi S, Namkoong H, Tanaka H, Lee H, Azekawa S, Otake S, Fukushima T, Morita A, Watase M, Sakurai K, Kusumoto T, Asakura T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Edahiro R, Murakami K, Sato Y, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Impact of upper and lower respiratory symptoms on COVID-19 outcomes: a multicenter retrospective cohort study. Respir Res. 2022 Nov 15;23(1):315. doi: 10.1186/s12931-022-02222-3.
72. Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJ, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A; COVID-19 Host Genetics Initiative; DeCOI Host Genetics Group; GEN-COVID Multicenter Study (Italy); Mount Sinai Clinical Intelligence Center; GEN-COVID consortium (Spain); GenOMICC Consortium; Japan COVID-19 Task Force; Regeneron Genetics Center, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet. 2022 Nov 3;18(11):e1010367. doi: 10.1371/journal.pgen.1010367.
73. Wang TW, Johmura Y, Suzuki N, Omori S, Migita T, Yamaguchi K, Hatakeyama S, Yamazaki S, Shimizu E, Imoto S, Furukawa Y, Yoshimura A, Nakanishi M. Blocking PD-L1-PD-1 improves senescence surveillance and ageing phenotypes. Nature, 2022 Nov 2. doi: 10.1038/s41586-022-05388-4.
74. Heryanto YD, Katayama K, Imoto S. Analyzing integrated network of methylation and gene expression profiles in lung squamous cell carcinoma. Scientific Reports, 2022 Sep 22;12(1):15799. doi: 10.1038/s41598-022-20232-5.
75. Kazama S, Yokoyama K, Ueki T, Kazumoto H, Satomi H, Sumi M, Ito I, Yusa N, Kasajima R, Shimizu E, Yamaguchi R, Imoto S, Miyano S, Tojo A, Kobayashi H. Case report: common clonal origin of concurrent langerhans cell histiocytosis and acute myeloid leukemia. Frontiers in Oncology, section Hematologic Malignancies, 2022 Sep 16:12:974307. doi: 10.3389/fonc.2022.974307.
76. Otake S, Chubachi S, Namkoong H, Nakagawara K, Tanaka H, Lee H, Morita A, Fukushima T, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Murakami K, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Clinical clustering with prognostic implications in Japanese COVID-19 patients: report from Japan COVID-19 Task Force, a nation-wide consortium to investigate COVID-19 host genetics. BMC Infect Dis. 2022 Sep 14;22(1):735. doi: 10.1186/s12879-022-07701-y.
77. Sahara N, Kobayashi S, Kitahara S, Matsunaga T, Fujii T, Yusa N, Shimizu E, Imoto S, Yokoyama K5 , Tojo A, Ohno N. Anti-inflammatory effects of ruxolitinib on chronic neutrophilic leukemia harboring CSF3R T618I mutation with bilateral renal abscesses. Leukemia Research Reports, 2022 Sep 6;18:100348. doi: 10.1016/j.lrr.2022.100348.
78. Shimazu Y, Kobayashi Y, Imoto S, Tsubokura M. A retrospective observational study analyzing work and study motivation based on the work environment of 15,677 Japanese clinicians in 2016. Scientific Reports, (2022) 12:14806. doi: 10.1038/s41598-022-19007-9.
79. Wang QS, Edahiro R, Namkoong H, Hasegawa T, Shirai Y, Sonehara K, Tanaka H, Lee H, Saiki R, Hyugaji T, Shimizu E, Katayama K, Kanai M, Naito T, Sasa N, Yamamoto K, Kato Y, Morita T, Takahashi K, Harada N, Naito T, Hiki M, Matsushita Y, Takagi H, Ichikawa M, Nakamura A, Harada S, Sandhu Y, Kabata H, Masaki K, Kamata H, Ikemura S, Chubachi S, Okamori S, Terai H, Morita A, Asakura T, Sasaki J, Morisaki H, Uwamino Y, Nanki K, Uchida S, Uno S, Nishimura T, Ishiguro T, Isono T, Shibata S, Matsui Y, Hosoda C, Takano K, Nishida T, Kobayashi Y, Takaku Y, Takayanagi N, Ueda S, Tada A, Miyawaki M, Yamamoto M, Yoshida E, Hayashi R, Nagasaka T, Arai S, Kaneko Y, Sasaki K, Tagaya E, Kawana M, Arimura K, Takahashi K, Anzai T, Ito S, Endo A, Uchimura Y, Miyazaki Y, Honda T, Tateishi T, Tohda S, Ichimura N, Sonobe K, Sassa CT, Nakajima J, Nakano Y, Nakajima Y, Anan R, Arai R, Kurihara Y, Harada Y, Nishio K, Ueda T, Azuma M, Saito R, Sado T, Miyazaki Y, Sato R, Haruta Y, Nagasaki T, Yasui Y, Hasegawa Y, Mutoh Y, Kimura T, Sato T, Takei R, Hagimoto S, Noguchi Y, Yamano Y, Sasano H, Ota S, Nakamori Y, Yoshiya K, Saito F, Yoshihara T, Wada D, Iwamura H, Kanayama S, Maruyama S, Yoshiyama T, Ohta K, Kokuto H, Ogata H, Tanaka Y, Arakawa K, Shimoda M, Osawa T, Tateno H, Hase I, Yoshida S, Suzuki S, Kawada M, Horinouchi H, Saito F, Mitamura K, Hagihara M, Ochi J, Uchida T, Baba R, Arai D, Ogura T, Takahashi H, Hagiwara S, Nagao G, Konishi S, Nakachi I, Murakami K, Yamada M, Sugiura H, Sano H, Matsumoto S, Kimura N, Ono Y, Baba H, Suzuki Y, Nakayama S, Masuzawa K, Namba S, Shiroyama T, Noda Y, Niitsu T, Adachi Y, Enomoto T, Amiya S, Hara R, Yamaguchi Y, Murakami T, Kuge T, Matsumoto K, Yamamoto Y, Yamamoto M, Yoneda M, Tomono K, Kato K, Hirata H, Takeda Y, Koh H, Manabe T, Funatsu Y, Ito F, Fukui T, Shinozuka K, Kohashi S, Miyazaki M, Shoko T, Kojima M, Adachi T, Ishikawa M, Takahashi K, Inoue T, Hirano T, Kobayashi K, Takaoka H, Watanabe K, Miyazawa N, Kimura Y, Sado R, Sugimoto H, Kamiya A, Kuwahara N, Fujiwara A, Matsunaga T, Sato Y, Okada T, Hirai Y, Kawashima H, Narita A, Niwa K, Sekikawa Y, Nishi K, Nishitsuji M, Tani M, Suzuki J, Nakatsumi H, Ogura T, Kitamura H, Hagiwara E, Murohashi K, Okabayashi H, Mochimaru T, Nukaga S, Satomi R, Oyamada Y, Mori N, Baba T, Fukui Y, Odate M, Mashimo S, Makino Y, Yagi K, Hashiguchi M, Kagyo J, Shiomi T, Fuke S, Saito H, Tsuchida T, Fujitani S, Takita M, Morikawa D, Yoshida T, Izumo T, Inomata M, Kuse N, Awano N, Tone M, Ito A, Nakamura Y, Hoshino K, Maruyama J, Ishikura H, Takata T, Odani T, Amishima M, Hattori T, Shichinohe Y, Kagaya T, Kita T, Ohta K, Sakagami S, Koshida K, Hayashi K, Shimizu T, Kozu Y, Hiranuma H, Gon Y, Izumi N, Nagata K, Ueda K, Taki R, Hanada S, Kawamura K, Ichikado K, Nishiyama K, Muranaka H, Nakamura K, Hashimoto N, Wakahara K, Koji S, Omote N, Ando A, Kodama N, Kaneyama Y, Maeda S, Kuraki T, Matsumoto T, Yokote K, Nakada TA, Abe R, Oshima T, Shimada T, Harada M, Takahashi T, Ono H, Sakurai T, Shibusawa T, Kimizuka Y, Kawana A, Sano T, Watanabe C, Suematsu R, Sageshima H, Yoshifuji A, Ito K, Takahashi S, Ishioka K, Nakamura M, Masuda M, Wakabayashi A, Watanabe H, Ueda S, Nishikawa M, Chihara Y, Takeuchi M, Onoi K, Shinozuka J, Sueyoshi A, Nagasaki Y, Okamoto M, Ishihara S, Shimo M, Tokunaga Y, Kusaka Y, Ohba T, Isogai S, Ogawa A, Inoue T, Fukuyama S, Eriguchi Y, Yonekawa A, Kan-O K, Matsumoto K, Kanaoka K, Ihara S, Komuta K, Inoue Y, Chiba S, Yamagata K, Hiramatsu Y, Kai H, Asano K, Oguma T, Ito Y, Hashimoto S, Yamasaki M, Kasamatsu Y, Komase Y, Hida N, Tsuburai T, Oyama B, Takada M, Kanda H, Kitagawa Y, Fukuta T, Miyake T, Yoshida S, Ogura S, Abe S, Kono Y, Togashi Y, Takoi H, Kikuchi R, Ogawa S, Ogata T, Ishihara S, Kanehiro A, Ozaki S, Fuchimoto Y, Wada S, Fujimoto N, Nishiyama K, Terashima M, Beppu S, Yoshida K, Narumoto O, Nagai H, Ooshima N, Motegi M, Umeda A, Miyagawa K, Shimada H, Endo M, Ohira Y, Watanabe M, Inoue S, Igarashi A, Sato M, Sagara H, Tanaka A, Ohta S, Kimura T, Shibata Y, Tanino Y, Nikaido T, Minemura H, Sato Y, Yamada Y, Hashino T, Shinoki M, Iwagoe H, Takahashi H, Fujii K, Kishi H, Kanai M, Imamura T, Yamashita T, Yatomi M, Maeno T, Hayashi S, Takahashi M, Kuramochi M, Kamimaki I, Tominaga Y, Ishii T, Utsugi M, Ono A, Tanaka T, Kashiwada T, Fujita K, Saito Y, Seike M, Watanabe H, Matsuse H, Kodaka N, Nakano C, Oshio T, Hirouchi T, Makino S, Egi M, Omae Y, Nannya Y, Ueno T, Takano T, Katayama K, Ai M, Kumanogoh A, Sato T, Hasegawa N, Tokunaga K, Ishii M, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K, Okada Y. The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force. Nature Communications, 2022 Aug 22;13(1):4830. doi: 10.1038/s41467-022-32276-2.
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00186.html
80. Kitajima M, Murakami M, Kadoya SS, Ando H, Kuroita T, Katayama H, Imoto S. Association of SARS-CoV-2 Load in Wastewater With Reported COVID-19 Cases in the Tokyo 2020 Olympic and Paralympic Village From July to September 2021. JAMA Network Open. 2022 Aug 1;5(8):e2226822. doi: 10.1001/jamanetworkopen.2022.26822.
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00188.html
81. Park H, Imoto S, Miyano S. PredictiveNetwork: Predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. BMC Bioinformatics, volume 23, Article number: 342 (2022) https://doi.org/10.1186/s12859-022-04871-z
82. Murakami M, Fujita T, Li P, Imoto S, Yasutaka T. Development of a COVID-19 risk assessment model for participants at outdoor music festivals: evaluation of the validity and control measure effectiveness based on two actual events in Japan and Spain. PeerJ, 2022, 10:e13846 https://doi.org/10.7717/peerj.13846
83. Lee H, Chubachi S, Namkoong H, Tanaka H, Otake S, Nakagawara K, Morita A, Fukushima T, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Murakami K, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. Effects of mild obesity on outcomes in Japanese patients with COVID-19: a nationwide consortium to investigate COVID-19 host genetics. Nutr Diabetes, 2022 Aug 9;12(1):38. doi: 10.1038/s41387-022-00217-z.
84. Namkoong H, Edahiro R, Takano T, Nishihara H, Shirai Y, Sonehara K, Tanaka H, Azekawa S, Mikami Y, Lee H, Hasegawa T, Okudela K, Okuzaki D, Motooka D, Kanai M, Naito T, Yamamoto K, Wang QS, Saiki R, Ishihara R, Matsubara Y, Hamamoto J, Hayashi H, Yoshimura Y, Tachikawa N, Yanagita E, Hyugaji T, Shimizu E, Katayama K, Kato Y, Morita T, Takahashi K, Harada N, Naito T, Hiki M, Matsushita Y, Takagi H, Aoki R, Nakamura A, Harada S, Sasano H, Kabata H, Masaki K, Kamata H, Ikemura S, Chubachi S, Okamori S, Terai H, Morita A, Asakura T, Sasaki J, Morisaki H, Uwamino Y, Nanki K, Uchida S, Uno S, Nishimura T, Ishiguro T, Isono T, Shibata S, Matsui Y, Hosoda C, Takano K, Nishida T, Kobayashi Y, Takaku Y, Takayanagi N, Ueda S, Tada A, Miyawaki M, Yamamoto M, Yoshida E, Hayashi R, Nagasaka T, Arai S, Kaneko Y, Sasaki K, Tagaya E, Kawana M, Arimura K, Takahashi K, Anzai T, Ito S, Endo A, Uchimura Y, Miyazaki Y, Honda T, Tateishi T, Tohda S, Ichimura N, Sonobe K, Sassa CT, Nakajima J, Nakano Y, Nakajima Y, Anan R, Arai R, Kurihara Y, Harada Y, Nishio K, Ueda T, Azuma M, Saito R, Sado T, Miyazaki Y, Sato R, Haruta Y, Nagasaki T, Yasui Y, Hasegawa Y, Mutoh Y, Kimura T, Sato T, Takei R, Hagimoto S, Noguchi Y, Yamano Y, Sasano H, Ota S, Nakamori Y, Yoshiya K, Saito F, Yoshihara T, Wada D, Iwamura H, Kanayama S, Maruyama S, Yoshiyama T, Ohta K, Kokuto H, Ogata H, Tanaka Y, Arakawa K, Shimoda M, Osawa T, Tateno H, Hase I, Yoshida S, Suzuki S, Kawada M, Horinouchi H, Saito F, Mitamura K, Hagihara M, Ochi J, Uchida T, Baba R, Arai D, Ogura T, Takahashi H, Hagiwara S, Nagao G, Konishi S, Nakachi I, Murakami K, Yamada M, Sugiura H, Sano H, Matsumoto S, Kimura N, Ono Y, Baba H, Suzuki Y, Nakayama S, Masuzawa K, Namba S, Suzuki K, Naito Y, Liu YC, Takuwa A, Sugihara F, Wing JB, Sakakibara S, Hizawa N, Shiroyama T, Miyawaki S, Kawamura Y, Nakayama A, Matsuo H, Maeda Y, Nii T, Noda Y, Niitsu T, Adachi Y, Enomoto T, Amiya S, Hara R, Yamaguchi Y, Murakami T, Kuge T, Matsumoto K, Yamamoto Y, Yamamoto M, Yoneda M, Kishikawa T, Yamada S, Kawabata S, Kijima N, Takagaki M, Sasa N, Ueno Y, Suzuki M, Takemoto N, Eguchi H, Fukusumi T, Imai T, Fukushima M, Kishima H, Inohara H, Tomono K, Kato K, Takahashi M, Matsuda F, Hirata H, Takeda Y, Koh H, Manabe T, Funatsu Y, Ito F, Fukui T, Shinozuka K, Kohashi S, Miyazaki M, Shoko T, Kojima M, Adachi T, Ishikawa M, Takahashi K, Inoue T, Hirano T, Kobayashi K, Takaoka H, Watanabe K, Miyazawa N, Kimura Y, Sado R, Sugimoto H, Kamiya A, Kuwahara N, Fujiwara A, Matsunaga T, Sato Y, Okada T, Hirai Y, Kawashima H, Narita A, Niwa K, Sekikawa Y, Nishi K, Nishitsuji M, Tani M, Suzuki J, Nakatsumi H, Ogura T, Kitamura H, Hagiwara E, Murohashi K, Okabayashi H, Mochimaru T, Nukaga S, Satomi R, Oyamada Y, Mori N, Baba T, Fukui Y, Odate M, Mashimo S, Makino Y, Yagi K, Hashiguchi M, Kagyo J, Shiomi T, Fuke S, Saito H, Tsuchida T, Fujitani S, Takita M, Morikawa D, Yoshida T, Izumo T, Inomata M, Kuse N, Awano N, Tone M, Ito A, Nakamura Y, Hoshino K, Maruyama J, Ishikura H, Takata T, Odani T, Amishima M, Hattori T, Shichinohe Y, Kagaya T, Kita T, Ohta K, Sakagami S, Koshida K, Hayashi K, Shimizu T, Kozu Y, Hiranuma H, Gon Y, Izumi N, Nagata K, Ueda K, Taki R, Hanada S, Kawamura K, Ichikado K, Nishiyama K, Muranaka H, Nakamura K, Hashimoto N, Wakahara K, Koji S, Omote N, Ando A, Kodama N, Kaneyama Y, Maeda S, Kuraki T, Matsumoto T, Yokote K, Nakada TA, Abe R, Oshima T, Shimada T, Harada M, Takahashi T, Ono H, Sakurai T, Shibusawa T, Kimizuka Y, Kawana A, Sano T, Watanabe C, Suematsu R, Sageshima H, Yoshifuji A, Ito K, Takahashi S, Ishioka K, Nakamura M, Masuda M, Wakabayashi A, Watanabe H, Ueda S, Nishikawa M, Chihara Y, Takeuchi M, Onoi K, Shinozuka J, Sueyoshi A, Nagasaki Y, Okamoto M, Ishihara S, Shimo M, Tokunaga Y, Kusaka Y, Ohba T, Isogai S, Ogawa A, Inoue T, Fukuyama S, Eriguchi Y, Yonekawa A, Kan-O K, Matsumoto K, Kanaoka K, Ihara S, Komuta K, Inoue Y, Chiba S, Yamagata K, Hiramatsu Y, Kai H, Asano K, Oguma T, Ito Y, Hashimoto S, Yamasaki M, Kasamatsu Y, Komase Y, Hida N, Tsuburai T, Oyama B, Takada M, Kanda H, Kitagawa Y, Fukuta T, Miyake T, Yoshida S, Ogura S, Abe S, Kono Y, Togashi Y, Takoi H, Kikuchi R, Ogawa S, Ogata T, Ishihara S, Kanehiro A, Ozaki S, Fuchimoto Y, Wada S, Fujimoto N, Nishiyama K, Terashima M, Beppu S, Yoshida K, Narumoto O, Nagai H, Ooshima N, Motegi M, Umeda A, Miyagawa K, Shimada H, Endo M, Ohira Y, Watanabe M, Inoue S, Igarashi A, Sato M, Sagara H, Tanaka A, Ohta S, Kimura T, Shibata Y, Tanino Y, Nikaido T, Minemura H, Sato Y, Yamada Y, Hashino T, Shinoki M, Iwagoe H, Takahashi H, Fujii K, Kishi H, Kanai M, Imamura T, Yamashita T, Yatomi M, Maeno T, Hayashi S, Takahashi M, Kuramochi M, Kamimaki I, Tominaga Y, Ishii T, Utsugi M, Ono A, Tanaka T, Kashiwada T, Fujita K, Saito Y, Seike M, Watanabe H, Matsuse H, Kodaka N, Nakano C, Oshio T, Hirouchi T, Makino S, Egi M; Biobank Japan Project, Omae Y, Nannya Y, Ueno T, Katayama K, Ai M, Fukui Y, Kumanogoh A, Sato T, Hasegawa N, Tokunaga K, Ishii M, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K, Okada Y. DOCK2 is involved in the host genetics and biology of severe COVID-19. Nature, 2022 Sep;609(7928):754-760. doi: 10.1038/s41586-022-05163-5. Online ahead of print.
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00185.html
85. Iwamoto R, Yamaguchi K, Arakawa C, Ando H, Haramoto E, Setsukinai K, Katayama K, Yamagishi T, Sorano S, Murakami M, Kyuwa S, Kobayashi H, Okabe S, Imoto S, Kitajima M. The detectability and removal efficiency of SARS-CoV-2 in a large-scale septic tank of a COVID-19 quarantine facility in Japan. Science of the Total Environment, 2022 Nov 25;849:157869. doi: 10.1016/j.scitotenv.2022.157869
86. Bai Z, Zhang Y-Z, Miyano S, Yamaguchi R, Fujimoto K, Uematsu S, Imoto S. Identification of bacteriophage genome sequences with representation learning. Bioinformatics, 2022 Sep 15;38(18):4264-4270. doi: 10.1093/bioinformatics/btac509.
87. Koyama T, Tokumasu R, Katayama K, Saito A, Kudo M, Imoto S. Cross-border transmissions of the Delta substrain AY.29 during Tokyo Olympic and Paralympic Games. Frontiers in Microbiology, section Virology, August 2022, Volume 13, Article 883849. https://doi.org/10.3389/fmicb.2022.883849
    Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00183.html
88. Fukushima T, Chubachi S, Namkoong H, Otake S, Nakagawara K, Tanaka H, Lee H, Morita A, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Murakami K, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K; Japan COVID-19 Task Force. U-shaped association between abnormal serum uric acid levels and COVID-19 severity: Reports from the Japan COVID-19 Task Force. International Journal of Infectious Disease, 2022 Jul 7:S1201-9712(22)00409-X. doi: 10.1016/j.ijid.2022.07.014. Online ahead of print.
89. Tai A-S, Lin R-T, Lin Y-C, Wang C-H, Lin S-H, Imoto S. Genome-wide causal mediation analysis identifies genetic loci associated with uterine fibroids mediated by age at menarche. Human Reproduction, 2022 Jun 11;deac136. doi: 10.1093/humrep/deac136. Online ahead of print.
90. Tomiyama E, Fujita K,Nakano K, Kuwahara K, Minami T, Kato T, Hatano K, Kawashima A, Uemura M, Takao T, Fushimi H, Katayama K, Imoto S, Yoshimura K, Imamura R, Uemura H, Nonomura N. Trop-2 in upper tract urothelial carcinoma. Current Oncology, 2022, 29(6), 3911-3921. doi: 10.3390/curroncol29060312
91. Park H, Yamaguchi R, Imoto S, Miyano S. Xprediction: Explainable EGFR-TKIs response prediction based on drug sensitivity specific gene networks. PLoS ONE, 2022 May 18;17(5):e0261630. doi: 10.1371/journal.pone.0261630.
92. Hasegawa T, Kakuta M, Yamaguchi R, Sato N, Mikami T, Murashita K, Nakaji S, Itoh K, Imoto S. Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in northern Japanese population. Scientific Reports, 2022 May 10;12(1):7628. doi: 10.1038/s41598-022-11730-7.
93. Maeda F, Kato A,Takeshima K, Shibazakia M, Sato R, Shibata T, Miyake K, Kozuka-Hata H, Oyama M, Shimizu E, Imoto S, Miyano S, Adachi S, Natsume T, Takeuchi K, Maruzuru Y, Koyanagi N, Arii J, Kawaguchi Y. Role of the orphan transporter SLC35E1 in the nuclear egress of herpes simplex virus 1. Journal of Virology, 2022 Apr 27:e0030622. doi: 10.1128/jvi.00306-22. Online ahead of print.
94. Masuhiro K, Tamiya M, Fujimoto K, Koyama S, Naito Y, Osa A, Hirai T, Suzuki H, Okamoto N, Shiroyama T, Nishino K, Adachi Y, Nii T, Kinugasa-Katayama Y, Kajihara A, Morita T, Imoto S, Uematsu S, Irie T, Okuzaki D, Aoshi T, Takeda Y, Kumagai T, Hirashima T, Kumanogoh A. Bronchoalveolar lavage fluid reveals factors contributing to the efficacy of PD-1 blockade in lung cancer. JCI insight, 2022 Apr 7;e157915. doi: 10.1172/jci.insight.157915. Online ahead of print.
95. Takeshita K, Takao H, Imoto S, Murayama Y. Improvement of the Japanese healthcare data system for the effective management of patients with COVID-19: a national survey. International Journal of Medical Informatics, Available online 24 March 2022, 104752, https://doi.org/10.1016/j.ijmedinf.2022.104752
96. Yasutaka T, Murakami M, Iwasaki Y, Naito W, Onishi M, Fujita T, Imoto S. Assessment of COVID-19 risk and prevention effectiveness among spectators of mass gathering events. Microbial Risk Analysis, 2022 Aug;21:100215. doi: 10.1016/j.mran.2022.100215.
97. Kamo M, Murakami M, Naito W, Takeshita J, Yasutaka T, Imoto S. COVID-19 testing systems and their effectiveness in small, semi-isolated groups for sports events. PLoS ONE, Published: March 29, 2022. https://doi.org/10.1371/journal.pone.0266197
98. Nakano K, Koh Y, Yamamichi G, Yumiba S, Tomiyama E, Matsushita M, Hayashi Y, Wang C, Ishizuya Y, Yamamoto Y, Kato T, Hatano K, Kawashima A, Ujike T, Fujita K, Kiyotani K, Katayama K, Yamaguchi R, Imoto S, Imamura R, Nonomura N, Uemura M. Perioperative circulating tumor DNA enables identification of patients with poor prognosis in upper tract urothelial carcinoma. Cancer Science, 2022 Mar 16. doi: 10.1111/cas.15334. Online ahead of print.
99. Takeda R, Yokoyama K, Fukuyama T, Kawamata T, Ito M, Yusa N, Kasajima R, Shimizu E, Ohno N, Uchimaru K, Yamaguchi R, Imoto S, Miyano S, Tojo A. Repeated lineage switches in an elderly case of refractory B-cell acute lymphoblastic leukemia with MLL gene amplification: A case report and literature review. Frontiers in Oncology, section Hematologic Malignancies, 2022, 23 March 2022 | https://doi.org/10.3389/fonc.2022.799982
100. Koh Y, Nakano K, Katayama K, Yamamichi G, Yumiba S, Tomiyama E, Matsushita M, Hayashi Y, Yamamoto Y, Kato T, Hatano K, Kawashima A, Ujike T, Imamura R, Yamaguchi R, Imoto S, Shiotsu Y, Nonomura N, Uemura M. Early dynamics of circulating tumor DNA predict clinical response to immune checkpoint inhibitors in metastatic renal cell carcinoma. International Journal of Urology, 2022 May;29(5):462-469. https://doi.org/10.1111/iju.14816
101. Ozato N, Yamaguchi T, Mori K, Katashima M, Kumagai M, Murashita K, Katsuragi Y, Tamada Y, Kakuta M, Imoto S, Ihara K, Nakaji S. Two Blautia species associated with visceral fat accumulation: a one-year longitudinal study. Biology 2022, 11(2), 318. https://doi.org/10.3390/biology11020318
102. Kitajima M, Murakami M, Iwamoto R, Katayama H, Imoto S. COVID-19 wastewater surveillance implemented in the Tokyo 2020 Olympic and Paralympic Village. Journal of Travel Medicine, 2022 May 31;29(3):taac004. doi: 10.1093/jtm/taac004. Online ahead of print.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00151.html
103. Park H, Yamaguchi R, Imoto S, Miyano S. Uncovering molecular mechanisms of drug resistance via network-constrained common structure identification. Journal of Computational Biology, 2022 Mar;29(3):257-275. doi: 10.1089/cmb.2021.0314. Online ahead of print.
104. Kamo M, Murakami M, Imoto S. Effects of test timing and isolation length to reduce the risk of COVID-19 infection associated with airplane travel, as determined by infectious disease dynamics modeling. Microbial Risk Analysis, Available online 11 December 2021, https://doi.org/10.1016/j.mran.2021.100199
105. Kosaka S, Nadatani Y, Higashimori A, Otani K, Fujimoto K, Ominami M, Fukunaga S, Hosomi S, Kamata N, Tanaka F, Nagami Y, Taira K, Imoto S, Uematsu S, Watanabe T, Fujiwara Y. The ovariectomy-induced dysbiosis may have a minor effect on bone in Mice. Microorganisms, 2021 Dec 10;9(12):2563. doi: 10.3390/microorganisms9122563.
106. Liu Y, Zhang Y-Z, Imoto S. Discovering microbe functionality in human disease with a gene-ontology-aware model. Proc. Biological Ontologies and Knowledge Bases 2021. 1873-1880.
107. Zhang Y-Z, Yamaguchi K, Hatakeyama S, Furukawa Y, Miyano S, Yamaguchi R, Imoto S. On the application of BERT models for nanopore methylation detection. Proc. IEEE International Conference on Bioinformatics and Biomedicine 2021. 320-327. (accepted 143 regular papers among 727 paper submissions (acceptance rate: 19.6%)).
108. Zhang Y-Z, Imoto S, Miyano S, Yamaguchi R. Enhancing breakpoint resolution with deep segmentation model: a general refinement method for read-depth based structural variant callers. PLoS Computational Biology, 2021 Oct 11;17(10):e1009186. doi: 10.1371/journal.pcbi.1009186
109. Kinoshita K, Ozato N, Yamaguchi T, Sudo M, Yamashiro Y, Mori K, Kumagai M, Sawada K, Katsuragi Y, Imoto S, Ihara K, Nakaji S. The effect of age on the association between daily gait speed and abdominal obesity in Japanese adults. Scientific Reports, 2021 Oct 7;11(1):19975. doi: 10.1038/s41598-021-98679-1.
110. Tanaka H, Lee H, Morita A, Chubachi S, Kabata H, Kamata H, Ishii M, Hasegawa N, Norihiro N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Murakami K, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Clinical characteristics of patients with coronavirus disease (COVID-19): preliminary baseline report of Japan COVID-19 Task Force, a nation-wide consortium to investigate host genetics of COVID-19. International Journal of Infectious Diseases, 2021 Sep 30;S1201-9712(21)00775-X. doi: 10.1016/j.ijid.2021.09.070. Online ahead of print.
111. Yata E, Kasajima R, Niida A, Imoto S, Miyano S, Miyagi Y, Sasada T, Wada S. Possible Role of cytochrome P450 1B1 in the mechanism of gemcitabine resistance in pancreatic cancer. Biomedicines 2021, 9(10), 1396; https://doi.org/10.3390/biomedicines9101396
112. Hasegawa T, Yamaguchi R, Kakuta M, Ando M, Songee J, Tokuda I, Murashita K, Imoto S. Application of state-space model with skew-t measurement noise to blood test value prediction. Applied Mathematical Modeling, 100: 365-378 (2021). https://doi.org/10.1016/j.apm.2021.08.007
113. Ishizaka A, Koga M, Mizutani T, Parbie P, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T, Yotsuyanagi H. Unique gut microbiome in HIV patients on ART suggests association with chronic inflammation. Microbiology Spectrum, 2021 Aug 11;e0070821. doi: 10.1128/Spectrum.00708-21. Online ahead of print.
114. Mizuno S, Yamaguchi R, Hasegawa T, Hayashi S, Fujita M, Zhang F, Koh Y, Lee S-Y, Yoon S-S, Shimizu E, Komura M, Fujimoto A, Nagai M, Kato M, Liang H, Miyano S, Zhang Z, Nakagawa H, Imoto S. Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories. Scientific Reports, 11, Article number: 15713 (2021). doi: 10.1038/s41598-021-95287-x.
115. Yasui H, Kobayashi M, Sato K, Kondoh K, Ishida T, Kaito Y, Tamura H, Honda H, Tsukune Y, Sasaki M, Komatsu N, Tanaka N, Tanaka J, Kizaki M, Kawamata T, Makiyama J, Yokoyama K, Imoto S, Tojo A, Imai Y. Circulating cell‐free DNA in the peripheral blood plasma of patients is an informative biomarker for multiple myeloma relapse. International Journal of Clinical Oncology, 2021 Nov;26(11):2142-2150. https://doi.org/10.1007/s10147-021-01991-z 
116. Saiki R, Momozawa Y, Nannya Y, Nakagawa M, Ochi Y, Yoshizato T, Terao C, Kuroda Y, Shiraishi Y, Chiba K, Tanaka H, Niida A, Imoto S, Matsuda K, Morisaki T, Murakami Y, Kamatani Y, Matsuda S, Kubo M, Miyano S, Makishima H, Ogawa S. Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis. Nature Medicine (2021). Jul 8. doi: 10.1038/s41591-021-01411-9. Online ahead of print.
117. COVID-19 Host Genetics Initiative. Mapping the human genetic architecture of COVID-19. Nature, 2021 Dec;600(7889):472-477. doi: 10.1038/s41586-021-03767-x. Epub 2021 Jul 8.
118. Yuki Y, Nojima M, Hosono O, Tanaka H, Kimura Y, Satoh T, Imoto S, Uematsu S, Kurokawa S, Kashima S, Mejima M, Nakahashi-Ouchida R, Uchida Y, Marui T, Yoshikawa N, Nagamura F, Fujihashi K, Kiyono H. Oral MucoRice-CTB vaccine for safety and microbiota-dependent immunogenicity in humans: a phase 1 randomised trial. The Lancet Microbe, 2021 Sep;2(9):E429-E440. doi:10.1016/S2666-5247(20)30196-8.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00104.html
119. Murakami M, Yasutaka T, Onishi M, Naito W, Shinohara N, Okuda T, Fujii K, Katayama K, Imoto S. Living with COVID-19: Mass gatherings and minimizing risk. QJM: An International Journal of Medicine, 114(7), July 2021, 437–439.  https://doi.org/10.1093/qjmed/hcab163
120. Konishi H, Yamaguchi R, Yamaguchi K, Furukawa Y, Imoto S. Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention. Bioinformatics, 2021 Jun 9;37(9):1211-1217. doi: 10.1093/bioinformatics/btaa953.
121. Wang Y, Coudray N, Zhao Y, Li F, Hu C, Zhang YZ, Imoto S, Tsirigos A, Webb GI, Daly RJ, Song J. HEAL: an automated deep learning framework for cancer histopathology image analysis. Bioinformatics, 2021 Nov 18;37(22):4291-4295. doi: 10.1093/bioinformatics/btab380.
122. Yamaguchi K, Kasajima R, Takane K, Hatakeyama S, Shimizu E, Yamaguchi R, Katayama K, Arai M, Ishioka C, Iwama T, Kaneko S, Matsubara N, Moriya Y, Nomizu T, Sugano K, Tamura K, Tomita N, Yoshida T, Sugihara K, Nakamura Y, Miyano S, Imoto S, Furukawa Y, Ikenoue T. Application of targeted nanopore sequencing for the screening and determination of structural variants in patients with Lynch syndrome. J Hum Genet, 2021 May 6. doi: 10.1038/s10038-021-00927-9. Online ahead of print.
123. Parbie PK, Mizutani T, Ishizaka A, Kawana-Tachikawa A, Runtuwene LR, Seki S, Abana C Z-Y, Kushitor D, Bonney EY, Ofori SB, Uematsu S, Imoto S, Kimura Y, Kiyono H, Ishikawa K, Kwabena W, Matano T. Dysbiotic fecal microbiome in HIV-1 infected individuals in Ghana. Frontiers in Cellular and Infection Microbiology, 2021 May 18;11:646467. doi: 10.3389/fcimb.2021.646467.
124. Murakami M, Miura F, Kitajima M, Fujii K, Yasutaka T, Iwasaki Y, Ono K, Shimazu Y, Sorano S, Okuda T, Ozaki A, Katayama K, Nishikawa Y, Kobashi Y, Sawano T, Abe T, Saito MM, Tsubokura M, Naito W, Imoto S. COVID-19 risk assessment at the opening ceremony of the Tokyo 2020 Olympic Games. Microbial Risk Analysis, 2021 Dec;19:100162. doi: 10.1016/j.mran.2021.100162. Epub 2021 Mar 21.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00082.html
125. Suzuki M, Kasajima R, Yokose T, Ito H, Shimizu E, Hatakeyama S, Yokoyama K, Yamaguchi R, Furukawa Y, Miyano S, Imoto S, Yoshioka E, Washimi K, Okubo Y, Kawachi K, Sato S, Miyagi Y. Comprehensive molecular analysis of genomic profiles and PD-L1 expression in lung adenocarcinoma with a high-grade fetal adenocarcinoma component. Translational Lung Cancer Research, 2021 Mar;10(3):1292-1304. http://dx.doi.org/10.21037/tlcr-20-1158
126. Park H, Imoto S, Miyano S. Automatic sparse principal component analysis. The Canadian Journal of Statistics, 49(3), 2021, 678–697.
127. Fujimoto K, Kimura Y, Allegretti JR, Yamamoto M, Zhang Y-Z, Katayama K, Tremmel G, Kawaguchi Y, Shimohigoshi M, Hayashi T, Uematsu M, Yamaguchi K, Furukawa Y, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, *Imoto S, *Uematsu S. Functional restoration of bacteriomes and viromes by fecal microbiota transplantation. Gastroenterology, 2021 May;160(6):2089-2102.e12. doi: 10.1053/j.gastro.2021.02.013.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00068.html
     Selected as Cover Image: https://www.gastrojournal.org/issue/S0016-5085(21)X0006-6
128. Johmura Y, Yamanaka T, Omori S, Wang T-W, Sugiura Y, Matsumoto M, Suzuki N, Kumamoto S, Yamaguchi K, Hatakeyama S, Takami T, Yamaguchi R, Shimizu E, Ikeda K, Okahashi N, Mikawa R, Suematsu M, Arita M, Sugimoto M, Nakayama K, Furukawa Y, Imoto S, and Nakanish M. Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders. Science, 15 Jan 2021:371(6526) 265-270. doi: 10.1126/science.abb5916
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00065.html
129. Ishida S, Kato K, Tanaka M, Odamaki T, Kubo R, Mitsuyama E, Xiao J, Yamaguchi R, Uematsu S, Imoto S, Miyano S. Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota. Communications Biology, 3, Article number: 686 (2020)
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00048.html
130. Park H, Maruhashi K, Yamaguchi R, Imoto S, Miyano S. Global gene network explorer based on explainable artificial intelligence approach. PLoS ONE, November 6, (2020). https://doi.org/10.1371/journal.pone.0241508
131. Omori S, Wang T-W, Johmura Y, Kanai T, Nakano Y, Kido T, Susaki E, Nakajima T, Shichino S, Ueha S, Ozawa M, Yokote K, Kumamoto S, Nishiyama A, Sakamoto T, Yamaguchi K, Hatakeyama S, Shimizu E, Katayama K, Yamada Y, Yamazaki S, Iwasaki K, Miyoshi C, Funato H, Yanagisawa M, Ueno H, Imoto S, Furukawa Y, Yoshida N, Matsushima K, Ueda H, Miyajima A, Nakanishi M. Generation of a p16 reporter mouse and its use to characterize and target p16high cells in vivo. Cell Metabolism, 2020 Nov 3;32(5):814-828.e6. doi: 10.1016/j.cmet.2020.09.006.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00033.html
132. Moriyama T, Imoto S, Miyano S, Yamaguchi R. Theoretical foundation of the performance of phylogeny-based somatic variant detection. Proc. 2nd International Symposium on Mathematical and Computational Oncology, Springer LNBI, 12508, 87-101.
133. Shimizu S, Mimura J, Imoto S, Hasegawa T, Tsushima M, Kasai S, Yamazaki H, Ushida Y, Suganuma H, Tomita H, Nakaji S, Itoh K. Association between single nucleotide polymorphism in NRF2 promoter and vascular stiffness with aging, PLoS ONE, 15(8): e0236834. https://doi.org/10.1371/journal.pone.0236834
134. Hasegawa T, Hayashi S, Shimizu E, Mizuno S, Niida A, Yamaguchi R, Miyano S, Nakagawa H, *Imoto S. Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens, Bioinformatics, 2020 Sep 15;36(18):4813-4816. doi: 10.1093/bioinformatics/btaa616.
135. Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y.
136. Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS; PCAWG Drivers and Functional Interpretation Group, Johnson R; PCAWG Consortium. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol. 2020 Feb 5;3(1):56. doi: 10.1038/s42003-019-0741-7.
137. Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 Feb 5;11(1):729. doi: 10.1038/s41467-020-14367-0.
138. Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris QD, Stein LD; PCAWG Consortium. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nat Commun. 2020 Feb 5;11(1):728. doi: 10.1038/s41467-019-13825-8.
139. Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group, Reimand J; PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2020 Feb 5;11(1):735. doi: 10.1038/s41467-019-13983-9.
140. Cmero M, Yuan K, Ong CS, Schröder J; PCAWG Evolution and Heterogeneity Working Group, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G; PCAWG Consortium. Inferring structural variant cancer cell fraction. Nat Commun. 2020 Feb 5;11(1):730. doi: 10.1038/s41467-020-14351-8.
141. Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG; PCAWG Evolution and Heterogeneity Working Group, Morris QD; PCAWG Consortium. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun. 2020 Feb 5;11(1):731. doi: 10.1038/s41467-020-14352-7.
142. Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, Creighton CJ; PCAWG Consortium. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w.
143. Bhandari V, Li CH, Bristow RG, Boutros PC; PCAWG Consortium. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2020 Feb 5;11(1):737. doi: 10.1038/s41467-019-14052-x.
144. Shuai S; PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein LD; PCAWG Consortium. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun. 2020 Feb 5;11(1):734. doi: 10.1038/s41467-019-13929-1.
145. Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2020 Feb 5;11(1):733. doi: 10.1038/s41467-019-13824-9.
146. Li CH, Prokopec SD, Sun RX, Yousif F,Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Sex differences in oncogenic mutational processes. Nature Communications, Published online 2020 Aug 28. doi: 10.1038/s41467-020-17359-2
147. Fujimoto K, Kimura Y, Shimohigoshi M, Satoh T, Sato S, Tremmel G, Uematsu M, Kawaguchi Y, Usui Y, Nakano Y, Hayashi T, Kashima K, Yuki Y, Yamaguchi K, Furukawa Y, Kakuta M, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, *Imoto S, *Uematsu S. Metagenome data on intestinal phage–bacteria associations aids the development of phage therapy against pathobionts, Cell Host & Microbe, 2020 Sep 9;28(3):380-389.e9. doi: 10.1016/j.chom.2020.06.005. Epub 2020 Jul 10.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00021.html
148. Fujimoto A, Fujita M, Hasegawa T, Wong J-H, Maejima K, Oku-Sasaki A, Nakano K, Shiraishi Y, Miyano S, Yamamoto G, Akagi K, Imoto S, Nakagawa H. (2020) Comprehensive analysis of indels in whole-genome microsatellite Regions and microsatellite instability across 21 cancer types, Genome Research, 2020, 30:334-346. doi: 10.1101/gr.255206.119
149. Takashima S, Tanaka F, Usui Y, Fujimoto K, Nadatani Y, Otani K, Hosomi S, Nagami S, Kamata N, Taira K, Tanigawa T, Watanabe T, Imoto S, Uematsu S, Fujiwara Y. Proton pump inhibitors enhance intestinal permeability via dysbiosis of gut microbiota under stressed conditions in mice. Neurogastroenterology and Motility, 2020 Apr 21;e13841. doi: 10.1111/nmo.13841. Online ahead of print.
150. Zhang Y-Z, Akdemir A, Tremmel G, Imoto S, Miyano S, Shibuya T, Yamaguchi R. Nanopore basecalling from a perspective of instance segmentation. BMC Bioinformatics, 2020 Apr 23;21(Suppl 3):136. doi: 10.1186/s12859-020-3459-0.
151. Sato N, Kakuta M, Hasegawa T, Yamaguchi R, Uchino E, Murashita K, Nakaji S, Imoto S, Yanagita M, Okuno Y. Metagenomic profiling of gut microbiome in early chronic kidney disease. Nephrology Dialysis Transplantation, 2020 Sep 1:gfaa172. doi: 10.1093/ndt/gfaa122. Online ahead of print..
152. Parbie PK, Mizutani T, Ishizaka A, Kawana-Tachikawa A, Runtuwene LR, Seki S, Abana CZ, Kushitor D, Bonney EY, Ofori SB, Uematsu S, Imoto S, Kimura Y, Kiyono H, Ishikawa K, Ampofo WK, Matano T. Fecal microbiome composition in healthy adults in Ghana. Jpn J Infect Dis, 2021 Jan 22;74(1):42-47. doi: 10.7883/yoken.JJID.2020.469. Epub 2020 Jun 30.
153. Hasegawa T, Yamaguchi R, Kakuta M, Sawada K, Kawatani K, Murashita K, Nakaji S, Imoto S. (2020) Prediction of blood test values under different lifestyle scenarios using time-series electronic health record. PLoS ONE, 15(3): e0230172.
154. Sato N, Kakuta M, Hasegawa T, Yamaguchi R, Uchino E, Kobayashi W, Sawada K, Tamura Y, Murashita K, Nakaji S, Imoto S, Yanagita M, Tokuda I, Okuno Y. (2020) Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers. npj Biofilms and Microbiomes, 6, Article number: 11.
155. Maeda-Minami A, Yoshino T, Katayama K, Horiba Y, Hikiami H, Shimada Y, Namiki T, Tahara E, Minamizawa K, Muramatsu S, Yamaguchi R, Imoto S, Miyano S, Mima H, Mimura M, Nakamura T, Watanabe K. Discrimination of prediction models between cold-heat and deficiency-excess patterns. Complement Ther Med, 2020 Mar;49:102353. doi: 10.1016/j.ctim.2020.102353.
156. Sato N, Kakuta M, Uchino E, Hasegawa T, Kojima R, Kobayashi W, Sawada K, Tamura Y, Tokuda I, Imoto S, Nakaji S, Murashita K, Yanagita M, Okuno Y. The relationship between cigarette smoking and the tongue microbiome in an East Asian population. J Oral Microbiol, 2020 Mar 25;12(1):1742527. doi: 10.1080/20002297.2020.1742527.
157. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature, Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5.
     Press Release: https://www.ims.u-tokyo.ac.jp/imsut/content/000000682.pdf
158. Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO, PCAWG Consortium. Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 2020 Feb 5. doi: 10.1038/s41587-019-0360-3. [Epub ahead of print]
159. Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H. Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations. EBioMedicine, 2020, 53, 102659.
160. Kasajima R, Yamaguchi R, Shimizu E, Tamada Y, Niida A, Tremmel G, Kishida T, Aoki I, Imoto S, Miyano S, Uemura H, Miyagi Y. Variant analysis of prostate cancer in Japanese patients and a new attempt to predict related biological pathways. Oncol Rep. 2020 Jan 27. doi: 10.3892/or.2020.7481. [Epub ahead of print]
161. Hijikata Y, Yokoyama K, Yokoyama N, Matsubara Y, Shimizu E, Nakashima M, Yamagishi M, Ota Y, Lim L, Yamaguchi R, Ito M, Tanaka Y, Denda T, Tani K, Yotsuyanagi H, Imoto S, Miyano S, Uchimaru K, Tojo A. Successful clinical sequencing by molecular tumor board in an elderly patient with refractory Sézary syndrome. JCO Precision Oncology, 4 (2020) 534-560.
162. Ozato N, Saito S, Yamaguchi T, Katashima, M, Tokuda I, Sawada K, Katsuragi Y, Kakuta M, Imoto S, Ihara K, Nakaji S. Association between breath methane concentration and visceral fat area: A population-based cross-sectional study. Journal of Breath Research, 2020 Feb 25;14(2):026008. doi: 10.1088/1752-7163/ab61c6.
163. Hirata M, Asano N, Katayama K, Yoshida A, Tsuda Y, Sekimizu M, Mitani S, Kobayashi E, Komiyama M, Fujimoto H, Goto T, Iwamoto Y, Naka N, Iwata S, Nishida Y, Hiruma T, Hiraga H, Kawano H, Motoi T, Oda Y, Matsubara D, Fujita M, Shibata T, Nakagawa H, Nakayama R, Kondo T, Imoto S, Miyano S, Kawai A, Yamaguchi R, Ichikawa H, Matsuda K. Integrated exome and RNA sequencing of dedifferentiated liposarcoma. Nature Communications, 2019 Dec 12;10(1):5683. doi: 10.1038/s41467-019-13286-z.
164. Ozato N, Saito S, Yamaguchi T, Katashima M, Tokuda I, Sawada K, Katsuragi Y, Imoto S, Ihara K, Nakaji S. Association between nutrients and visceral fat in healthy Japanese adults: a 2-year longitudinal study. Nutrients, 2019 Nov 7;11(11) 2698. pii: E2698. doi: 10.3390/nu11112698.
165. Hasegawa T, Yamaguchi R, Niida A, Miyano S, Imoto S. Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model, Journal of the Franklin Institute, 357(5) March 2020, 2916-2933. https://doi.org/10.1016/j.jfranklin.2019.10.015
166. Takeda R, Yokoyama K, Kawamata T, Nakamura S, Fukuyama T, Ito M, Yusa N, Shimizu E, Ohno N, Yamaguchi R, Imoto S, Miyano S, Uchimaru K, Tojo S, Kobayashi S. An unusually short latent period of therapy-related myeloid neoplasm harboring a rare MLL-EP300 rearrangement: case report and literature review. Case Reports in Hematology, 2019 Oct 2;2019:4532434. doi: 10.1155/2019/4532434. eCollection 2019.
167. Ozato N, Saito S, Yamaguchi T, Katashima M, Tokuda I, Sawada K, Katsuragi Y, Kakuta M, Imoto S, Ihara K, Nakaji S. (2019) Blautia genus associated with visceral fat accumulation independent of BMI and waist circumference in adults 20-76 years of age. npj Biofilms and Microbiomes, 5, Article number: 28.
     Press Release: https://www.kao.com/jp/corporate/news/rd/2019/20191028-001/
     (Nature Blog: https://naturemicrobiologycommunity.nature.com/users/321769-shigeyuki-nakaji/posts/55270-the-iwaki-health-promotion-project-is-unique-big-health-data-from-healthy-individuals)
168. Yang F, Kim D-K, Nakagawa H, Hayashi S, Imoto S, Stein L, Roth FP. (2019) Quantifying immune-based counterselection of somatic mutations. PLoS Genetics, 15(7):e1008227. doi: 10.1371/journal.pgen.1008227.
169. 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(1):267. doi: 10.1186/s12859-019-2853-y.
170. Maeda-Minami A, Yoshino T, Katayama K, Horiba Y, Hikiami H, Shimada Y, Namiki T, Tahara E, Minamizawa K, Muramatsu S, Yamaguchi R, Imoto S, Miyano S, Mima H, Mimura M, Nakamura T, Watanabe K. (2019) Prediction of deficiency-excess pattern in Japanese Kampo medicine: multi-centre data collection-. Complementary Therapies in Medicine, 45:228-233. doi: 10.1016/j.ctim.2019.07.003.
171. Yoshino T, Katayama K, Yamaguchi R, Imoto S, Miyano S, Mima H, Watanabe K. (2019) Classification of patients with cold sensation by a review of systems database: a single-centre observational study. Complementary Therapies in Medicine, 45:7-13. doi: 10.1016/j.ctim.2019.05.011.
172. Tsuda Y, Hirata M, Katayama K, Motoi T, Matsubara D, Oda Y, Fujita M, Kobayashi H, Kawano H, Nishida Y, Sakai T, Okuma T, Goto T, Ogura K, Kawai A, Ae K, Anazawa U, Suehara Y, Iwata S, Miyano S, Imoto S, Shibata T, Nakagawa H, Yamaguchi R, Tanaka S, Matsuda K. (2019) Massively parallel sequencing of tenosynovial giant cell tumors reveals novel CSF1 fusion transcripts and novel somatic CBL mutations. International Journal of Cancer, 145(12):3276-3284. doi: 10.1002/ijc.32421.
173. Yamaguchi K, Shimizu E, Yamaguchi R, Imoto S, Komura M, Hatakeyama S, Noguchi R, Takane K, Ikenoue T, Gohda Y, Yano H, Miyano S, Furukawa Y. (2019) Development of an MSI-positive colon tumor with aberrant DNA methylation in a PPAP patient, Journal of Human Genetics, 64(8):729-740. doi: 10.1038/s10038-019-0611-7.
174. Nakamura S, Yokoyama K, Shimizu E, Yusa N, Kondoh K, Ogawa M, Takei T, Kobayashi A, Ito M, Isobe M, Konuma T, Kato S, Kasajima R, Wada Y, Nagamura-Inoue T, Yamaguchi R, Takahashi S, Imoto S, Miyano S, Tojo A. (2019) Prognostic impact of circulating tumor DNA status post-allogeneic hematopoietic stem cell transplantation in AML and MDS, Blood, 133(25):2682-2695. doi: 10.1182/blood-2018-10-880690.
175. Takeda R, Yokoyama K, Ogawa M, Kawamata T, Fukuyama T, Kondoh K, Takei T,  Nakamura S, Ito M, Yusa N, Shimizu E, Ohno N, Uchimaru K, Yamaguchi R, Imoto S, Miyano S, Tojo A. (2019) The first case of elderly TCF3-HLF-positive B-cell acute lymphoblastic leukemia, Leukemia and Lymphoma, 6:1-4. doi: 10.1080/10428194.2019.1602267.
176. Park H, Yamada M, Imoto S, Miyano S. (2019) Robust sample-specific stability selection with effective error control. Journal of Computational Biology, 26(3):202-217.
177. Moriyama T, Imoto S, Hayashi S, Shiraishi Y, Miyano S, Yamaguchi R. (2019) A Bayesian model integration for mutation calling through data partitioning, Bioinformatics, 35, 4247–4254. doi: 10.1093/bioinformatics/btz233. [Epub ahead of print]
178. Hayashi S, Moriyama T, Yamaguchi R, Mizuno S, Komura M, Miyano S, Nakagawa H, Imoto S. (2019) ALPHLARD-NT: Bayesian method for HLA genotyping and mutation calling through simultaneous analysis of normal and tumor whole-genome sequence data, Journal of Computational Biology, 26(9):923-937. doi: 10.1089/cmb.2018.0224.
179. Hayashi S, Yamaguchi R, Mizuno S, Komura M, Miyano S, Nakagawa H, Imoto S. ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data, BMC Genomics, 2018 Nov 1;19(1):790. doi: 10.1186/s12864-018-5169-9.
180. Muraoka D, Seo N, Hayashi T, Tahara Y, Fujii K, Tawara I, Miyahara Y, Okamori K, Yagita H, Imoto S, Yamaguchi R, Komura M, Miyano S, Goto M, Sawada S, Asai A, Ikeda H, Akiyoshi K, Harada N, Shiku H. (2019) Antigen delivery targeting tumor-associated macrophages overcomes tumor immune resistance, Journal of Clinical Investigation, 129(3):1278-1294. doi: 10.1172/JCI97642.
181. Yokoyama K, Shimizu E, Yokoyama N, Nakamura S, Kasajima R, Ogawa M, Takei T, Ito M, Kobayashi A, Yamaguchi R, Imoto S, Miyano S, Tojo A. (2018) Cell-lineage level–targeted sequencing to identify acute myeloid leukemia with myelodysplasia-related changes, Blood Advances, 2(19):2513-2521. DOI 10.1182/ bloodadvances.2017010744.
182. Nakamura S, Yokoyama K, Yusa N, Ogawa M, Takei T, Kobayashi A, Ito M, Shimizu E, Kasajima R, Wada Y, Yamaguchi R, Imoto S, Nagamura-Inoue T, Miyano S, Tojo A. (2018) Circulating tumor DNA dynamically predicts response and/or relapse in patients with hematological malignancies. Int J Hematol. 108(4):402-410. doi: 10.1007/s12185-018-2487-2.
183. Usui Y, Kimura Y, Satoh T, Takemura N, Ouchi Y, Ohmiya H, Kobayashi K, Suzuki H, Koyama S, Hagiwara S, Tanaka H, Imoto S, Eberl G, Asami Y, Fujimoto K, Uematsu S. (2018) Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp. bulgaricus 2038 and Streptococcus thermophilus 1131 on mice. Int Immunol. 30(7):319-331. doi: 10.1093/intimm/dxy035.
184. Inoue D, Fujino T, Sheridan P, Zhang Y-Z, Nagase R, Horikawa S, Li Z, Matsui H, Kanai A, Saika M, Yamaguchi R, Kozuka-Hata H, Kawabata K, Yokoyama A, Goyama S, Inaba T, Imoto S, Miyano S, Xu M, Yang F-C, Oyama M, and Kitamura T. A novel ASXL1-OGT axis plays roles in H3K4 methylation and tumor suppression in myeloid malignancies, Leukemia, 32, 1327–1337 (2018)
185. Park H, Shimamura T, Imoto S, Miyano S. Adaptive NetworkProfiler for identifying cancer characteristic-specific gene regulatory networks. Journal of Computational Biology, 25(2):130-145, (2018). doi: 10.1089/cmb.2017.0120.
186. VanderWeele DJ, Finney R, Katayama K, Gillard M, Paner G, Imoto S, Yamaguchi R, Wheeler D, Cam M, Maejima K, Sasaki-Oku A, Nakano K, Tanaka H, Pontier A, Grigoryev D, Kubo M, Ratain M, Miyano S, Nakagawa H. Genomic heterogeneity within individual prostate cancer foci impacts predictive biomarkers of targeted therapy, European Urology Focus, 2019 May; 5(3): 416–424. doi: 10.1016/j.euf.2018.01.006. (Published online 2018 Feb 15.)
187. Fujita K, Chen X, Homma H, Tagawa K, Amano M, Saito A, Imoto S, Akatsu H, Hashizume Y, Kaibuchi K, Miyano S, Okazawa H. Targeting Tyro3 signals ameliorates PGRN-mutant FTLD-TDP model via tau-mediated synapse pathology, Nature Communications, 9:433, (2018)
188. Ogawa M, Yokoyama K, Hirano M, Jimbo K, Ochi K, Kawamata T, Ohno N, Shimizu E, Yokoyama N, Yamaguchi R, Imoto S, Uchimaru K, Takahashi N, Miyano S, Imai Y, Tojo A. Different clonal dynamics of chronic myeloid leukaemia between bone marrow and the central nervous system, British Journal of Haematology, 183(5):842-845 (2018). doi: 10.1111/bjh.15065
189. Kiyotani K, Mai T, Yamaguchi R, Yew P-Y, Kulis M, Orgel K, Imoto S, Miyano S, Burks A.W, Nakamura Y. Characterization of the B-cell receptor repertoires in peanut allergic subjects undergoing oral immunotherapy, Journal of Human Genetics, 63, 239-248, (2018)
190. Zhang Y-Z, Imoto S, Miyano S, Yamaguchi R. Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning, International Workshop on Deep Learning in Bioinformatics, Biomedicine, and Healthcare Informatics, 1227-1232 (2017) doi: 10.1109/BIBM.2017.8217832
191. Kobayashi M, Yokoyama K, Shimizu E, Yusa N, Ito M, Yamaguchi R, Imoto S, Miyano S, Tojo A. Phenotype-based gene analysis allowed successful diagnosis of X-linked neutropenia associated with a novel WASp mutation. Ann Hematol. 97(2):367-369 (2018) doi: 10.1007/s00277-017-3134-3.
192. Sato R, Shibata T, Tanaka Y, Kato C, Yamaguchi K, Furukawa Y, Shimizu E, Yamaguchi R, Imoto S, Miyano S, Miyake K. Requirement of glycosylation machinery in TLR responses revealed by CRISPR/Cas9 screening, International Immunology, 29(8):347-355 (2017).
193. Tanikawa C, Zhang Y-Z, Yamamoto R, Tsuda Y, Tanaka M, Funauchi Y, Mori J, Imoto S, Yamaguchi R, Nakamura Y, Miyano S, Nakagawa H, Matsuda K. The Transcriptional Landscape of p53 Signalling Pathway. EBioMedicine, 109-119, (2017).
194. Miyamoto T, Tanikawa C, Yodsurang V, Zhang Y-Z, Imoto S, Yamaguchi R, Miyano S, Nakagawa H, Matsuda K. Identification of a p53-repressed gene module in breast cancer cells, Oncotarget, 8(34):55821-55836, (2017).
195. Nagata H, Kozaki K, Muramatsu T, Hiramoto H, Tanimoto K, Fujiwara N, Imoto S, Ichikawa D, Otsuji E, Miyano S, Kawano T, Inazawa J. Genome-wide screening of DNA methylation associated with lymph node metastasis in esophageal squamous cell carcinoma, Oncotarget, 8(23):37740-37750, (2017)
196. Fujii K, Miyahara Y, Harada N, Muraoka D, Komura M, Yamaguchi R, Yagita H, Nakamura J, Sugino S, Okumura S, Imoto S, Miyano S, Shiku H. Identification of an immunogenic neo-epitope encoded by mouse sarcoma using CXCR3 ligand mRNAs as sensors, OncoImmunology, 6(5): e1306617 (2017)
197. Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian mutation calling method utilizing overlapping paired-end reads, IEEE Transactions on NanoBioscience, 16(2):1-7 (2017) 10.1109/TNB.2017.2670601
198. Park H, Shiraishi Y, Imoto S, Miyano S. A novel adaptive penalized logistic regression for uncovering biomarker associated with anti-cancer drug sensitivity, IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14:771-782 (2017)
199. Tsuda Y, Tanikawa C, Miyamoto T, Hirata M, Yodsurang V, Zhang Y-Z, Imoto S, Yamaguchi R, Miyano S, Takayanagi H, Kawano H, Nakagawa H, Tanaka S, Matsuda K. Identification of a p53 target, CD137L, that mediates growth suppression and immune response of osteosarcoma cells. Scientific Reports, 2017 Sep 6;7(1):10739. doi: 10.1038/s41598-017-11208-x.
200. Zhang Y-Z, Yamaguchi R, Imoto S, Miyano S, Sequence-specific bias correction for RNA-seq data using recurrent neural networks, BMC Genomics, 18(Suppl 1):1044 (2017).
201. Park H, Niida A, Imoto S, Miyano S, Interaction based feature selection for uncovering cancer driver genes via copy number driven expression level, Journal of Computational Biology, 24:138-152 (2017)
202. Yamaguchi K, Nagayama S, Shimizu E, Komura M, Yamaguchi R, Shibuya T, Arai M, Hatakeyama S, Ikenoue T, Ueno M, Miyano S, Imoto S, Furukawa Y, Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis, Scientific Reports, 6:26011 (2016) doi: 10.1038/srep26011.
203. Chapman CG, Yamaguchi R, Tamura K, Weidner J, Imoto S, Kwon J, Fang H, Yew PY, Marino SR, Miyano S, Nakamura Y, Kiyotani K. Characterization of T-cell receptor repertoire in inflamed tissues of patients with Crohn's disease through deep sequencing, Inflamm Bowel Dis. 22(6):1275-85 (2016)
204. Hasegawa T, Hayashi S, Shimizu E, Mizuno S, Yamaguchi R, Miyano S, Nakagawa H, Imoto S. An in silico automated pipeline to identify tumor specific neoantigens from whole genome and exome sequencing data. Proc. 12th International Symposium on Bioinformatics Research and Applications, 2016.
205. Yoshino T, Katayama K, Horiba Y, Munakata K, Yamaguchi R, Imoto S, Miyano S, Mima H, Watanabe K. Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study, BMC Medical Informatics and Decision Making, 16:118 (2016)
206. Mao Y, Tamura T, Yuki Y, Abe D, Tamada Y, Imoto S, Tanaka H, Homma H, Miyano S, Okazawa H. The hnRNP-Htt axis regulates necrotic cell death induced by transcriptional repression through impaired RNA splicing, Cell Death & Disease, 7:e2207 (2016)
207. Muramatsu T, Kozaki K-i, Imoto S, Yamaguchi R, Tsuda H, Kawano T, Fujiwara N, Morishita M, Miyano S, Inazawa J. The hypusine cascade promotes cancer progression and metastasis through the regulation of RhoA in squamous cell carcinoma, Oncogene, 35(40):5304-5316 (2016)
208. Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian mutation calling method utilizing overlapping paired-end reads, Lecture Notes in Computer Science, 9683, 40-51 (2016).
209. Kato T, Inoue H, Imoto S, Tamada Y, Miyamoto T, Matsuo Y, Nakamura Y, Park JH. Oncogenic roles of TOPK and MELK, and effective growth suppression by small molecular inhibitors in kidney cancer cells, Oncotarget, 7, 17652-17664 (2016).
210. Kayano M, Matsui H, Yamaguchi R, Imoto S, Miyano S. Gene set differential analysis of time course expression profiles via sparse estimation in functional logistic model with application to time-dependent biomarker detection, Biostatistics, 17(2):235-248 (2016).
211. Park H, Imoto S, Miyano S. Recursive random lasso (RRLasso) for identifying anti-cancer drug targets, PLoS ONE, 10, e0141869 (2015).
212. Hasegawa T, Niida A, Moria T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S. A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models, Computational Statistics and Data Analysis, 94, 63-74 (2016).
213. Yoshino T, Katayama K, Horiba Y, Munakata K, Yamaguchi R, Imoto S, Miyano S, Mima H, Watanabe K, Mimura M. The Difference between the Two Representative Kampo Formulas for Treating Dysmenorrhea: An Observational Study, Evidence-Based Complementary and Alternative Medicine, Article ID 3159617 (2016)
214. Nakata A, Yoshida R, Yamaguchi R, Yamauchi M, Tamada Y, Fujita A, Shimamura T, Imoto S, Higuchi T, Nomura M, Kimura T, Nokihara H, Higashiyama M, Kondoh K, Nishihara H, Tojo A, Yano S, Miyano S, Gotoh N. Elevated beta-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs, Scientific Reports, 5, 13076 (2015).
215. Sainia H, Raicara G, Sharma A, Lala S, Dehzangib A, Lyonsb J, Paliwalb KK, Imoto S, Miyano S. Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳s pseudo amino acid composition for protein fold recognition, J Theoretical Biology, 380, 291–298 (2015).
216. Yew PY, Alachkar H, Yamaguchi R, Kiyotani K, Fang H, Yap KL, Liu HT, Wickrema A, Artz A, Besien KV, Imoto S, Miyano S, Bishop M, Stock W, Nakamura Y. Quantitative characterization of T cell repertoire in allogeneic hematopoietic stem cell transplant recipients, Bone Marrow Transplantation, 50, 1227-1234 (2015).
217. Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T. Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks, BMC Systems Biology, 9:14 (2015).
218. Iwakawa R, Kohno T, Totoki Y, Shibata T, Tsuchihara K, Mimaki S, Tsuta K, Narita Y, Nishikawa R, Noguchi M, Harris CC, Robles AI, Yamaguchi R, Imoto S, Miyano S, Totsuka H, Yoshida T, Yokota J. Expression and clinical significance of genes frequently mutated in small cell lung cancers defined by whole exome/RNA sequencing, Carcinogenesis, 36, 616-621 (2015).
219. Ayada E, Niida A, Hasegawa T, Miyano S, Imoto S. Binary contingency table method for analyzing gene mutation in cancer genome, Proc. 11th International Symposium on Bioinformatics Research and Applications, Lecture Note in Computer Science, Springer-Verlag, 9096, 12-23 (2015).
220. Kobayashi K, Sakurai K, Hiramatsu H, Inada K, Shiogama K, Nakamura S, Suemasa F, Kobayashi K, Imoto S, Haraguchi T, Ito H,Ishizaka A, Tsutsumi Y, Iba H. The miR-199a/Brm/EGR1 axis is a determinant of anchorage-independent growth in epithelial tumor cell lines, Scientific Reports, 5, 8428 (2015).
221. Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S. Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinformatics, 31(1), 116-118 (2015).
222. Chikahara Y, Niida A, Yamaguchi R, Imoto S, Miyano S. Integrative clustering of cancer genome data using infinite relational models. Proc the 7th International Conference on Bioinformatics and Computational Biology (BICoB-2015), 11-18 (2015).
223. Ikenoue T, Yamaguchi K, Komura M, Imoto S, Yamaguchi R, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Miyano S, Furukawa Y. Attenuated familial adenomatous polyposis with desmoids by an APC mutation. Human Genome Variation, 2, 15011 (2015).
224. Ito H, Shiwaku H, Yoshida C, Homma H, Luo H, Chen X, Fujita K, Musante L, Fischer U, Frints SGM, Romano C, Ikeuchi Y, Shimamura T, Imoto S, Miyano S, Muramatsu S, Kawauchi T, Hoshino M, Sudol M, Arumughan A, Wanker EE, Rich T, Schwartz C, Matsuzaki F, Bonni A, Kalscheuer VM, Okazawa H. In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells. Molecular Psychiatry, 20, 459-471 (2015).
225. Park H, Niida A, Miyano S, Imoto S. Sparse overlapping group lasso for integrative multi-omics analysis. Journal of Computational Biology, 22(2), 73-84 (2015).
226. Saini H, Raicar G, Lal S, Dehzangi A, Lyons J, Paliwal KK, Imoto S, Miyano S, Sharma A. Genetic algorithm for an optimized weighted voting scheme incorporating k-separated bigram transition probabilities to improve protein fold recognition. Asia-Pacific World Congress on Computer Science and Engineering, 1-7. (DOI: 10.1109/APWCCSE.2014.7053846)
227. Tagawa K, Homma H, Saito A, Fujita K, Chen X, Imoto S, Oka T, Ito H, Motoki K, Yoshida C, Hatsuta H, Murayama S, Iwatsubo T, Miyano S, Okazawa H. Comprehensive phosphoproteome analysis unravels the core signaling network that initiates the earliest synapse pathology in preclinical Alzheimer’s disease brain. Human Molecular Genetics, 24(2), 540-558 (2015).
228. Tamura K, Hazama S, Yamaguchi R, Imoto S, Takenouchi H, Inoue Y, Kanekiyo S, Shindo Y, Miyano S, Nakamura Y, Kiyotani K. Characterization of T cell repertoire in tumor tissues and blood in advanced colorectal cancers through deep T cell receptor sequencing. Oncology Letters, 11(6): 3643-3649 (2016) DOI: 10.3892/ol.2016.4465
229. Yamaguchi K, Komura M, Yamaguchi R, Imoto S, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Takahashi N, Ikenoue T, Hata K, Tsurita G, Shinozaki M, Suzuki Y, Sugano S, Miyano S, Furukawa Y. Detection of APC germline mosaicism by next-generation sequencing in an FAP patient. Journal of Human Genetics, 60, 227-231 (2015).
230. Arima C, Kajino T, Tamada Y, Imoto S, Shimada Y, Nakatochi M, Suzuki M, Isomura H, Yatabe Y, Yamaguchi T, Yanagisawa K, Miyano S, Takahashi T. Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features. Carcinogenesis, 35(10), 2224-2231 (2014).
231. Fang H, Yamaguchi R, Liu X, Daigo Y, Yew PY, Tanikawa C, Matsuda K, Imoto S, Miyano S, Nakamura Y. Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor α and β chains using next-generation sequencing (NGS). OncoImmunology, 3(12), e968467 (2014).
232. Barclay SS, Tamura T, Ito H, Fujita K, Tagawa K, Shimamura T, Katsuta A, Shiwaku H, Sone M, Imoto S, Miyano S, Okazawa, H. Systems biology analysis of Drosophila in vivo screen data elucidates core networks for DNA damage repair in SCA1. Human Molecular Genetics, 23(5), 1345-1364 (2014).
233. Hasegawa T, Mori T, Yamaguchi R, Imoto S, Miyano S, Akutsu T. An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. Journal of Computational Biology, 21(11), 785-798 (2014).
234. Hasegawa T, Nagasaki M, Yamaguchi R, Imoto S, Miyano S. An efficient method of exploring simulation models by assimilating literature and biological observational data. BioSystems, 121, 54-66 (2014).
235. Hasegawa T, Yamaguchi R, Nagasaki M, Miyano S, Imoto S. Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization. PLoS One, 9(8), e105942 (2014).
236. Nishiura H, Ejima K, Mizumoto K, Nakaoka S, Inaba H, Imoto S, Yamaguchi R, Saito MM. Cost-effective length and timing of school closure during an influenza pandemic depend on the severity. Theoretical Biology and Medical Modelling, 11, 5 (2014).
237. Sugimachi K, Niida A, Yamamoto K, Shimamura T, Imoto S, Iinuma H, Shinden Y, Eguchi H, Sudo T, Watanabe M, Tanaka J, Kudo S, Hase K, Kusunoki M, Yamada K, Shimada Y, Sugihara K, Maehara Y, Miyano S, Mori M, Mimori K. Allelic imbalance at an 8q24 oncogenic SNP is involved in activating MYC in human colorectal cancer, Annals of Surgical Oncology, 21, Suppl 4, S515-21 (2014).
238. Park H, Shimamura T, Miyano S, Imoto S. Robust prediction of anti-cancer drug sensitivity and sensitivity-specific biomarker. PLoS One, 9(10), e108990 (2014).
239. Sharma A, Dehzangi A, Lyons J, Imoto S, Miyano S, Nakai K, Patil A. Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function, PLoS One. 9(2), e89890 (2014).
240. Takahashi R, Nagayama S, Furu M, Kajita Y, Jin Y-H, Kato T, Imoto S, Sakai Y, Toguchida J. AFAP1L1, a novel associating partner with vinculin, modulates cellular morphology and motility, and promotes the progression of colorectal cancers. Cancer Medicine. 3(4), 759–774 (2014).
241. Tokunaga H, Munakata K, Katayama K, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Clinical data mining related to the Japanese Kampo concept "Hie" (oversensivity to coldness) in men and pre- and postmenopausal women. Evidence-Based Complementary and Alternative Medicine. Article ID: 832824 (2014).
242. Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S. HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations. Bioinformatics. 30(23), 3302-3309 (2014).
243. Affara M, Sanders D, Araki H, Tamada Y, Dunmore BJ, Humphreys S, Imoto S, Savoie C, Miyano S, Kuhara S, Jeffries D, Print C, Charnock-Jones DS. Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis. BMC Genomics. 14(1), 23 (2013).
244. Katayama K, Yamaguchi R, Imoto S, Watanabe K, Miyano S. Analysis of questionnaire for traditional medicine and development of decision support system. Evidence-Based Complementary and Alternative Medicine. Article ID: 974139 (2013).
245. Katayama K, Yoshino T, Munakata K, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Prescription of Kampo drugs in the Japanese Health Care Insurance Program. Evidence-Based Complementary and Alternative Medicine. Article ID: 576973 (2013).
246. Kayano M, Imoto S, Yamaguchi R, Miyano S. Multi-omics approach for estimating metabolic networks using low-order partial correlations. J Computational Biology. 20(8), 571-582 (2013).
247. Komatsu M, Yoshimaru T, Matsuo T, Kiyotani K, Miyoshi Y, Tanahashi T, Rokutan K, Yamaguchi R, Saito A, Imoto S, Miyano S, Nakamura Y, Sasa M, Shimada M, Katagiri T. Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. International J Oncology. 42(2), 478-506 (2013).
248. Niida A, Tremmel G, Imoto S, Miyano S. Multilayer cluster heat map visualizing biological tensor data. Lecture Notes in Bioinformatics. 8213, 116-125 (2013).
249. Saito MM, Imoto S, Yamaguchi R, Sato H, Nakada H, Kami M, Miyano S, Higuchi T. Extension and verification of the SEIR model on the 2009 influenza A (H1N1) pandemic in Japan.  Mathematical Biosciences. 246(1), 47-54 (2013).
250. Saito MM, Imoto S, Yamaguchi R, Tsubokura M, Kami M, Nakada H, Sato H, Miyano S, Higuchi T. Enhancement of collective immunity by selective vaccination against emerging influenza pandemic. PLoS One. 8(9), e72866 (2013).
251. Sharma A, Paliwal KK, Dehzangi A, Lyons J, Imoto S, Miyano S. A Strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. BMC Bioinformatics. 14, 233 (2013).
252. Sharma A, Paliwal KK, Imoto S, Miyano S. A feature selection method using improved regularized linear discriminant analysis. Machine Vision and Applications. 25(3), 775-786 (2013).
253. Sharma A, Paliwal KK, Imoto S, Miyano S, Sharma V, Ananthanarayanan R. A feature selection method using fixed-point algorithm for DNA microarray gene expression data. International J Knowledge-Based and Intelligent Engineering Systems. 18, 55-59 (2013).
254. Takatsuno Y, Mimori K, Yamamoto K, Sato T, Niida A, Inoue H, Imoto S, Kawano S, Yamaguchi R, Toh H, Iinuma H, Ishimaru S, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka J, Kudo S, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Miyano S, Sugihara K, Mori M. The rs6983267 SNP Is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer. Annals of Surgical Oncology. 20(4), 1395-1402 (2013).
255. Tamura T, Sone M, Nakamura Y, Shimamura T, Imoto S, Miyano S, Okazawa H. A restricted level of PQBP1 is needed for the best longevity of Drosophila. Neurobiology of Aging. 34(1): 356.e11-20 (2013).
256. Yamaguchi K, Yamaguchi R, Takahashi N, Ikenoue T, Fujii T, Shinozaki M, Tsurita G, Hata K, Niida A, Imoto S, Miyano S, Nakamura Y, Furukawa Y. Overexpression of cohesion establishment factor DSCC1 through E2F in colorectal cancer. PLoS One. 9(1), e85750 (2013).
257. Yamaguchi R, Imoto S, Kami M, Watanabe K, Miyano S, Yuji K. Does Twitter trigger bursts in signature collections? PLoS One. 8(3), e58252 (2013).
258. Yokobori T, Iinuma H, Shimamura T, Imoto S, Ishii H, Sugimachi K, Iwatsuki M, Ota D, Ohkuma M, Iwaya T, Nishida N, Kogo R, Sudo T, Tanaka F, Shibata K, Toh H, Sato T, Barnard GF, Fukagawa T, Yamamoto S, Nakanishi H, Sasaki S, Miyano S, Watanabe T, Kuwano H, Mimori K, Pantel K, Mori M. Plastin3 is a novel marker for circulating tumor cells undergoing the epitheial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Research. 73(7), 2059-2069 (2013).
259. Yoshimaru T, Komatsu M, Matsuo T, Chen Y-A, Murakami Y, Mizuguchi K, Mizohata E, Inoue T, Akiyama M, Yamaguchi R, Imoto S, Miyano S, Miyoshi Y, Sasah M, Nakamura Y, Katagiri T. Targeting the BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells. Nature Communications. 4, 2443 (2013).
260. Yoshino T, Katayama K, Munakata K, Horiba Y, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Statistical Analysis of Hie (cold sensation) and Hiesho (cold disorder) in Kampo Clinic. Evidence-Based Complementary and Alternative Medicine. Article ID: 398458 (2013).
261. Hurley D, Araki H, Tamada T, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG. Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Research. 40(6), 2377-2398 (2012).
262. Ishimaru S, Mimori K, Yamamoto K, Inoue H, Imoto S, Kawano, S, Yamaguchi R, Sato T, Toh H, Iinuma,H, Maeda T, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka J, Kudo S, Sugihara K, Hase K, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Barnard GF, Miyano S, Mori M. Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24. Annals of Surgical Oncology. 19(9), 2853-2858 (2012).
263. Kojima K, Imoto S, Yamaguchi R, Fujita A, Yamauchi M, Gotoh N, Miyano S. Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. BMC Genomics. 13(Suppl 1), S6 (2012).
264. Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Analysis of questionnaire for Traditional Medical and develop decision support system. Proc. International Workshop on Biomedical and Health Informatics. 762-763 (2012).
265. Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S. Identifying gene pathways associated with cancer characteristics via sparse statistical methods. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9(4), 966-972 (2012).
266. Niida A, Imoto S, Shimamura T, Miyano S. Statistical model-based testing to evaluate the recurrence of genomic aberrations. Bioinformatics. 28, i115-i120 (2012).
267. Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S. Computational gene network analysis reveals TNF-induced angiogenesis. BMC Systems Biology. 6(Suppl 2), S12 (2012).
268. Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Identifiability of local transmissibility parameters in agent-based pandemic simulation. Proc. 14th International Conference on Information FUSION. 2466-2471 (2012).
269. Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Parallel agent-based simulator for influenza pandemic. Lecture Notes in Computer Science. 7068, 361-370 (2012).
270. Sharma A, Imoto S, Miyano S. A between-class overlapping filter-based method for transcriptome data analysis. J Bioinformatics and Computational Biology. 10(5), 1250010 (2012).
271. Sharma A, Imoto S, Miyano S. A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9(3), 754-64 (2012).
272. Sharma A, Imoto S, Miyano S. A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data. Current Bioinformatics. 7(3), 289-294 (2012).
273. Sharma A, Imoto S, Miyano S, Sharma V. Null space based feature selection method for gene expression data. International J Machine Learning and Cybernetics. 3(4), 269-276 (2012).
274. Sharma A, Paliwal KK, Imoto S, Miyano S Principal component analysis using QR decomposition. International J Machine Learning and Cybernetics. (10.1007/s13042-012-0131-7) (2012). (Online)
275. Wang L, Hurley D, Watkins W, Araki H, Tamada Y, Muthukaruppan, A, Ranjard L, Derkac E, Imoto S, Miyano S, Crampin E, Print C. Cell cycle gene networks are associated with melanoma prognosis. PLoS One. 7(4), e34247 (2012).
276. Yamauchi M, Yamaguchi R, Nakata A, Kohno T, Nagasaki M, Shimamura T, Imoto S, Saito A, Ueno K, Hatanaka Y, Yoshida R, Higuchi T, Nomura M, Beer DG, Yokota J, Miyano S, Gotoh N. Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma. PLoS One. 7(9), e43923 (2012).
277. Yamamoto M, Yamaguchi R, Muanakata K, Takashima K, Nishiyama M, Hioki K, Ohnishi Y, Nagasaki M, Imoto S, Miyano S, Ishige A, Watanabe K. A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. BMC Genomics. 13, 335 (2012).
278. Yuji K,* Imoto S,* Yamaguchi R, Matsumura T, Murashige N, Kodama Y, Miyano S, Imai K, Kami M. Forecasting Japan's physician shortage in 2035 as the first full-fledged aged society.  PLoS One. 7(11), e50410 (2012). (*Equal contribution)
279. Furu M, Kajita Y, Nagayama S, Ishibe T, Shima Y, Uejima D, Aoyama T, Nakayama T, Nakamura T, Nakashima Y, Ikegawa M, Imoto S, Katagiri T, Nakamura Y, Toguchida J. Identification of AFAP1L1 as a prognostic marker for spindle cell sarcomas. Oncogene. 30, 4015-4025 (2011).
280. Hasegawa T, Yamaguchi R, Nagasaki M, Imoto S, Miyano S. Comprehensive pharmacogenomic pathway screening by data assimilation. Lecture Notes in Computer Science. 6674, 160-171 (2011).
281. Imoto S, Kojima K, Perrier E, Tamada Y, Miyano S. Searching optimal Bayesian network structure on constraint search space: super-structure approach. Lecture Notes in Computer Science. 6797, 210-218 (2011).
282. Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Clustering for visual analogue scale data in symbolic data analysis. Procedia Computer Science. 6, 370-374 (2011).
283. Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Transform of visual analogue scale data and their clustering. International J Knowledge Engineering and Soft Data Paradigms. 3(2), 143-151 (2011).
284. Katayama K, Yamaguchi R, Imoto S, Tokunaga H, Imazu Y, Matuura K, Watanabe K, Miyano S. Symbolic hierarchical clustering for visual analogue scale data. KES-Springer Smart Innovations, Systems and Technologies Series. 10, 799-805 (2011).
285. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. Long non-coding RNA HOTAIR regulates Polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Research. 71(20), 6320-6326 (2011).
286. Saito M, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Estimation of macroscopic parameter in agent-based pandemic simulation. Proc. 13th International Conference on Information Fusion. 1-6 (2011).
287. Sharma A, Hock Koh, C, Imoto S, Miyano S. A strategy of finding the optimal number of features on gene expression data. Electronics Letters. 47(8), 480-482 (2011).
288. Shimamura T, Imoto S, Shimada Y, Hosono Y, Niida A, Nagasaki M, Yamaguchi R, Takahashi T, Miyano S. A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS One. 6(6), e20804 (2011).
289. Sogawa Y, Shimizu S, Shimamura T, Hyvarinen A, Washio T, Imoto S. Estimating exogenous variables in data with more variables than observations. Neural Networks. 24(8), 875-880 (2011).
290. Tamada Y, Imoto S, Araki H, Nagasaki M, Print C, Charnock-Jones S, Miyano S. Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(3), 683-697 (2011).
291. Tamada Y, Imoto S, Miyano S. Parallel algorithm for learning optimal Bayesian network structure. J Machine Learning Research. 12, 2437-2459 (2011).
292. Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S. SiGN: large-scale gene network estimation environment for high performance computing. Genome Informatics. 25, 40-52 (2011).
293. Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S. SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinformatics. 27(8), 1172-1173 (2011).
294. Yamauchi M, Yoshino I, Yamaguchi R, Shimamura T, Nagasaki M, Imoto S, Niida A, Koizumi F, Kohno T, Yokota J, Miyano S, Gotoh N. N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. American J Cancer Research. 1, 823-833 (2011).
295. Fujita A, Nagasaki M, Imoto S, Saito A, Ikeda E, Shimamura T, Yamaguchi R, Suzuki H, Hayashizaki Y, Miyano S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. Genome Informatics. 24, 56-68 (2010).
296. Higashigaki T, Kojima K, Yamaguchi R, Inoue, M, Imoto S, Miyano S. Identifying hidden confounders in gene networks by Bayesian networks. Proc. 10th IEEE Bioinformatics and Bioengineering. 168-173 (2010).
297. Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S. Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. Proc. IEEE Bioinformatics and Biomedicine. 253-258 (2010).
298. Kojima K, Imoto S, Nagasaki M, Miyano S. Gene regulatory network clustering for graph layout based on microarray gene expression data. Genome Informatics. 24, 84-95 (2010).
299. Kojima K, Perrier E, Imoto S, Miyano S. Optimal search on clustered structural constraint for learning Bayesian network structure. J Machine Learning Research. 11, 285-310 (2010).
300. Niida A, Imoto S, Yamaguchi R, Nagasaki M, Fujita A, Shimamura T, Miyano S. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics. 26, 3090-3097 (2010).
301. Niida A, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS One, 5(6), e10910 (2010).
302. Sato H,* Nakada H,* Yamaguchi R,* Imoto S,* Miyano S, Kami M. When should we intervene to control the 2009 influenza A (H1N1) pandemic? Euro Surveillance. 15(1), pii=19455 (2010). (*Equal contribution)
303. Shimamura T, Imoto S, Nagasaki M, Yamauchi M, Yamaguchi R, Fujita A, Tamada Y, Gotoh N, Miyano S. Collocation-based sparse estimation for inferring continuous-time dynamic gene networks. Genome Informatics. 24, 164-178 (2010).
304. Shimamura T, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics. 26(8), 1064-1072 (2010).
305. Sogawa Y, Shimizu S, Hyvarinen A, Washio T, Shimamura T, Imoto S. Discovery of exogenous variables in data with more variables than observations. Proc. 20th International Conference on Artificial Neural Networks. 67-76 (2010).
306. Yamaguchi R, Imoto S, Miyano S. Network-based predictions and simulations by biological state space models: search for drug mode of action. J Computer Science and Technology. 25(1), 131-153 (2010).
307. Araki H,* Tamada Y,* Imoto S,* Dunmore, B, Sanders D, Humphrey S, Nagasaki M, Doi A, Nakanishi Y, Yasuda K, Tomiyasu Y, Tashiro K, Print C, Charnock-Jones DS, Kuhara S, Miyano S. Analysis of PPAR alpha-dependent and PPAR alpha-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis. 12(3), 221-229 (2009). (*Equal contribution)
308. Kojima K, Yamaguchi R, Imoto S, Yamauchi M, Nagasaki M, Yoshida R, Shimamura T, Ueno K, Higuchi T, Gotoh N, Miyano S. A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Informatics. 22, 56-68 (2009).
309. Niida A, Imoto S, Nagasaki M, Yamaguchi R, Miyano S. A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells. Genome Informatics. 22, 121-131 (2009).
310. Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T. Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics. 10, 71 (2009).
311. Shimamura T, Imoto S, Yamaguchi R, Fujita A, Nagasaki M, Miyano S. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Systems Biology. 3, 41 (2009).
312. Tamada Y,* Araki H,* Imoto S,* Nagasaki M, Doi A, Nakinishi Y, Tomiyasu Y, Yasuda K, Dunmore B, Sanders D, Humphries S, Print C, Charnock-Jones DS, Tashiro K, Kuhara S, Miyano S. Unraveling dynamic activities of autoacine pathways that control drug-response transcriptome networks. Pacific Symposium on Biocomputing. 14, 251-263 (2009). (*Equal contribution)
313. Yoshikawa N, Nagasaki M, Sano M, Tokudome S, Ueno K, Shimizu N, Imoto S, Miyano S, Suematsu M, Fukuda K, Morimoto C, Tanaka H. Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. American J Physiology, Endocrinology and Metabolism. 296, E1363-E1373 (2009).
314. Ando T, Konishi S, Imoto S. Nonlinear regression modeling via regularized radial basis function networks. J Statistical Planning and Inference. 138(11), 3616-3633 (2008).
315. Hirose O, Yoshida R, Yamaguchi R, Imoto S, Higuchi T, Miyano S. Analyzing time course gene expression data with biological and technical replicates to estimate gene networks by state space models. Proc. 2nd Asia International Conference on Modeling & Simulation. 940-946 (2008).
316. Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, Charnock-Jones SD, Print C, Miyano S. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics. 24(7), 932-942 (2008).
317. Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada T, Imoto S, Kinoshita K, Nakai K, Miyano S. A novel strategy to search conserved transcription factor binding sites among coexpressing genes. Genome Informatics. 20, 212-221 (2008).
318. Kojima K, Fujita A, Shimamura T, Imoto S, Miyano S. Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Informatics. 20, 37-51 (2008).
319. Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T. Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics. 9, 404 (2008).
320. Numata K, Imoto S, Miyano S. Partial order-based Bayesian network learning algorithm for estimating gene networks. Proc. IEEE Bioinformatics and Biomedicine. 357-360 (2008).
321. Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S. ExonMiner: web service for analysis of GeneChip Exon Array data. BMC Bioinformatics. 9, 494 (2008).
322. Perrier E, Imoto S, Miyano S. Finding optimal Bayesian network given a super-structure. J Machine Learning Research. 9, 2251-2286 (2008).
323. Watanabe Y, Yamamoto M, Miura N, Fukutake M, Ishige A, Yamaguchi R, Nagasaki M, Imoto S, Miyano S, Takeda J, Watanabe K. Orengedokuto and berberine improve indomethacin- induced small intestinal injury via adenosine. J Gastroenterology. 44, 380-389 (2008).
324. Yamaguchi R, Imoto S, Yamauchi M, Nagasaki M, Yoshida R, Shimamura T, Hatanaka Y, Ueno K, Higuchi T, Gotoh N, Miyano S. Predicting differences in gene regulatory systems by state space models. Genome Informatics. 21, 101-113 (2008).
325. Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T. Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics. 24(22), 2592-2601 (2008).
326. Affara M, Dunmore B, Savoie CJ, Imoto S, Tamada Y, Araki H, Charnock-Jones DS, Miyano S, Print C. Understanding endothelial cell apoptosis: what can the transcriptome glycome and proteome reveal? Philosophical Transactions of Royal Society. 62(1484), 1469-1487 (2007).
327. Gupta PK, Yoshida R, Imoto S, Yamaguchi R, Miyano S. Statistical absolute evaluation of gene ontology terms with gene expression data. Lecture Notes in Bioinformatics. 4463, 146-157 (2007).
328. Hirose O, Yoshida R, Yamaguchi R, Imoto S, Higuchi T, Miyano S. Clustering with time course gene expression profiles and the mixture of state space models. Genome Informatics. 18, 258-266 (2007).
329. Numata K, Imoto S, Miyano S. A structure learning algorithm for inference of gene networks from microarray gene expression data using Bayesian networks. Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering. 1280-1284 (2007).
330. Shimamura T, Yamaguchi R, Imoto S, Miyano S. Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Informatics. 19, 142-153 (2007).
331. Termier A, Tamada Y, Numata K, Imoto S, Washio T, Higuchi T. DIGDAG, a first algorithm to mine closed frequent embedded sub-DAGs. Proc. 5th International Workshop on Mining and Learning with Graphs. CR-ROM (2007).
332. Yamaguchi R, Yamamoto M, Imoto S, Nagasaki M, Yoshida R, Tsuiji K, Ishige A, Asou H, Watanabe K, Miyano S. Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice. Genome Informatics. 18, 119-129 (2007).
333. Yamaguchi R, Yoshida R, Imoto S, Higuchi T, Miyano S. Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data. IEEE Signal Processing Magazine. 24(1), 37-46 (2007).
334. Yoshida R, Numata K, Imoto S, Nagasaki M, Doi A, Ueno K, Miyano S. Computational discovery of aberrant splice variations with genome-wide exon expression profiles. Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering. 715-722 (2007).
335. Imoto S, Higuchi T, Goto T, Miyano S. Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks. Statistical Methodology. 3(1), 1-16 (2006).
336. Imoto S,* Tamada Y,* Araki H,* Yasuda K, Print CG, Charnock-Jones SD, Sanders, D, Savoie CJ, Tashiro K, Kuhara S, Miyano S. Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pacific Symposium on Biocomputing. 11, 559-571 (2006). (*Equal contribution)
337. Imoto S, Tamada Y, Savoie CJ, Miyano S. Analysis of gene networks for drug target discovery and validation. Methods in Molecular Biology. 360, 33-56 (2006).
338. Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T. Genomic data assimilation for estimating hybrid functional petri net from time-course gene expression data. Genome Informatics. 17(1), 46-61 (2006).
339. Nakamichi R, Imoto S, Miyano S. Statistical model selection method to analyze combinatorial effects of SNPs and environmental factors for binary disease. International J Artificial Intelligence Tools. 15(5), 711-724 (2006).
340. Termier A, Tamada Y, Imoto S, Washio T, Higuchi T. From closed tree mining towards closed DAG mining. Proc. International Workshop on Data Mining and Statistical Science. 1-7 (2006).
341. Yoshida R, Numata K, Imoto S, Nagasaki M, Doi A, Ueno K, Miyano S. A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays. Genome Informatics. 17(1), 88-99 (2006).
342. Yoshida R, Higuchi T, Imoto S, Miyano S. ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. Bioinformatics. 22, 1538-1539 (2006).
343. Hirose O, Nariai N, Tamada Y, Bannai H, Imoto S, Miyano S. Estimating gene networks from expression data and binding location data via Boolean networks. Lecture Notes in Computer Science. 3482, 349-356 (2005).
344. Nariai N, Tamada Y, Imoto S, Miyano S. Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics, 21, Suppl.2, ii206-ii212 (2005).
345. Tamada Y, Bannai H, Imoto S, Katayama T, Kanehisa M, Miyano S. Utilizing evolutionary information and gene expression data for estimating gene regulations with Bayesian network models. J Bioinformatics and Computational Biology, 3(6), 1295-1313 (2005).
346. Tamada Y, Imoto S, Tashiro K, Kuhara S, Miyano S. Identifying drug active pathways from gene networks estimated by gene expression data. Genome Informatics, 16(1), 182-191 (2005).
347. Yoshida R, Imoto S, Higuchi T. Estimating time-dependent gene networks from time series microarray data by dynamic linear models with Markov switching. Proc. 4th Computational Systems Bioinformatics, 289-298 (2005).
348. Yoshida R, Imoto S, Higuchi T. A penalized likelihood estimation on transcriptional module-based clustering. Lecture Notes in Computer Science, 3482, 389-401 (2005).
349. Ando T, Imoto S, Konishi S. Adaptive learning machines for nonlinear classification and Bayesian information criterion. Bulletin of Informatics and Cybernetics, 36, 147-162 (2004).
350. Ando T, Imoto S, Miyano S. Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities. Genome Informatics, 15(2), 201-210 (2004).
351. Ando T, Imoto S, Miyano S. Functional data analysis of the dynamics of gene regulatory networks. Lecture Notes in Computer Science, 3303, 69-83 (2004).
352. Araki Y, Konishi S, Imoto S. Functional discriminant analysis for time-seriese gene expression data via radial basis function expansion. COMPSTAT, 613-620 (2004).
353. De Hoon MJL, Imoto S, Kobayashi K, Ogasawara N, Miyano S. Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pacific Symposium on Biocomputing, 9, 276-287 (2004).
354. De Hoon MJL, Makita Y, Imoto S, Kobayashi K, Ogasawara N, Nakai K, Miyano S. Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. Bioinformatics, 20 Suppl.1, i101-i108 (2004).
355. De Hoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics, 20(9), 1453-1454 (2004).
356. Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S. Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. J Bioinformatics and Computational Biology, 2(1), 77-98 (2004).
357. Imoto S, Higuchi T, Kim S, Jeong E, Miyano S. Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data.  Lecture Notes in Bioinformatics, 3082, 149-160 (2004).
358. Kim S, Imoto S, Miyano S. Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. BioSystems, 75(1-3), 57-65 (2004).
359. Konishi S, Ando T, Imoto S. Bayesian information criteria and smoothing parameter selection in radial basis function networks. Biometrika, 91(1), 27-43 (2004).
360. Nakamichi R, Imoto S, Miyano S. Case-control study of binary trait considering interactions between SNPs and environmental effects using logistic regression. Proc. 4th IEEE Bioinformatics and Bioengineering, 73-78 (2004).
361. Nariai N, Kim S, Imoto S, Miyano S. Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks. Pacific Symposium on Biocomputing, 9, 336-347 (2004).
362. Ott S, Imoto S, Miyano S. Finding optimal models for small gene networks. Pacific Symposium on Biocomputing, 9, 557-567 (2004).
363. Yoshida R, Higuchi T, Imoto S. A mixed factors model for dimension reduction and extraction of a group structure in gene expression data. Proc. 3rd Computational Systems Bioinformatics, 161-172 (2004).
364. De Hoon MJL, Imoto S, Kobayashi K, Ogasawara N, Miyano S. Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pacific Symposium on Biocomputing, 8, 17-28 (2003).
365. De Hoon MJL, Ott S, Imoto S, Miyano S. Validation of noisy dynamical system models of gene regulation inferred from time-course gene expression data at arbitrary time intervals. Proc. 2nd European Conference on Computational Biology, 26-28 (2003).
366. Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S. Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc. 2nd Computational Systems Bioinformatics, 104-113 (2003).
367. Imoto S, Kim S, Goto T, Aburatani S, Tashiro K, Kuhara S, Miyano S. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J Bioinformatics and Computational Biology, 1(2), 231-252 (2003).
368. Imoto S, Konishi S. Selection of smoothing parameters in B-spline nonparametric regression models using information criteria. Annals of the Institute of Statistical Mathematics, 55(4), 671-687 (2003).
369. Imoto S, Savoie CJ, Aburatani S, Kim S, Tashiro K, Kuhara S, Miyano S. Use of gene networks for identifying and validating drug targets. J Bioinformatics and Computational Biology, 1(3), 459-474 (2003).
370. Kim S, Imoto S, Miyano S. Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Lecture Notes in Computer Science, 2602, 104-113 (2003).
371. Savoie CJ, Aburatani S, Watanabe S, Eguchi Y, Muta S, Imoto S, Miyano S, Kuhara S, Tashiro K. Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Research, 10, 19-25 (2003).
372. Tamada Y, Kim S, Bannai H, Imoto S, Tashiro K, Kuhara S, Miyano S. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics, 19,  ii227-ii236 (2003).
373. De Hoon MJL, Imoto S, Miyano S. Inferring gene regulatory networks from time-ordered gene expression data using differential equations. Lecture Notes in Artificial Intelligence, 2534, 267-274 (2002).
374. De Hoon MJL, Imoto S, Miyano S. Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinformatics, 18, 1477-1485 (2002).
375. Imoto S, Kim S, Goto T, Aburatani S, Tashiro K, Kuhara S, Miyano S. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Proc. 1st IEEE Computer Society Bioinformatics Conference, 219-227 (2002).
376. Imoto S, Goto T, Miyano S. Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression. Pacific Symposium on Biocomputing, 7, 175-186 (2002).

2) Review papers

1. Zhang YZ, Imoto S. Genome analysis through image processing with deep learning models. J Hum Genet. 2024 Jul 31. doi: 10.1038/s10038-024-01275-0. Online ahead of print.
2. Hayashi S, Imoto S. HLA Typing and Mutation Calling from Normal and Tumor Whole Genome Sequencing Data with ALPHLARD-NT. Methods Mol Biol. 2024;2809:101-113. doi: 10.1007/978-1-0716-3874-3_7.
3. MARCO (MAss gathering Risk COntrol and COmmunication). Implementing Solution-Focused Risk Assessment and Control for Mass Gathering Events. Japanese Journal of Risk Analysis, 31(3): 173–179 (2022)
4. Murakami M, Kitajima M, Imoto S. Applying quantitative microbial risk assessment and wastewater-based epidemiology to mass gathering risk control and communication. Health Related Water Microbiology Specialist Group Newsletter, 23, 5 (2021)
5. Ogawa M, Yokoyama K, Imoto S, Tojo A. Role of circulating tumor DNA in hematological malignancy. Cancers, 2021, 13(9), 2078; https://doi.org/10.3390/cancers13092078.
6. Imoto S, Hasegawa T, Yamaguchi R. Data science and precision healthcare. Nutrition Reviews, 2020 Dec 1;78(Supplement_3):53-57. doi: 10.1093/nutrit/nuaa110.
7. Miyano S, Yamaguchi R, Tamada Y, Nagasaki M, Imoto S. Gene networks viewed through two models. Lecture Notes in Bioinformatics, 4652, 54-66 (2009).
8. Kim S, Imoto S, Miyano S. Inferring gene networks from time series microarray data using dynamic Bayesian networks. Briefings in Bioinformatics, 4(3), 228-235 (2003).

3) Books, Chapters, others

1. Uematsu S, Imoto S. A virus-derived enzyme can destroy the membrane structures that protect bacteria. Nature Research Briefings. 2024, Oct 3, published online. doi: https://doi.org/10.1038/d41586-024-03188-6
2. Yasutaka T, Fujita T, Naito W, Onishi M, Murakami M, Imoto S, Okuda T. Infection risk assessment of COVID-19 at graduation and entrance ceremonies. Japanese Journal of Risk Analysis. 2024, 33(4): 167–178. doi: 10.11447/jjra.O-23-001
3. Momose H, Kurita N, Nishikii H, Yusa N, Yokoyama K, Shimizu E, Imoto S, Nanmoku T, Maruyama Y, Sakamoto T, Yokoyama Y, Kato T, Matsuoka R, Obara N, Sakata-Yanagimoto M, Chiba S. Durable remission of T-cell prolymphocytic leukemia with CLEC16A::IL2 after allogeneic hematopoietic stem cell transplantation. Rinsho Ketsueki. 2024, 65(1):35-40. doi: 10.11406/rinketsu.65.35.
4. Tasutaka T, Fujita T, Naito W, Onishi M, Murakami M, Imoto S, Okuda T. Infection risk assessment of COVID-19 at graduation and entrance ceremonies. Japanese Journal of Risk Analysis. in press. (Japanese with English abstract)
5. Sato M, Shino M, Yokoyama K, Ishida T, Hirao M, Kamoda Y, Iizuka H, Kida M, Imoto S, Tojo A, Usuki K. The efficacy of alemtuzumab for pure red cell aplasia associated with autoimmune polyendocrine syndrome type 1. Rinsho Ketsueki. 2022;63(3):189-193. doi: 10.11406/rinketsu.63.189.
6. Yamaguchi R, Imoto S, Miyano S. A TCR Sequence Data Analysis Pipeline: Tcrip, Y. Nakamura (Ed.), Immunopharmacogenomics, Springer Japan, pp. 27-43 (2015)
7. Imoto S, Matsuno H, Miyano S. Gene Networks: Estimation, Modeling and Simulation. In R. Eils and A. Kriete (Eds.), Computational Systems Biology, 2nd Edition, Academic Press, pp. 89-112 (2014).
8. Imoto S, Tamada Y, Araki H, Miyano S. Computational Drug Target Pathway Discovery: A Bayesian Network Approach. In H. Lu, B. Schokop, H. Zhao (Eds.), Handbook of Computational Statistics: Statistical Bioinformatics, Springer-Verlag. pp. 501-532 (2010).
9. Imoto S, Miyano S. Bayesian Network Approach to Estimate Gene Networks. In A. Mittal, A. Kassim, T. Tan (Eds.), Bayesian Network Technologies: Applications and Graphical Models, Idea Group Publishers, USA. pp. 269-299 (2007).