2020s

2025 2024 2023 2022 2021 2020

2025

1. Morita A, Ishii M, Asakura T, Yotsukura M, Hegab AE, Kusumoto T, Namkoong H, Ogawa T, Nakatake Y, Oda M, Saito F, Kamata H, Hamamoto J, Okamori S, Ebisudani T, Yasuda H, Sugimoto S, Kuze Y, Seki M, Suzuki Y, Hasegawa N, Asamura H, Watanabe H, Ko M, Sato T, Ieda M, Fukunaga K. Direct reprogramming of mouse fibroblasts into self-renewable alveolar epithelial-like cells. NPJ Regen Med. 2025 Jun 23;10(1):30. doi: 10.1038/s41536-025-00411-4. PMID: 40550799
2. Kaneda T, Matsuda-Imai N, Kosako H, Shoji K, Suzuki MG, Suzuki Y, Kiuchi T, Katsuma S. The Masc-PSI complex directly induces male-type doublesex splicing in silkworms. Commun Biol. 2025 Jun 14;8(1):927. doi: 10.1038/s42003-025-08350-y. PMID: 40517142
3. Sakai S, Maeda Y, Saeki M, Konno D, Kawaji K, Matsuzaki F, Suzuki Y, Gotoh Y, Kishi Y.　In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex. Development. 2025 Jun 12:dev.204564. doi: 10.1242/dev.204564. Online ahead of print. PMID: 40501413
4. Ishiyama T, Sano D, Takahashi H, Oridate N, Suzuki Y, Fujii S. Ligand-Receptor Interactions Between Squamous and Endothelial Cells Induce Head and Neck Squamous Cell Carcinoma. Cancer Sci. 2025 May 26. doi: 10.1111/cas.70085. Online ahead of print. PMID: 40418639
5. Yamamoto Y, Shirai Y, Sonehara K, Namba S, Ojima T, Yamamoto K, Edahiro R, Suzuki K, Kanai A; BioBank Japan Project; Oda Y, Suzuki Y, Morisaki T, Narita A, Takeda Y, Tamiya G, Yamamoto M, Matsuda K, Kumanogoh A, Yamauchi T, Kadowaki T, Okada Y. Dissecting cross-population polygenic heterogeneity across respiratory and cardiometabolic diseases. Nat Commun. 2025 Apr 28;16(1):3765. doi: 10.1038/s41467-025-58149-y. PMID: 40295474
6. Ueda S, Kitamura C, Tateoka Y, Kanai A, Suzuki Y, Fukuda I, Shirai Y. Single-Nucleus RNA Sequencing Reveals Muscle-Region-Specific Differences in Fibro-Adipogenic Progenitors Driving Intramuscular Fat Accumulation. Metabolites. 2025 Mar 28;15(4):231. doi: 10.3390/metabo15040231. PMID: 40278360
7. Morita K, Hatano A, Kokaji T, Sugimoto H, Tsuchiya T, Ozaki H, Egami R, Li D, Terakawa A, Ohno S, Inoue H, Inaba Y, Suzuki Y, Matsumoto M, Takahashi M, Izumi Y, Bamba T, Hirayama A, Soga T, Kuroda S. Structural robustness and temporal vulnerability of the starvation-responsive metabolic network in healthy and obese mouse liver. Sci Signal. 2025 Apr 22;18(883):eads2547. doi: 10.1126/scisignal.ads2547. Epub 2025 Apr 22. PMID: 40261956
8. Wang K, Suyama R, Mizutani N, Matsuo M, Peng Y, Seki M, Suzuki Y, Luscombe NM, Dantec C, Lemaire P, Toyoda A, Nishida H, Onuma TA. Transcriptomes of a fast-developing chordate uncover drastic differences in transcription factors and localized maternal RNA composition compared with those of ascidians. Development. 2025 Mar 15;152(6):DEV202666. doi: 10.1242/dev.202666. Epub 2025 Mar 18. PMID: 40099490
9. Sonehara K, Uwamino Y, Saiki R, Takeshita M, Namba S, Uno S, Nakanishi T, Nishimura T, Naito T, Sato G, Kanai M, Liu A, Uchida S, Kurafuji T, Tanabe A, Arai T, Ohno A, Shibata A, Tanaka S, Wakui M, Kashimura S, Tomi C, Hara A, Yoshikawa S, Gotanda K, Misawa K, Tanaka H, Azekawa S, Wang QS, Edahiro R, Shirai Y, Yamamoto K, Nagao G, Suzuki T, Kiyoshi M, Ishii-Watabe A, Higashiue S, Kobayashi S, Yamaguchi H, Okazaki Y, Matsumoto N, Masumoto A, Koga H, Kanai A; Japan COVID-19 Task Force; Biobank Japan Project; Oda Y, Suzuki Y, Matsuda K, Kitagawa Y, Koike R, Kimura A, Kumanogoh A, Yoshimura A, Imoto S, Miyano S, Kanai T, Fukunaga K, Hasegawa N, Murata M, Matsushita H, Ogawa S, Okada Y, Namkoong H. Germline variants and mosaic chromosomal alterations affect COVID-19 vaccine immunogenicity. Cell Genom. 2025 Mar 12;5(3):100783. doi: 10.1016/j.xgen.2025.100783. Epub 2025 Mar 4. PMID: 40043710
10. Sato T, Yamaguchi T, Minato T, Hoshizaki M, Yamamoto A, Morita M, Suzuki T, Fujio Y, Imai Y, Suzuki Y, Yamamoto T, Watanabe H, Kuba K. CNOT6L deadenylase suppresses cardiac remodeling in heart failure through downregulation of tenascin-C mRNA. J Pharmacol Exp Ther. 2025 Feb;392(2):100052. doi: 10.1016/j.jpet.2024.100052. Epub 2024 Nov 30. PMID: 40023604
11. Yokomoto-Umakoshi M, Fujita M, Umakoshi H, Ogasawara T, Iwahashi N, Nakatani K, Kaneko H, Fukumoto T, Nakao H, Haji S, Kawamura N, Shimma S, Seki M, Suzuki Y, Izumi Y, Oda Y, Eto M, Ogawa S, Bamba T, Ogawa Y. Multiomics analysis unveils the cellular ecosystem with clinical relevance in aldosterone-producing adenomas with KCNJ5 mutations. Proc Natl Acad Sci U S A. 2025 Mar 4;122(9):e2421489122.  doi: 10.1073/pnas.2421489122. Epub 2025 Feb 26. PMID: 40009643
12. Sakai SA, Nomura R, Nagasawa S, Chi S, Suzuki A, Suzuki Y, Imai M, Nakamura Y, Yoshino T, Ishikawa S, Tsuchihara K, Kageyama SI, Yamashita R. SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data. PLoS Comput Biol. 2025 Feb 18;21(2):e1012854. doi: 10.1371/journal.pcbi.1012854. eCollection 2025 Feb. PMID: 39965034
13. Yoshida K, Yokoi A, Suzuki H, Tamauchi S, Kitagawa M, Inami E, Nakayama J, Mori Y, Okamoto K, Suzuki Y, Yoshida H, Kato T, Kajiyama H, Yamamoto Y. Single-Nucleus RNA Sequencing and Spatial Transcriptomics for Squamous Cell Carcinoma Arising From Ovarian Mature Teratoma. Cancer Sci. 2025 May;116(5):1339-1351. doi: 10.1111/cas.70022. Epub 2025 Feb 13. PMID: 39948701
14. Furusawa Y, Kiso M, Uraki R, Sakai-Tagawa Y, Nagai H, Koga M, Kashima Y, Hojo M, Iwamoto N, Iwatsuki-Horimoto K, Ohmagari N, Suzuki Y, Yotsuyanagi H, Halfmann PJ, Kamitani W, Yamayoshi S, Kawaoka Y. Amino acid substitutions in NSP6 and NSP13 of SARS-CoV-2 contribute to superior virus growth at low temperatures. J Virol. 2025 Mar 18;99(3):e0221724. doi: 10.1128/jvi.02217-24. Epub 2025 Feb 12. PMID: 39936915
15. Miura F, Shibata Y, Miura M, Inatomi K, Suzuki Y, Ito T. Identification of an enzyme with strong single-stranded DNA ligation activity and its application for sequencing. Nucleic Acids Res. 2025 Jan 24;53(3):gkaf054. doi: 10.1093/nar/gkaf054. PMID: 39883008
16. Miyahara J, Omata Y, Chijimatsu R, Okada H, Ishikura H, Higuchi J, Tachibana N, Nagata K, Tani S, Kono K, Kawaguchi K, Yamagami R, Inui H, Taketomi S, Iwanaga Y, Terashima A, Yano F, Seki M, Suzuki Y, Baron R, Tanaka S, Saito T. CD34hi subset of synovial fibroblasts contributes to fibrotic phenotype of human knee osteoarthritis. JCI Insight. 2025 Jan 23;10(2):e183690. doi: 10.1172/jci.insight.183690. PMID: 39846253
17. Nolte T, Halabian R, Israel S, Suzuki Y, Avelar RA, Palmer D, Fuellen G, Makalowski W, Boiani M. Animal and vegetal materials of mouse oocytes segregate at first zygotic cleavage: a simple mechanism that makes the two-cell blastomeres differ reciprocally from the start. Mol Hum Reprod. 2025 Jan 17;31(1):gaae045. doi: 10.1093/molehr/gaae045. PMID: 39786543
18. Yamada Y, Sadahiro T, Nakano K, Honda S, Abe Y, Akiyama T, Fujita R, Nakamura M, Maeda T, Kuze Y, Onishi M, Seki M, Suzuki Y, Takeuchi C, Iwasaki YW, Murano K, Sakata-Yanagimoto M, Chiba S, Kato H, Sakamoto H, Hiramatsu Y, Ieda M. Cardiac Reprogramming and Gata4 Overexpression Reduce Fibrosis and Improve Diastolic Dysfunction in Heart Failure With Preserved Ejection Fraction. Circulation. 2025 Feb 11;151(6):379-395. doi: 10.1161/CIRCULATIONAHA.123.067504. Epub 2024 Dec 14. PMID: 39673349v
19. Sakai SA, Saeki K, Chi S, Hamaya Y, Du J, Nakamura M, Hojo H, Kojima T, Nakamura Y, Bando H, Kojima M, Suzuki A, Suzuki Y, Akimoto T, Tsuchihara K, Haeno H, Yamashita R, Kageyama SI. Mathematical Modeling Predicts Optimal Immune Checkpoint Inhibitor and Radiotherapy Combinations and Timing of Administration. Cancer Immunol Res. 2025 Mar 4;13(3):353-364. doi: 10.1158/2326-6066.CIR-24-0610. PMID: 39666379
20. Ishizaka A, Tamura A, Koga M, Mizutani T, Yamayoshi S, Iwatsuki-Horimoto K, Yasuhara A, Yamamoto S, Nagai H, Adachi E, Suzuki Y, Kawaoka Y, Yotsuyanagi H. Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection. Microbiol Spectr. 2025 Jan 7;13(1):e0099824. doi: 10.1128/spectrum.00998-24. Epub 2024 Dec 10. PMID: 39656008
21. Mizuike J, Suzuki K, Tosaka S, Kuze Y, Kobayashi S, Nakashima M, Jimbo K, Nannya Y, Suzuki Y, Uchimaru K, Yamagishi M. Rewired chromatin structure and epigenetic gene dysregulation during HTLV-1 infection to leukemogenesis. Cancer Sci. 2025 Feb;116(2):513-523. doi: 10.1111/cas.16388. Epub 2024 Nov 19. PMID: 39561277

2024

1. Takano Y, Suzuki J, Nomura K, Fujii G, Zenkoh J, Kawai H, Kuze Y, Kashima Y, Nagasawa S, Nakamura Y, Kojima M, Tsuchihara K, Seki M, Kanai A, Matsubara D, Kohno T, Noguchi M, Nakaya A, Tsuboi M, Ishii G, Suzuki Y, Suzuki A. Spatially resolved gene expression profiling of tumor microenvironment reveals key steps of lung adenocarcinoma development. Nat Commun. 2024 Dec 6;15(1):10637. doi: 10.1038/s41467-024-54671-7. PMID: 39639005
2. Shu X, Kato M, Takizawa S, Suzuki Y, Carninci P. RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions. Nucleic Acids Res. 2024 Dec 11;52(22):e104. doi: 10.1093/nar/gkae1054. PMID: 39558168
3. Kume K, Iida M, Iwaya T, Yashima-Abo A, Koizumi Y, Endo A, Wade K, Hiraki H, Calvert V, Wulfkuhle J, Espina V, Siwak DR, Lu Y, Takemoto K, Suzuki Y, Sasaki Y, Tokino T, Petricoin E 3rd, Liotta LA, Mills GB, Nishizuka SS. Targeted Dynamic Phospho-Proteogenomic Analysis of Gastric Cancer Cells Suggests Host Immunity Provides Survival Benefit Mol Cell Proteomics. 2024 Dec;23(12):100870. doi: 10.1016/j.mcpro.2024.100870. Epub 2024 Oct 25. PMID: 39461475
4. Kuribayashi H, Iwagawa T, Murakami A, Kawamura T, Suzuki Y, Watanabe S. NMNAT1 Is Essential for Human iPS Cell Differentiation to the Retinal Lineage. Invest Ophthalmol Vis Sci. 2024 Oct 1;65(12):37. doi: 10.1167/iovs.65.12.37. PMID: 39446354
5. Taniue K, Sugawara A, Zeng C, Han H, Gao X, Shimoura Y, Ozeki AN, Onoguchi-Mizutani R, Seki M, Suzuki Y, Hamada M, Akimitsu N. The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons. Nat Commun. 2024 Oct 17;15(1):8684. doi: 10.1038/s41467-024-51981-8. PMID: 39419981
6. Noguchi K, Suzuki H, Abe R, Horiuchi K, Onoguchi-Mizutani R, Akimitsu N, Ogawa S, Akiyama T, Ike Y, Ino Y, Kimura Y, Ryo A, Doi H, Tanaka F, Suzuki Y, Toyoda A, Yamaguchi Y, Takahashi H. Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation. Cell Rep. 2024 Sep 24;43(9):114734. doi: 10.1016/j.celrep.2024.114734. Epub 2024 Sep 15. PMID: 39283744
7. Tomizawa SI, Fellows R, Ono M, Kuroha K, Dočkal I, Kobayashi Y, Minamizawa K, Natsume K, Nakajima K, Hoshi I, Matsuda S, Seki M, Suzuki Y, Aoto K, Saitsu H, Ohbo K. The non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis. Development. 2024 Sep 15;151(18):dev202834. doi: 10.1242/dev.202834. Epub 2024 Sep 17. PMID: 39222051
8. Tateishi S, Hamada K, Emoto N, Abe K, Abe K, Kawasaki Y, Sunohara M, Moriya K, Katayama H, Tsutsumi T, Murakami Y, Suzuki Y, Yotsuyanagi H, Yanagimoto S. Facility wastewater monitoring as an effective tool for pandemic infection control: An experience in COVID-19 pandemic with long-term monitoring. J Infect Chemother. 2025 Jan;31(1):102499. doi: 10.1016/j.jiac.2024.08.014. Epub 2024 Aug 21. PMID: 39173741
9. Maeshima Y, Kataoka TR, Vandenbon A, Hirata M, Takeuchi Y, Suzuki Y, Fukui Y, Kawashima M, Takada M, Ibi Y, Haga H, Morita S, Toi M, Kawaoka S, Kawaguchi K. Intra-patient spatial comparison of non-metastatic and metastatic lymph nodes reveals the reduction of CD169+ macrophages by metastatic breast cancers. EBioMedicine. 2024 Sep;107:105271. doi: 10.1016/j.ebiom.2024.105271. Epub 2024 Aug 21. PMID: 39173531
10. Mukohara F, Iwata K, Ishino T, Inozume T, Nagasaki J, Ueda Y, Suzawa K, Ueno T, Ikeda H, Kawase K, Saeki Y, Kawashima S, Yamashita K, Kawahara Y, Nakamura Y, Honobe-Tabuchi A, Watanabe H, Dansako H, Kawamura T, Suzuki Y, Honda H, Mano H, Toyooka S, Kawazu M, Togashi Y. Somatic mutations in tumor-infiltrating lymphocytes impact on antitumor immunity. Proc Natl Acad Sci U S A. 2024 Aug 27;121(35):e2320189121. doi: 10.1073/pnas.2320189121. Epub 2024 Aug 21. PMID: 39167601
11. Ishizaka A, Koga M, Mizutani T, Suzuki Y, Matano T, Yotsuyanagi H. Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy. BMC Microbiol. 2024 Jul 24;24(1):274. doi: 10.1186/s12866-024-03431-0. PMID: 39044127
12. Nagasawa S, Zenkoh J, Suzuki Y, Suzuki A. Spatial omics technologies for understanding molecular status associated with cancer progression. Cancer Sci. 2024 Oct;115(10):3208-3217. doi: 10.1111/cas.16283. Epub 2024 Jul 23. PMID: 39042942 Review.
13. Debette S, Caro I, Western D, Namba S, Sun N, Kawaguchi S, He Y, Fujita M, Roshchupkin G, D’Aoust T, Duperron MG, Sargurupremraj M, Tsuchida A, Koido M, Ahmadi M, Yang C, Timsina J, Ibanez L, Matsuda K, Suzuki Y, Oda Y, Kanai A, Jandaghi P, Munter HM, Auld D, Astafeva I, Puerta R, Rotter J, Psaty B, Bis J, Longstreth W, Couffinhal T, Garcia-Gonzalez P, Pytel V, Marquié M, Cano A, Boada M, Joliot M, Lathrop M, Le Grand Q, Launer L, Wardlaw J, Heiman M, Ruiz A, Matthews P, Seshadri S, Fornage M, Adams H, Mishra A, Trégouët DA, Okada Y, Kellis M, De Jager P, Tzourio C, Kamatani Y, Matsuda F, Cruchaga C. Proteogenomics in cerebrospinal fluid and plasma reveals new biological fingerprint of cerebral small vessel disease. Res Sq [Preprint]. 2024 Jul 2:rs.3.rs-4535534. doi: 10.21203/rs.3.rs-4535534/v1. PMID: 39011113 Preprint.
14. Eldeeb D, Okada H, Suzuki Y, Seki M, Tanaka J, Mishima K, Chung UI, Ohba S, Hojo H. Exploring the role of DNMT1 in dental papilla cell fate specification during mouse tooth germ development through integrated single-cell transcriptomics and bulk RNA sequencing. J Oral Biosci. 2024 Sep;66(3):530-538. doi: 10.1016/j.job.2024.06.010. Epub 2024 Jun 26. PMID: 38942194
15. Fujita S, Plianchaisuk A, Deguchi S, Ito H, Nao N, Wang L, Nasser H, Tamura T, Kimura I, Kashima Y, Suzuki R, Suzuki S, Kida I, Tsuda M, Oda Y, Hashimoto R, Watanabe Y, Uriu K, Yamasoba D, Guo Z, Hinay AA Jr, Kosugi Y, Chen L, Pan L, Kaku Y, Chu H, Donati F, Temmam S, Eloit M, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Suzuki Y; Genotype to Phenotype Japan (G2P-Japan) Consortium; Ito J, Ikeda T, Tanaka S, Matsuno K, Fukuhara T, Takayama K, Sato K. Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236. EBioMedicine. 2024 Jun;104:105181. doi: 10.1016/j.ebiom.2024.105181. Epub 2024 Jun 4. PMID: 38838469
16. Wang Y, Tsukioka D, Oda S, Suzuki MG, Suzuki Y, Mitani H, Aoki F. Involvement of H2A variants in DNA damage response of zygotes. Cell Death Discov. 2024 May 14;10(1):231. doi: 10.1038/s41420-024-01999-0. PMID: 38744857
17. Iwahashi N, Umakoshi H, Fujita M, Fukumoto T, Ogasawara T, Yokomoto-Umakoshi M, Kaneko H, Nakao H, Kawamura N, Uchida N, Matsuda Y, Sakamoto R, Seki M, Suzuki Y, Nakatani K, Izumi Y, Bamba T, Oda Y, Ogawa Y. Single-cell and spatial transcriptomics analysis of human adrenal aging. Mol Metab. 2024 Jun;84:101954. doi: 10.1016/j.molmet.2024.101954. Epub 2024 May 6. PMID: 38718896
18. Hara T, Meng S, Sato H, Tatekawa S, Sasaki K, Takeda Y, Tsuji Y, Arao Y, Ofusa K, Kitagawa T, Yamada D, Takahashi H, Kobayashi S, Motooka D, Suzuki Y, Rennie S, Uchida S, Mori M, Ogawa K, Doki Y, Eguchi H, Ishii H. High N6-methyladenosine-activated TCEAL8 mRNA is a novel pancreatic cancer marker. Cancer Sci. 2024 Jul;115(7):2360-2370. doi: 10.1111/cas.16152. Epub 2024 Apr 24. PMID: 38659235
19. Naoi Y, Morinaga T, Nagasaki J, Ariyasu R, Ueda Y, Yamashita K, Zhou W, Kawashima S, Kawase K, Honobe-Tabuchi A, Ohnuma T, Kawamura T, Umeda Y, Kawahara Y, Nakamura Y, Kiniwa Y, Yamasaki O, Fukushima S, Kawazu M, Suzuki Y, Nishikawa H, Hanazawa T, Ando M, Inozume T, Togashi Y. CD106 in Tumor-Specific Exhausted CD8+ T Cells Mediates Immunosuppression by Inhibiting TCR Signaling. Cancer Res. 2024 Jul 2;84(13):2109-2122. doi: 10.1158/0008-5472.CAN-23-0453. PMID: 38635899
20. Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K. Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis. EBioMedicine. 2024 May;103:105102. doi: 10.1016/j.ebiom.2024.105102. Epub 2024 Apr 12. PMID: 38614865
21. Ezura K, Lu Y, Suzuki Y, Mitsuda N, Ariizumi T. Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit. Plant J. 2024 Jun;118(6):2037-2054. doi: 10.1111/tpj.16727. Epub 2024 Apr 5. PMID: 38577750
22. Fukumoto T, Umakoshi H, Iwahashi N, Ogasawara T, Yokomoto-Umakoshi M, Kaneko H, Fujita M, Uchida N, Nakao H, Kawamura N, Matsuda Y, Sakamoto R, Miyazawa T, Seki M, Eto M, Oda Y, Suzuki Y, Ogawa S, Ogawa Y. Steroids-producing nodules: a two-layered adrenocortical nodular structure as a precursor lesion of cortisol-producing adenoma. EBioMedicine. 2024 May;103:105087. doi: 10.1016/j.ebiom.2024.105087. Epub 2024 Apr 2. PMID: 38570222
23. Funaya S, Takahashi Y, Suzuki MG, Suzuki Y, Aoki F. H3.1/3.2 regulate the initial progression of the gene expression program. Nucleic Acids Res. 2024 Jun 24;52(11):6158-6170. doi: 10.1093/nar/gkae214. PMID: 38567720
24. Bai Y, Morita K, Kokaji T, Hatano A, Ohno S, Egami R, Pan Y, Li D, Yugi K, Uematsu S, Inoue H, Inaba Y, Suzuki Y, Matsumoto M, Takahashi M, Izumi Y, Bamba T, Hirayama A, Soga T, Kuroda S. Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity. iScience. 2024 Feb 26;27(3):109121. doi: 10.1016/j.isci.2024.109121. eCollection 2024 Mar 15. PMID: 38524370
25. Xu S, Shiomi H, Yamashita Y, Koyama S, Horie T, Baba O, Kimura M, Nakashima Y, Sowa N, Hasegawa K, Suzuki A, Suzuki Y, Kimura T, Ono K. CRISPR-Cas9-guided amplification-free genomic diagnosis for familial hypercholesterolemia using nanopore sequencing. PLoS One. 2024 Mar 20;19(3):e0297231. doi: 10.1371/journal.pone.0297231. eCollection 2024. PMID: 38507394 Free article.
26. Wattanathavorn W, Seki M, Suzuki Y, Buranapraditkun S, Kitkumthorn N, Sasivimolrattana T, Bhattarakosol P, Chaiwongkot A. Downregulation of LAMB3 Altered the Carcinogenic Properties of Human Papillomavirus 16-Positive Cervical Cancer Cells. Int J Mol Sci. 2024 Feb 22;25(5):2535. doi: 10.3390/ijms25052535. PMID: 38473784 Free PMC article.
27. Yamano K, Haseda A, Iwabuchi K, Osabe T, Sudo Y, Pachakkil B, Tanaka K, Suzuki Y, Toyoda A, Hirakawa H, Onodera Y. QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules. PLoS One. 2024 Feb 23;19(2):e0296675. doi: 10.1371/journal.pone.0296675. eCollection 2024. PMID: 38394294
28. Yamagishi M, Kuze Y, Kobayashi S, Nakashima M, Morishima S, Kawamata T, Makiyama J, Suzuki K, Seki M, Abe K, Imamura K, Watanabe E, Tsuchiya K, Yasumatsu I, Takayama G, Hizukuri Y, Ito K, Taira Y, Nannya Y, Tojo A, Watanabe T, Tsutsumi S, Suzuki Y, Uchimaru K. Mechanisms of action and resistance in histone methylation-targeted therapy. Nature. 2024 Mar;627(8002):221-228. doi: 10.1038/s41586-024-07103-x. Epub 2024 Feb 21. PMID: 38383791
29. Zhou W, Kawashima S, Ishino T, Kawase K, Ueda Y, Yamashita K, Watanabe T, Kawazu M, Dansako H, Suzuki Y, Nishikawa H, Inozume T, Nagasaki J, Togashi Y.Stem-like progenitor and terminally differentiated TFH-like CD4+ T cell exhaustion in the tumor microenvironment. Cell Rep. 2024 Feb 27;43(2):113797. doi: 10.1016/j.celrep.2024.113797. Epub 2024 Feb 15. PMID: 38363680
30. Sato A, Mihirogi Y, Wood C, Suzuki Y, Truebano M, Bishop J. Heterogeneity in maternal mRNAs within clutches of eggs in response to thermal stress during the embryonic stage. BMC Ecol Evol. 2024 Feb 12;24(1):21. doi: 10.1186/s12862-024-02203-8. PMID: 38347459
31. Kunitake K, Motohashi N, Inoue T, Suzuki Y, Aoki Y. Characterization of CD90/Thy-1 as a crucial molecular signature for myogenic differentiation in human urine-derived cells through single-cell RNA sequencing. Sci Rep. 2024 Jan 28;14(1):2329. doi: 10.1038/s41598-024-52530-5. PMID: 38282008
32. Hongo H, Kosaka T, Takayama KI, Baba Y, Yasumizu Y, Ueda K, Suzuki Y, Inoue S, Beltran H, Oya M. G-protein signaling of oxytocin receptor as a potential target for cabazitaxel-resistant prostate cancer. PNAS Nexus. 2024 Jan 4;3(1):pgae002. doi: 10.1093/pnasnexus/pgae002. eCollection 2024 Jan. PMID: 38250514
33. Maruki T, Nomoto H, Iwamoto N, Yamamoto K, Kurokawa M, Iwatsuki-Horimoto K, Yamayoshi S, Suzuki Y, Kawaoka Y, Ohmagari N. Successful management of persistent COVID-19 using combination antiviral therapy (nirmatrelvir/ritonavir and remdesivir) and intravenous immunoglobulin transfusion in an immunocompromised host who had received CD20 depleting therapy for follicular lymphoma. J Infect Chemother. 2024 Jan 17:S1341-321X(24)00012-6. doi: 10.1016/j.jiac.2024.01.008. Online ahead of print. PMID: 38242284
34. Azuma I, Mizuno T, Morita K, Suzuki Y, Kusuhara H. Investigation of the usefulness of liver-specific deconvolution method by establishing a liver benchmark dataset. NAR Genom Bioinform. 2024 Jan 5;6(1):lqad111. doi: 10.1093/nargab/lqad111. eCollection 2024 Mar. PMID: 38187088
35. Sakahara M, Okamoto T, Srivastava U, Natsume Y, Yamanaka H, Suzuki Y, Obama K, Nagayama S, Yao R. Paneth-like cells produced from OLFM4+ stem cells support OLFM4+ stem cell growth in advanced colorectal cancer. Commun Biol. 2024 Jan 5;7(1):27. doi: 10.1038/s42003-023-05504-8. PMID: 38182890
36. Ishizaka A, Koga M, Mizutani T, Yamayoshi S, Iwatsuki-Horimoto K, Adachi E, Suzuki Y, Kawaoka Y, Yotsuyanagi H. Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV. BMC Microbiol. 2024 Jan 3;24(1):6. doi: 10.1186/s12866-023-03157-5. PMID: 38172680
37. Hagihara M, Hayashi H, Nakashima S, Imai Y, Nakano H, Uchida T, Inoue M, Sakai-Tagawa Y, Ito M, Yamayoshi S, Iwatsuki-Horimoto K, Suzuki Y, Kawaoka Y. Clinical Efficacy of Imdevimab/Casirivimab for Persistent Omicron SARS-CoV-2 Infection in Patients with Hematological Malignancies. Intern Med. 2024 Jan 2. doi: 10.2169/internalmedicine.2900-23. Online ahead of print. PMID: 38171874
38. Sato R, Nanasato Y, Takata N, Nagano S, Fukatsu E, Fujino T, Yamaguchi K, Moriguchi Y, Shigenobu S, Suzuki Y, Kasahara M, Ueno S. Efficient selection of a biallelic and nonchimeric gene-edited tree using Oxford Nanopore Technologies sequencing. Tree Physiol. 2024 Feb 11;44(2):tpad158. doi: 10.1093/treephys/tpad158. PMID: 38145493

2023

1. Characterization of a SARS-CoV-2 EG.5.1 clinical isolate in vitro and in vivo. Uraki R, Kiso M, Iwatsuki-Horimoto K, Yamayoshi S, Ito M, Chiba S, Sakai-Tagawa Y, Imai M, Kashima Y, Koga M, Fuwa N, Okumura N, Hojo M, Iwamoto N, Kato H, Nakajima H, Ohmagari N, Yotsuyanagi H, Suzuki Y, Kawaoka Y.Cell Rep. 2023 Dec 26;42(12):113580. doi: 10.1016/j.celrep.2023.113580. Epub 2023 Dec 15.PMID: 38103202
2. Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma.Haga Y, Sakamoto Y, Kajiya K, Kawai H, Oka M, Motoi N, Shirasawa M, Yotsukura M, Watanabe SI, Arai M, Zenkoh J, Shiraishi K, Seki M, Kanai A, Shiraishi Y, Yatabe Y, Matsubara D, Suzuki Y, Noguchi M, Kohno T, Suzuki A. Nat Commun. 2023 Dec 15;14(1):8375. doi: 10.1038/s41467-023-43732-y. PMID: 38102134
3. ABA signaling converts stem cell fate by substantiating a tradeoff between cell polarity, growth and cell cycle progression and abiotic stress responses in the moss Physcomitrium patens. Beier MP, Jinno C, Noda N, Nakamura K, Sugano S, Suzuki Y, Fujita T. Front Plant Sci. 2023 Nov 29;14:1303195. doi: 10.3389/fpls.2023.1303195. eCollection 2023. PMID: 38093991
4. Comprehensive single-cell analysis demonstrates radiotherapy-induced infiltration of macrophages expressing immunosuppressive genes into tumor in esophageal squamous cell carcinoma. Oyoshi H, Du J, Sakai SA, Yamashita R, Okumura M, Motegi A, Hojo H, Nakamura M, Hirata H, Sunakawa H, Kotani D, Yano T, Kojima T, Nakamura Y, Kojima M, Suzuki A, Zenkoh J, Tsuchihara K, Akimoto T, Shibata A, Suzuki Y, Kageyama SI. Sci Adv. 2023 Dec 15;9(50):eadh9069. doi: 10.1126/sciadv.adh9069. Epub 2023 Dec 13. PMID: 38091397
5. Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma. Tamura D, Abe M, Hiraki H, Sasaki N, Yashima-Abo A, Ikarashi D, Kato R, Kato Y, Maekawa S, Kanehira M, Takata R, Maejima K, Sasagawa S, Fujita M, Suzuki Y, Nakagawa H, Iwaya T, Nishizuka SS, Obara W. Cancer Sci. 2024 Feb;115(2):529-539. doi: 10.1111/cas.16025. Epub 2023 Dec 11. PMID: 38083992
6. Mint3-depletion-induced energy stress sensitizes triple-negative breast cancer to chemotherapy via HSF1 inactivation. Tanaka N, Okada H, Yamaguchi K, Seki M, Matsubara D, Gotoh N, Suzuki Y, Furukawa Y, Yamashita T, Inoue JI, Kaneko S, Sakamoto T. Cell Death Dis. 2023 Dec 11;14(12):815. doi: 10.1038/s41419-023-06352-4. PMID: 38081808
7. Progression of adult T-cell leukemia/lymphoma from smoldering to acute type due to branched subclonal evolution. Jimbo K, Yamagishi M, Suzuki Y, Suzuki K, Mizukami M, Yokoyama K, Sato A, Nagamura-Inoue T, Nannya Y, Uchimaru K. EJHaem. 2023 Aug 24;4(4):1188-1190. doi: 10.1002/jha2.776. eCollection 2023 Nov. PMID: 38024629
8. Tumor heterogeneity and immune-evasive T follicular cell lymphoma phenotypes at single-cell resolution. Suma S, Suehara Y, Fujisawa M, Abe Y, Hattori K, Makishima K, Sakamoto T, Sawa A, Bando H, Kaji D, Sugio T, Kato K, Akashi K, Matsue K, Carreras J, Nakamura N, Suzuki A, Suzuki Y, Ito K, Shiiba H, Chiba S, Sakata-Yanagimoto M. Leukemia. 2024 Feb;38(2):340-350. doi: 10.1038/s41375-023-02093-7. Epub 2023 Nov 27. PMID: 38012392
9. An improved method for the highly specific detection of transcription start sites. Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y. Nucleic Acids Res. 2024 Jan 25;52(2):e7. doi: 10.1093/nar/gkad1116. PMID: 37994784
10. Transcriptome profile of subsynaptic myonuclei at the neuromuscular junction in embryogenesis. Ohkawara B, Kurokawa M, Kanai A, Imamura K, Chen G, Zhang R, Masuda A, Higashi K, Mori H, Suzuki Y, Kurokawa K, Ohno K. J Neurochem. 2023 Nov 23. doi: 10.1111/jnc.16013. Online ahead of print. PMID: 37994470
11. FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters. Li M, Nishimura T, Takeuchi Y, Hongu T, Wang Y, Shiokawa D, Wang K, Hirose H, Sasahara A, Yano M, Ishikawa S, Inokuchi M, Ota T, Tanabe M, Tada KI, Akiyama T, Cheng X, Liu CC, Yamashita T, Sugano S, Uchida Y, Chiba T, Asahara H, Nakagawa M, Sato S, Miyagi Y, Shimamura T, Nagai LAE, Kanai A, Katoh M, Nomura S, Nakato R, Suzuki Y, Tojo A, Voon DC, Ogawa S, Okamoto K, Foukakis T, Gotoh N. J Clin Invest. 2023 Nov 15;133(22):e166666. doi: 10.1172/JCI166666. PMID: 37966117
12. Rat Deconvolution as Knowledge Miner for Immune Cell Trafficking from Toxicogenomics Databases. Morita K, Mizuno T, Azuma I, Suzuki Y, Kusuhara H. Toxicol Sci. 2023 Nov 6;197(2):121-31. doi: 10.1093/toxsci/kfad117. Online ahead of print. PMID: 37941435
13. DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle. Maehara H, Kokaji T, Hatano A, Suzuki Y, Matsumoto M, Nakayama KI, Egami R, Tsuchiya T, Ozaki H, Morita K, Shirai M, Li D, Terakawa A, Uematsu S, Hironaka KI, Ohno S, Kubota H, Araki H, Miura F, Ito T, Kuroda S. Sci Rep. 2023 Nov 5;13(1):19118. doi: 10.1038/s41598-023-46393-5. PMID: 37926704
14. Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections. Aso H, Ito J, Ozaki H, Kashima Y, Suzuki Y, Koyanagi Y, Sato K. Gigascience. 2022 Dec 28;12:giad086. doi: 10.1093/gigascience/giad086. PMID: 37848618
15. HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation. Kuwayama N, Kujirai T, Kishi Y, Hirano R, Echigoya K, Fang L, Watanabe S, Nakao M, Suzuki Y, Ishiguro KI, Kurumizaka H, Gotoh Y. Nat Commun. 2023 Oct 12;14(1):6420. doi: 10.1038/s41467-023-42094-9. PMID: 37828010
16. Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan. Kashima Y, Mizutani T, Okimoto Y, Maeda M, Musashino K, Nishide RI, Matsukura A, Nagase J, Suzuki Y. DNA Res. 2023 Oct 1;30(5):dsad020. doi: 10.1093/dnares/dsad020. PMID: 37712596
17. A single-nucleotide substitution of CjTKPR1 determines pollen production in the gymnosperm plant Cryptomeria japonica. Kakui H, Ujino-Ihara T, Hasegawa Y, Tsurisaki E, Futamura N, Iwai J, Higuchi Y, Fujino T, Suzuki Y, Kasahara M, Yamaguchi K, Shigenobu S, Otani M, Nakano M, Nameta M, Shibata S, Ueno S, Moriguchi Y. PNAS Nexus. 2023 Aug 8;2(8):pgad236. doi: 10.1093/pnasnexus/pgad236. eCollection 2023 Aug. PMID: 37559748
18. Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways. Du J, Kageyama SI, Yamashita R, Tanaka K, Okumura M, Motegi A, Hojo H, Nakamura M, Hirata H, Sunakawa H, Kotani D, Yano T, Kojima T, Hamaya Y, Kojima M, Nakamura Y, Suzuki A, Suzuki Y, Tsuchihara K, Akimoto T. Commun Biol. 2023 Aug 5;6(1):818. doi: 10.1038/s42003-023-05080-x. PMID: 37543704
19. Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5. Tamura T, Yamasoba D, Oda Y, Ito J, Kamasaki T, Nao N, Hashimoto R, Fujioka Y, Suzuki R, Wang L, Ito H, Kashima Y, Kimura I, Kishimoto M, Tsuda M, Sawa H, Yoshimatsu K, Yamamoto Y, Nagamoto T, Kanamune J, Suzuki Y, Ohba Y; Genotype to Phenotype Japan (G2P-Japan) Consortium; Yokota I, Matsuno K, Takayama K, Tanaka S, Sato K, Fukuhara T. Commun Biol. 2023 Jul 24;6(1):772. doi: 10.1038/s42003-023-05081-w. PMID: 37488344
20. TIMP3 promotes the maintenance of neural stem-progenitor cells in the mouse subventricular zone. Fang L, Kuniya T, Harada Y, Yasuda O, Maeda N, Suzuki Y, Kawaguchi D, Gotoh Y. Front Neurosci. 2023 Jun 28;17:1149603. doi: 10.3389/fnins.2023.1149603. eCollection 2023. PMID: 37456993
21. Research article antibody induction and immune response in nasal cavity by third dose of SARS-CoV-2 mRNA vaccination. Ishizaka A, Koga M, Mizutani T, Uraki R, Yamayoshi S, Iwatsuki-Horimoto K, Yamamoto S, Imai M, Tsutsumi T, Suzuki Y, Kawaoka Y, Yotsuyanagi H. Virol J. 2023 Jul 13;20(1):146. doi: 10.1186/s12985-023-02113-z. PMID: 37443091
22. Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex. Kawaguchi YW, Tsuchikane Y, Tanaka K, Taji T, Suzuki Y, Toyoda A, Ito M, Watano Y, Nishiyama T, Sekimoto H, Tsuchimatsu T. Genome Biol Evol. 2023 Aug 1;15(8):evad115. doi: 10.1093/gbe/evad115. PMID: 37348049
23. Efficacy of antivirals and mRNA vaccination against an XBF clinical isolate. Uraki R, Ito M, Kiso M, Yamayoshi S, Iwatsuki-Horimoto K, Sakai-Tagawa Y, Imai M, Koga M, Yamamoto S, Adachi E, Saito M, Tsutsumi T, Otani A, Kashima Y, Kikuchi T, Theiler J, Yotsuyanagi H, Suzuki Y, Korber B, Kawaoka Y. Lancet Reg Health West Pac. 2023 May;34:100777. doi: 10.1016/j.lanwpc.2023.100777. Epub 2023 May 11. PMID: 37193320
24. Long-term safety and efficacy of mogamulizumab (anti-CCR4) for treating virus-associated myelopathy. Sato T, Yamauchi J, Yagishita N, Araya N, Takao N, Ohta Y, Inoue E, Takahashi M, Yamagishi M, Suzuki Y, Uchimaru K, Matsumoto N, Hasegawa Y, Yamano Y. Brain. 2023 Aug 1;146(8):3181-3191. doi: 10.1093/brain/awad139. PMID: 37093965
25. Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma. Kitagawa A, Osawa T, Noda M, Kobayashi Y, Aki S, Nakano Y, Saito T, Shimizu D, Komatsu H, Sugaya M, Takahashi J, Kosai K, Takao S, Motomura Y, Sato K, Hu Q, Fujii A, Wakiyama H, Tobo T, Uchida H, Sugimachi K, Shibata K, Utsunomiya T, Kobayashi S, Ishii H, Hasegawa T, Masuda T, Matsui Y, Niida A, Soga T, Suzuki Y, Miyano S, Aburatani H, Doki Y, Eguchi H, Mori M, Nakayama KI, Shimamura T, Shibata T, Mimori K. Br J Cancer. 2023 Jun;128(12):2206-2217. doi: 10.1038/s41416-023-02256-4. Epub 2023 Apr 19. PMID: 37076565
26. Masculinizer is not post-transcriptionally regulated by female-specific piRNAs during sex determination in the Asian corn borer, Ostrinia furnacalis. Fukui T, Shoji K, Kiuchi T, Suzuki Y, Katsuma S. Insect Biochem Mol Biol. 2023 May;156:103946. doi: 10.1016/j.ibmb.2023.103946. Epub 2023 Apr 17. PMID: 37075905
27. The histone H3K36 demethylase Fbxl11 plays pivotal roles in the development of retinal late-born cell types. Iwagawa T, Fukushima M, Takeuchi S, Kawamura Y, Aihara Y, Ozawa M, Yakushiji-Kaminatsui N, Aihara M, Koseki H, Suzuki Y, Watanabe S. Genes Cells. 2023 Jul;28(7):482-495. doi: 10.1111/gtc.13028. Epub 2023 Apr 19. PMID: 37073980
28. The dataset of de novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo, a bloom-forming, cosmopolitan raphidophyte. Sato M, Seki M, Suzuki Y, Ueki S. Data Brief. 2023 Mar 22;48:109071. doi: 10.1016/j.dib.2023.109071. eCollection 2023 Jun. PMID: 37066092
29. Condensed but liquid-like domain organization of active chromatin regions in living human cells. Nozaki T, Shinkai S, Ide S, Higashi K, Tamura S, Shimazoe MA, Nakagawa M, Suzuki Y, Okada Y, Sasai M, Onami S, Kurokawa K, Iida S, Maeshima K. Sci Adv. 2023 Apr 5;9(14):eadf1488. doi: 10.1126/sciadv.adf1488. Epub 2023 Apr 5. PMID: 37018405
30. Stem cell-based modeling and single-cell multiomics reveal gene-regulatory mechanisms underlying human skeletal development. Tani S, Okada H, Onodera S, Chijimatsu R, Seki M, Suzuki Y, Xin X, Rowe DW, Saito T, Tanaka S, Chung UI, Ohba S, Hojo H. Cell Rep. 2023 Apr 25;42(4):112276. doi: 10.1016/j.celrep.2023.112276. Epub 2023 Mar 24. PMID: 36965484
31. Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures. Ito Y, Uda S, Kokaji T, Hirayama A, Soga T, Suzuki Y, Kuroda S, Kubota H. Sci Rep. 2023 Mar 23;13(1):4758. doi: 10.1038/s41598-023-31547-2. PMID: 36959243
32. Mixed Response to Cancer Immunotherapy is Driven by Intratumor Heterogeneity and Differential Interlesion Immune Infiltration. Morinaga T, Inozume T, Kawazu M, Ueda Y, Sax N, Yamashita K, Kawashima S, Nagasaki J, Ueno T, Lin J, Ohara Y, Kuwata T, Yukami H, Kawazoe A, Shitara K, Honobe-Tabuchi A, Ohnuma T, Kawamura T, Umeda Y, Kawahara Y, Nakamura Y, Kiniwa Y, Morita A, Ichihara E, Kiura K, Enokida T, Tahara M, Hasegawa Y, Mano H, Suzuki Y, Nishikawa H, Togashi Y. Cancer Res Commun. 2022 Jul 28;2(7):739-753. doi: 10.1158/2767-9764.CRC-22-0050. eCollection 2022 Jul. PMID: 36923281
33. B cell receptor repertoire analysis from autopsy samples of COVID-19 patients. Iwabuchi S, Tsukahara T, Okayama T, Kitabatake M, Motobayashi H, Shichino S, Imafuku T, Yamaji K, Miyamoto K, Tamura S, Ueha S, Ito T, Murata SI, Kondo T, Ikeo K, Suzuki Y, Matsushima K, Kohara M, Torigoe T, Yamaue H, Hashimoto S. Front Immunol. 2023 Feb 23;14:1034978. doi: 10.3389/fimmu.2023.1034978. eCollection 2023. PMID: 36911681
34. Efficacy of antivirals and bivalent mRNA vaccines against SARS-CoV-2 isolate CH.1.1. Uraki R, Ito M, Kiso M, Yamayoshi S, Iwatsuki-Horimoto K, Sakai-Tagawa Y, Furusawa Y, Imai M, Koga M, Yamamoto S, Adachi E, Saito M, Tsutsumi T, Otani A, Kashima Y, Kikuchi T, Yotsuyanagi H, Suzuki Y, Kawaoka Y. Lancet Infect Dis. 2023 May;23(5):525-526. doi: 10.1016/S1473-3099(23)00132-9. Epub 2023 Mar 7. PMID: 36898405
35. Regulation of MEK inhibitor selumetinib sensitivity by AKT phosphorylation in the novel BRAF L525R mutant. Nakai C, Mimaki S, Matsushima K, Shinozaki E, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shitara K, Bando H, Suzuki Y, Akagi K, Nomura S, Fujii S, Sugiyama M, Nishida N, Mizokami M, Koh Y, Koshizaka T, Okada H, Abe Y, Ohtsu A, Yoshino T, Tsuchihara K. Int J Clin Oncol. 2023 May;28(5):654-663. doi: 10.1007/s10147-023-02318-w. Epub 2023 Mar 1. PMID: 36856908
36. Prognostic analysis of smoldering ATLL with skin eruptions based on genomic aberrations. Mochida K, Nakahata S, Suzuki Y, Inoue K, Moriguchi S, Yamashita A, Amano M, Morishita K. J Dermatol Sci. 2023 Feb;109(2):80-88. doi: 10.1016/j.jdermsci.2023.02.001. Epub 2023 Feb 14. PMID: 36842846
37. Detection of Pretreatment Circulating Tumor DNA Predicts Recurrence after High-Dose Proton Beam Therapy for Early-Stage Non-Small Cell Lung Cancer. Nakamura M, Kageyama SI, Hirata H, Tochinai T, Hojo H, Motegi A, Kanai A, Suzuki Y, Tsuchihara K, Akimoto T. Int J Radiat Oncol Biol Phys. 2023 Aug 1;116(5):1085-1090. doi: 10.1016/j.ijrobp.2023.02.021. Epub 2023 Feb 22. PMID: 36822372
38. Optogenetic decoding of Akt2-regulated metabolic signaling pathways in skeletal muscle cells using transomics analysis. Kawamura G, Kokaji T, Kawata K, Sekine Y, Suzuki Y, Soga T, Ueda Y, Endo M, Kuroda S, Ozawa T. Sci Signal. 2023 Feb 21;16(773):eabn0782. doi: 10.1126/scisignal.abn0782. Epub 2023 Feb 21. PMID: 36809024
39. Long-Read Whole-Genome Sequencing Using a Nanopore Sequencer and Detection of Structural Variants in Cancer Genomes. Haga Y, Sakamoto Y, Arai M, Suzuki Y, Suzuki A. Methods Mol Biol. 2023;2632:177-189. doi: 10.1007/978-1-0716-2996-3_13. PMID: 36781729
40. De Novo Genome Assembly of Japanese Black Cattle as Model of an Economically Relevant Animal.Sasaki S, Haga Y, Wakaguri H, Abe K, Suzuki Y. Methods Mol Biol. 2023;2632:41-55. doi: 10.1007/978-1-0716-2996-3_4. PMID: 36781720
41. Staphylococcus aureus MazG hydrolyzes oxidized guanine nucleotides and contributes to oxidative stress resistance.Nigo F, Nakagawa R, Hirai Y, Imai L, Suzuki Y, Furuta K, Kaito C. Biochimie. 2023 Jun;209:52-60. doi: 10.1016/j.biochi.2023.02.001. Epub 2023 Feb 4. PMID: 36746255
42. Multimodal single-cell analyses of peripheral blood mononuclear cells of COVID-19 patients in Japan. Kashima Y, Mizutani T, Nakayama-Hosoya K, Moriyama S, Matsumura T, Yoshimura Y, Sasaki H, Horiuchi H, Miyata N, Miyazaki K, Tachikawa N, Takahashi Y, Suzuki T, Sugano S, Matano T, Kawana-Tachikawa A, Suzuki Y. Sci Rep. 2023 Feb 2;13(1):1935. doi: 10.1038/s41598-023-28696-9. PMID: 36732528
43. Murine breast cancers disorganize the liver transcriptome in a zonated manner. Vandenbon A, Mizuno R, Konishi R, Onishi M, Masuda K, Kobayashi Y, Kawamoto H, Suzuki A, He C, Nakamura Y, Kawaguchi K, Toi M, Shimizu M, Tanaka Y, Suzuki Y, Kawaoka S. Commun Biol. 2023 Jan 24;6(1):97. doi: 10.1038/s42003-023-04479-w. PMID: 36694005
44. Mutated genes on ctDNA detecting postoperative recurrence presented reduced neoantigens in primary tumors in colorectal cancer cases. Nagayama S, Kobayashi Y, Fukunaga M, Sakimura S, Sugimachi K, Sasaki S, Masuda T, Mafune KI, Oshima M, Shibata T, Suzuki Y, Mimori K. Sci Rep. 2023 Jan 24;13(1):1366. doi: 10.1038/s41598-023-28575-3. PMID: 36693917
45. Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer. Ozato Y, Kojima Y, Kobayashi Y, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Kagawa K, Goto Y, Utou M, Fukunaga M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Niida A, Hirose H, Hayashi S, Koseki J, Oki E, Fukuchi S, Murakami K, Tobo T, Nagayama S, Uemura M, Sakamoto T, Oshima M, Doki Y, Eguchi H, Mori M, Iwasaki T, Oda Y, Shibata T, Suzuki Y, Shimamura T, Mimori K. Cell Rep. 2023 Jan 31;42(1):111929. doi: 10.1016/j.celrep.2022.111929. Epub 2023 Jan 18. PMID: 36656712
46. Establishment of experimental salivary gland cancer models using organoid culture and patient-derived xenografting. Aizawa Y, Takada K, Aoyama J, Sano D, Yamanaka S, Seki M, Kuze Y, Ramilowski JA, Okuda R, Ueno Y, Nojima Y, Inayama Y, Hatakeyama H, Hatano T, Takahashi H, Nishimura G, Fujii S, Suzuki Y, Taniguchi H, Oridate N. Cell Oncol (Dordr). 2023 Apr;46(2):409-421. doi: 10.1007/s13402-022-00758-6. Epub 2022 Dec 20. PMID: 36538240
47. A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium. Sekimoto H, Komiya A, Tsuyuki N, Kawai J, Kanda N, Ootsuki R, Suzuki Y, Toyoda A, Fujiyama A, Kasahara M, Abe J, Tsuchikane Y, Nishiyama T. New Phytol. 2023 Mar;237(5):1636-1651. doi: 10.1111/nph.18662. Epub 2023 Jan 9. PMID: 36533897
48. Direct Reprogramming Improves Cardiac Function and Reverses Fibrosis in Chronic Myocardial Infarction. Tani H, Sadahiro T, Yamada Y, Isomi M, Yamakawa H, Fujita R, Abe Y, Akiyama T, Nakano K, Kuze Y, Seki M, Suzuki Y, Fujisawa M, Sakata-Yanagimoto M, Chiba S, Fukuda K, Ieda M. Circulation. 2023 Jan 17;147(3):223-238. doi: 10.1161/CIRCULATIONAHA.121.058655. Epub 2022 Dec 12.PMID: 36503256
49. Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines. Hamaya Y, Suzuki A, Suzuki Y, Tsuchihara K, Yamashita R. Jpn J Clin Oncol. 2023 Jan 28;53(2):97-104. doi: 10.1093/jjco/hyac175. PMID: 36465011

2022

1. Single-cell RNA sequencing unravels heterogeneity of skeletal progenitors and cell-cell interactions underlying the bone repair process. Nakayama M, Okada H, Seki M, Suzuki Y, Chung UI, Ohba S, Hojo H. Regen Ther. 2022 May 18;21:9-18. doi: 10.1016/j.reth.2022.05.001. eCollection 2022 Dec. PMID: 35619947
2. Lack of Hikeshi activates HSF1 activity under normal conditions and disturbs the heat-shock response. Kose S, Imai K, Watanabe A, Nakai A, Suzuki Y, Imamoto N. Life Sci Alliance. 2022 May 17;5(9):e202101241. doi: 10.26508/lsa.202101241. Print 2022 Sep. PMID: 35580988
3. Intensive single-cell analysis reveals immune-cell diversity among healthy individuals. Kashima Y, Kaneko K, Reteng P, Yoshitake N, Runtuwene LR, Nagasawa S, Onishi M, Seki M, Suzuki A, Sugano S, Sakata-Yanagimoto M, Imai Y, Nakayama-Hosoya K, Kawana-Tachikawa A, Mizutani T, Suzuki Y. Life Sci Alliance. 2022 Apr 5;5(7):e202201398. doi: 10.26508/lsa.202201398. Print 2022 Jul. PMID: 35383111
4. The 3′ Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies. Suzuki H, Abe R, Shimada M, Hirose T, Hirose H, Noguchi K, Ike Y, Yasui N, Furugori K, Yamaguchi Y, Toyoda A, Suzuki Y, Yamamoto T, Saitoh N, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Takahashi H. Nat Commun. 2022 May 25;13(1):2905. doi: 10.1038/s41467-022-30632-w. PMID: 35614107
5. Differing impact of phosphoglycerate mutase 1-deficiency on brown and white adipose tissue. Yoshida Y, Shimizu I, Hsiao YT, Suda M, Katsuumi G, Seki M, Suzuki Y, Okuda S, Soga T, Minamino T. iScience. 2022 Apr 18;25(5):104268. doi: 10.1016/j.isci.2022.104268. eCollection 2022 May 20. PMID: 35521515
6. Multiomics identifies the link between intratumor steatosis and the exhausted tumor immune microenvironment in hepatocellular carcinoma. Murai H, Kodama T, Maesaka K, Tange S, Motooka D, Suzuki Y, Shigematsu Y, Inamura K, Mise Y, Saiura A, Ono Y, Takahashi Y, Kawasaki Y, Iino S, Kobayashi S, Idogawa M, Tokino T, Hashidate-Yoshida T, Shindou H, Miyazaki M, Imai Y, Tanaka S, Mita E, Ohkawa K, Hikita H, Sakamori R, Tatsumi T, Eguchi H, Morii E, Takehara T. Hepatology. 2022 May 14. doi: 10.1002/hep.32573. Online ahead of print. PMID: 3556754
7. Dengue fever as a reemerging disease in upper Egypt: Diagnosis, vector surveillance and genetic diversity using RT-LAMP assay. Gaber M, Ahmad AA, El-Kady AM, Tolba M, Suzuki Y, Mohammed SM, Elossily NA. PLoS One. 2022 May 2;17(5):e0265760. doi: 10.1371/journal.pone.0265760. eCollection 2022. PMID: 35499983
8. Oppositional poly(A) tail length regulation by FMRP and CPEB1. Shin J, Paek KY, Chikhaoui L, Jung S, Ponny S, Suzuki Y, Padmanabhan K, Richter JD. RNA. 2022 May;28(5):756-765. doi: 10.1261/rna.079050.121. Epub 2022 Feb 25. PMID: 35217597
9. Correlation Analysis between Gut Microbiota Alterations and the Cytokine Response in Patients with Coronavirus Disease during Hospitalization. Mizutani T, Ishizaka A, Koga M, Ikeuchi K, Saito M, Adachi E, Yamayoshi S, Iwatsuki-Horimoto K, Yasuhara A, Kiyono H, Matano T, Suzuki Y, Tsutsumi T, Kawaoka Y, Yotsuyanagi H. Microbiol Spectr. 2022 Apr 27;10(2):e0168921. doi: 10.1128/spectrum.01689-21. Epub 2022 Mar 7. PMID: 35254122
10. Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice. Jangid A, Fukuda S, Suzuki Y, Taylor TD, Ohno H, Prakash T. Sci Rep. 2022 Apr 25;12(1):6748. doi: 10.1038/s41598-022-10762-3. PMID: 35468931
11. Glycoprotein nonmetastatic melanoma protein B regulates lysosomal integrity and lifespan of senescent cells. Suda M, Shimizu I, Katsuumi G, Hsiao CL, Yoshida Y, Matsumoto N, Yoshida Y, Katayama A, Wada J, Seki M, Suzuki Y, Okuda S, Ozaki K, Nakanishi-Matsui M, Minamino T. Sci Rep. 2022 Apr 20;12(1):6522. doi: 10.1038/s41598-022-10522-3. PMID: 35444208
12. OCT1-target neural gene PFN2 promotes tumor growth in androgen receptor-negative prostate cancer. Obinata D, Funakoshi D, Takayama K, Hara M, Niranjan B, Teng L, Lawrence MG, Taylor RA, Risbridger GP, Suzuki Y, Takahashi S, Inoue S. Sci Rep. 2022 Apr 12;12(1):6094. doi: 10.1038/s41598-022-10099-x. PMID: 35413990
13. Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism. Chong YK, Tartey S, Yoshikawa Y, Imami K, Li S, Yoshinaga M, Hirabayashi A, Liu G, Vandenbon A, Hia F, Uehata T, Mino T, Suzuki Y, Noda T, Ferrandon D, Standley DM, Ishihama Y, Takeuchi O. Sci Signal. 2022 Apr 12;15(729):eabm5011. doi: 10.1126/scisignal.abm5011. Epub 2022 Apr 12. PMID: 35412849
14. Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms. Chiba A, Seki M, Suzuki Y, Kinjo Y, Mizunoe Y, Sugimoto S. NPJ Biofilms Microbiomes. 2022 Apr 4;8(1):17. doi: 10.1038/s41522-022-00278-z. PMID: 35379830
15. Retraction: Transcriptome analysis reveals a role for the endothelial ANP-GC-A signaling in interfering with pre-metastatic niche formation by solid cancers. Nojiri T, Arai M, Suzuki Y, Kumazoe M, Tokudome T, Miura K, Hino J, Hosoda H, Miyazato M, Okumura M, Kawaoka S, Kangawa K. Oncotarget. 2022 Mar 24;13:551-552. doi: 10.18632/oncotarget.28223. eCollection 2022. PMID: 35359748
16. Preoperative Chemoradiotherapy plus Nivolumab before Surgery in Patients with Microsatellite Stable and Microsatellite Instability-High Locally Advanced Rectal Cancer. Bando H, Tsukada Y, Inamori K, Togashi Y, Koyama S, Kotani D, Fukuoka S, Yuki S, Komatsu Y, Homma S, Taketomi A, Uemura M, Kato T, Fukui M, Wakabayashi M, Nakamura N, Kojima M, Kawachi H, Kirsch R, Yoshida T, Suzuki Y, Sato A, Nishikawa H, Ito M, Yoshino T. Clin Cancer Res. 2022 Mar 15;28(6):1136-1146. doi: 10.1158/1078-0432.CCR-21-3213. PMID: 35063964
17. Clonal Selection and Evolution of HTLV-1-Infected Cells Driven by Genetic and Epigenetic Alteration. Yamagishi M, Suzuki Y, Watanabe T, Uchimaru K. Viruses. 2022 Mar 12;14(3):587. doi: 10.3390/v14030587. PMID: 35336993
18. Efficient prediction of a spatial transcriptomics profile better characterizes breast cancer tissue sections without costly experimentation. Monjo T, Koido M, Nagasawa S, Suzuki Y, Kamatani Y. Sci Rep. 2022 Mar 8;12(1):4133. doi: 10.1038/s41598-022-07685-4. PMID: 35260632
19. Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing. Zaha S, Sakamoto Y, Nagasawa S, Sugano S, Suzuki A, Suzuki Y, Seki M. Bio Protoc. 2022 Mar 5;12(5):e4345. doi: 10.21769/BioProtoc.4345. eCollection 2022 Mar 5. PMID: 35592605
20. TSS-seq of Toxoplasma gondii sporozoites revealed a novel motif in stage-specific promoters. Kidaka T, Sugi T, Hayashida K, Suzuki Y, Xuan X, Dubey JP, Yamagishi J. Infect Genet Evol. 2022 Mar;98:105213. doi: 10.1016/j.meegid.2022.105213. Epub 2022 Jan 15. PMID: 35041968
21. Spatial and single-cell transcriptome analysis reveals changes in gene expression in response to drug perturbation in rat kidney. Onoda N, Kawabata A, Hasegawa K, Sakakura M, Urakawa I, Seki M, Zenkoh J, Suzuki A, Suzuki Y. DNA Res. 2022 Feb 27;29(2):dsac007. doi: 10.1093/dnares/dsac007. PMID: 35325072
22. Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. Uematsu S, Ohno S, Tanaka KY, Hatano A, Kokaji T, Ito Y, Kubota H, Hironaka KI, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S. iScience. 2022 Feb 4;25(2):103787. doi: 10.1016/j.isci.2022.103787. eCollection 2022 Feb 18. PMID: 35243212
23. Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing. Runtuwene LR, Sathirapongsasuti N, Srisawat R, Komalamisra N, Tuda JSB, Mongan AE, Aboge GO, Shabardina V, Makalowski W, Nesti DR, Artama WT, Nguyen-Thi LA, Wan KL, Na BK, Hall W, Pain A, Eshita Y, Maeda R, Yamagishi J, Suzuki Y. BMC Res Notes. 2022 Feb 12;15(1):44. doi: 10.1186/s13104-022-05927-2. PMID: 35151353
24. Impact of dietary fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion. Jangid A, Fukuda S, Kato T, Seki M, Suzuki Y, Taylor TD, Ohno H, Prakash T. 3 Biotech. 2022 Feb;12(2):56. doi: 10.1007/s13205-022-03116-3. Epub 2022 Feb 2. PMID: 35186653
25. PD-1 blockade therapy promotes infiltration of tumor-attacking exhausted T cell clonotypes. Nagasaki J, Inozume T, Sax N, Ariyasu R, Ishikawa M, Yamashita K, Kawazu M, Ueno T, Irie T, Tanji E, Morinaga T, Honobe A, Ohnuma T, Yoshino M, Iwata T, Kawase K, Sasaki K, Hanazawa T, Kochin V, Kawamura T, Matsue H, Hino M, Mano H, Suzuki Y, Nishikawa H, Togashi Y. Cell Rep. 2022 Feb 1;38(5):110331. doi: 10.1016/j.celrep.2022.110331. PMID: 35108529
26. TUBB3 E410K Syndrome With Childhood-Onset Nonalcoholic Steatohepatitis. Mori J, Umemura A, Satake W, Cha PC, Suzuki Y, Itoh K, Chiyonobu T. J Clin Endocrinol Metab. 2022 Jan 1;107(1):e38-e43. doi: 10.1210/clinem/dgab628. PMID: 34435630
27. Bile acid dysmetabolism in the gut-microbiota-liver axis under hepatitis C virus infection. Inoue T, Funatsu Y, Ohnishi M, Isogawa M, Kawashima K, Tanaka M, Moriya K, Kawaratani H, Momoda R, Iio E, Nakagawa H, Suzuki Y, Matsuura K, Fujiwara K, Nakajima A, Yoshiji H, Nakayama J, Tanaka Y. Liver Int. 2022 Jan;42(1):124-134. doi: 10.1111/liv.15041. Epub 2021 Sep 5. PMID: 34411400

2021

1. HTLV-1 infection promotes excessive T cell activation and transformation into adult T cell leukemia/lymphoma. Tan BJ, Sugata K, Reda O, Matsuo M, Uchiyama K, Miyazato P, Hahaut V, Yamagishi M, Uchimaru K, Suzuki Y, Ueno T, Suzushima H, Katsuya H, Tokunaga M, Uchiyama Y, Nakamura H, Sueoka E, Utsunomiya A, Ono M, Satou Y. J Clin Invest. 2021 Dec 15;131(24):e150472. doi: 10.1172/JCI150472. PMID: 34907908
2. The proteome, not the transcriptome, predicts that oocyte superovulation affects embryonic phenotypes in mice. Taher L, Israel S, Drexler HCA, Makalowski W, Suzuki Y, Fuellen G, Boiani M. Sci Rep. 2021 Dec 9;11(1):23731. doi: 10.1038/s41598-021-03054-9. PMID: 34887460
3. IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. Ando M, Magi S, Seki M, Suzuki Y, Kasukawa T, Lefaudeux D, Hoffmann A, Okada M. NPJ Syst Biol Appl. 2021 Dec 1;7(1):42. doi: 10.1038/s41540-021-00204-7. PMID: 34853340
4. Gene expression signatures as candidate biomarkers of response to PD-1 blockade in non- small cell lung cancers. Aiba T, Hattori C, Sugisaka J, Shimizu H, Ono H, Domeki Y, Saito R, Kawana S, Kawashima Y, Terayama K, Toi Y, Nakamura A, Yamanda S, Kimura Y, Suzuki Y, Niida A, Sugawara S. PLoS One. 2021 Nov 29;16(11):e0260500. doi: 10.1371/journal.pone.0260500. eCollection 2021. PMID: 34843570
5. Transcriptomic Analysis of the Effects of Chemokine Receptor CXCR3 Deficiency on Immune Responses in the Mouse Brain during Toxoplasma gondii Infection. Umeda K, Goto Y, Watanabe K, Ushio N, Fereig RM, Ihara F, Tanaka S, Suzuki Y, Nishikawa Y. Microorganisms. 2021 Nov 12;9(11):2340. doi: 10.3390/microorganisms9112340. PMID: 34835465
6. Cell cycle arrest determines adult neural stem cell ontogeny by an embryonic Notch- nonoscillatory Hey1 module. Harada Y, Yamada M, Imayoshi I, Kageyama R, Suzuki Y, Kuniya T, Furutachi S, Kawaguchi D, Gotoh Y. Nat Commun. 2021 Nov 12;12(1):6562. doi: 10.1038/s41467-021-26605-0. PMID: 34772946
7. TIGIT/CD155 axis mediates resistance to immunotherapy in patients with melanoma with the inflamed tumor microenvironment. Kawashima S, Inozume T, Kawazu M, Ueno T, Nagasaki J, Tanji E, Honobe A, Ohnuma T, Kawamura T, Umeda Y, Nakamura Y, Kawasaki T, Kiniwa Y, Yamasaki O, Fukushima S, Ikehara Y, Mano H, Suzuki Y, Nishikawa H, Matsue H, Togashi Y. J Immunother Cancer. 2021 Nov;9(11):e003134. doi: 10.1136/jitc-2021-003134. PMID: 34795004
8. The Evolving Genomic Landscape of Esophageal Squamous Cell Carcinoma Under Chemoradiotherapy. Hirata H, Niida A, Kakiuchi N, Uchi R, Sugimachi K, Masuda T, Saito T, Kageyama SI, Motomura Y, Ito S, Yoshitake T, Tsurumaru D, Nishimuta Y, Yokoyama A, Hasegawa T, Chiba K, Shiraishi Y, Du J, Miura F, Morita M, Toh Y, Hirakawa M, Shioyama Y, Ito T, Akimoto T, Miyano S, Shibata T, Mori M, Suzuki Y, Ogawa S, Ishigami K, Mimori K. Cancer Res. 2021 Oct 1;81(19):4926-4938. doi: 10.1158/0008-5472.CAN-21-0653. Epub 2021 Aug 19. PMID: 34413060
9. H3K4me3 histone modification in baculovirus-infected silkworm cells. Shoji K, Kokusho R, Kawamoto M, Suzuki Y, Katsuma S. Virus Genes. 2021 Oct;57(5):459-463. doi: 10.1007/s11262-021-01858-5. Epub 2021 Jun 29. PMID: 34185196
10. Cell shape-based chemical screening reveals an epigenetic network mediated by focal adhesions. Kanazawa T, Michida H, Uchino Y, Ishihara A, Zhang S, Tabata S, Suzuki Y, Imamoto A, Okada M. FEBS J. 2021 Oct;288(19):5613-5628. doi: 10.1111/febs.15840. Epub 2021 Apr 22. PMID: 33768715
11. A combination approach of pseudotime analysis and mathematical modeling for understanding drug-resistant mechanisms. Magi S, Ki S, Ukai M, Domínguez-Hüttinger E, Naito AT, Suzuki Y, Okada M. Sci Rep. 2021 Sep 16;11(1):18511. doi: 10.1038/s41598-021-97887-z. PMID: 34531471
12. Single-Cell Analyses Reveal Diverse Mechanisms of Resistance to EGFR Tyrosine Kinase Inhibitors in Lung Cancer. Kashima Y, Shibahara D, Suzuki A, Muto K, Kobayashi IS, Plotnick D, Udagawa H, Izumi H, Shibata Y, Tanaka K, Fujii M, Ohashi A, Seki M, Goto K, Tsuchihara K, Suzuki Y, Kobayashi SS. Cancer Res. 2021 Sep 15;81(18):4835-4848. doi: 10.1158/0008-5472.CAN-20-2811. Epub 2021 Jul 9. PMID: 34247147
13. Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation. Ishizaka A, Koga M, Mizutani T, Parbie PK, 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. Microbiol Spectr. 2021 Sep 3;9(1):e0070821. doi: 10.1128/Spectrum.00708-21. Epub 2021 Aug 11. PMID: 34378948
14. Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis. Yuasa H, Kajitani R, Nakamura Y, Takahashi K, Okuno M, Kobayashi F, Shinoda T, Toyoda A, Suzuki Y, Thongtham N, Forsman Z, Bronstein O, Seveso D, Montalbetti E, Taquet C, Eyal G, Yasuda N, Itoh T. DNA Res. 2021 Aug 25;28(4):dsab012. doi: 10.1093/dnares/dsab012. PMID: 34387305
15. Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing. Sakamoto Y, Zaha S, Nagasawa S, Miyake S, Kojima Y, Suzuki A, Suzuki Y, Seki M. Nucleic Acids Res. 2021 Aug 20;49(14):e81. doi: 10.1093/nar/gkab397. PMID: 34019650
16. Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma. Yamagishi M, Kubokawa M, Kuze Y, Suzuki A, Yokomizo A, Kobayashi S, Nakashima M, Makiyama J, Iwanaga M, Fukuda T, Watanabe T, Suzuki Y, Uchimaru K. Nat Commun. 2021 Aug 10;12(1):4821. doi: 10.1038/s41467-021-25101-9. PMID: 34376672
17. Predictive markers based on transcriptome modules for vinorelbine-based adjuvant chemotherapy for lung adenocarcinoma patients. Nakasone S, Suzuki A, Okazaki H, Onodera K, Zenkoh J, Ishii G, Suzuki Y, Tsuboi M, Tsuchihara K. Lung Cancer. 2021 Aug;158:115-125. doi: 10.1016/j.lungcan.2021.06.011. Epub 2021 Jun 10. PMID: 34157583
18. Application of long-read sequencing to the detection of structural variants in human cancer genomes. Sakamoto Y, Zaha S, Suzuki Y, Seki M, Suzuki A. Comput Struct Biotechnol J. 2021 Jul 28;19:4207-4216. doi: 10.1016/j.csbj.2021.07.030. eCollection 2021. PMID: 34527193
19. Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition. Nagasawa S, Kashima Y, Suzuki A, Suzuki Y. Inflamm Regen. 2021 Jul 16;41(1):22. doi: 10.1186/s41232-021-00170-x. PMID: 34271973
20. m6 A-mediated alternative splicing coupled with nonsense-mediated mRNA decay regulates SAM synthetase homeostasis. Watabe E, Togo-Ohno M, Ishigami Y, Wani S, Hirota K, Kimura-Asami M, Hasan S, Takei S, Fukamizu A, Suzuki Y, Suzuki T, Kuroyanagi H. EMBO J. 2021 Jul 15;40(14):e106434. doi: 10.15252/embj.2020106434. Epub 2021 Jun 21. PMID: 34152017
21. Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy-Refractory Cancer Growth. Takayama KI, Honma T, Suzuki T, Kondoh Y, Osada H, Suzuki Y, Yoshida M, Inoue S. Cancer Res. 2021 Jul 1;81(13):3495-3508. doi: 10.1158/0008-5472.CAN-20-3819. Epub 2021 May 11. PMID: 33975881
22. Maintenance of neural stem-progenitor cells by the lysosomal biosynthesis regulators TFEB and TFE3 in the embryonic mouse telencephalon. Yuizumi N, Harada Y, Kuniya T, Sunabori T, Koike M, Wakabayashi M, Ishihama Y, Suzuki Y, Kawaguchi D, Gotoh Y. Stem Cells. 2021 Jul;39(7):929-944. doi: 10.1002/stem.3359. Epub 2021 Mar 10. PMID: 33609411
23. A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. Hirakawa H, Toyoda A, Itoh T, Suzuki Y, Nagano AJ, Sugiyama S, Onodera Y. DNA Res. 2021 Jun 25;28(3):dsab004. doi: 10.1093/dnares/dsab004. PMID: 34142133
24. Subtype-specific collaborative transcription factor networks are promoted by OCT4 in the progression of prostate cancer. Takayama KI, Kosaka T, Suzuki T, Hongo H, Oya M, Fujimura T, Suzuki Y, Inoue S. Nat Commun. 2021 Jun 18;12(1):3766. doi: 10.1038/s41467-021-23974-4. PMID: 34145268
25. Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Yoshitake K, Kimura G, Sakami T, Watanabe T, Taniuchi Y, Kakehi S, Kuwata A, Yamaguchi H, Kataoka T, Kawachi M, Ikeo K, Tan E, Igarashi Y, Ohtsubo M, Watabe S, Suzuki Y, Asakawa S, Ishino S, Tashiro K, Ishino Y, Kobayashi T, Mineta K, Gojobori T. Sci Rep. 2021 Jun 9;11(1):12222. doi: 10.1038/s41598-021-91615-3. PMID: 34108585
26. Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L. Mehraj H, Takahashi S, Miyaji N, Akter A, Suzuki Y, Seki M, Dennis ES, Fujimoto R. Front Plant Sci. 2021 Jun 7;12:659634. doi: 10.3389/fpls.2021.659634. eCollection 2021. PMID: 34163501
27. Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants. Shirai K, Sato MP, Nishi R, Seki M, Suzuki Y, Hanada K. Genome Res. 2021 Jun;31(6):1060-1068. doi: 10.1101/gr.271726.120. Epub 2021 May 18. PMID: 34006571
28. Interleukin-6 sensitizes TNF-α and TRAIL/Apo2L dependent cell death through upregulation of death receptors in human cancer cells. Sano E, Kazaana A, Tadakuma H, Takei T, Yoshimura S, Hanashima Y, Ozawa Y, Yoshino A, Suzuki Y, Ueda T. Biochim Biophys Acta Mol Cell Res. 2021 Jun;1868(7):119037. doi: 10.1016/j.bbamcr.2021.119037. Epub 2021 Apr 9. PMID: 33839168
29. A single m6A modification in U6 snRNA diversifies exon sequence at the 5′ splice site. Ishigami Y, Ohira T, Isokawa Y, Suzuki Y, Suzuki T. Nat Commun. 2021 May 28;12(1):3244. doi: 10.1038/s41467-021-23457-6. PMID: 34050143
30. Importance of lymph node immune responses in MSI-H/dMMR colorectal cancer. Inamori K, Togashi Y, Fukuoka S, Akagi K, Ogasawara K, Irie T, Motooka D, Kobayashi Y, Sugiyama D, Kojima M, Shiiya N, Nakamura S, Maruyama S, Suzuki Y, Ito M, Nishikawa H. JCI Insight. 2021 May 10;6(9):e137365. doi: 10.1172/jci.insight.137365. PMID: 33755600
31. Setd1a Plays Pivotal Roles for the Survival and Proliferation of Retinal Progenitors via Histone Modifications of Uhrf1. Deng X, Iwagawa T, Fukushima M, Suzuki Y, Watanabe S. Invest Ophthalmol Vis Sci. 2021 May 3;62(6):1. doi: 10.1167/iovs.62.6.1. PMID: 33938913
32. Identification of novel heat shock-induced long non-coding RNA in human cells. Onoguchi-Mizutani R, Kishi Y, Ogura Y, Nishimura Y, Imamachi N, Suzuki Y, Miyazaki S, Akimitsu N. J Biochem. 2021 Apr 29;169(4):497-505. doi: 10.1093/jb/mvaa126. PMID: 33170212
33. Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus. Maeda T, Takahashi S, Yoshida T, Shimamura S, Takaki Y, Nagai Y, Toyoda A, Suzuki Y, Arimoto A, Ishii H, Satoh N, Nishiyama T, Hasebe M, Maruyama T, Minagawa J, Obokata J, Shigenobu S. Elife. 2021 Apr 27;10:e60176. doi: 10.7554/eLife.60176. PMID: 33902812
34. Tsga8 is required for spermatid morphogenesis and male fertility in mice. Kobayashi Y, Tomizawa SI, Ono M, Kuroha K, Minamizawa K, Natsume K, Dizdarević S, Dočkal I, Tanaka H, Kawagoe T, Seki M, Suzuki Y, Ogonuki N, Inoue K, Matoba S, Anastassiadis K, Mizuki N, Ogura A, Ohbo K. Development. 2021 Apr 15;148(8):dev196212. doi: 10.1242/dev.196212. Epub 2021 Apr 26. PMID: 33766931
35. Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer. Okamoto T, duVerle D, Yaginuma K, Natsume Y, Yamanaka H, Kusama D, Fukuda M, Yamamoto M, Perraudeau F, Srivastava U, Kashima Y, Suzuki A, Kuze Y, Takahashi Y, Ueno M, Sakai Y, Noda T, Tsuda K, Suzuki Y, Nagayama S, Yao R. Stem Cell Reports. 2021 Apr 13;16(4):954-967. doi: 10.1016/j.stemcr.2021.02.012. Epub 2021 Mar 11. PMID: 33711267
36. Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast. Nagasawa S, Kuze Y, Maeda I, Kojima Y, Motoyoshi A, Onishi T, Iwatani T, Yokoe T, Koike J, Chosokabe M, Kubota M, Seino H, Suzuki A, Seki M, Tsuchihara K, Inoue E, Tsugawa K, Ohta T, Suzuki Y. Commun Biol. 2021 Apr 1;4(1):438. doi: 10.1038/s42003-021-01959-9. PMID: 33795819
37. Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle. Sasaki S, Watanabe T, Ibi T, Hasegawa K, Sakamoto Y, Moriwaki S, Kurogi K, Ogino A, Yasumori T, Wakaguri H, Muraki E, Miki Y, Yoshida Y, Inoue Y, Tabuchi I, Iwao K, Arishima T, Kawashima K, Watanabe M, Sugano S, Sugimoto Y, Suzuki Y. Sci Rep. 2021 Mar 23;11(1):6687. doi: 10.1038/s41598-021-86225-y. PMID: 33758295
38. Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle. Egami R, Kokaji T, Hatano A, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka KI, Uematsu S, Terakawa A, Bai Y, Pan Y, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S. iScience. 2021 Feb 20;24(3):102217. doi: 10.1016/j.isci.2021.102217. eCollection 2021 Mar 19. PMID: 33748705
39. Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by regnase-1. Nakatsuka Y, Yaku A, Handa T, Vandenbon A, Hikichi Y, Motomura Y, Sato A, Yoshinaga M, Tanizawa K, Watanabe K, Hirai T, Chin K, Suzuki Y, Uehata T, Mino T, Tsujimura T, Moro K, Takeuchi O. Eur Respir J. 2021 Mar 11;57(3):2000018. doi: 10.1183/13993003.00018-2020. Print 2021 Mar. PMID: 32978308
40. MCM10 compensates for Myc-induced DNA replication stress in breast cancer stem-like cells. Murayama T, Takeuchi Y, Yamawaki K, Natsume T, Li M, Marcela RN, Nishimura T, Kogure Y, Nakata A, Tominaga K, Sasahara A, Yano M, Ishikawa S, Ohta T, Ikeda K, Horie-Inoue K, Inoue S, Seki M, Suzuki Y, Sugano S, Enomoto T, Tanabe M, Tada KI, Kanemaki MT, Okamoto K, Tojo A, Gotoh N. Cancer Sci. 2021 Mar;112(3):1209-1224. doi: 10.1111/cas.14776. Epub 2021 Jan 22. PMID: 33340428
41. A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle. Sasaki S, Miki Y, Ibi T, Wakaguri H, Yoshida Y, Sugimoto Y, Suzuki Y. BMC Genomics. 2021 Feb 6;22(1):107. doi: 10.1186/s12864-021-07415-6. PMID: 33549039
42. CRISPR/Cas9-mediated mutagenesis of Ago2 and Siwi in silkworm cultured cells. Katsuma S, Shoji K, Suzuki Y, Kiuchi T. Gene. 2021 Feb 5;768:145314. doi: 10.1016/j.gene.2020.145314. Epub 2020 Nov 18. PMID: 33220342
43. DOCK11 and DENND2A play pivotal roles in the maintenance of hepatitis B virus in host cells. Hashimoto S, Shirasaki T, Yamashita T, Iwabuchi S, Suzuki Y, Takamura Y, Ukita Y, Deshimaru S, Okayama T, Ikeo K, Kuroki K, Kawaguchi K, Mizukoshi E, Matsushima K, Honda M, Kaneko S. PLoS One. 2021 Feb 4;16(2):e0246313. doi: 10.1371/journal.pone.0246313. eCollection 2021. PMID: 33539396
44. Directed induction of alveolar type I cells derived from pluripotent stem cells via Wnt signaling inhibition. Kanagaki S, Ikeo S, Suezawa T, Yamamoto Y, Seki M, Hirai T, Hagiwara M, Suzuki Y, Gotoh S. Stem Cells. 2021 Feb;39(2):156-169. doi: 10.1002/stem.3302. Epub 2020 Nov 26. PMID: 33241896
45. Potential for small RNA production against Bombyx mori latent virus in Bombyx mori ovaries. Katsuma S, Shoji K, Suzuki Y, Iwanaga M. Arch Insect Biochem Physiol. 2021 Feb;106(2):e21761. doi: 10.1002/arch.21761. Epub 2020 Nov 22. PMID: 33225529
46. Impaired tumor immune response in metastatic tumors is a selective pressure for neutral evolution in CRC cases. Sakimura S, Nagayama S, Fukunaga M, Hu Q, Kitagawa A, Kobayashi Y, Hasegawa T, Noda M, Kouyama Y, Shimizu D, Saito T, Niida A, Tsuruda Y, Otsu H, Matsumoto Y, Uchida H, Masuda T, Sugimachi K, Sasaki S, Yamada K, Takahashi K, Innan H, Suzuki Y, Nakamura H, Totoki Y, Mizuno S, Ohshima M, Shibata T, Mimori K. PLoS Genet. 2021 Jan 21;17(1):e1009113. doi: 10.1371/journal.pgen.1009113. eCollection 2021 Jan. PMID: 33476333
47. Genome assembly and annotation of the California harvester ant Pogonomyrmex californicus. Bohn J, Halabian R, Schrader L, Shabardina V, Steffen R, Suzuki Y, Ernst UR, Gadau J, Makałowski W. G3 (Bethesda). 2021 Jan 18;11(1):jkaa019. doi: 10.1093/g3journal/jkaa019. PMID: 33561225
48. E74-Like Factor 3 Is a Key Regulator of Epithelial Integrity and Immune Response Genes in Biliary Tract Cancer. Suzuki M, Saito-Adachi M, Arai Y, Fujiwara Y, Takai E, Shibata S, Seki M, Rokutan H, Maeda D, Horie M, Suzuki Y, Shibata T, Kiyono T, Yachida S. Cancer Res. 2021 Jan 15;81(2):489-500. doi: 10.1158/0008-5472.CAN-19-2988. Epub 2020 Dec 8. PMID: 33293429
49. Potentiality of multiple modalities for single-cell analyses to evaluate the tumor microenvironment in clinical specimens. Kashima Y, Togashi Y, Fukuoka S, Kamada T, Irie T, Suzuki A, Nakamura Y, Shitara K, Minamide T, Yoshida T, Taoka N, Kawase T, Wada T, Inaki K, Chihara M, Ebisuno Y, Tsukamoto S, Fujii R, Ohashi A, Suzuki Y, Tsuchihara K, Nishikawa H, Doi T. Sci Rep. 2021 Jan 11;11(1):341. doi: 10.1038/s41598-020-79385-w. PMID: 33431933
50. Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. Yahara K, Suzuki M, Hirabayashi A, Suda W, Hattori M, Suzuki Y, Okazaki Y. Nat Commun. 2021 Jan 4;12(1):27. doi: 10.1038/s41467-020-20199-9. PMID: 33397904
51. Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. Oka M, Xu L, Suzuki T, Yoshikawa T, Sakamoto H, Uemura H, Yoshizawa AC, Suzuki Y, Nakatsura T, Ishihama Y, Suzuki A, Seki M. Genome Biol. 2021 Jan 4;22(1):9. doi: 10.1186/s13059-020-02240-8. PMID: 33397462
52. Transcript Identification Through Long-Read Sequencing. Seki M, Oka M, Xu L, Suzuki A, Suzuki Y. Methods Mol Biol. 2021;2284:531-541. doi: 10.1007/978-1-0716-1307-8_29. PMID: 33835462
53. The genome sequence of Samia ricini, a new model species of lepidopteran insect. Lee J, Nishiyama T, Shigenobu S, Yamaguchi K, Suzuki Y, Shimada T, Katsuma S, Kiuchi T. Mol Ecol Resour. 2021 Jan;21(1):327-339. doi: 10.1111/1755-0998.13259. Epub 2020 Oct 16. PMID: 32985129

2020

英語論文

1. Mitobe Y, Iino K, Takayama KI, Ikeda K, Suzuki T, Aogi K, Kawabata H, Suzuki Y, Horie-Inoue K, Inoue S.
   PSF promotes ER-positive breast cancer progression via posttranscriptional regulation of ESR1 and SCFD2.
   Cancer Res. 2020 Mar 25:canres.3095.2019. doi: 10.1158/0008-5472.CAN-19-3095.
2. Jangid A, Fukuda S, Seki M, Horiuchi T, Suzuki Y, Taylor TD, Ohno H, Prakash T.
   Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice.
   PLoS One. 2020 Mar 24;15(3):e0228358. doi: 10.1371/journal.pone.0228358. eCollection 2020.
3. Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y,
   Takigawa I, Tsukiyama T,Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y,
   Matsumoto M, Nakayama KI, Washburn MP, Saraf A, Florens L, Sato S,
   The role of Mediator and Little Elongation Complex in transcription termination.
   Tomomori-Sato C, Conaway RC, Conaway JW, Hatakeyama S.
4. Imamoto A, Ki S, Li L, Iwamoto K, Maruthamuthu V, Devany J, Lu O, Kanazawa T, Zhang S, Yamada T, Hirayama A, Fukuda S,
   Suzuki Y, Okada M.,Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis.
   Life Sci Alliance. 2020 Feb 10;3(2). pii: e201900635. doi: 10.26508/lsa.201900635. Print 2020 Feb.
5. Ozawa Y, Yamamuro S, Sano E, Tatsuoka J, Hanashima Y, Yoshimura S, Sumi K, Hara H, Nakayama T, Suzuki Y, Yoshino A.
   Indoleamine 2,3-dioxygenase 1 is highly expressed in glioma stem cells.
   Biochem Biophys Res Commun. 2020 Feb 5. pii: S0006-291X(20)30231-X. doi: 10.1016/j.bbrc.2020.01.148. [Epub ahead of print]
6. Izumi N, Shoji K, Suzuki Y, Katsuma S, Tomari Y.
   Zucchini consensus motifs determine the mechanism of pre-piRNA production.
   Nature. 2020 Feb;578(7794):311-316. doi: 10.1038/s41586-020-1966-9. Epub 2020 Jan 29.
7. Fujimoto S, Kawamoto M, Shoji K, Suzuki Y, Katsuma S, Iwanaga M.
   Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain.
   Virus Genes. 2020 Jan 7. doi: 10.1007/s11262-019-01727-2. [Epub ahead of print]
8. Suzuki Y.
   Advent of a new sequencing era: long-read and on-site sequencing.
   J Hum Genet. 2020 Jan;65(1):1. doi: 10.1038/s10038-019-0683-4. Epub 2020 Jan 6. No abstract available.
9. Shabardina V, Kashima Y, Suzuki Y, Makalowski W.
   Emergence and Evolution of ERM Proteins and Merlin in Metazoans.
   Genome Biol Evol. 2020 Jan 1;12(1):3710-3724. doi: 10.1093/gbe/evz265