Research

1. Amano R, Takahashi M, Haga K, Yamamoto M, Goto K, Ichinose A, Hamada M, Gohda J, Inoue J, Kawaguchi Y, Moi ML, Nakamura Y. A chimeric RNA consisting of siRNA and aptamer for inhibiting dengue virus replication. NAR Mol Med. 1(4):ugae025. https://doi.org/10.1093/narmme/ugae025 (2024) 

2. Katoh H, Kimura R, Sekizuka T, Matsuoka K, Hosogi M, Kitai Y, Akahori Y, Kato F, Kataoka M, Kobayashi H, Nagata N, Suzuki T, Ohkawa Y, Oki S, Takeda M. Structural and molecular properties of mumps virus inclusion bodies. Science Advances. 10(49):eadr0359. https://doi.org/10.1126/sciadv.adr0359 (2024)

3. Kobayashi M, Kobayashi N, Deguchi K, Omori S, Nagai M, Fukui R, Song I, Fukuda S, Miyake K, Ichinohe T. TNF-α exacerbates SARS-CoV-2 infection by stimulating CXCL1 production from macrophages. Plos Pathogens. 20(12):e1012776. https://doi.org/10.1371/journal.ppat.1012776 (2024)

4. Zhou NE, Tang S, Bian X, Parai MK, Krieger IV, Flores A, Jaiswal PK, Bam R, Wood JL, Shi Z, Stevens LJ, Scobey T, Diefenbacher MV, Moreira FR, Baric TJ, Acharya A, Shin J, Rathi MM, Wolff KC, Riva L, Bakowski MA, Mcnamara CW, Catanzaro NJ, Graham RL, Schultz DC, Cherry S, Kawaoka Y, Halfmann PJ, Baric RS, Denison MR, Sheahan TP, Sacchettini JC. An oral non-covalent non-peptidic inhibitor of SARS-CoV-2 Mpro ameliorates viral replication and pathogenesis in vivo. Cell Reports. 43(11):114929. https://doi.org/10.1016/j.celrep.2024.114929 (2024)

5. Oshima HS, Ogawa A, Sano FK, Akasaka H, Kawakami T, Iwama A, Okamoto HH, Nagiri C, Wei F, Shihoya W, Nureki O. Structural insights into the agonist selectivity of the adenosine A3 receptor. Nature Communications. 15(1):9294. https://doi.org/10.1038/s41467-024-53473-1 (2024)

6. Muro R, Nitta T, Nitta S, Tsukasaki M, Asano T, Nakano K, Okamura T, Nakashima T, Okamoto K, Takayanagi H. Transcript splicing optimizes the thymic self-antigen repertoire to suppress autoimmunity. J Clin Invest. 134(20):e179612. https://doi.org/10.1172/JCI179612 (2024)

7. Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T. Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nature Communications. 15(1):8574. https://doi.org/10.1038/s41467-024-52808-2 (2024)

8. Gao P, Morita N, Shinkura R. Role of mucosal IgA antibodies as novel therapies to enhance mucosal barriers. Semin Immunopathol. 47(1):1–4. https://doi.org/10.1007/s00281-024-01027-4 (2024)

9. Shimoyama M, Nakada-Tsukui K, Nozaki T. EhRacM differentially regulates macropinocytosis and motility in the enteric protozoan parasite Entamoeba histolytica. PLoS Pathog. 20(11):e1012364. https://doi.org/10.1371/journal.ppat.1012364 (2024)

10. Kawataki S, Kubota Y, Katayama K, Imoto S, Takekawa M. GADD45beta-MTK1 signaling axis mediates oncogenic stress-induced activation of the p38 and JNK pathways. Cancer Sci. https://doi.org/10.1111/cas.16389 (2024)

11. Kuwata T, Kaku Y, Biswas S, Matsumoto K, Shimizu M, Kawanami Y, Uraki R, Okazaki K, Minami R, Nagasaki Y, Nagashima M, Yoshida I, Sadamasu K, Yoshimura K, Ito M, Kiso M, Yamayoshi S, Imai M, Ikeda T, Sato K, Toyoda M, Ueno T, Inoue T, Tanaka Y, Kimura KT, Hashiguchi T, Sugita Y, Noda T, Morioka H, Kawaoka Y, Matsushita S, Genotype to Phenotype Japan (G2P-Japan) Consortium. Induction of IGHV3-53 public antibodies with broadly neutralising activity against SARS-CoV-2 including Omicron subvariants in a Delta breakthrough infection case. EBioMedicine. 110:105439. https://doi.org/10.1016/j.ebiom.2024.105439 (2024)

12. Gu C, Maemura T, Guan L, Eisfeld AJ, Biswas A, Kiso M, Uraki R, Ito M, Trifkovic S, Wang T, Babujee L, Presler RJ, Dahn R, Suzuki Y, Halfmann PJ, Yamayoshi S, Neumann G, Kawaoka Y. A human isolate of bovine H5N1 is transmissible and lethal in animal models. Nature.  636(8043)  https://doi.org/10.1038/s41586-024-08254-7 (2024)

13. Yajima H, Nomai T, Okumura K, Maenaka K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Hashiguchi T, Sato K. Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants. mBio. 15(10):e0322023–23. Epub 2024 Sep 16. https://doi.org/10.1128/mbio.03220-23 (2024)

14. Chiba S, Kiso M, Yamada S, Someya K, Onodera Y, Yamaguchi A, Matsunaga S, Uraki R, Iwatsuki-Horimoto K, Yamayoshi S, Takeshita F, Kawaoka Y. An mRNA vaccine candidate encoding H5HA clade 2.3.4.4b protects mice from clade 2.3.2.1a virus infection. NPJ Vaccines. 9(1):189–9. https://doi.org/10.1038/s41541-024-00988-9 (2024)

15. Chiba S, Kiso M, Yamada S, Someya K, Onodera Y, Yamaguchi A, Matsunaga S, Jounai N, Yamayoshi S, Takeshita F, Kawaoka Y. Protective effects of an mRNA vaccine candidate encoding H5HA clade 2.3.4.4b against the newly emerged dairy cattle H5N1 virus. eBioMedicine. 109:105408. https://doi.org/10.1016/j.ebiom.2024.105408 (2024) 

16. Yaku H, Takahashi K, Okada H, Kobiyama K, Shiokawa M, Uza N, Kodama Y, Ishii KJ, Seno H. Near-infrared photoimmunotherapy as a complementary modality to in situ vaccine in a preclinical pancreatic cancer model. Biochem Biophys Res Commun. 737:150534. https://doi.org/10.1016/j.bbrc.2024.150534 (2024)

17. Jiang H, Santos HJ, Nozaki T. Tetraspanin-enriched microdomains play an important role in pathogenesis in the protozoan parasite Entamoeba histolytica. PLoS Pathog. 20(10):e1012151. https://doi.org/10.1371/journal.ppat.1012151 (2024)

18. Kaku Y, Okumura KA-K, Kawakubo S, Uriu K, Chen L, Kosugi Y, Uwamino Y, Begum MM, Leong S, Ikeda T, Sadamasu K, Asakura H, Nagashima M, Yoshimura K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Sato K. Virological characteristics of the SARS-CoV-2 XEC variant. Lancet Infect Dis. 24(12):e736–X. Epub 2024 Nov 6. https://doi.org/10.1016/S1473-3099(24)00731-X (2024)

19. Wulansari D, Jeelani G, Yazaki E, Nozaki T. Identification and characterization of archaeal-type FAD synthase as a novel tractable drug target from the parasitic protozoa Entamoeba histolytica. mSphere. 9(9):e0034724–24. Epub 2024 Aug 27. https://doi.org/10.1128/msphere.00347-24 (2024)

20. Kiso M, Uraki R, Yamayoshi S, Imai M, Kawaoka Y. Drug susceptibility and the potential for drug-resistant SARS-CoV-2 emergence in immunocompromised animals. Iscience. 27(9):110729. https://doi.org/10.1016/j.isci.2024.110729 (2024)

21. Miyauchi K, Kimura S, Akiyama N, Inoue K, Ishiguro K, Vu T, Srisuknimit V, Koyama K, Hayashi G, Soma A, Nagao A, Shirouzu M, Okamoto A, Waldor MK, Suzuki T. A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis. Nat Chem Biol. https://doi.org/10.1038/s41589-024-01726-x (2024)

22. Tanaka T, Hososhima S, Yamashita Y, Sugimoto T, Nakamura T, Shigemura S, Iida W, Sano FK, Oda K, Uchihashi T, Katayama K, Furutani Y, Tsunoda SP, Shihoya W, Kandori H, Nureki O. The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4. Mol Cell. 84(18) https://doi.org/10.1016/j.molcel.2024.08.016 (2024)

23. Muraoka D, Moi ML, Muto O, Nakatsukasa T, Deng S, Takashima C, Yamaguchi R, Sawada S, Hayakawa H, Nguyen TTN, Haseda Y, Soga T, Matsushita H, Ikeda H, Akiyoshi K, Harada N. Low-frequency CD8(+) T cells induced by SIGN-R1(+) macrophage-targeted vaccine confer SARS-CoV-2 clearance in mice. NPJ Vaccines. 9(1):173–6. https://doi.org/10.1038/s41541-024-00961-6 (2024)

24. Inoue T, Baba Y, Kurosaki T. BCR signaling in germinal center B cell selection. Trends Immunol. 45(9):693–704. https://doi.org/10.1016/j.it.2024.07.005 (2024)

25. Neumann G, Kawaoka Y. Highly pathogenic H5N1 avian influenza virus outbreak in cattle: the knowns and unknowns. Nature Reviews Microbiology. 22(9):525–526. https://doi.org/10.1038/s41579-024-01087-1 (2024)

26. Takashita E, Ichikawa M, Fujisaki S, Morita H, Nagata S, Miura H, Watanabe S, Hasegawa H, Kawaoka Y. Antiviral susceptibility of SARS-CoV-2 and influenza viruses from 3 co-infecte d pe diatric patients. International Journal of Infectious Diseases. 146:107134. https://doi.org/10.1016/j.ijid.2024.107134 (2024)

27. Liu S, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. Impact of the interaction between herpes simplex virus 1 ICP22 and FACT on viral gene expression and pathogenesis. J Virol. 98(8):e0073724–24. Epub 2024 Jul 17. https://doi.org/10.1128/jvi.00737-24 (2024)

28. Manabe S, Iwamoto S, Nagatoishi S, Hoshinoo A, Mitani A, Sumiyoshi W, Kinoshita T, Yamaguchi Y, Tsumoto K. Systematic Preparation of a 66-IgG Library with Symmetric and Asymmetric Homogeneous Glycans and Their Functional Evaluation. J Am Chem Soc. 146(33):23426–23436. https://doi.org/10.1021/jacs.4c06558 (2024)

29. Mizutani T, Ishizaka A*. Poliovirus capsid protein VP3 can penetrate vascular endothelial cells. FEBS Lett. 598(15):1909–1918. https://doi.org/10.1002/1873-3468.14974 (2024)

30. Huynh NC, Ling R, Komagamine M, Shi T, Tsukasaki M, Matsuda K, Okamoto K, Asano T, Muro R, Pluemsakunthai W, Kollias G, Kaneko Y, Takeuchi T, Tanaka S, Komatsu N, Takayanagi H. Oncostatin M-driven macrophage-fibroblast circuits as a drug target in autoimmune arthritis. Inflamm Regen. 44(1):36-0. https://doi.org/10.1186/s41232-024-00347-0 (2024)

31. 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. 24(1):274-0. https://doi.org/10.1186/s12866-024-03431-0 (2024)

32. Kato A, Iwasaki R, Takeshima K, Maruzuru Y, Koyanagi N, Natsume T, Kusano H, Adachi S, Kawano S, Kawaguchi Y. Identification of a novel neurovirulence factor encoded by the cryptic orphan gene UL31.6 of herpes simplex virus 1. J Virol. 98(7):e0074724-24. Epub 2024 May 31. https://doi.org/10.1128/jvi.00747-24 (2024)

33. Iijima N, Hayashi T, Niino M, Miyamoto Y, Oka M, Ishii KJ. Tridecylcyclohexane in incomplete Freund's adjuvant is a critical component in inducing experimental autoimmune diseases. Eur J Immunol. :e2350957. https://doi.org/10.1002/eji.202350957 (2024)

34. Eisfeld AJ, Biswas A, Guan L, Gu C, Maemura T, Trifkovic S, Wang T, Babujee L, Dahn R, Halfmann PJ, Barnhardt T, Neumann G, Suzuki Y, Thompson A, Swinford AK, Dimitrov KM, Poulsen K, Kawaoka Y. Pathogenicity and transmissibility of bovine H5N1 influenza virus. Nature. https://doi.org/10.1038/s41586-024-07766-6 (2024)

35. Guan L, Eisfeld AJ, Pattinson D-PD, Gu C, Biswas A, Maemura T, Trifkovic S, Babujee L, Presler RJ, Dahn R, Halfmann PJ, Barnhardt T, Neumann G, Thompson A, Swinford AK, Dimitrov KM, Poulsen K, Kawaoka Y. Cow's Milk Containing Avian Influenza A(H5N1) Virus - Heat Inactivation and Infectivity in Mice. N Engl J Med. 391(1):87-90. https://doi.org/10.1056/NEJMc2405495 (2024)

36. Nakane T, Nakagawa R, Ishiguro S, Okazaki S, Mori H, Shuto Y, Yamashita K, Yachie N, Nishimasu H, Nureki O. Structure and engineering of Brevibacillus laterosporus Cas9. Commun Biol. 7(1):803-z. https://doi.org/10.1038/s42003-024-06422-z (2024)

37. Inoue T, Matsumoto Y, Kawai C, Ito M, Nada S, Okada M, Kurosaki T. Csk restrains BCR-mediated ROS production and contributes to germinal center selection and affinity maturation. J Exp Med. 221(7):e20231996. doi: 10.1084/jem.20231996. Epub 2024 May 16. https://doi.org/10.1084/jem.20231996 (2024)

38. Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O. Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature. 631(8019):224–231. https://doi.org/10.1038/s41586-024-07497-8 (2024)

39. Asano R, Nakakido M, Perez JF, Ise T, Caaveiro JMM, Nagata S, Tsumoto K. Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab. Biochem Biophys Res Commun. 714:149969. https://doi.org/10.1016/j.bbrc.2024.149969 (2024)

40. Iwama A, Kise R, Akasaka H, Sano FK, Oshima HS, Inoue A, Shihoya W, Nureki O. Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103. Nat Commun. 15(1):4769-5. https://doi.org/10.1038/s41467-024-49030-5 (2024)

41. Lee MSJ, Matsuo-Dapaah J, Del Rosario Zorrilla C, Omatsu Y, Nagasawa T, Uemura S, Iwama A, Ishii KJ, Coban C. Acute malaria suppresses the B lymphocytic niche in the bone marrow through the alteration of CXCL12-abundant reticular cells. Int Immunol. 36(7):339–352. https://doi.org/10.1093/intimm/dxae012 (2024)

42. 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 AAJ, 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. 104:105181. https://doi.org/10.1016/j.ebiom.2024.105181 (2024)

43. Ito S, Matsunaga R, Nakakido M, Komura D, Katoh H, Ishikawa S, Tsumoto K. High-throughput system for the thermostability analysis of proteins. Protein Sci. 33(6):e5029. https://doi.org/10.1002/pro.5029 (2024)

44. Shimizu K, Kawakami C, Matsuzaki Y, Fujisaki S, Nagata S, Morita H, Watanabe K, Miura H, Momoki T, Saikusa M, Ozawa H, Kumazaki M, Usuku S, Tanaka N, Senda R, Okubo I, Watanabe S, Hasegawa H, Kawaoka Y, Takashita E. Monitoring Influenza C and D Viruses in Patients With Respiratory Diseases in Japan, January 2018 to March 2023. Influenza Other Respir Viruses. 18(6):e13345. https://doi.org/10.1111/irv.13345 (2024)

45. Yoshioka D, Nakamura T, Kubota Y, Takekawa M. Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms. J Biochem. 175(6):629-641. https://doi.org/10.1093/jb/mvae009 (2024)

46. Setoguchi R, Sengiku T, Kono H, Kawakami E, Kubo M, Yamamoto T, Hori S. Memory CD8 T cells are vulnerable to chronic IFN-gamma signals but not to CD4 T cell deficiency in MHCII-deficient mice. Nat Commun. 15(1):4418-4. https://doi.org/10.1038/s41467-024-48704-4 (2024)

47. Kitai Y, Watanabe O, Ohmiya S, Kisu T, Ota R, Kawakami K, Katoh H, Fukuzawa K, Takeda M, Nishimura H. Detailed analysis of low temperature inactivation of respiratory syncytial virus. Sci Rep. 14(1):11823-z. https://doi.org/10.1038/s41598-024-62658-z (2024)

48. Yamamoto K, Nagatoishi S, Nakakido M, Kuroda D, Tsumoto K. Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain V H H antibodies. Biochem Biophys Res Commun. 709:149839. https://doi.org/10.1016/j.bbrc.2024.149839 (2024)

49. Muehlemann B, Wilks SH, Baracco L, Bekliz M, Carreno JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara V, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Roessler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar MS, Tuereli S, Wang W, Weiss CD, Smith DJ. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays. Science Translational Medicine. 16(747):eadl1722. https://doi.org/10.1126/scitranslmed.adl1722 (2024)

50. Wang W, Harimurti S, Inoue D, Nayeem MOG, Wang J, Okuda C, Hashizume D, Lee S, Fukuda K, Yokota T, Someya T. Janus Membrane-Based Wearable pH Sensor with Sweat Absorption, Gas Permeability, and Self-Adhesiveness. Acs Applied Materials & Interfaces. 16(21):27065–27074. https://doi.org/10.1021/acsami.4c02189 (2024)

51. Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T. Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nature Structural & Molecular Biology. 31(5) https://doi.org/10.1038/s41594-024-01238-1 (2024)

52. Sasaki I, Fukuda-Ohta Y, Nakai C, Wakaki-Nishiyama N, Okamoto C, Okuzaki D, Morita S, Kaji S, Furuta Y, Hemmi H, Kato T, Yamamoto A, Tosuji E, Saitoh S, Tanaka T, Hoshino K, Fukuda S, Miyake K, Kuroda E, Ishii KJ, Iwawaki T, Furukawa K, Kaisho T. A stress sensor, IRE1α, is required for bacterial-exotoxin-induced interleukin-1β production in tissue-resident macrophages. Cell Rep. 43(4):113981. https://doi.org/10.1016/j.celrep.2024.113981 (2024)

53. Tolentino JE, Lytras S, Ito J, Sato K. Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV. Virol J. 21(1):84-2. https://doi.org/10.1186/s12985-024-02358-2 (2024)

54. Goto M, Takahashi H, Yoshida R, Itamiya T, Nakano M, Nagafuchi Y, Harada H, Shimizu T, Maeda M, Kubota A, Toda T, Hatano H, Sugimori Y, Kawahata K, Yamamoto K, Shoda H, Ishigaki K, Ota M, Okamura T, Fujio K. Age-associated CD4(+) T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity. Sci Immunol. 9(93):eadk1643. https://doi.org/10.1126/sciimmunol.adk1643 (2024)

55. Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T. Structure of the human Bre1 complex bound to the nucleosome. Nat Commun. 15(1):2580-8. https://doi.org/10.1038/s41467-024-46910-8 (2024)

56. Katayama M, Murakami S, Ishida H, Matsugo H, Sekine W, Ohira K, Takenaka-Uema A, Horimoto T. Antigenic commonality and divergence of hemagglutinin-esterase-fusion protein among influenza D virus lineages revealed using epitope mapping. J Virol. 98(3):e0190823-23. Epub 2024 Feb 12. https://doi.org/10.1128/jvi.01908-23 (2024)

57. Shihoya W, Iwama A, Sano FK, Nureki O. Cryo-EM advances in GPCR structure determination. J Biochem. https://doi.org/10.1093/jb/mvae029 (2024)

58. Serafini N, Di Santo JP. Group 3 innate lymphoid cells: A trained Gutkeeper. Immunol Rev. https://doi.org/10.1111/imr.13322 (2024)

59. Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K. Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun. 15(1):2404-1. https://doi.org/10.1038/s41467-024-46747-1 (2024)

60. Halfmann PJ, Iwatsuki-Horimoto K, Kuroda M, Hirata Y, Yamayoshi S, Iida S, Uraki R, Ito M, Ueki H, Furusawa Y, Sakai-Tagawa Y, Kiso M, Armbrust T, Spyra S, Maeda K, Wang Z, Imai M, Suzuki T, Kawaoka Y. Characterization of Omicron BA.4.6, XBB, and BQ.1.1 subvariants in hamsters. Commun Biol. 7(1):331-w. https://doi.org/10.1038/s42003-024-06015-w (2024)

61. Inada T, Beckmann R. Mechanisms of Translation-coupled Quality Control. J Mol Biol. 436(6):168496. https://doi.org/10.1016/j.jmb.2024.168496 (2024)

62. Song I, Yang J, Saito M, Hartanto T, Nakayama Y, Ichinohe T, Fukuda S. Prebiotic inulin ameliorates SARS-CoV-2 infection in hamsters by modulating the gut microbiome. NPJ Sci Food. 8(1):18-z. https://doi.org/10.1038/s41538-024-00248-z (2024)

63. Begum MSTM, Ichihara K, Takahashi O, Nasser H, Jonathan M, Tokunaga K, Yoshida I, Nagashima M, Sadamasu K, Yoshimura K, Sato K, Ikeda T, Genotype Phenotype Japan G2P Japan. Virological characteristics correlating with SARS-CoV-2 spike protein fusogenicity. Frontiers in Virology. 4:1353661. https://doi.org/10.3389/fviro.2024.1353661 (2024)

64. Temizoz B, Shibahara T, Hioki K, Hayashi T, Kobiyama K, Lee MSJ, Surucu N, Sag E, Kumanogoh A, Yamamoto M, Gursel M, Ozen S, Kuroda E, Coban C, Ishii KJ. 5,6-dimethylxanthenone-4-acetic acid (DMXAA), a partial STING agonist, competes for human STING activation. Front Immunol. 15:1353336. https://doi.org/10.3389/fimmu.2024.1353336 (2024)

65. Hiranuma R, Sato R, Yamaguchi K, Nakamizo S, Asano K, Shibata T, Fukui R, Furukawa Y, Kabashima K, Miyake K. Aberrant monocytopoiesis drives granuloma development in sarcoidosis. Int Immunol. 36(4):183-196. https://doi.org/10.1093/intimm/dxad054 (2024)

66. Guo Z, Murakami M, Saito K, Kato H, Toriyama M, Tominaga M, Ishii KJ, Fujita F. Integrin alpha5 regulates motility of human monocyte-derived Langerhans cells during immune response. Exp Dermatol. 33(3):e15021. https://doi.org/10.1111/exd.15021 (2024)

67. Kosugi Y, Kaku Y, Hinay AAJ, Guo Z, Uriu K, Kihara M, Saito F, Uwamino Y, Kuramochi J, Shirakawa K, Takaori-Kondo A, Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato K. Antiviral humoral immunity against SARS-CoV-2 omicron subvariants induced by XBB.1.5 monovalent vaccine in infection-naive and XBB-infected individuals. Lancet Infect Dis. 24(3):e147-e148. https://doi.org/10.1016/S1473-3099(23)00784-3 (2024)

68. Jo-Watanabe A, Inaba T, Osada T, Hashimoto R, Nishizawa T, Okuno T, Ihara S, Touhara K, Hattori N, Oh-Hora M, Nureki O, Yokomizo T. Bicarbonate signalling via G protein-coupled receptor regulates ischaemia-reperfusion injury. Nat Commun. 15(1):1530-3. https://doi.org/10.1038/s41467-024-45579-3 (2024)

69. Ando Y, Tsukasaki M, Huynh NC, Zang S, Yan M, Muro R, Nakamura K, Komagamine M, Komatsu N, Okamoto K, Nakano K, Okamura T, Yamaguchi A, Ishihara K, Takayanagi H. The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis. Int J Oral Sci. 16(1):18-8. https://doi.org/10.1038/s41368-023-00275-8 (2024)

70. Gu C, Fan S, Dahn R, Babujee L, Chiba S, Guan L, Maemura T, Pattinson D, Neumann G, Kawaoka Y. Characterization of a human H3N8 influenza virus. EBioMedicine. 101:105034. https://doi.org/10.1016/j.ebiom.2024.105034 (2024)

71. Nobe M, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. MYBBP1A is required for efficient replication and gene expression of herpes simplex virus 1. Microbiol Immunol. https://doi.org/10.1111/1348-0421.13120 (2024)

72. Fan S, Kong H, Babujee L, Presler R,Jr, Jester P, Burke D, Pattinson D, Barr I, Smith D, Neumann G, Kawaoka Y. Assessment of the antigenic evolution of a clade 6B.1 human H1N1pdm influenza virus revealed differences between ferret and human convalescent sera. EBioMedicine. 101:105013. https://doi.org/10.1016/j.ebiom.2024.105013 (2024)

73. Tamura T, Mizuma K, Nasser H, Deguchi S, Padilla-Blanco M, Oda Y, Uriu K, Tolentino JEM, Tsujino S, Suzuki R, Kojima I, Nao N, Shimizu R, Wang L, Tsuda M, Jonathan M, Kosugi Y, Guo Z, Hinay AAJ, Putri O, Kim Y, Tanaka YL, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito A, Ito J, Irie T, Tanaka S, Zahradnik J, Ikeda T, Takayama K, Matsuno K, Fukuhara T, Sato K. Virological characteristics of the SARS-CoV-2 BA.2.86 variant. Cell Host Microbe. 32(2):170-180.e12. https://doi.org/10.1016/j.chom.2024.01.001 (2024)

74. Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Yang JE, Wright ER, Kawaoka Y, Kane RS. Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine. Nat Commun. 15(1):1284-6. https://doi.org/10.1038/s41467-024-45495-6 (2024)

75. Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Sawa H, Kawabata R, Watanabe Y, Sakamoto A, Yasuhara N, Suzuki T, Nakajima Y, Ferdous Z, Shishido K, Mugita Y, Takahashi O, Ichihara K, Kaku Y, Misawa N, Guo Z, Hinay A, Jr., Kosugi Y, Fujita S, Tolentino JM, Chen L, Pan L, Suganami M, Chiba M, Yoshimura R, Yasuda K, Iida K, Ohsumi N, Strange AP, Shibatani Y, Nishiuchi T, Tanaka S, Putri O, Joas G, Kim Y, Yamasoba D, Yoshimura K, Sadamasu K, Nagashima M, Asakura H, Yoshida I, Nakagawa S, Takaori-Kondo A, Shirakawa K, Nagata K, Nomura R, Horisawa Y, Tashiro Y, Kawai Y, Ueno T, Motozono C, Toyoda M, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, Fukuhara T, Genotype Phenotype Japan G. Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant. Nature Communications. 15(1):1176. https://doi.org/10.1038/s41467-024-45274-3 (2024)

76. Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O. Structural basis for lysophosphatidylserine recognition by GPR34. Nat Commun. 15(1):902-z. https://doi.org/10.1038/s41467-024-45046-z (2024)

77. Kaku Y, Padilla-Blanco M, Kosugi Y, Uriu K, Hinay AAJ, Chen L, Plianchaisuk A, Kobiyama K, Ishii KJ, Genotype to Phenotype Japan (G2P-Japan) Consortium, Zahradnik J, Ito J, Sato K. Virological characteristics of the SARS-CoV-2 JN.1 variant. Lancet Infect Dis. 24(2):e82-7. Epub 2024 Jan 3. https://doi.org/10.1016/S1473-3099(23)00813-7 (2024)

78. Belongia EA, Petrie JG, Feldstein LR, Guan L, Halfmann PJ, King JP, Neumann G, Pattinson D, Rolfes MA, McLean HQ, Kawaoka Y. Neutralizing Immunity Against Antigenically Advanced Omicron BA.5 in Children After SARS-CoV-2 Infection. J Pediatric Infect Dis Soc. 13(1):100-104. https://doi.org/10.1093/jpids/piad109 (2024)

79. Takeda M. Cleavage-Activation of Respiratory Viruses - Half a Century of History from Sendai Virus to SARS-CoV-2. Jpn J Infect Dis. 77(1):1–6. https://doi.org/10.7883/yoken.JJID.2023.353 (2024)

80. Yamayoshi S, Nagai E, Mitamura K, Hagihara M, Kobayashi R, Takahashi S, Shibata A, Uwamino Y, Hasegawa N, Iqbal A, Kamimaki I, Iwatsuki-Horimoto K, Nagamura-Inoue T, Kawaoka Y. Seroprevalence of severe acute respiratory syndrome coronavirus 2 N antibodies between December 2021 and march 2023 in Japan. Epidemiol Infect. 152:e24. https://doi.org/10.1017/S0950268824000141 (2024)

81. Oshima HS, Sano FK, Akasaka H, Iwama A, Shihoya W, Nureki O. Optimizing cryo-EM structural analysis of G(i)-coupling receptors via engineered G(t) and Nb35 application. Biochem Biophys Res Commun. 693:149361. https://doi.org/10.1016/j.bbrc.2023.149361 (2024)

82. 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. https://doi.org/10.1016/j.jiac.2024.01.008 (2024)

83. Kosugi Y, Plianchaisuk A, Putri O, Uriu K, Kaku Y, Hinay AAJ, Chen L, Kuramochi J, Sadamasu K, Yoshimura K, Asakura H, Nagashima M, Ito J, Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato K. Characteristics of the SARS-CoV-2 omicron HK.3 variant harbouring the FLip substitution. Lancet Microbe. 5(4):e313–7. Epub 2024 Jan 11. https://doi.org/10.1016/S2666-5247(23)00373-7 (2024)

84. Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs. J Proteome Res. 23(1):149-160. https://doi.org/10.1021/acs.jproteome.3c00506 (2024)

85. Maharana J, Sano FK, Sarma P, Yadav MK, Duan L, Stepniewski TM, Chaturvedi M, Ranjan A, Singh V, Saha S, Mahajan G, Chami M, Shihoya W, Selent J, Chung KY, Banerjee R, Nureki O, Shukla AK. Molecular insights into atypical modes of β-arrestin interaction with seven transmembrane receptors. Science. 383(6678):101-108. https://doi.org/10.1126/science.adj3347 (2024)

86. Komatsu M, Inada T, Noda NN. The UFM1 system: Working principles, cellular functions, and pathophysiology. Mol Cell. 84(1):156–169. https://doi.org/10.1016/j.molcel.2023.11.034 (2024)

87. 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. 24(1):6-5. https://doi.org/10.1186/s12866-023-03157-5 (2024)

88. Uraki R, Imai M, Ito M, Yamayoshi S, Kiso M, Jounai N, Miyaji K, Iwatsuki-Horimoto K, Takeshita F, Kawaoka Y. An mRNA vaccine encoding the SARS-CoV-2 receptor-binding domain protects mice from various Omicron variants. NPJ Vaccines. 9(1):4-0. https://doi.org/10.1038/s41541-023-00800-0 (2024)

89. Ekemen S, Bilir E, Soultan HEA, Zafar S, Demir F, Tabandeh B, Toprak S, Yapicier O, Coban C. The Programmed Cell Death Ligand 1 and Lipocalin 2 Expressions in Primary Breast Cancer and Their Associations with Molecular Subtypes and Prognostic Factors. Breast Cancer (Dove Med Press). 16:1–13. https://doi.org/10.2147/BCTT.S444077 (2024)

90. 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. https://doi.org/10.2169/internalmedicine.2900-23 (2024)

91. Hiraizumi M, Akashi T, Murasaki K, Kishida H, Kumanomidou T, Torimoto N, Nureki O, Miyaguchi I. Transport and inhibition mechanism of the human SGLT2-MAP17 glucose transporter. Nat Struct Mol Biol. 31(1):159-169. https://doi.org/10.1038/s41594-023-01134-0 (2024)

92. Chiba S, Maemura T, Loeffler K, Frey SJ, Gu C, Biswas A, Hatta M, Kawaoka Y, Kane RS. Single immunization with an influenza hemagglutinin nanoparticle-based vaccine elicits durable protective immunity. Bioengineering & Translational Medicine. https://doi.org/10.1002/btm2.10689 (2024)

93. Miyake K, Shibata T, Fukui R, Murakami Y, Sato R, Hiranuma R. Endosomal Toll-Like Receptors as Therapeutic Targets for Autoimmune Diseases. Basic Immunology and its Clinical Application. 1444:97–108. https://doi.org/10.1007/978-981-99-9781-7_7 (2024)

1. Watanabe N, Saito-Nakano Y, Kurisawa N, Otomo K, Suenaga K, Nakano K, Nozaki T. Fumagillin inhibits growth of the enteric protozoan parasite Entamoeba histolytica by covalently binding to and selectively inhibiting methionine aminopeptidase 2. Antimicrob Agents Chemother. 67(11):e0056023. https://doi.org/10.1128/aac.00560-23 (2023)

2. Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, Sato K. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. J Virol. 97(10):e0101123-23. Epub 2023 Oct 5. https://doi.org/10.1128/jvi.01011-23 (2023)

3. 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. Characterization of a SARS-CoV-2 EG.5.1 clinical isolate in vitro and in vivo. Cell Rep. 42(12):113580. https://doi.org/10.1016/j.celrep.2023.113580 (2023)

4. Masuda Y, Nasser H, Zahradnik J, Mitoma S, Shimizu R, Nagata K, Takaori-Kondo A, Schreiber G, Shirakawa K, Saito A, Ikeda T, Ito J, Sato K. Characterization of the evolutionary and virological aspects of mutations in the receptor binding motif of the SARS-CoV-2 spike protein. Frontiers in Virology. 3:1328229. https://doi.org/10.3389/fviro.2023.1328229 (2023)

5. Yamanouchi D, Kasuya G, Nakajo K, Kise Y, Nureki O. Dual allosteric modulation of voltage and calcium sensitivities of the Slo1-LRRC channel complex. Mol Cell. 83(24):4555-4569.e4. https://doi.org/10.1016/j.molcel.2023.11.005 (2023)

6. Safari C, Ghosh S, Andersson R, Johannesson J, Bath P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Borjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, Branden G. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. Sci Adv. 9(49):eadh4179. https://doi.org/10.1126/sciadv.adh4179 (2023)

7. Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, Suzuki T, Suzuki T. Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell. 186(25) https://doi.org/10.1016/j.cell.2023.10.026 (2023)

8. Yamayoshi S, Ito M, Iwatsuki-Horimoto K, Yasuhara A, Okuda M, Hamabata T, Murakami J, Duong C, Yamamoto T, Kuroda Y, Maeda K, Kawaoka Y. Seroprevalence of SARS-CoV-2 antibodies in dogs and cats during the early and mid-pandemic periods in Japan. One Health. 17:100588. https://doi.org/10.1016/j.onehlt.2023.100588 (2023)

9. Hiramoto T, Inaba H, Baatartsogt N, Kashiwakura Y, Hayakawa M, Kamoshita N, Nishimasu H, Nureki O, Kinai E, Ohmori T. Genome editing of patient-derived iPSCs identifies a deep intronic variant causing aberrant splicing in hemophilia A. Blood Adv. 7(22):7017-7027. https://doi.org/10.1182/bloodadvances.2023010838 (2023)

10. Kingstad-Bakke B, Cleven T, Bussan H, Yount BL,Jr, Uraki R, Iwatsuki-Horimoto K, Koga M, Yamamoto S, Yotsuyanagi H, Park H, Mishra JS, Kumar S, Baric RS, Halfmann PJ, Kawaoka Y, Suresh M. Airway surveillance and lung viral control by memory T cells induced by COVID-19 mRNA vaccine. JCI Insight. 8(22):e172510. doi: 10.1172/jci.insight.172510. https://doi.org/10.1172/jci.insight.172510 (2023)

11. Iwatsuki-Horimoto K, Ito M, Okuda-Hamabata M, Takagi H, Imai M, Kawaoka Y. Cardiomyopathy Does Not Exacerbate the Severity of Pneumonia Caused by a SARS-CoV-2 Delta Variant in the J2N-k Hamster Model. Viruses. 15(12):2280. doi: 10.3390/v15122280. https://doi.org/10.3390/v15122280 (2023)

12. Kuroda M, Halfmann PJ, Thackray LB, Diamond MS, Feldmann H, Marzi A, Kawaoka Y. An Antiviral Role for TRIM14 in Ebola Virus Infection. J Infect Dis. 228:S514-S521. https://doi.org/10.1093/infdis/jiad325 (2023a)

13. Halfmann PJ, Borisevich V, Levine CB, Mire CE, Fenton KA, Geisbert TW, Kawaoka Y, Cross RW. The Mucin-Like Domain of the Ebola Glycoprotein Does Not Impact Virulence or Pathogenicity in Ferrets. J Infect Dis. 228:S587-S593. https://doi.org/10.1093/infdis/jiad240 (2023)

14. Kuroda M, Halfmann PJ, Kawaoka Y. Ebola Virus Infection Induces HCAR2 Expression Leading to Cell Death. J Infect Dis. 228:S508-S513. https://doi.org/10.1093/infdis/jiad344 (2023b)

15. Kobayashi D, Kai I, Faizah AN, Moi ML, Tajima S, Takasaki T, Sasaki T, Isawa H. Comparative analysis of the susceptibility of Aedes aegypti and Japanese Aedes albopictus to all dengue virus serotypes. Trop Med Health. 51(1):61-5. https://doi.org/10.1186/s41182-023-00553-5 (2023)

16. Maemura T, Guan L, Gu C, Eisfeld A, Biswas A, Halfmann P, Neumann G, Kawaoka Y. Characterization of highly pathogenic clade 2.3.4.4b H5N1 mink influenza viruses. EBioMedicine. 97:104827. https://doi.org/10.1016/j.ebiom.2023.104827 (2023)

17. Ota M, Nakano M, Nagafuchi Y, Kobayashi S, Hatano H, Yoshida R, Akutsu Y, Itamiya T, Ban N, Tsuchida Y, Shoda H, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Multimodal repertoire analysis unveils B cell biology in immune-mediated diseases. Ann Rheum Dis. 82(11):1455-1463. https://doi.org/10.1136/ard-2023-224421 (2023)

18. Uriu K, Ito J, Kosugi Y, Tanaka YL, Mugita Y, Guo Z, Hinay AAJ, Putri O, Kim Y, Shimizu R, Begum MM, Jonathan M, Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito A, Ikeda T, Sato K. Transmissibility, infectivity, and immune evasion of the SARS-CoV-2 BA.2.86 variant. Lancet Infect Dis. 23(11):e460-e461. https://doi.org/10.1016/S1473-3099(23)00575-3 (2023)

19. Dzau V, Swaminathan S, Baker C, Bright RA, Castillo J, Chuan TC, Draghia-Akli R, Eardley-Patel R, Gao GF, Ishii K, Tebeje YK, Lambe T, Machingaidze S, Rottingen J, Shaligram U, Simao M, Swarup R, Toussaint J, Wairagkar NS. The 100 Days Mission: how a new medical-countermeasures network can deliver equity and innovation. Lancet. 402(10412):1507-1510. https://doi.org/10.1016/S0140-6736(23)01775-0 (2023)

20. Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O. An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell. 186(22):4920-4935.e23. https://doi.org/10.1016/j.cell.2023.08.031 (2023)

21. Shoda H, Natsumoto B, Fujio K. Investigation of immune-related diseases using patient-derived induced pluripotent stem cells. Inflamm Regen. 43(1):51-4. https://doi.org/10.1186/s41232-023-00303-4 (2023)

22. Wang Y, Morishima T, Sezaki M, Sato R, Nakato G, Fukuda S, Kobiyama K, Ishii KJ, Li Y, Takizawa H. Akkermansia muciniphila induces slow extramedullary hematopoiesis via cooperative IL-1R/TLR signals. EMBO Rep. :e57485. https://doi.org/10.15252/embr.202357485 (2023)

23. Fujita S, Uriu K, Pan L, Nao N, Tabata K, Kishimoto M, Itakura Y, Sawa H, Kida I, Tamura T, Fukuhara T, Ito J, Matsuno K, Sato K, Consortium G. Impact of Imprinted Immunity Induced by mRNA Vaccination in an Experimental Animal Model. J Infect Dis. 228(8):1060–1065. https://doi.org/10.1093/infdis/jiad230 (2023)

24. Koda T, Natsumoto B, Shoda H, Fujio K. Nonepisodic Angioedema with Eosinophilia Following Receipt of the BNT162b2 mRNA COVID-19 Vaccine. Intern Med. 62(20):3063-3067. https://doi.org/10.2169/internalmedicine.1788-23 (2023)

25. Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya J, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. Science. 382(6666):eadj0070. https://doi.org/10.1126/science.adj0070 (2023)

26. 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, Fukushi S, Watanabe S, Suzuki T, Kikuchi T, Yotsuyanagi H, Maeda K, Kawaoka Y. Antiviral efficacy against and replicative fitness of an XBB.1.9.1 clinical isolate. iScience. 26(11):108147. https://doi.org/10.1016/j.isci.2023.108147 (2023)

27. Kikuchi C, Antonopoulos A, Wang S, Maemura T, Karamanska R, Lee C, Thompson AJ, Dell A, Kawaoka Y, Haslam SM, Paulson JC. Glyco-engineered MDCK cells display preferred receptors of H3N2 influenza absent in eggs used for vaccines. Nat Commun. 14(1):6178-0. https://doi.org/10.1038/s41467-023-41908-0 (2023)

28. Scarno G, Mazej J, Laffranchi M, Di Censo C, Mattiola I, Candelotti AM, Pietropaolo G, Stabile H, Fionda C, Peruzzi G, Brooks SR, Tsai WL, Mikami Y, Bernardini G, Gismondi A, Sozzani S, Di Santo JP, Vosshenrich CAJ, Diefenbach A, Gadina M, Santoni A, Sciume G. Divergent roles for STAT4 in shaping differentiation of cytotoxic ILC1 and NK cells during gut inflammation. Proc Natl Acad Sci U S A. 120(40):e2306761120. https://doi.org/10.1073/pnas.2306761120 (2023)

29. Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol. https://doi.org/10.1038/s41577-023-00937-y (2023)

30. Kaku Y, Kosugi Y, Uriu K, Ito J, Hinay AAJ, Kuramochi J, Sadamasu K, Yoshimura K, Asakura H, Nagashima M, Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato K. Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against omicron subvariants including EG.5. Lancet Infect Dis. 23(10):e395-e396. https://doi.org/10.1016/S1473-3099(23)00553-4 (2023)

31. Kashima Y, Mizutani T, Okimoto Y, Maeda M, Musashino K, Nishide R, Matsukura A, Nagase J, Suzuki Y. 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. DNA Res. 30(5):dsad020. doi: 10.1093/dnares/dsad020. https://doi.org/10.1093/dnares/dsad020 (2023)

32. Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schafer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE,Jr, Kawaoka Y, Baric RS. Host range, transmissibility and antigenicity of a pangolin coronavirus. Nat Microbiol. 8(10):1820-1833. https://doi.org/10.1038/s41564-023-01476-x (2023)

33. Hirano M, Yamada Y. Reprogramming of pancreatic islet cells for regeneration and rejuvenation. Curr Opin Genet Dev. 82:102099. https://doi.org/10.1016/j.gde.2023.102099 (2023)

34. Zhang Z, Shibata T, Fujimura A, Kitaura J, Miyake K, Ohto U, Shimizu T. Structural basis for thioredoxin-mediated suppression of NLRP1 inflammasome. Nature. 622(7981):188-194. https://doi.org/10.1038/s41586-023-06532-4 (2023)

35. Shihoya W, Sano FK, Nureki O. Structural insights into endothelin receptor signalling. J Biochem. 174(4):317-325. https://doi.org/10.1093/jb/mvad055 (2023)

36. Zhuo S, Noda N, Hioki K, Jin S, Hayashi T, Hiraga K, Momose H, Li W, Zhao L, Mizukami T, Ishii KJ, Li Y, Uesugi M. Identification of a Self-Assembling Small-Molecule Cancer Vaccine Adjuvant with an Improved Toxicity Profile. J Med Chem. 66(18):13266-13279. https://doi.org/10.1021/acs.jmedchem.3c01252 (2023)

37. Dott T, Culina S, Chemali R, Mansour CA, Dubois F, Jagla B, Doisne JM, Rogge L, Huetz F, Jonsson F, Commere P, Di Santo J, Terrier B, Quintana-Murci L, Duffy D, Hasan M, Milieu IC. Standardized high-dimensional spectral cytometry protocol and panels for whole blood immune phenotyping in clinical and translational studies. Cytometry A. https://doi.org/10.1002/cyto.a.24801 (2023)

38. Yao L, Chemaitelly H, Goldman E, Gudina EK, Khalil A, Ahmed R, James AB, Roca A, Fallah MP, Macnab A, Cho WC, Eikelboom J, Qamar FN, Kremsner P, Oliu-Barton M, Sisa I, Tadesse BT, Marks F, Wang L, Kim JH, Meng X, Wang Y, Fly AD, Wang C, Day SW, Howard SC, Graff JC, Maida M, Ray K, Franco-Paredes C, Mashe T, Ngongo N, Kaseya J, Ndembi N, Hu Y, Bottazzi ME, Hotez PJ, Ishii KJ, Wang G, Sun D, Aleya L, Gu W. Time to establish an international vaccine candidate pool for potential highly infectious respiratory disease: a community's view. EClinicalMedicine. 64:102222. https://doi.org/10.1016/j.eclinm.2023.102222 (2023)

39. Chiba S, Halfmann PJ, Iida S, Hirata Y, Sato Y, Kuroda M, Armbrust T, Spyra S, Suzuki T, Kawaoka Y. Recombinant spike protein vaccines coupled with adjuvants that have different modes of action induce protective immunity against SARS-CoV-2. Vaccine. 41(41):6025-6035. https://doi.org/10.1016/j.vaccine.2023.08.054 (2023)

40. Fujita S, Kosugi Y, Kimura I, Tokunaga K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Sato K. Determination of the factors responsible for the tropism of SARS-CoV-2-related bat coronaviruses to Rhinolophus bat ACE2. J Virol. :e0099023. https://doi.org/10.1128/jvi.00990-23 (2023)

41. Komagamine M, Komatsu N, Ling R, Okamoto K, Tianshu S, Matsuda K, Takeuchi T, Kaneko Y, Takayanagi H. Effect of JAK inhibitors on the three forms of bone damage in autoimmune arthritis: joint erosion, periarticular osteopenia, and systemic bone loss. Inflamm Regen. 43(1):44-3. https://doi.org/10.1186/s41232-023-00293-3 (2023)

42. Inoue M, Nagafuchi Y, Ota M, Tsuchiya H, Tateishi S, Kanda H, Fujio K. Carriers of HLA-DRB1*04:05 have a better clinical response to abatacept in rheumatoid arthritis. Sci Rep. 13(1):15250-6. https://doi.org/10.1038/s41598-023-42324-6 (2023)

43. Shibata T, Sato R, Taoka M, Saitoh S, Komine M, Yamaguchi K, Goyama S, Motoi Y, Kitaura J, Izawa K, Yamauchi Y, Tsukamoto Y, Ichinohe T, Fujita E, Hiranuma R, Fukui R, Furukawa Y, Kitamura T, Takai T, Tojo A, Ohtsuki M, Ohto U, Shimizu T, Ozawa M, Yoshida N, Isobe T, Latz E, Mukai K, Taguchi T, Hemmi H, Akira S, Miyake K. TLR7/8 stress response drives histiocytosis in SLC29A3 disorders. J Exp Med. 220(9):e20230054. doi: 10.1084/jem.20230054. Epub 2023 Jul 18. https://doi.org/10.1084/jem.20230054 (2023)

44. Kimura A, Takagi T, Thamamongood T, Sakamoto S, Ito T, Seki I, Okamoto M, Aono H, Serada S, Naka T, Imataka H, Miyake K, Ueda T, Miyanokoshi M, Wakasugi K, Iwamoto N, Ohmagari N, Iguchi T, Nitta T, Takayanagi H, Yamashita H, Kaneko H, Tsuchiya H, Fujio K, Handa H, Suzuki H. Extracellular aaRSs drive autoimmune and inflammatory responses in rheumatoid arthritis via the release of cytokines and PAD4. Ann Rheum Dis. 82(9):1153-1161. https://doi.org/10.1136/ard-2023-224055 (2023)

45. Fukui A, Maruzuru Y, Ohno S, Nobe M, Iwata S, Takeshima K, Koyanagi N, Kato A, Kitazume S, Yamaguchi Y, Kawaguchi Y. Dual impacts of a glycan shield on the envelope glycoprotein B of HSV-1: evasion from human antibodies in vivo and neurovirulence. mBio. 14(4):e0099223-23. Epub 2023 Jun 27. https://doi.org/10.1128/mbio.00992-23 (2023)

46. Chiba S, Kong H, Neumann G, Kawaoka Y. Influenza H3 hemagglutinin vaccine with scrambled immunodominant epitopes elicits antibodies directed toward immunosubdominant head epitopes. mBio. 14(4):e0062223-23. Epub 2023 Jul 19. https://doi.org/10.1128/mbio.00622-23 (2023)

47. Abeygoonawardena H, Wijesinghe N, Navaratne V, Balasuriya A, Nguyen TTN, Moi ML, De Silva AD. Serological Evidence of Zika virus Circulation with Dengue and Chikungunya Infections in Sri Lanka from 2017. J Glob Infect Dis. 15(3):113-120. https://doi.org/10.4103/jgid.jgid_195_22 (2023)

48. Mise-Omata S, Ando M, Srirat T, Nakagawara K, Hayakawa T, Iizuka-Koga M, Nishimasu H, Nureki O, Ito M, Yoshimura A. SOCS3 deletion in effector T cells confers an anti-tumorigenic role of IL-6 to the pro-tumorigenic cytokine. Cell Rep. 42(8):112940. https://doi.org/10.1016/j.celrep.2023.112940 (2023)

49. Thaller AL, Jonsson F, Fiquet O, Marie S, Doisne J, Girelli-Zubani G, Eri T, Fernandes P, Tatirovsky E, Langa-Vives F, Bruhns P, Strick-Marchand H, Di Santo JP. A human immune system (HIS) mouse model that dissociates roles for mouse and human FcR(+) cells during antibody-mediated immune responses. Eur J Immunol. :e2350454. https://doi.org/10.1002/eji.202350454 (2023)

50. Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. Sci Adv. 9(33):eadh3635. https://doi.org/10.1126/sciadv.adh3635 (2023)

51. Guan L, Ping J, Lopes TJS, Fan S, Presler R, Neumann G, Kawaoka Y. Development of an Enhanced High-Yield Influenza Vaccine Backbone in Embryonated Chicken Eggs. Vaccines (Basel). 11(8):1364. doi: 10.3390/vaccines11081364. https://doi.org/10.3390/vaccines11081364 (2023)

52. Yan M, Tsukasaki M, Muro R, Ando Y, Nakamura K, Komatsu N, Nitta T, Okamura T, Okamoto K, Takayanagi H. Identification of an intronic enhancer regulating RANKL expression in osteocytic cells. Bone Res. 11(1):43-6. https://doi.org/10.1038/s41413-023-00277-6 (2023)

53. Tomoda E, Nagao A, Shirai Y, Asano K, Suzuki T, Battersby BJ, Suzuki T. Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases. Nucleic Acids Res. 51(14):7563-7579. https://doi.org/10.1093/nar/gkad139 (2023)

54. Takashita E, Fujisaki S, Morita H, Nagata S, Miura H, Nagashima M, Watanabe S, Takeda M, Kawaoka Y, Hasegawa H. Assessment of the frequency of SARS-CoV-2 Omicron variant escape from RNA-dependent RNA polymerase inhibitors and 3C-like protease inhibitors. Antiviral Res. 216:105671. https://doi.org/10.1016/j.antiviral.2023.105671 (2023)

55. Omura SN, Nakagawa R, Südfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O. Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat Struct Mol Biol. 30(8):1172-1182. https://doi.org/10.1038/s41594-023-01042-3 (2023)

56. Ohta S, Yamada Y. Exploring the potential of in vivo reprogramming for studying embryonic development, tissue regeneration, and organismal aging. Curr Opin Genet Dev. 81:102067. https://doi.org/10.1016/j.gde.2023.102067 (2023)

57. 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, Tabata K, Yokota I, Matsuno K, Takayama K, Tanaka S, Sato K, Fukuhara T, Genotype Phenotype Japan G2P-Japan. Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5. Communications Biology. 6(1):772. https://doi.org/10.1038/s42003-023-05081-w (2023)

58. Guan L, Babujee L, Browning VL, Presler R, Pattinson D, Nguyen HLK, Hoang VMP, Le MQ, van Bakel H, Neumann G, Kawaoka Y. Continued Circulation of Highly Pathogenic H5 Influenza Viruses in Vietnamese Live Bird Markets in 2018-2021. Viruses. 15(7):1596. doi: 10.3390/v15071596. https://doi.org/10.3390/v15071596 (2023)

59. Yamada S, Nagafuchi Y, Fujio K. Pathophysiology and stratification of treatment-resistant rheumatoid arthritis. Immunol Med. :1-12. https://doi.org/10.1080/25785826.2023.2235734 (2023)

60. Kiso M, Yamayoshi S, Iida S, Furusawa Y, Hirata Y, Uraki R, Imai M, Suzuki T, Kawaoka Y. In vitro and in vivo characterization of SARS-CoV-2 resistance to ensitrelvir. Nat Commun. 14(1):4231-1. https://doi.org/10.1038/s41467-023-40018-1 (2023)

61. Li J, Chen Z, Kim G, Luo J, Hori S, Wu C. Cathepsin W restrains peripheral regulatory T cells for mucosal immune quiescence. Sci Adv. 9(28):eadf3924. https://doi.org/10.1126/sciadv.adf3924 (2023)

62. 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. Research article antibody induction and immune response in nasal cavity by third dose of SARS-CoV-2 mRNA vaccination. Virol J. 20(1):146-z. https://doi.org/10.1186/s12985-023-02113-z (2023)

63. Kiso M, Yamayoshi S, Kawaoka Y. Efficacy of favipiravir against influenza virus resistant to both baloxavir and neuraminidase inhibitors. J Antimicrob Chemother. 78(7):1649-1657. https://doi.org/10.1093/jac/dkad145 (2023)

64. Kiso M, Furusawa Y, Uraki R, Imai M, Yamayoshi S, Kawaoka Y. In vitro and in vivo characterization of SARS-CoV-2 strains resistant to nirmatrelvir. Nat Commun. 14(1):3952-x. https://doi.org/10.1038/s41467-023-39704-x (2023)

65. Muramoto Y, Takahashi S, Halfmann PJ, Gotoh S, Noda T, Kawaoka Y. Replicative capacity of SARS-CoV-2 omicron variants BA.5 and BQ.1.1 at elevated temperatures. Lancet Microbe. 4(7):e486-3. Epub 2023 Apr 24. https://doi.org/10.1016/S2666-5247(23)00100-3 (2023)

66. Das K, Nozaki T. Non-Vesicular Lipid Transport Machinery in Leishmania donovani: Functional Implications in Host-Parasite Interaction. International Journal of Molecular Sciences. 24(13):10637. https://doi.org/10.3390/ijms241310637 (2023)

67. Nagai M, Moriyama M, Ishii C, Mori H, Watanabe H, Nakahara T, Yamada T, Ishikawa D, Ishikawa T, Hirayama A, Kimura I, Nagahara A, Naito T, Fukuda S, Ichinohe T. High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nat Commun. 14(1):3863. https://doi.org/10.1038/s41467-023-39569-0 (2023) 

68. Yamamoto S, Yamayoshi S, Ito M, Sakai-Tagawa Y, Nakachi I, Baba R, Kamimoto S, Ogura T, Hagiwara S, Kato H, Nakajima H, Uwamino Y, Yagi K, Sugaya N, Nagai H, Saito M, Adachi E, Koga M, Tsutsumi T, Duong C, Okuda M, Murakami J, Furusawa Y, Ujie M, Iwatsuki-Horimoto K, Yotsuyanagi H, Kawaoka Y. Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination. iScience. 26(7):107208. https://doi.org/10.1016/j.isci.2023.107208 (2023)

69. Halfmann PJ, Uraki R, Kuroda M, Iwatsuki-Horimoto K, Yamayoshi S, Ito M, Kawaoka Y. Transmission and re-infection of Omicron variant XBB.1.5 in hamsters. eBioMedicine. 93:104677. https://doi.org/10.1016/j.ebiom.2023.104677 (2023) 

70. Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Lin Q, Sakuma M, Kawahara E, Yamazaki I, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Hisano T, Moriyama S, Takahashi Y, Ito M, Imai M, Maemura T, Furusawa Y, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T, Keio DP. Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents. iScience. 26(6):106955. https://doi.org/10.1016/j.isci.2023.106955 (2023)

71. Moser MJ, Hill-Batorski L, Bowen RA, Matejka SM, Marshall D, Kawaoka Y, Neumann G, Bilsel P. Intranasal Single-Replication Influenza Vector Induces Cross-Reactive Serum and Mucosal Antibodies against SARS-CoV-2 Variants. Vaccines (Basel). 11(6):1063. doi: 10.3390/vaccines11061063. https://doi.org/10.3390/vaccines11061063 (2023)

72. Nakajima-Takagi Y, Oshima M, Takano J, Koide S, Itokawa N, Uemura S, Yamashita M, Andoh S, Aoyama K, Isshiki Y, Shinoda D, Saraya A, Arai F, Yamaguchi K, Furukawa Y, Koseki H, Ikawa T, Iwama A. Polycomb repressive complex 1.1 coordinates homeostatic and emergency myelopoiesis. Elife. 12:10.7554/eLife.83004. https://doi.org/10.7554/eLife.83004 (2023)

73. Kobayashi K, Kawakami K, Kusakizako T, Tomita A, Nishimura M, Sawada K, Okamoto HH, Hiratsuka S, Nakamura G, Kuwabara R, Noda H, Muramatsu H, Shimizu M, Taguchi T, Inoue A, Murata T, Nureki O. Class B1 GPCR activation by an intracellular agonist. Nature. 618(7967):1085-1093. https://doi.org/10.1038/s41586-023-06169-3 (2023)

74. Yamada S, Nagafuchi Y, Wang M, Ota M, Hatano H, Takeshima Y, Okubo M, Kobayashi S, Sugimori Y, Masahiro N, Yoshida R, Hanata N, Suwa Y, Tsuchida Y, Iwasaki Y, Sumitomo S, Kubo K, Shimane K, Setoguchi K, Azuma T, Kanda H, Shoda H, Zhang X, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance. Ann Rheum Dis. 82(6):809-819. https://doi.org/10.1136/ard-2022-223645 (2023)

75. Tamura D, Kawaoka Y. Omicron proliferation in the nasal cavity may explain its high infectivity. J Infect. 86(6):584-587. https://doi.org/10.1016/j.jinf.2023.03.006 (2023)

76. Yamasoba D, Uriu K, Plianchaisuk A, Kosugi Y, Pan L, Zahradnik J, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Sato K.  Virological characteristics of the SARS-CoV-2 omicron XBB.1.16 variant. Lancet Infect Dis. 23(6):655-656. https://doi.org/10.1016/S1473-3099(23)00278-5 (2023)

77. Saito Y, Takahashi T, Hiramatsu K, Serada S, Fujimoto M, Ohkawara T, Sugase T, Nishigaki T, Tanaka K, Miyazaki Y, Makino T, Kurokawa Y, Nakajima K, Yamasaki M, Ishii KJ, Eguchi H, Doki Y, Naka T. Nano-particulate Toll-like Receptor 9 Agonist Potentiates the Antitumor Activity of Anti-Glypican-1 Antibody. Anticancer Res. 43(6):2425-2432. https://doi.org/10.21873/anticanres.16410 (2023)

78. Fujikawa D, Nakamura T, Yoshioka D, Li Z, Moriizumi H, Taguchi M, Tokai-Nishizumi N, Kozuka-Hata H, Oyama M, Takekawa M. Stress granule formation inhibits stress-induced apoptosis by selectively sequestering executioner caspases. Curr Biol. 33(10):1967-1981.e8. https://doi.org/10.1016/j.cub.2023.04.012 (2023)

79. Nakamura Y, Moi ML, Shiina T, Shin-I T, Suzuki R. Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases. Viruses-Basel. 15(5):1186. https://doi.org/10.3390/v15051186 (2023)

80. Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Quality control of protein synthesis in the early elongation stage. Nat Commun. 14(1):2704-5. https://doi.org/10.1038/s41467-023-38077-5 (2023)

81. Shibata K, Oda K, Nishizawa T, Hazama Y, Ono R, Takaramoto S, Bagherzadeh R, Yawo H, Nureki O, Inoue K, Akiyama H. Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2. J Am Chem Soc. 145(19):10779-10789. https://doi.org/10.1021/jacs.3c01879 (2023)

82. Tamura T, Ito J, Uriu K, Zahradnik J, Kida I, Anraku Y, Nasser H, Shofa M, Oda Y, Lytras S, Nao N, Itakura Y, Deguchi S, Suzuki R, Wang L, Begum MM, Kita S, Yajima H, Sasaki J, Sasaki-Tabata K, Shimizu R, Tsuda M, Kosugi Y, Fujita S, Pan L, Sauter D, Yoshimatsu K, Suzuki S, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Schreiber G, Maenaka K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Hashiguchi T, Ikeda T, Fukuhara T, Saito A, Tanaka S, Matsuno K, Takayama K, Sato K. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun. 14(1):2800-3. https://doi.org/10.1038/s41467-023-38435-3 (2023)

83. Ikeuchi K, Ivic N, Buschauer R, Cheng J, Froehlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R. Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nat Commun. 14(1):2730. https://doi.org/10.1038/s41467-023-38161-w (2023)

84. Ito J, Suzuki R, Uriu K, Itakura Y, Zahradnik J, Kimura KT, Deguchi S, Wang L, Lytras S, Tamura T, Kida I, Nasser H, Shofa M, Begum MM, Tsuda M, Oda Y, Suzuki T, Sasaki J, Sasaki-Tabata K, Fujita S, Yoshimatsu K, Ito H, Nao N, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Kuramochi J, Schreiber G, Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito A, Matsuno K, Takayama K, Hashiguchi T, Tanaka S, Fukuhara T, Ikeda T, Sato K. Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant. Nat Commun. 14(1):2671-z. https://doi.org/10.1038/s41467-023-38188-z (2023)

85. 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. Efficacy of antivirals and mRNA vaccination against an XBF clinical isolate. Lancet Reg Health West Pac. 34:100777. https://doi.org/10.1016/j.lanwpc.2023.100777 (2023) 

86. 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. Efficacy of antivirals and bivalent mRNA vaccines against SARS-CoV-2 isolate CH.1.1. Lancet Infect Dis. 23(5):525-526. https://doi.org/10.1016/S1473-3099(23)00132-9 (2023)

87. Furusawa Y, Kiso M, Iida S, Uraki R, Hirata Y, Imai M, Suzuki T, Yamayoshi S, Kawaoka Y. In SARS-CoV-2 delta variants, Spike-P681R and D950N promote membrane fusion, Spike-P681R enhances spike cleavage, but neither substitution affects pathogenicity in hamsters. EBioMedicine. 91:104561. https://doi.org/10.1016/j.ebiom.2023.104561 (2023)

88. Amada K, Hijiya N, Ikarimoto S, Yanagihara K, Hanada T, Hidano S, Kurogi S, Tsukamoto Y, Nakada C, Kinoshita K, Hirashita Y, Uchida T, Shin T, Yada K, Hirashita T, Kobayashi T, Murakami K, Inomata M, Shirao K, Aoki M, Takekawa M, Moriyama M. Involvement of clusterin expression in the refractory response of pancreatic cancer cells to a MEK inhibitor. Cancer Sci. 114(5):2189-2202. https://doi.org/10.1111/cas.15735 (2023)

89. Sakai-Tagawa Y, Yamayoshi S, Halfmann PJ, Wilson N, Bobholz M, Vuyk WC, Wei W, Ries H, O'Connor DH, Friedrich TC, Sordillo EM, van Bakel H, Simon V, Kawaoka Y. Sensitivity of rapid antigen tests for Omicron subvariants of SARS-CoV-2. J Med Virol. 95(5):e28788. https://doi.org/10.1002/jmv.28788 (2023)

90. Chowdhury SI, Inui M, Yamazaki T, Tomono S, Takagi H, Biswas M, Saitoh S, Miyake K, Akashi-Takamura S. The anti-TLR4 monoclonal antibody Sa15-21 enhances inflammatory cytokine production in LPS-stimulated macrophages. FEBS Lett. 597(9):1246-1260. https://doi.org/10.1002/1873-3468.14619 (2023)

91. Otsuka Saito K, Fujita F, Toriyama M, Utami RA, Guo Z, Murakami M, Kato H, Suzuki Y, Okada F, Tominaga M, Ishii KJ. Roles of TRPM4 in immune responses in keratinocytes and identification of a novel TRPM4-activating agent. Biochem Biophys Res Commun. 654:1-9. https://doi.org/10.1016/j.bbrc.2023.02.062 (2023)

92. Guan L, Zhong G, Fan S, Plisch EM, Presler R, Gu C, Babujee L, Pattinson D, Le Khanh Nguyen H, Hoang VMP, Le MQ, van Bakel H, Neumann G, Kawaoka Y. Highly Pathogenic H5 Influenza Viruses Isolated between 2016 and 2017 in Vietnamese Live Bird Markets. Viruses-Basel. 15(5):1093. https://doi.org/10.3390/v15051093 (2023)

93. Ekemen S, Comunoglu C, Kayhan CK, Bilir E, Cavusoglu I, Etiler N, Bilgi S, Ince U, Coban C, Erden HF. Endometrial Staining of CD56 (Uterine Natural Killer), BCL-6, and CD138 (Plasma Cells) Improve Diagnosis and Clinical Pregnancy Outcomes in Unexplained Infertility and Recurrent IVF Failures: Standardization of Diagnosis with Digital Pathology. Diagnostics. 13(9):1557. https://doi.org/10.3390/diagnostics13091557 (2023)

94. Sano F, Akasaka H, Shihoya W, Nureki O. Cryo-EM structure of the endothelin-1-ET(B)-G(i) complex. Elife. 12:10.7554/eLife.85821. https://doi.org/10.7554/eLife.85821 (2023)

95. Hiramoto T, Kashiwakura Y, Hayakawa M, Baatartsogt N, Kamoshita N, Abe T, Inaba H, Nishimasu H, Uosaki H, Hanazono Y, Nureki O, Ohmori T. PAM-flexible Cas9-mediated base editing of a hemophilia B mutation in induced pluripotent stem cells. Commun Med (Lond). 3(1):56-w. https://doi.org/10.1038/s43856-023-00286-w (2023)

96. Changrob S, Halfmann PJ, Liu H, Torres JL, McGrath JJC, Ozorowski G, Li L, Wilbanks GD, Kuroda M, Maemura T, Huang M, Zheng N, Turner HL, Erickson SA, Fu Y, Yasuhara A, Singh G, Monahan B, Mauldin J, Srivastava K, Simon V, Krammer F, Sather DN, Ward AB, Wilson IA, Kawaoka Y, Wilson PC. Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants. J Clin Invest. 133(8):e166844. doi: 10.1172/JCI166844. https://doi.org/10.1172/JCI166844 (2023)

97. Hill-Batorski L, Hatta Y, Moser MJ, Sarawar S, Neumann G, Kawaoka Y, Bilsel P. Quadrivalent Formulation of Intranasal Influenza Vaccine M2SR (M2-Deficient Single Replication) Protects against Drifted Influenza A and B Virus Challenge. Vaccines (Basel). 11(4):798. doi: 10.3390/vaccines11040798. https://doi.org/10.3390/vaccines11040798 (2023)

98. Uraki R, Ito M, Kiso M, Yamayoshi S, Iwatsuki-Horimoto K, Furusawa Y, Sakai-Tagawa Y, Imai M, Koga M, Yamamoto S, Adachi E, Saito M, Tsutsumi T, Otani A, Kikuchi T, Yotsuyanagi H, Halfmann PJ, Pekosz A, Kawaoka Y. Antiviral and bivalent vaccine efficacy against an omicron XBB.1.5 isolate. Lancet Infect Dis. 23(4):402-403. https://doi.org/10.1016/S1473-3099(23)00070-1 (2023)

99. Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O. Cryo-EM structure of the transposon-associated TnpB enzyme. Nature. 616(7956):390-397. https://doi.org/10.1038/s41586-023-05933-9 (2023)

News Release　Study reveals the 3D structure of a protein involved in genome editing

100. Moriizumi H, Kubota Y, Tsuchiya T, Naka R, Takekawa M. Caspase 3-specific cleavage of MEK1 suppresses ERK signaling and sensitizes cells to stress-induced apoptosis. FEBS Open Bio. 13(4):684-700. https://doi.org/10.1002/2211-5463.13574 (2023)

101. Saitoh H, Sakai-Tagawa Y, Nagasawa S, Torimitsu S, Kubota K, Hirata Y, Iwatsuki-Horimoto K, Motomura A, Ishii N, Okaba K, Horioka K, Abe H, Ikemura M, Rokutan H, Hinata M, Iwasaki A, Yasunaga Y, Nakajima M, Yamaguchi R, Tsuneya S, Kira K, Kobayashi S, Inokuchi G, Chiba F, Hoshioka Y, Mori A, Yamamoto I, Nakagawa K, Katano H, Iida S, Suzuki T, Akitomi S, Hasegawa I, Ushiku T, Yajima D, Iwase H, Makino Y, Kawaoka Y. High titers of infectious SARS-CoV-2 in corpses of patients with COVID-19. Int J Infect Dis. 129:103-109. https://doi.org/10.1016/j.ijid.2023.01.046 (2023)

102. Sun X, Hosomi K, Shimoyama A, Yoshii K, Lan H, Wang Y, Yamaura H, Nagatake T, Ishii KJ, Akira S, Kiyono H, Fukase K, Kunisawa J. TLR4 agonist activity of Alcaligenes lipid a utilizes MyD88 and TRIF signaling pathways for efficient antigen presentation and T cell differentiation by dendritic cells. Int Immunopharmacol. 117:109852. https://doi.org/10.1016/j.intimp.2023.109852 (2023)

103. Ito D, Ito H, Ando T, Sakai Y, Ideta T, Ishii KJ, Ishikawa T, Shimizu M. Spermidine enhances the efficacy of adjuvant in HBV vaccination in mice. Hepatol Commun. 7(4):e0104. doi: 10.1097/HC9.0000000000000104. eCollection 2023 Apr 1. https://doi.org/10.1097/HC9.0000000000000104 (2023)

104. Uraki R, Iida S, Halfmann PJ, Yamayoshi S, Hirata Y, Iwatsuki-Horimoto K, Kiso M, Ito M, Furusawa Y, Ueki H, Sakai-Tagawa Y, Kuroda M, Maemura T, Kim T, Mine S, Iwamoto N, Li R, Liu Y, Larson D, Fukushi S, Watanabe S, Maeda K, Wang Z, Ohmagari N, Theiler J, Fischer W, Korber B, Imai M, Suzuki T, Kawaoka Y. Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates. Nat Commun. 14(1):1620-x. https://doi.org/10.1038/s41467-023-37059-x (2023)

105. Furusawa Y, Yamayoshi S, Kawaoka Y. The accuracy of reverse genetics systems for SARS-CoV-2: Circular polymerase extension reaction versus bacterial artificial chromosome. Influenza Other Respir Viruses. 17(3):e13109. https://doi.org/10.1111/irv.13109 (2023)

106. Sukegawa S, Nureki O, Toki S, Saika H. Genome editing in rice mediated by miniature size Cas nuclease SpCas12f. Front Genome Ed. 5:1138843. https://doi.org/10.3389/fgeed.2023.1138843 (2023)

107. Tatsuma T, Nakakido M, Ichinohe T, Kuroiwa Y, Tomioka K, Liu C, Miyamae N, Onuki T, Tsumoto K, Hashimoto K, Wakihara T. Inactivation and spike protein denaturation of novel coronavirus variants by CuxO/TiO2 nano-photocatalysts. Sci Rep. 13(1) https://doi.org/10.1038/s41598-023-30690-0 (2023)

108. Petrie JG, King JP, McClure DL, Rolfes MA, Meece JK, Pattinson D, Neumann G, Kawaoka Y, Belongia EA, McLean HQ. Effectiveness of first and second COVID-19 mRNA vaccine monovalent booster doses during a period of circulation of Omicron variant sublineages: December 2021-July 2022. Influenza Other Respir Viruses. 17(3):e13104. https://doi.org/10.1111/irv.13104 (2023)

109. Uriu K, Ito J, Zahradnik J, Fujita S, Kosugi Y, Schreiber G, Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato K. Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant. Lancet Infect Dis. 23(3):280-281. https://doi.org/10.1016/S1473-3099(23)00051-8 (2023)

110. Fukui A, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. Establishment of a system to quantify wild-type herpes simplex virus-induced cell-cell fusion reveals a role of N-glycosylation of HSV-1 envelope glycoprotein B in cell-cell fusion. Microbiol Immunol. 67(3):114-119. https://doi.org/10.1111/1348-0421.13050 (2023)

111. Bramer LM, Hontz RD, Eisfeld AJ, Sims AC, Kim Y, Stratton KG, Nicora CD, Gritsenko MA, Schepmoes AA, Akasaka O, Koga M, Tsutsumi T, Nakamura M, Nakachi I, Baba R, Tateno H, Suzuki S, Nakajima H, Kato H, Ishida K, Ishii M, Uwamino Y, Mitamura K, Paurus VL, Nakayasu ES, Attah IK, Letizia AG, Waters KM, Metz TO, Corson K, Kawaoka Y, Gerbasi VR, Yotsuyanagi H, Iwatsuki-Horimoto K. Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections. Heliyon. 9(3):e13795. https://doi.org/10.1016/j.heliyon.2023.e13795 (2023)

112. Chazan A, Das I, Fujiwara T, Murakoshi S, Rozenberg A, Molina-Marquez A, Sano FK, Tanaka T, Gomez-Villegas P, Larom S, Pushkarev A, Malakar P, Hasegawa M, Tsukamoto Y, Ishizuka T, Konno M, Nagata T, Mizuno Y, Katayama K, Abe-Yoshizumi R, Ruhman S, Inoue K, Kandori H, Leon R, Shihoya W, Yoshizawa S, Sheves M, Nureki O, Beja O. Phototrophy by antenna-containing rhodopsin pumps in aquatic environments. Nature. 615(7952):535-540. https://doi.org/10.1038/s41586-023-05774-6 (2023)

113. Kiso M, Uraki R, Ito M, Yamayoshi S, Kotani Y, Imai M, Kohda N, Kawaoka Y. Oral intake of heat-killed Lactiplantibacillus pentosus ONRICb0240 partially protects mice against SARS-CoV-2 infection. Frontiers in Virology. 3:1137133. https://doi.org/10.3389/fviro.2023.1137133 (2023)

114. Kuchitsu Y, Mukai K, Uematsu R, Takaada Y, Shinojima A, Shindo R, Shoji T, Hamano S, Ogawa E, Sato R, Miyake K, Kato A, Kawaguchi Y, Nishitani-Isa M, Izawa K, Nishikomori R, Yasumi T, Suzuki T, Dohmae N, Uemura T, Barber GN, Arai H, Waguri S, Taguchi T. STING signalling is terminated through ESCRT-dependent microautophagy of vesicles originating from recycling endosomes. Nat Cell Biol. 25(3):453-466. https://doi.org/10.1038/s41556-023-01098-9 (2023)

115. Okamoto K, Takayanagi H. Effect of T cells on bone. Bone. 168:116675. https://doi.org/10.1016/j.bone.2023.116675 (2023)

116. Wijaya TJ, Yokota T, Lee S, Okano R, Kobayashi M, Someya T. Photostability Improvement of Organic Photodiodes with ZnO Electron Transport Layer. Adv Photon Res. 4(3) https://doi.org/10.1002/adpr.202200355 (2023)

117. Higashi-Kuwata N, Tsuji K, Hayashi H, Bulut H, Kiso M, Imai M, Ogata-Aoki H, Ishii T, Kobayakawa T, Nakano K, Takamune N, Kishimoto N, Hattori S, Das D, Uemura Y, Shimizu Y, Aoki M, Hasegawa K, Suzuki S, Nishiyama A, Saruwatari J, Shimizu Y, Sukenaga Y, Takamatsu Y, Tsuchiya K, Maeda K, Yoshimura K, Iida S, Ozono S, Suzuki T, Okamura T, Misumi S, Kawaoka Y, Tamamura H, Mitsuya H. Identification of SARS-CoV-2 M(pro) inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2. Nat Commun. 14(1):1076-0. https://doi.org/10.1038/s41467-023-36729-0 (2023)

118. McLean HQ, Petrie JG, Hanson KE, Meece JK, Rolfes MA, Sylvester GC, Neumann G, Kawaoka Y, Belongia EA. Interim Estimates of 2022-23 Seasonal Influenza Vaccine Effectiveness - Wisconsin, October 2022-February 2023. MMWR Morb Mortal Wkly Rep. 72(8):201-205. https://doi.org/10.15585/mmwr.mm7208a1 (2023)

119. Yotsuyanagi H, Ohmagari N, Doi Y, Imamura T, Sonoyama T, Ichihashi G, Sanaki T, Tsuge Y, Uehara T, Mukae H. A phase 2/3 study of S-217622 in participants with SARS-CoV-2 infection (Phase 3 part). Medicine (Baltimore). 102(8):e33024. https://doi.org/10.1097/MD.0000000000033024 (2023)

120. Nakayama T, Azegami T, Kiso M, Imai M, Uraki R, Hayashi K, Hishikawa A, Yoshimoto N, Nakamichi R, Sugita-Nishimura E, Yoshida-Hama E, Kawaoka Y, Itoh H. Plasminogen activator inhibitor 1 is not a major causative factor for exacerbation in a mouse model of SARS-CoV-2 infection. Sci Rep. 13(1):3103-8. https://doi.org/10.1038/s41598-023-30305-8 (2023)

121. Iwatsuki-Horimoto K, Ueki H, Ito M, Nagasawa S, Hirata Y, Hashizume K, Ushiwata K, Iwase H, Makino Y, Ushiku T, Akitomi S, Imai M, Saitoh H, Kawaoka Y. SARS-CoV-2 Transmission from Virus-Infected Dead Hamsters. mSphere. 8(1):e0041122-22. Epub 2023 Jan 10. https://doi.org/10.1128/msphere.00411-22 (2023)

122. Yoshioka Y, Kobiyama K, Hayashi T, Onishi M, Yanagida Y, Nakagawa T, Hashimoto M, Nishinaka A, Hirose J, Asaoka Y, Tajiri M, Hayata A, Ishida S, Omoto S, Nagira M, Ishii KJ. A-910823, a squalene-based emulsion adjuvant, induces T follicular helper cells and humoral immune responses via alpha-tocopherol component. Front Immunol. 14:1116238. https://doi.org/10.3389/fimmu.2023.1116238 (2023)

123. Best K, Ikeuchi K, Kater L, Best D, Musial J, Matsuo Y, Berninghausen O, Becker T, Inada T, Beckmann R. Structural basis for clearing of ribosome collisions by the RQT complex. Nat Commun. 14(1):921-8. https://doi.org/10.1038/s41467-023-36230-8 (2023)

124. Tesina P, Ebine S, Buschauer R, Thoms M, Matsuo Y, Inada T, Beckmann R. Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. Mol Cell. 83(4):607-621.e4. https://doi.org/10.1016/j.molcel.2023.01.020 (2023)

125. Soga T, Duong C, Pattinson D, Sakai-Tagawa Y, Tokita A, Izumida N, Nishino T, Hagiwara H, Wada N, Miyamoto Y, Kuroki H, Hayashi Y, Seki M, Kasuya N, Koga M, Adachi E, Iwatsuki-Horimoto K, Yotsuyanagi H, Yamayoshi S, Kawaoka Y. Characterization of Influenza A(H1N1)pdm09 Viruses Isolated in the 2018-2019 and 2019-2020 Influenza Seasons in Japan. Viruses. 15(2):535. https://doi.org/10.3390/v15020535 (2023)

126. Mahita J, Ha B, Gambiez A, Schendel SL, Li H, Hastie KM, Dennison SM, Li K, Kuzmina N, Periasamy S, Bukreyev A, Munt JE, Osei-Twum M, Atyeo C, Overton JA, Vita R, Guzman-Orozco H, Mendes M, Kojima M, Halfmann PJ, Kawaoka Y, Alter G, Gagnon L, Baric RS, Tomaras GD, Germann T, Bedinger D, Greenbaum JA, Saphire EO, Peters B. Coronavirus Immunotherapeutic Consortium Database. Database (Oxford). 2023:10.1093/database/baac112. https://doi.org/10.1093/database/baac112 (2023)

127. Miyashita R, Nishiyama A, Qin W, Chiba Y, Kori S, Kato N, Konishi C, Kumamoto S, Kozuka-Hata H, Oyama M, Kawasoe Y, Tsurimoto T, Takahashi TS, Leonhardt H, Arita K, Nakanishi M. The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5. Elife. 12:10.7554/eLife.79013. https://doi.org/10.7554/eLife.79013 (2023)

128. Chen S, Quan DH, Sam G, Ozberk V, Wang XT, Halfmann P, Pandey M, Good MF, Kawaoka Y, Britton WJ, Rehm BHA. Assembly of Immunogenic Protein Particles toward Advanced Synthetic Vaccines. Small. 19(8):e2205819. https://doi.org/10.1002/smll.202205819 (2023)

129. Sugimori Y, Iwasaki Y, Takeshima Y, Okubo M, Kobayashi S, Hatano H, Yamada S, Nakano M, Yoshida R, Ota M, Tsuchida Y, Nagafuchi Y, Shimane K, Yoshida K, Kurosaka D, Sumitomo S, Shoda H, Yamamoto K, Okamura T, Fujio K. Transcriptome Profiling of Immune Cell Types in Peripheral Blood Reveals Common and Specific Pathways Involved in the Pathogenesis of Myositis-Specific Antibody-Positive Inflammatory Myopathies. ACR Open Rheumatol. 5(2):93-102. https://doi.org/10.1002/acr2.11521 (2023)

130. Neumann G, Kawaoka Y. The COVID-19 Pandemic-A Potential Role for Antivirals in Mitigating Pandemics. Viruses. 15(2):303. https://doi.org/10.3390/v15020303 (2023)

131. Braun KM, Haddock Iii LA, Crooks CM, Barry GL, Lalli J, Neumann G, Watanabe T, Imai M, Yamayoshi S, Ito M, Moncla LH, Koelle K, Kawaoka Y, Friedrich TC. Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals. Virus Evol. 9(1):vead004. https://doi.org/10.1093/ve/vead004 (2023)

132. Ly MHP, Nguyen CT, Nguyen TV, Nguyen TTN, Nabeshima T, Adungo F, Takamatsu Y, Huy NT, Le TQM, Morita K, Hasebe F, Moi ML. Differential Infectivity of Human Neural Cell Lines by a Dengue Virus Serotype-3 Genotype-III with a Distinct Nonstructural Protein 2A (NS2A) Amino Acid Substitution Isolated from the Cerebrospinal Fluid of a Dengue Encephalitis Patient. Can J Infect Dis Med Microbiol. 2023:2635383. https://doi.org/10.1155/2023/2635383 (2023)

133. Muro R, Narita T, Nitta T, Takayanagi H. Spleen tyrosine kinase mediates the γδTCR signaling required for γδT cell commitment and γδT17 differentiation. Front Immunol. 13:1045881. https://doi.org/10.3389/fimmu.2022.1045881 (2023)

134. Moritoyo T, Nishimura N, Hasegawa K, Ishii S, Kirihara K, Takata M, Svensson AK, Umeda-Kameyama Y, Kawarasaki S, Ihara R, Sakanaka C, Wakabayashi Y, Niizuma K, Tominaga T, Yamazaki T, Hasumi K. A first-in-human study of the anti-inflammatory profibrinolytic TMS-007, an SMTP family triprenyl phenol. Br J Clin Pharmacol. https://doi.org/10.1111/bcp.15651 (2023)

135. Tomomatsu S, Watanabe A, Tesina P, Hashimoto S, Ikeuchi K, Li S, Matsuo Y, Beckmann R, Inada T. Two modes of Cue2-mediated mRNA cleavage with distinct substrate recognition initiate no-go decay. Nucleic Acids Res. 51(1):253-270. https://doi.org/10.1093/nar/gkac1172 (2023)

136. Matsuo Y, Uchihashi T, Inada T. Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex. Nat Commun. 14(1):79-4. https://doi.org/10.1038/s41467-022-35608-4 (2023)

137. Minagawa Y, Nakata S, Date M, Ii Y, Noji H. On-Chip Enrichment System for Digital Bioassay Based on Aqueous Two-Phase System. ACS Nano. 17(1):212-220. https://doi.org/10.1021/acsnano.2c06007 (2023)

138. Neumann G, Kawaoka Y. Which Virus Will Cause the Next Pandemic? Viruses. 15(1):199. https://doi.org/10.3390/v15010199 (2023)

139. Chiba S, Hatta M, Pattinson D, Yasuhara A, Neumann G, Kawaoka Y. Ferret model to mimic the sequential exposure of humans to historical H3N2 influenza viruses. Vaccine. 41(2):590-597. https://doi.org/10.1016/j.vaccine.2022.12.005 (2023)

140. Imai M, Ito M, Kiso M, Yamayoshi S, Uraki R, Fukushi S, Watanabe S, Suzuki T, Maeda K, Sakai-Tagawa Y, Iwatsuki-Horimoto K, Halfmann PJ, Kawaoka Y. Efficacy of Antiviral Agents against Omicron Subvariants BQ.1.1 and XBB. N Engl J Med. 388(1):89-91. https://doi.org/10.1056/NEJMc2214302 (2023)

141. Jin J, Ogawa T, Hojo N, Kryukov K, Shimizu K, Ikawa T, Imanishi T, Okazaki T, Shiroguchi K. Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes. Proc Natl Acad Sci U S A. 120(1):e2210283120. https://doi.org/10.1073/pnas.2210283120 (2023)

142. Takashita E, Watanabe S, Hasegawa H, Kawaoka Y. Are twindemics occurring? Influenza Other Respir Viruses. 17(1):e13090. https://doi.org/10.1111/irv.13090 (2023)

143. Bae C, Katoh H, Wakata A, Sakata M, Kato F, Takeda M. Demonstration of bacterium-free very rapid reverse genetics system using mumps virus. Microbiol Immunol. 67(1):44-47. https://doi.org/10.1111/1348-0421.13032 (2023)

144. Koga M, Iwatsuki-Horimoto K, Kikuchi T, Yamayoshi S, Kawaoka Y, Yotsuyanagi H. Previous omicron infection may be protective against reinfection with omicron variant BA.5 for at least 5 months. Clin Microbiol Infect. 29(1):120-121. https://doi.org/10.1016/j.cmi.2022.09.009 (2023)

145. Uraki R, Ito M, Furusawa Y, Yamayoshi S, Iwatsuki-Horimoto K, Adachi E, Saito M, Koga M, Tsutsumi T, Yamamoto S, Otani A, Kiso M, Sakai-Tagawa Y, Ueki H, Yotsuyanagi H, Imai M, Kawaoka Y. Humoral immune evasion of the omicron subvariants BQ.1.1 and XBB. Lancet Infect Dis. 23(1):30-32. https://doi.org/10.1016/S1473-3099(22)00816-7 (2023)

146. Furuya G, Katoh H, Atsumi S, Hashimoto I, Komura D, Hatanaka R, Senga S, Hayashi S, Akita S, Matsumura H, Miura A, Mita H, Nakakido M, Nagatoishi S, Sugiyama A, Suzuki R, Konishi H, Yamamoto A, Abe H, Hiraoka N, Aoki K, Kato Y, Seto Y, Yoshimura C, Miyadera K, Tsumoto K, Ushiku T, Ishikawa S. Nucleic acid-triggered tumoral immunity propagates pH-selective therapeutic antibodies through tumor-driven epitope spreading. Cancer Sci. 114(1):321-338. https://doi.org/10.1111/cas.15596 (2023)

147. Atsumi Y, Toriyama M, Kato H, Nakamura M, Morita A, Takaishi M, Saito K, Tanaka M, Okada F, Tominaga M, Ishii KJ, Fujita F. Anti-Inflammatory Role of TRPV4 in Human Macrophages. Immunohorizons. 7(1):81-96. https://doi.org/10.4049/immunohorizons.2200100 (2023) 

1. Eiden J, Fierro C, Schwartz H, Adams M, Ellis KJ, Aitchison R, Herber R, Hatta Y, Marshall D, Moser MJ, Belshe R, Greenberg H, Coelingh K, Kawaoka Y, Neumann G, Bilsel P. Intranasal M2SR (M2-Deficient Single Replication) H3N2 Influenza Vaccine Provides Enhanced Mucosal and Serum Antibodies in Adults. J Infect Dis. 227(1):103-112. https://doi.org/10.1093/infdis/jiac433 (2022)

2. Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T. Potent SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models. iScience. 25(12):105596. https://doi.org/10.1016/j.isci.2022.105596 (2022)

3. Takeshima K, Maruzuru Y, Koyanagi N, Kato A, Kawaguchi Y. Redundant and Specific Roles of A-Type Lamins and Lamin B Receptor in Herpes Simplex Virus 1 Infection. J Virol. 96(24):1429. https://doi.org/10.1128/jvi.01429-22 (2022)

4. Ishimura R, El-Gowily AH, Noshiro D, Komatsu-Hirota S, Ono Y, Shindo M, Hatta T, Abe M, Uemura T, Lee-Okada H, Mohamed TM, Yokomizo T, Ueno T, Sakimura K, Natsume T, Sorimachi H, Inada T, Waguri S, Noda NN, Komatsu M. The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Nat Commun. 13(1):7857-0. https://doi.org/10.1038/s41467-022-35501-0 (2022)

5. Kawasaki T, Ikegawa M, Yunoki K, Otani H, Ori D, Ishii KJ, Kuroda E, Takamura S, Kitabatake M, Ito T, Isotani A, Kawai T. Alveolar macrophages instruct CD8(+) T cell expansion by antigen cross-presentation in lung. Cell Rep. 41(11):111828. https://doi.org/10.1016/j.celrep.2022.111828 (2022)

6. Sarawar S, Gabaglia CR, Sanchez A, Hatta Y, Dias P, Neumann G, Kawaoka Y, Bilsel P. Longevity and Mechanism of Heterosubtypic Protection Induced by M2SR (M2-Deficient Single-Replication) Live Influenza Virus Vaccine in Mice. Vaccines (Basel). 10(12):2131. doi: 10.3390/vaccines10122131. https://doi.org/10.3390/vaccines10122131 (2022)

7. Ohe S, Kubota Y, Yamaguchi K, Takagi Y, Nashimoto J, Kozuka-Hata H, Oyama M, Furukawa Y, Takekawa M. ERK-mediated NELF-A phosphorylation promotes transcription elongation of immediate-early genes by releasing promoter-proximal pausing of RNA polymerase II. Nat Commun. 13(1):7476-4. https://doi.org/10.1038/s41467-022-35230-4 (2022)

8. Boon ACM, Darling TL, Halfmann PJ, Franks J, Webby RJ, Barouch DH, Port JR, Munster VJ, Diamond MS, Kawaoka Y. Reduced airborne transmission of SARS-CoV-2 BA.1 Omicron virus in Syrian hamsters. PLoS Pathog. 18(12):e1010970. https://doi.org/10.1371/journal.ppat.1010970 (2022)

9. Uraki R, Halfmann PJ, Iida S, Yamayoshi S, Furusawa Y, Kiso M, Ito M, Iwatsuki-Horimoto K, Mine S, Kuroda M, Maemura T, Sakai-Tagawa Y, Ueki H, Li R, Liu Y, Larson D, Fukushi S, Watanabe S, Maeda K, Pekosz A, Kandeil A, Webby RJ, Wang Z, Imai M, Suzuki T, Kawaoka Y. Characterization of SARS-CoV-2 Omicron BA.4 and BA.5 isolates in rodents. Nature. 612(7940):540-545. https://doi.org/10.1038/s41586-022-05482-7 (2022)

10. Tsukamoto Y, Kurogi S, Shibata T, Suzuki K, Hirashita Y, Fumoto S, Yano S, Yanagihara K, Nakada C, Mieno F, Kinoshita K, Fuchino T, Mizukami K, Ueda Y, Etoh T, Uchida T, Hanada T, Takekawa M, Daa T, Shirao K, Hironaka S, Murakami K, Inomata M, Hijiya N, Moriyama M. Enhanced phosphorylation of c-Jun by cisplatin treatment as a potential predictive biomarker for cisplatin response in combination with patient-derived tumor organoids. Lab Invest. 102(12):1355-1366. https://doi.org/10.1038/s41374-022-00827-2 (2022)

11. Takashita E, Yamayoshi S, Halfmann P, Wilson N, Ries H, Richardson A, Bobholz M, Vuyk W, Maddox R, Baker DA, Friedrich TC, O'Connor DH, Uraki R, Ito M, Sakai-Tagawa Y, Adachi E, Saito M, Koga M, Tsutsumi T, Iwatsuki-Horimoto K, Kiso M, Yotsuyanagi H, Watanabe S, Hasegawa H, Imai M, Kawaoka Y. In Vitro Efficacy of Antiviral Agents against Omicron Subvariant BA.4.6. N Engl J Med. 387(22):2094-2097. https://doi.org/10.1056/NEJMc2211845 (2022)

12. Murakami S, Kitamura T, Matsugo H, Kamiki H, Oyabu K, Sekine W, Takenaka-Uema A, Sakai-Tagawa Y, Kawaoka Y, Horimoto T. Isolation of Bat Sarbecoviruses, Japan. Emerg Infect Dis. 28(12):2500-2503. https://doi.org/10.3201/eid2812.220801 (2022)

13. Halfmann PJ, Frey SJ, Loeffler K, Kuroda M, Maemura T, Armbrust T, Yang JE, Hou YJ, Baric R, Wright ER, Kawaoka Y, Kane RS. Multivalent S2-based vaccines provide broad protection against SARS-CoV-2 variants of concern and pangolin coronaviruses. EBioMedicine. 86:104341. https://doi.org/10.1016/j.ebiom.2022.104341 (2022)

14. Hata K, Kobayashi N, Sugimura K, Qin W, Haxholli D, Chiba Y, Yoshimi S, Hayashi G, Onoda H, Ikegami T, Mulholland CB, Nishiyama A, Nakanishi M, Leonhardt H, Konuma T, Arita K. Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger. Nucleic Acids Res. 50(21):12527-12542. https://doi.org/10.1093/nar/gkac1082 (2022)

15. Nagai H, Saito M, Adachi E, Sakai-Tagawa Y, Yamayoshi S, Kiso M, Kawamata T, Koga M, Kawaoka Y, Tsutsumi T, Yotsuyanagi H. Casirivimab/Imdevimab for Active COVID-19 Pneumonia Which Persisted for Nine Months in a Patient with Follicular Lymphoma during Anti-CD20 Therapy. Jpn J Infect Dis. 75(6):608-611. https://doi.org/10.7883/yoken.JJID.2022.092 (2022)

16. Otsubo R, Minamitani T, Kobiyama K, Fujita J, Ito T, Ueno S, Anzai I, Tanino H, Aoyama H, Matsuura Y, Namba K, Imadome K, Ishii KJ, Tsumoto K, Kamitani W, Yasui T. Human antibody recognition and neutralization mode on the NTD and RBD domains of SARS-CoV-2 spike protein. Sci Rep. 12(1):20120-4. https://doi.org/10.1038/s41598-022-24730-4 (2022)

17. Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S, Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A, Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A, Nakanishi M, Defossez P, Arita K. Structural basis for activation of DNMT1. Nat Commun. 13(1):7130-4. https://doi.org/10.1038/s41467-022-34779-4 (2022)

18. Halfmann PJ, Minor NR, Haddock Iii LA, Maddox R, Moreno GK, Braun KM, Baker DA, Riemersa KK, Prasad A, Alman KJ, Lambert MC, Florek K, Bateman A, Westergaard R, Safdar N, Andes DR, Kawaoka Y, Fida M, Yao JD, Friedrich TC, O'Connor DH. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual. Virus Evol. 9(2):veac104. https://doi.org/10.1093/ve/veac104 (2022)

19. Yasuhara A, Yamayoshi S, Kiso M, Sakai-Tagawa Y, Okuda M, Kawaoka Y. A broadly protective human monoclonal antibody targeting the sialidase activity of influenza A and B virus neuraminidases. Nat Commun. 13(1):6602-0. https://doi.org/10.1038/s41467-022-34521-0 (2022)

20. Wang T, 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. 611(7935):358-364. https://doi.org/10.1038/s41586-022-05388-4 (2022)

21. Hanata N, Ota M, Tsuchida Y, Nagafuchi Y, Okamura T, Shoda H, Fujio K. Serum extracellular traps associate with the activation of myeloid cells in SLE patients with the low level of anti-DNA antibodies. Sci Rep. 12(1):18397. https://doi.org/10.1038/s41598-022-23076-1 (2022)

22. Yamayoshi S, Iwatsuki-Horimoto K, Okuda M, Ujie M, Yasuhara A, Murakami J, Duong C, Hamabata T, Ito M, Chiba S, Kobayashi R, Takahashi S, Mitamura K, Hagihara M, Shibata A, Uwamino Y, Hasegawa N, Ebina T, Izumi A, Kato H, Nakajima H, Sugaya N, Seki Y, Iqbal A, Kamimaki I, Yamazaki M, Kawaoka Y, Furuse Y. Age-Stratified Seroprevalence of SARS-CoV-2 Antibodies before and during the Vaccination Era, Japan, February 2020-March 2022. Emerg Infect Dis. 28(11):2198-2205. https://doi.org/10.3201/eid2811.221127 (2022)

23. Narita M, Denk T, Matsuo Y, Sugiyama T, Kikuguchi C, Ito S, Sato N, Suzuki T, Hashimoto S, Machova I, Tesina P, Beckmann R, Inada T. A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation. Nat Commun. 13(1):6411-9. https://doi.org/10.1038/s41467-022-34097-9 (2022)

24. Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O. Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility. Nat Commun. 13(1):6208-x. https://doi.org/10.1038/s41467-022-34017-x (2022)

25. Ohta M, Kambayashi Y, Mita H, Kuroda T, Bannai H, Tsujimura K, Yamanaka T, Garvey M, Cullinane A, Yamayoshi S, Kawaoka Y, Nemoto M. Protective efficacy of a reverse genetics-derived inactivated vaccine against equine influenza virus in horses. Vaccine. 40(44):6362-6366. https://doi.org/10.1016/j.vaccine.2022.09.047 (2022)