Publications

Journal articles (†, equal contribution; *, corresponding author）

Please see Google Scholar Citations for the citation 

Preprint

ii. Koichi Kitao, Kenji Ichiyanagi, So Nakagawa. Birth of protein-coding exons by ancient domestication of LINE retrotransposon. bioRxiv doi: https://doi.org/10.1101/2024.04.25.591049

i. Masato Ohtsuka, Jurai Imafuku, Shuho Hori, Aki Kurosaki, Ayaka Nakamura, Tsubasa Nakahara, Takashi Yahata, Kolari Bhat, Steven Papastefan, So Nakagawa, Rolen M Quadros, Hiromi Miura, Channabasavaiah B Gurumurthy. Delivering mRNAs to mouse tissues using the SEND system. bioRxiv doi: https://www.biorxiv.org/content/10.1101/2023.01.28.522652v1

Peer-reviewed

84. Sakaguchi S*, Nakano T, Nakagawa S*, (2024) NeoRdRp2 with improved seed data, annotations, and scoring. Frontiers in Virology 4: 1378695. DOI: 10.3389/fviro.2024.1378695  Web PDF

83. Takada K, Orba Y, Kida Y, Wu J, Ono C, Matsuura Y, Nakagawa S, Sawa H, Watanabe T. (2024) Genes involved in the limited spread of SARS-CoV-2 in the lower respiratory airways of hamsters may be associated with adaptive evolution. Journal of Virology. 16:e0178423 doi: 10.1128/jvi.01784-23. Web PDF

82. Oka A*, Hadano S, Ueda MT, Nakagawa S, Komaki G, Ando T. (2024) Rare CRHR2 and GRM8 variants identified as candidate factors associated with eating disorders in Japanese patients by whole exome sequencing. Heliyon 2024: e28643. DOI: doi.org/10.1016/j.heliyon.2024.e28643. Web PDF

81. Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K*. (2024) Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Reports 43(2): 113697.  DOI: 10.1016/j.celrep.2024.113697. Web PDF

80. Nakagawa S†*, Katayama T†, Jin L†, Wu J, Kryukov K, Oyachi R, Takeuchi JS, Fujisawa T, Asano S, Komatsu M, Onami J, Abe T*, Arita M*.  (2023) SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan. Genes & Genetic Systems 98(5): 221-237. DOI: 10.1266/ggs.23-00085 Web PDF

79. 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*. (2023) Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. Journal of Virology 97(10): e0101123. DOI: 10.1128/jvi.01011-23 Web PDF

78. Kameda K†, Yanagiya R†, Miyatake Y†, Carreras J, Higuchi H, Murayama H, Ishida T, Ito A, Iida S, Fukuhara N, Harigae H, Fujioka Y, Takahashi N, Wada H, Ishida F, Nakazawa H, Ishihara R, Murakami Y, Tagawa H, Matsuura T, Nakagawa S, Iwabuchi S, Hashimoto S, Imadome KI, Nakamura N, Ishizawa K, Kanda Y, Ando K, Kotani A.* (2023) Hepatic niche leads to aggressive natural killer cell leukemia proliferation through transferrin-transferrin receptor 1 axis. Blood 142(4): 352-364. DOI: 10.1182/blood.2022018597 Web PDF 

77. Kitao K*, Shoji H, Miyazawa T, Nakagawa S*. (2023) Dynamic evolution of retroviral envelope genes in egg-laying mammalian genomes. Molecular Biology and Evolution. 40(5): msad090. DOI: 10.1093/molbev/msad090 Web PDF

76. Takada K, Ueda MT, Shichinohe S, Kida Y, Ono C, Matsuura Y, Watanabe T*, Nakagawa S*. (2023) Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene. iScience 26(3):106210. DOI: 10.1016/j.isci.2023.106210 Web PDF

75. Ohkura S*, Horie M, Shimizu M, Nakagawa S, Osanai H, Miyagawa Y, Morita R. Characterization of Megabat-Favored, CA-Dependent Susceptibility to Retrovirus Infection. Journal of Virology 97(3): e0180322. DOI: 10.1128/jvi.01803-22 Web PDF

74. Shoji H†, Kitao K†, Miyazawa T*, Nakagawa S*. Potentially reduced fusogenicity of syncytin-2 in New World monkeys. FEBS Open Bio 13(3): 459-467. DOI: 10.1002/2211-5463.13555 Web PDF

73. Kimura I†, Yamasoba D†, Nasser H†, Zahradnik J†, Kosugi Y†, Wu J†, Nagata K, Uriu K, Tanaka YL, Ito J, Shimizu R, Tan TS, Butlertanaka EP, Asakura H, Sadamasu K, Yoshimura K, Ueno K, Takaori-Kondo A, Schreiber G, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Toyoda M, Shirakawa K, Irie T, Saito A*, Nakagawa S*, Ikeda T*, Sato K*. The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant. iScience 25(12): 105720. DOI: 10.1016/j.isci.2022.105720 Web PDF

72. Kitao K, Miyazawa T*, Nakagawa S*. (2022) Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase. Virus Evolution 8(2): veac084 Web PDF

71. Sakaguchi S, Urayama S, Takaki Y, Wu H, Suzuki Y, Nunoura T, Nakano T*, Nakagawa S*. (2022) NeoRdRp: A Comprehensive Dataset for Identifying RNA-dependent RNA Polymerases of Various RNA Viruses from Metatranscriptomic Data. Microbes and Environments 37(3): ME22001 Web PDF

70. Miyake A, Ngo MH, Wulandari S, Shimojima M, Nakagawa S, Kawasaki J, Nishigaki K. (2022) Convergent evolution of antiviral machinery derived from endogenous retrovirus truncated envelope genes in multiple species. Proceedings of the National Academy of Sciences of the United States of America 119(26): e2114441119. DOI: doi.org/10.1073/pnas.2114441119 Web PDF

69. Takeuchi K*, Ikeda Y, Senda M, Harada A, Okuwaki K, Fukuzawa K, Nakagawa S, Yu HY, Nagase L, Imai M, Sasaki M, Lo YH, Ito D, Osaka N, Fujii Y, Sasaki AT*, Senda T*. (2022) The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity. Structure 30(6): 886-899. DOI: doi.org/10.1016/j.str.2022.04.004 Web PDF

68. Komiya S, Matsuo Y*, Nakagawa S, Morimoto Y, Kryukov K, Okada H, Hirota K. (2022) MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting. BMC Medical Genomics. 15(1): 68. DOI: 10.1186/s12920-022-01218-8. Web PDF 

67. Sakai H*, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada S, Ohkawa Y, Kikugawa T, Saika T, Imai, Y*. (2022) Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience 25(3): 103928. DOI: 10.1016/j.isci.2022.103928  Web PDF 

66. Saito A, Irie T, Suzuki R, Maemura T, Nasser H, Uriu K, Kosugi Y, Shirakawa K, Sadamasu K, Kimura I, Ito J, Wu J, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Loeber S, Tsuda M, Wang L, Ozono S, Butlertanaka EP, Tanaka YL, Shimizu R, Shimizu K, Yoshimatsu K, Kawabata R, Sakaguchi T, Tokunaga K, Yoshida I, Asakura H, Nagashima M, Kazuma Y, Nomura R, Horisawa Y, Yoshimura K, Takaori-Kondo A, Imai M; Genotype to Phenotype Japan (G2P-Japan) Consortium, Tanaka S*, Nakagawa S*, Ikeda T*, Fukuhara T*, Kawaoka Y*, Sato K.* (2022) Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature. 602(7896): 300–306. DOI: 10.1038/s41586-021-04266-9. Web PDF

Media:  Science, The Medical News

65. Kimura I, Kosugi Y, Wu J, Zahradnik J, Yamasoba D, Butlertanaka EP, Tanaka YL, Uriu K, Liu Y, Morizako N, Shirakawa K, Kazuma Y, Nomura R, Horisawa Y, Tokunaga K, Ueno T, Takaori-Kondo A, Schreiber G, Arase H, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Motozono C, Saito A, Nakagawa S*, Sato K*. (2022) The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Reports 38(2): 110218. DOI: 10.1016/j.celrep.2021.110218 Web PDF

64. Kitao K, Sumiyoshi A, Nakagawa S, Matsumoto Y, Mizuno T, Miyazawa T* (2021) Systematic identification of endogenous retroviral protein-coding genes expressed in canine oral malignant melanoma. Frontiers in Virology. 1: 785678. DOI: 10.3389/fviro.2021.785678. Web PDF

63. Kitao K, Nakagawa S, Miyazawa T* (2021) An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation. Retrovirology 18(1): 36 (2021). DOI: 10.1186/s12977-021-00580-2. Web PDF 

62. Uriu K, Kimura I, Shirakawa K, Takaori-Kondo A, Nakada TA, Kaneda A, Nakagawa S, Sato K*; Genotype to Phenotype Japan (G2P-Japan) Consortium. (2021) Neutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum. New England Journal of Medicine. 385(25): 2397-2399. DOI: 10.1056/NEJMc2114706 Web PDF

61. Hirabayashi A, Yahara K, Mitsuhashi S, Nakagawa S, Imanishi T, Ha VTT, Nguyen AV, Nguyen ST, Shibayama K, Suzuki M* (2021) Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam. PLOS ONE. 16(7): e0231119. DOI: 10.1371/journal.pone.0231119 Web PDF

60. Motozono C, Toyoda M†, Zahradnik J†, Saito A†, Nasser H†, Tan TS, Ngare I, Kimura I, Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J, Torii S, Yonekawa A, Shimono N, Nagasaki Y, Minami R, Toya T, Sekiya N, Fukuhara T, Matsuura Y, Schreiber G, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda T*, Nakagawa S*, Ueno T*, Sato K*. (2021) SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host & Microbe 29(7): 1124-1136. PMID: 34171266  PMCID: PMC8205251  DOI: 10.1016/j.chom.2021.06.006 Web PDF

Media: NewsMedical.net,

59. Matsuzawa A, Lee J, Nakagawa S, Itoh J, Takahashi Ueda M, Mitsuhashi S, Kochi Y, Kaneko-Ishino T, Ishino F.* (2021) HERV-derived ERVPb1 is conserved in Simiiformes, exhibiting expression in hematopoietic cell lineages including macro-phages. International Journal of Molecular Sciences. 22(9): 4504. PMID: 33925887 DOI: 10.3390/ijms22094504 Web PDF

58. Kimura I, Konno Y, Uriu K, Hopfensperge K, Sauter D, Nakagawa S, Sato K* (2021) Sarbecovirus ORF6 proteins hamper the Induction of interferon signaling by blocking mRNA nuclear export. Cell Reports. 34: 108916. PMID: 33765414  PMCID: PMC7953434 DOI: 10.1016/j.celrep.2021.108916 Web PDF

57. Mitsuhashi S, Nakagawa S, Sasaki-Honda M, Sakurai H, Frith MC, Mitsuhashi H* (2021) Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells. Human Molecular Genetics 30(7): 552–563. PMID: 33693705 DOI: 10.1093/hmg/ddab063 Web PDF

56. Shiraishi Y, Kryukov K, Tomomatsu K, Sakamaki F, Inoue S, Nakagawa S, Imanishi T, Asano K* (2021) Diagnosis of pleural empyema/parapneumonic effusion by next-generation sequencing. Infectious Diseases 53(6): 450-459. PMID: 33689538 DOI: 10.1080/23744235.2021.1892178 Web PDF

55. Chikuma S*, Yamanaka S†, Nakagawa S†, Ueda MT†, Hayabuchi H, Tokifuji Y, Kanayama M, Okamura T, Arase H, Yoshimura A. (2021) TRIM28 expression on dendritic cells prevents excessive T cell priming by silencing endogenous retrovirus. Journal of Immunology 206(7):1528-1539. PMID: 33619215  DOI: 10.4049/jimmunol.2001003 Web PDF

54. Ohno A, Umezawa K, Asai S, Kryukov K, Nakagawa S, Miyachi H, Imanishi T* (2021) Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer. Scientific Reports 11: 3436. PMID: 33564026  DOI: 10.1038/s41598-021-82903-z Web PDF

53. Matsuo Y*, Komiya S, Yasumizu Y, Yasuoka Y, Mizushima K, Takagi Y, Kryukov K, Fukuda A, Morimoto Y, Naito Y, Okada H, Bono H, Nakagawa S, Hirota K. (2021) Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. BMC Microbiology 21: 35. PMID: 33499799  PMCID: PMC7836573  DOI: 10.1186/s12866-021-02094-5 Web PDF

52. Kojima S, Yoshikawa K, Ito J, Nakagawa S, Parrish NF, Horie M, Kawano S*, Tomonaga K.* (2021) Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome. Proceedings of the National Academy of Sciences of the United States of America 118(5): e2010758118. PMID: 33495343  DOI: 10.1073/pnas.2010758118 Web PDF

Media: Phys.org

51. Nakagawa S†*, Kawashima M†, Miyatake Y†, Kudo K, Kotaki R, Ando K, Kotani A.* (2021) Expression of ERV3-1 in leukocytes of acute myelogenous leukemia patients. Gene 773: 145363. PMID: 33338509  DOI: 10.1016/j.gene.2020.145363 Web PDF

50. Orba, Y.*, Matsuno, K., Nakao, R., Kryukov, K., Saito, Y., Kawamori, F., Vega, A.L., Watanabe, T., Maemura, T., Sasaki, M., Hall, W.W., Hall, R.A., Pereira, J.A., Nakagawa, S., Sawa, H. (2021) Diverse mosquito specific flaviviruses in the Bolivian Amazon basin. Journal of General Virology. 102(3): 001518. PMID: 33416463  DOI: 10.1099/jgv.0.001518 Web PDF

49. Ueda, M.T., Kryukov, K., Mitsuhashi, S, Mitsuhashi, H, Imanishi, T, and Nakagawa, S.* (2020) Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains. Mobile DNA 11: 29. PMID: 32963593  PMCID: PMC7499964  DOI: 10.1186/s13100-020-00224-w Web PDF

48. Konno Y†, Kimura I†, Uriu K, Fukushi M, Irie T, Koyanagi Y, Sauter D, Gifford RJ; USFQ-COVID19 Consortium, Nakagawa S, Sato K.* (2020) SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant. Cell Reports 32: 108185.  PMID: 32941788  DOI: 10.1016/j.celrep.2020.108185 Web PDF

Media: The Scientist, Forbes, STAT

47. Nakano, Y., Yamamoto, K., Ueda, M. T., Soper, A., Konno, Y., Kimura, I., Uriu, K., Kumata, R., Aso, H., Misawa, N., Nagaoka, S., Shimizu, S., Mitsumune, K., Kosugi, Y., Juarez-Fernandez, G., Ito, J., Nakagawa, S., Ikeda, T., Koyanagi, Y., Harris, R. S. and Sato, K.* (2020) A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans. PLoS Pathogens 16(9): e1008812. PMID: 32913367  DOI: 10.1371/journal.ppat.1008812 Web PDF

46. Kotaki R, Kawashima M, Yamaguchi A, Suzuki N, Koyama-Nasu R, Ogiya D, Okuyama K, Yamamoto Y, Takamatsu M, Kurosaki N, Ando K, Murata A, Ohtsuka M, Nakagawa S, Katagiri K, Kotani A. (2020) Overexpression of miR-669m inhibits erythroblast differentiation. Scientific Reports 10(1):13554. PMID: 32782283  DOI: 10.1038/s41598-020-70442-y Web PDF

45. Saito M*, Hasegawa H*, Yamauchi S, Nakagawa S, Sasaki D, Nao N, Tanio M, Wada Y, Matsudaira T, Momose H, Kuramitsu M, Yamagishi M, Nakashima M, Nakahata S, Iha H, Ogata M, Imaizumi Y, Uchimaru K, Morishita K, Watanabe T, Miyazaki Y, Yanagihara K. (2020) A high-throughput detection method for the clonality of Human T-cell leukemia virus type-1-infected cells in vivo. International Journal of Hematology 112(3):300-306. PMID: 32725607  DOI: 10.1007/s12185-020-02935-5 Web PDF

44. Kryukov, K.*, Ueda, M.T., Nakagawa, S.  and Imanishi, T. (2020) Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. GigaScience 9(7): giaa072. PMID: 32627830 DOI: 10.1093/gigascience/giaa072  Web PDF

43. Oka A*, Takagi A, Komiyama E, Yoshihara N, Mano S, Hosomichi K, Suzuki S, Haida Y, Motosugi N, Hatanaka T, Kimura M, Ueda MT, Nakagawa, S, Miura H, Ohtsuka M, Tanaka M, Komiyama T, Otomo A, Hadano S, Mabuchi T, Beck S, Inoko H, Ikeda S.* (2020) Alopecia areata susceptibility variant in MHC region impacts expressions of genes contributing to hair keratinization and is involved in hair loss. EBioMedicine 57:102810. PMID: 32580135 DOI: 10.1016/j.ebiom.2020.102810  Web PDF

42. Otomo, A.*†, Ueda, M.T.†, Fujie, T., Hasebe, A., Suematsu, Y., Okamura, Y., Takeoka, S., Hadano, S., and Nakagawa, S.* (2020) Efficient differentiation and polarization of primary cultured neurons on poly(lactic acid) scaffolds with microgrooved structures. Scientific Reports 10: 6716. PMID: 32317746  DOI: 10.1038/s41598-020-63537-z Web PDF

41. Ishihara, T., Watanabe, N., Inoue, S., Aoki, H., Tsuji, T., Yamamoto, B., Yanagi, H., Oki, M., Kryukov, K., Nakagawa, S., Inokuchi, S., Ozawa, H., and Imanishi, T.* (2020) Usefulness of next-generation DNA sequencing for the diagnosis of urinary tract infection. Drug Discoveries & Therapeutics 14(1):42-49. PMID: 32101813 DOI: 10.5582/ddt.2020.01000 Web PDF

40. Hashimoto-Gotoh, A.†, Yoshikawa, R.†, Nakagawa, S., Okamoto, M., and Miyazawa, T.* (2020) Phylogenetic analyses of simian foamy virus from Yakushima macaques (Macaca fuscata yakui) reveal ancient sub-speciation event took place in Japanese macaques. Gene 734: 144382. PMID: 31978513 DOI: 10.1016/j.gene.2020.144382 Web PDF

39. Sakaguchi, S.*, Nakagawa, S., Mitsuhashi, S., Ogawa, M., Sugiyama, K., Tamukai, K., Koide, R., Katayama, Y., Nakano, T., Makino, S., Imanishi, T., Miyazawa, T., and Mizutani, T. (2020) Molecular characterization of feline paramyxovirus in Japanese cat populations. Archives of Virology  165(2): 413-418. PMID: 31823012  DOI: 10.1007/s00705-019-04480-x Web PDF

38. Nakagawa, S., Inoue, S.*, Kryukov, K., Yamagishi, J., Ohno, A., Hayashida, K., Nakazwe, R., Kalumbi, M., Mwenya, D., Asami, N., Sugimoto, C., Mutengo, M. M., Imanishi, T.* (2019) Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia. Clinical & Translational Immunology 8: e1087. PMID: 31709051 PMCID: PMC6831930 DOI: 10.1002/cti2.1087 Web PDF

   Oxford Nanopore Webpage

37. Mukai, Y., Tomita, Y., Kryukov, K., Nakagawa, S., Ozawa, M., Matsui, T., Tomonaga, K., Imanishi, T., Kawaoka, Y., Watanabe, T.*, Horie, M.* (2019) Identification of a distinct lineage of aviadenovirus from crane feces. Virus Genes 55(6): 815-824. PMID: 31549291 DOI: 10.1007/s11262-019-01703-w Web PDF

36. Tanaka, H., Matsuo, Y., Nakagawa, S., Nishi, K., Okamoto, A., Kai, S., Iwai, T., Tabata, Y., Tajima, T., Satoh, M., Kryukov, K., Imanishi, T., Hirota, K.* (2019) Real-time diagnostic analysis of MinION™-based metagenomic sequencing in clinical microbiology evaluation: a case report. JA Clinical Reports 5:24. PMID: 32025980 DOI: 10.1186/s40981-019-0244-z Web PDF

35. Kryukov, K.*, Ueda, M.T., Nakagawa, S.  and Imanishi, T. (2019) Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences. Bioinformatics 35(19): 3826–3828. PMID: 30799504 DOI: 10.1093/bioinformatics/btz144 Web PDF

34. Kai, S., Matsuo, Y.*, Nakagawa, S., Kryukov, K., Matsukawa, S., Tanaka, H., Iwai, T., Imanishi, T., and Hirota K.* (2019) Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer. FEBS Open Bio, 9: 548-557. PMID: 30868063 PMCID: PMC6396348 DOI: 10.1002/2211-5463.12590 Web PDF

   The most downloaded article was published in 2019

33. Koide, R., Yoshikawa, R., Okamoto, M.*, Sakaguchi, S., Suzuki, J., Isa, T., Nakagawa, S., Sakawaki, H., Miura, T., Miyazawa, T.* (2019) Experimental infection of Japanese macaques with simian retrovirus 5. Journal of General Virology, 100(2): 266-277. PMID: 30608228 DOI: 10.1099/jgv.0.001199 Web PDF

32. Kryukov, K., Ueda, M.T., Imanishi, T. and Nakagawa, S.* (2019) Systematic survey of non-retroviral virus-like elements in eukaryotic genomes.  Virus Research, 262:30-36. PMID: 29425804 DOI: 10.1016/j.virusres.2018.02.002. Web PDF

31. Sato, K., Otomo, A., Ueda, M.T., Hiratsuka, Y., Suzuki-Utsunomiya, K., Sugiyama, J., Murakoshi, S., Mitsui, S., Ono, S., Nakagawa, S., Shang, H.F., and Hadano, S.* (2018) Altered oligomeric states in pathogenic ALS2 variants associated with juvenile motor neuron diseases cause loss of ALS2-mediated endosomal function. Journal of Biological Chemistry, 293(44): 17135-17153. PMID: 30224357 PMCID: PMC6222102 DOI: 10.1074/jbc.RA118.003849 Web PDF

30. Watanabe, N., Kryukov, K., Nakagawa, S., Takeuchi, J.S., Takeshita, M., Kirimura, Y., Mitsuhashi, S., Ishihara, T., Aoki, H., Inokuchi, S., Imanishi, T., and Inoue, S.* (2018) Detection of pathogenic bacteria in the blood from sepsis patients using 16S rRNA gene amplicon sequencing analysis. PLOS ONE, 13(8): e0202049.  PMID: 30110400 DOI: 10.1371/journal.pone.0202049 Web PDF

29. Konno, Y., Nagaoka, S., Kimura, I., Yamamoto, K., Kagawa, Y., Kumata, R., Aso, H., Ueda, M.T., Nakagawa, S., Kobayashi, T., Koyanagi, Y. and Sato, K.* (2018) New World feline APOBEC3 potently controls inter-genus lentiviral transmission. Retrovirology, 15: 31. PMID: 29636069 PMCID: PMC5894237 DOI: 10.1186/s12977-018-0414-5  Web PDF

28. Konno, Y.†, Nagaoka, S.†, Kimura, I.†, Ueda, M.T., Kumata, R., Ito, J., Nakagawa, S., Kobayashi, T., Koyanagi, Y. and Sato, K.* (2018) A naturally occurring feline APOBEC3 variant that loses anti-lentiviral activity by lacking two amino acid residues. Journal of General Virology, 99(5): 704-709. PMID: 29611801 DOI: 10.1099/jgv.0.001046  Web PDF

27. Kurosaki, Y.†*, Ueda, M.T.†, Nakano, Y., Yasuda, J., Koyanagi, Y., Sato, K. and Nakagawa, S.* (2018) Different effects of two mutations on the infectivity of Ebola virus glycoprotein in nine mammalian species. Journal of General Virology. 99(2): 181-186. PMID: 29300152 DOI: 10.1099/jgv.0.000999 Web PDF

26. Mitsuhashi,S.*, Nakagawa, S., Ueda M.T., Imanishi, T., Frith M. C., and Mitsuhashi, H. (2017) Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy. Scientific Reports, 7: 14789. PMID: 29093467 PMCID: PMC5665936 DOI: 10.1038/s41598-017-13712-6 Web PDF

Oxford Nanopore Technologies

25. Sakurai, T., Nakagawa, S., Bai, H., Bai, R., Kusama, K., Ideta, A., Aoyagi, Y., Kaneko, K., Iga, K., Yasuda, J., Miyazawa, T., and Imakawa, K.* (2017) Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling. Biochemical Journal, 474: 3499-3512. PMID: 28899944 PMCID: PMC5633919 DOI: 10.1042/BCJ20170531 Web PDF

24. Mitsuhashi,S.†, Kryukov, K.†, Nakagawa, S.†, Takeuchi, J.S., Shiraishi, Y., Asano, K. and Imanishi, T.* (2017) A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer. Scientific Reports,7: 5657. PMID: 29093467 PMCID: PMC5665936 DOI: 10.1038/s41598-017-13712-6 Web PDF

Oxford Nanopore Technologies, Nature Japan

23. Oka, A.*, Asano, Y., Hasegawa, M., Fujimoto, M., Ishikawa, O., Kuwana, M., Kawaguchi, Y., Yamamoto, T., Takahashi, H., Goto, D., Endo, H., Jinnin, M., Mano, S., Hosomichi, K., Mabuchi, T., Ueda, M.T., Nakagawa, S., Beck, S., Bahram, S., Takehara, K., Sato, S. and Ihn, H. (2017) RXRB is a MHC-encoded susceptibility gene associated with anti-topoisomerase I antibody-positive systemic sclerosis. Journal of Investigative Dermatology, 137(9):1878-1886. PMID: 28506627 DOI: 10.1016/j.jid.2017.04.028 Web PDF

22. Nakagawa, S.*, Niimura, Y. and Gojobori, T. (2017) Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes. Nucleic Acids Research, 45(7): 3922-3931. PMID: 28334743 PMCID: PMC5397173 DOI: 10.1093/nar/gkx124 Web PDF

21. Ueda, M.T.†*, Kurosaki, Y.†, Izumi, T., Nakano, Y., Oloniniyi, O.K., Yasuda, J., Koyanagi, Y., Sato, K.* and Nakagawa, S.* (2017) Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in infection efficiency. Genes to Cells, 22(2):148-159. PMID: 28084671 DOI: 10.1111/gtc.12463 Web PDF

報道：日経産業新聞、日刊工業新聞など

Most Accessed Articles published in 2016-2017

20. Nakagawa, S.* and Takahashi, M.U. (2016) gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. Database (Oxford), 2016: baw087. PMID: 27242033 PMCID: PMC4885607 DOI: 10.1093/database/baw087 Web PDF

19. Akihito, Akishinonomiya, F., Ikeda, Y., Aizawa, M., Nakagawa, S., Umehara, Y., Yonezawa, T., Mano, S., Hasegawa, M., Nakabo, T. and Gojobori, T.* (2016) Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses. Gene 576(2): 593-602. PMID: 26475939 DOI: 10.1016/j.gene.2015.10.014 Web PDF

18. Miyaho, R.N., Nakagawa, S.*, Hashimoto-Gotoh, A., Nakaya, Y., Shimode, S., Sakaguchi, S., Yoshikawa, R., Takahashi, M.U., Miyazawa, T.* (2015) Susceptibility of domestic animals to a pseudotype virus bearing RD-114 virus envelope protein. Gene 567(2): 189-195. PMID: 25936996 DOI: 10.1016/j.gene.2015.04.079 Web PDF

Please see the correction as well: Web PDF

17. Kawamura, M., Watanabe, S., Odahara, Y., Nakagawa, S., Endo, Y., Tsujimoto, H., Nishigaki, K.* (2015) Genetic diversity in the feline leukemia virus gag gene. Virus Research 204:74-81. PMID: 25892717 DOI: 10.1016/j.virusres.2015.04.008 Web PDF

16. Yoshikawa, R., Okamoto, M., Sakaguchi, S., Nakagawa, S., Miura, T., Hirai, H., Miyazawa, T.* (2015) Simian Retrovirus 4 Induces Lethal Acute Thrombocytopenia in Japanese Macaques. Journal of Virology 89:3965-3975. PMID: 25609821 PMCID: PMC4403420 DOI: 10.1128/JVI.03611-14 Web PDF

15. Shimode, S., Nakagawa, S., Miyazawa, T.* (2015) Multiple invasions of infectious retrovirus in cat genomes. Scientific Reports 5, 8164. PMID: 25641657 PMCID: PMC4313119 DOI: 10.1038/srep08164 Web PDF

14. Yoshikawa, R.†, Nakagawa, S.†*, Okamura, M. and Miyazawa, T*. (2014) Construction of an infectious clone of simian foamy virus of Japanese macaque (SFVjm) and phylogenetic analyses of SFVjm isolates.  Gene 548(1):149-154. PMID: 25017058 DOI: 10.1016/j.gene.2014.07.025 Web PDF

13. Sakaguchi, S., Nakagawa, S., Yoshikawa, R., Kuwahara, C., Hagiwara, H., Asai, K., Kawakami, K., Yamamoto, Y., Ogawa, M. and Miyazawa, T.* (2014) Genetic diversity of feline morbilliviruses isolated in Japan. Journal of General Virology 95(7):1464-1468. PMID: 24728711 DOI: 10.1099/vir.0.065029-0 Web PDF

12. Shimode, S.†, Nakagawa, S.†, Yoshikawa, R., Shojima, T. and Miyazawa, T.* (2014) Heterogeneity of koala retrovirus isolates. FEBS Letters 588(1):41-46. PMID: 24239536 DOI: 10.1016/j.febslet.2013.10.046 Web PDF

11. Sakurai, T.†, Nakagawa, S.†, Kim, MS.†, Bai, H., Bai, R., Li, JY., Min, KS., Ideta, A., Aoyagi, Y. and Imakawa, K.* (2013) Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese Black cattle during peri-implantation period. PLoS ONE 8(11), e80427. PMID: 24348910 PMCID: PMC3857836 DOI: 10.1371/journal.pone.0080427 Web PDF

10. Nakaya, Y., Koshi, K., Nakagawa, S., Hashizume, K. and Miyazawa, T.* (2013) Fematrin-1 is involved in fetomaternal cell-to-cell fusion in Bovinae placenta and contributed to diversity of ruminant placentation. Journal of Virology 87(19):10563-72. PMID: 23864631 PMCID: PMC3807419 DOI: 10.1128/JVI.01398-13 Web PDF

Nature Japan , Optronics

9. Shojima, T., Yoshikawa, R., Hoshino, S., Shimode, S., Nakagawa, S., Ohata, T., Nakaoka, R. and Miyazawa, T.* (2013) Identification of a Novel Subgroup of Koala Retrovirus from Koalas in Japanese Zoos. Journal of Virology 87(17):9943-9948. PMID: 23824806 PMCID: PMC3754120 DOI: 10.1128/JVI.01385-13 Web PDF

8. Nakagawa, S.†, Gisselbrecht, S. S.†, Rogers, J. M.†, Hartl, D. L.* and Bulyk, M. L.* (2013) DNA binding specificity changes in the evolution of forkhead transcription factors.  Proceedings of the National Academy of Sciences of the United States of America. 110(30):12349-12354. PMID: 23836653 PMCID: PMC3725104 DOI: 10.1073/pnas.1310430110 Web PDF

Media: Science Editors' Choice (Vol. 341, No. 6145, 2013)

7. Watanabe, S., Kawamura, M., Anai, Y., Ochi, H., Odahara, Y., Nakagawa, S., Endo, Y., Tsujimoto, H. and Nishigaki, K.* (2013) Phylogenetic and Structural Diversity in the Feline Leukemia Virus Env Gene. PLoS ONE 8(4): e61009. PMID: 23593376 PMCID: PMC3623909 DOI: 10.1371/journal.pone.0061009 Web PDF

6. Nakagawa, S., Bai, H., Sakurai, T., Nakaya, Y., Konno, T., Miyazawa, T., Gojobori, T. and Imakawa, K.* (2013) Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation. Genome Biology and Evolution 5(2):296-306. PMID: 23335121 PMCID: PMC3590765 DOI: 10.1093/gbe/evt007 Web PDF

5. Takeda, E., Nakagawa, S., Nakaya, Y., Tanaka, A., Miyazawa, T. and Yasuda, J.* (2012) Identification and Functional Analysis of Three Isoforms of Bovine BST-2. PLoS ONE 7(7): e41483. PMID: 22911799 PMCID: PMC3401110 DOI: 10.1371/journal.pone.0041483 Web PDF

4. Anai, Y.†, Ochi, H.†, Watanabe, S.†, Nakagawa, S., Kawamura, M., Gojobori, T. and Nishigaki, K.* (2012) Infectious endogenous retroviruses in cats and emergence of recombinant viruses. Journal of Virology 86(16):8634-44. PMID: 22674983 PMCID: PMC3421742 DOI: 10.1128/JVI.00280-12 Web PDF

3. Nakagawa, S., Niimura, Y., Miura, K. and Gojobori, T.* (2010) Dynamic evolution of translation initiation mechanisms in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America 107(14):6382-7. PMID: 20308567 PMCID: PMC2851962 DOI: 10.1073/pnas.1002036107 Web PDF

2. Hase, T., Tanaka, H., Suzuki, Y., Nakagawa, S. and Kitano, H.* (2009) Structure of protein interaction networks and their implications on drug design. PLoS Computational Biology 5(10): e1000550. PMID: 19876376 PMCID: PMC2760708 DOI: 10.1371/journal.pcbi.1000550 Web PDF

1. Nakagawa, S., Niimura, Y., Gojobori, T., Tanaka, H.* and Miura, K. (2008) Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Research, 36(3):861-871. PMID: 18086709 PMCID: PMC2241899 DOI: 10.1093/nar/gkm1102  Web PDF

Peer-reviewed (as a consortium member)

14. 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. Nature Communication. 14(1): 2671 (2023).

13. 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 Infectious Diseases, in press.

12. Torii S, Kim KS, Koseki J, Suzuki R, Iwanami S, Fujita Y, Jeong YD, Ito J, Asakura H, Nagashima M, Sadamasu K, Yoshimura K; Genotype to Phenotype Japan (G2P-Japan) Consortium; Sato K, Matsuura Y, Shimamura T, Iwami S, Fukuhara T. Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir. PLoS Pathogen, 19(3): e1011231 (2023).

11. 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 Infectious Diseases, 23(3): 280-281 (2023).

10. Saito A, Tamura T, Zahradnik J, Deguchi S, Tabata K, Anraku Y, Kimura I, Ito J, Yamasoba D, Nasser H, Toyoda M, Nagata K, Uriu K, Kosugi Y, Fujita S, Shofa M, Monira Begum M, Shimizu R, Oda Y, Suzuki R, Ito H, Nao N, Wang L, Tsuda M, Yoshimatsu K, Kuramochi J, Kita S, Sasaki-Tabata K, Fukuhara H, Maenaka K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Ueno T, Schreiber G, Takaori-Kondo A; Genotype to Phenotype Japan (G2P-Japan) Consortium, Shirakawa K, Sawa H, Irie T, Hashiguchi T, Takayama K, Matsuno K, Tanaka S, Ikeda T, Fukuhara T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant. Cell Host & Microbe 30(11): 1540-1555.e1 (2022).

9. Nasser H, Shimizu R, Ito J; Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito A, Sato K, Ikeda T. Monitoring fusion kinetics of viral and target cell membranes in living cells using a SARS-CoV-2 spike-protein-mediated membrane fusion assay. STAR Protocol 3(4): 101773 (2022).

8. Kimura I, Yamasoba D, Tamura T, Nao N, Suzuki T, Oda Y, Mitoma S, Ito J, Nasser H, Zahradnik J, Uriu K, Fujita S, Kosugi Y, Wang L, Tsuda M, Kishimoto M, Ito H, Suzuki R, Shimizu R, Begum MM, Yoshimatsu K, Kimura KT, Sasaki J, Sasaki-Tabata K, Yamamoto Y, Nagamoto T, Kanamune J, Kobiyama K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Shirakawa K, Takaori-Kondo A, Kuramochi J, Schreiber G, Ishii KJ; Genotype to Phenotype Japan (G2P-Japan) Consortium, Hashiguchi T, Ikeda T, Saito A, Fukuhara T, Tanaka S, Matsuno K, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell 185(21): 3992-4007 (2022).

7. Yamasoba D, Kosugi Y, Kimura I, Fujita S, Uriu K, Ito J, Sato K; Genotype to Phenotype Japan (G2P-Japan) Consortium. Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies. Lancet Infectious Diseases 22(7): 942-943 (2022).

6. Yamasoba D, Kimura I, Nasser H, Morioka Y, Nao N, Ito J, Uriu K, Tsuda M, Zahradnik J, Shirakawa K, Suzuki R, Kishimoto M, Kosugi Y, Kobiyama K, Hara T, Toyoda M, Tanaka YL, Butlertanaka EP, Shimizu R, Ito H, Wang L, Oda Y, Orba Y, Sasaki M, Nagata K, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Kuramochi J, Seki M, Fujiki R, Kaneda A, Shimada T, Nakada TA, Sakao S, Suzuki T, Ueno T, Takaori-Kondo A, Ishii KJ, Schreiber G; Genotype to Phenotype Japan (G2P-Japan) Consortium, Sawa H, Saito A, Irie T, Tanaka S, Matsuno K, Fukuhara T, Ikeda T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell 185(12): 2103-2115 (2022).

5. Uriu K, Cárdenas P, Muñoz E, Barragan V, Kosugi Y, Shirakawa K, Takaori-Kondo A, Ecuador-COVID19 Consortium, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato K. Characterization of the immune resistance of SARS-CoV-2 Mu variant and the robust immunity induced by Mu infection. Journal of Infectious Diseases 226(7): 1200-1203 (2022).

4. Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ; CITIID-NIHR BioResource COVID- Collaboration; Genotype to Phenotype Japan (GP-Japan) Consortium members; Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer K, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature 603(7902): 706–714 (2022).

3. Suzuki R, Yamasoba D, Kimura I, Wang L, Kishimoto M, Ito J, Morioka Y, Nao N, Nasser H, Uriu K, Kosugi Y, Tsuda M, Orba Y, Sasaki M, Shimizu R, Kawabata R, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K; Genotype to Phenotype Japan (G2P-Japan) Consortium, Sawa H, Ikeda T, Irie T, Matsuno K, Tanaka S, Fukuhara T, Sato K. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature 603(7902): 700–705 (2022).

2. Mlcochova P, Kemp S, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal DC, Goel N, Satwik A, Vaishya R, Agarwal M; Indian SARS-CoV-2 Genomics Consortium (INSACOG); Genotype to Phenotype Japan (G2P-Japan) Consortium; CITIID-NIHR BioResource COVID-19 Collaboration, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599(7883): 114-119 (2021).

1. Ferreira IATM, Kemp SA, Datir R, Saito A, Meng B, Rakshit P, Takaori-Kondo A, Kosugi Y, Uriu K, Kimura I, Shirakawa K, Abdullahi A, Agarwal A, Ozono S, Tokunaga K, Sato K, Gupta RK; CITIID-NIHR BioResource COVID-19 Collaboration, Indian SARS-CoV-2 Genomics Consortium; Genotype to Phenotype Japan (G2P-Japan) Consortium. SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. Journal of Infectious Diseases 224(6): 989-994 (2021).