研究業績

 (†: equal contribution, *: corresponding author）

2024

  1. 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
  2. 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
  3. 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. Web PDF
  4. 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. Web PDF

2023

  1. 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. Web PDF
  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*. (2023) Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. Journal of Virology 97(10): e0101123. Web PDF
  3. Nakagawa S*, Sakaguchi S, Ogura A, Mineta K, Endo T, Suzuki Y, Gojobori T. (2023) Current trends in RNA virus detection through metatranscriptome sequencing data. FEBS Open Bio 13(6): 992-1000. Web PDF
  4. 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. Web
  5. 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. Web PDF
  6. Shiraishi Y, Suzuki Y, Imanishi T, Asano K, et al. A Method to Evaluate and Eliminate Fungal Contamination in Household Air Conditioners. Indoor Air, vol. 2023, Article ID 8984619, 10 pages, 2023. Web
  7. 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. Web PDF
  8. Takeuchi K, Senda M, Ikeda Y, Okuwaki K, Fukuzawa K, Nakagawa S, Sasaki M, Sasaki AT, Senda T.* (2023) Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. FEBS Journal 290(18):4419-4428. Web PDF
  9. Ohkura S*, Shimizu M, Horie M, Nakagawa S, Osanai H, Miyagawa Y, Morita R*. (2023) Characterization of megabat-favored, CA-dependent susceptibility to retrovirus infection. Journal of Virology, 97(3):e0180322 Web PDF
  10. Kryukov, K., Imanishi, T., Nakagawa, S.* (2023) Nanopore sequencing data analysis of 16S rRNA genes using GenomeSync-GSTK system. Methods in Molecular Biology, 2632: 215-226 Web
  11. Jin J, Ogawa T, Hojo N, Kryukov K, Shimizu K, Ikawa T, Imanishi T, Okazaki T, Shiroguchi K. (2023) Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes. Proc Natl Acad Sci U S A. 120(1):e2210283120.  Web PDF
  12. Shoji H†, Kitao K†, Miyazawa T*, Nakagawa S*. (2023) Potentially reduced fusogenicity of syncytin-2 in New World monkeys. FEBS Open Bio. 13(3): 459-467. Web PDF
  13. 中川草 (2023) EVE研究に役立つデータベース. 実験医学 41(14): 2264-2266. Web

2022

  1. 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: 105720. (2022) Web PDF
  2. Cui G, Shimba A, Jin J, Ogawa T, Muramoto Y, Miyachi H, Abe S, Asahi T, Tani-Ichi S, Dijkstra JM, Iwamoto Y, Kryukov K, Zhu Y, Takami D, Hara T, Kitano S, Xu Y, Morita H, Zhang M, Zreka L, Miyata K, Kanaya T, Okumura S, Ito T, Hatano E, Takahashi Y, Watarai H, Oike Y, Imanishi T, Ohno H, Ohteki T, Minato N, Kubo M, Holländer GA, Ueno H, Noda T, Shiroguchi K, and Ikuta K (2022) A circulating subset of iNKT cells mediates antitumor and antiviral immunity. Science Immunology 7(76):eabj8760. PubMed Sci Immunol
  3. Kitao K, Miyazawa T*, Nakagawa S*. (2022) Monotreme-Specific Conserved Putative Proteins Derived from Retroviral Reverse Transcriptase. Virus Evolution 8(2):veac084. Web PDF
  4. 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
  5. Imakawa K, Kusama K, Kaneko-Ishino T, Nakagawa S, Kitao K, Miyazawa T, Ishino F. (2022) Endogenous Retroviruses and Placental Evolution, Development, and Diversity. Cells. 11(15):2458. Web PDF
  6. Kryukov K, Jin L, Nakagawa S*. (2022) Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format (NAF). Patterns 3(9):100562. Web PDF
  7. 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
  8. 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
  9. Yamaguchi R, Matsudaira I, Takeuchi H, Imanishi T, Kimura R, Tomita H, Kawashima R, and Taki Y (2022) RELN rs7341475 associates with brain structure in Japanese healthy females. Neuroscience 494: 38-50.
  10. Shinozuka Y, Suzuki N, Kaneko S, Kawai K, Kurumisawa T, Shimizu Y, Imanishi T, Ohno A, Takahashi M, and Isobe N (2022) Regression tree analysis of the relationship between the concentrations of antimicrobial components and the microbiota of normal milk from dairy cows. Journal of Veterinary Medical Science 84 (3): 310-318.
  11. Takeuchi H, Tomita H, Taki Y, Kikuchi Y, Ono Tanaka C, Yu Z, Matsudaira I, Nouchi R, Imanishi T, and Kawashima R (2022) A psychiatric disorder risk polymorphism of ITIH3 is associated with multiple neuroimaging phenotypes in young healthy adults. Psychiatry Clin Neurosci. (in press) doi: 10.1111/pcn.13347.
  12. Tanahashi M, Yamada S, Imanishi T, and Yamamoto Y (2021) Choropleth map of newly infected people with COVID-19 in the prefecture. 2021 19th International Conference on ICT and Knowledge Engineering (ICT&KE). 1-5. doi: 10.1109/ICTKE52386.2021.9665704.
  13. 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. Web PDF DOI: 10.1186/s12920-022-01218-8.
  14. 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. Web PDF
  15. 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; 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: 110218. Web PDF
  16. 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. Web PDF
  17. 中川草 新型コロナウイルスのゲノム解析 実験医学 40(6): 887-891. 2022. Web

2021

  1. 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
  2. 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). Web PDF
  3. 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 (2021) Web PDF
  4. Takeuchi H, Kimura R, Tomita H, Taki Y, Kikuchi Y, Matsudaira I, Nouchi R, Yokoyama R, Kotozaki Y, Nakagawa S, Hanawa S, Iizuka K, Sekiguchi A, Araki T, Miyauchi C, Ikeda S, Sakaki K, Kawata K, Nozawa T, Yokota S, Magistro D, Imanishi T, and Kawashima R (2021) Polygenic risk score for bipolar disorder associates with divergent thinking and brain structures of the prefrontal cortex. Human Brain Mapping 42(18): 6028-6037. PubMed PDF
  5. Shinozuka Y, Kawai K, Kurumisawa T, Shimizu Y, Imanishi T, Ohno A, Takahashi M, Kaneko S, and Suzuki N (2021) Examination of the microbiota of normal cow milk using MinIONTM nanopore sequencing. The Journal of Veterinary Science 83(11): 1620-1627. PubMed PDF
  6. Kutsuzawa N, Takihara T, Shiraishi Y, Kajiwara H, Imanishi T, Fukutomi Y, Kamei K, Takahashi M, Enokida K, Horio Y, Ito Y, Hayama N, Oguma T, and Asano K (2021) Occupational hypersensitivity pneumonitis in a Japanese citrus farmer. Internal Medicine 60(22): 3581-3584.PubMed PDF
  7. 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. Web PDF
  8. 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. Web PDF
  9. Jiaqi Wu, Takahiro Yonezawa, and Hirohisa Kishino (2021) Evolution of reproductive life history in mammals and the associated change of functional constraints. Genes 2021, 12(5), 740. [Genes]
  10. 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. Web PDF
  11. 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. Web PDF
  12. 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. Web PDF
  13. Chikuma S*, Yamanaka S†, Nakagawa S†, Ueda MT†, Hayabuchi H, Tokifuji Y, Kanayama M, Okamura T, Arase H, Yoshimura A. (2021)  RIM28 expression on dendritic cells prevents excessive T cell priming by silencing endogenous retrovirus. Journal of Immunology 206(7):1528-1539.
  14. Shiraishi Y, Kryukov K, Tomomatsu K, Sakamaki F, Inoue S, Nakagawa S, Imanishi T, and Asano K (2021) Diagnosis of pleural empyema/parapneumonic effusion by next-generation sequencing. Infectious Diseases 53(6): 450-459.[Inf Dis] [PubMed]
  15. Ohno A, Umezawa K, Asai S, Kryukov K, Nakagawa S, Miyachi H, and Imanishi T (2021) Rapid profiling of drug resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer. Scientific Reports 11: 3436. [Sci Rep] [PubMed]
  16. 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. Web PDF
  17. 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. Web PDF
  18. 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. Web PDF
  19. 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 Web
  20. 中川草 新型コロナウイルスの遺伝子と変異 生物の科学 遺伝 75(1): 47-51, 2021.
  21. 中川草 新型コロナウイルスのゲノム進化 実験医学増刊 39(2): 178-184. 2021.

2020

  1. 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. Web PDF
  2. 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. Web PDF
  3. 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. Web PDF
  4. 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. Web
  5. Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, and Oota H (2020) Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Communications Biology 3(1):437. [PubMed]
  6. Tanabe K, Ikeda M, Hayashi M, Matsuo K, Yasaka M, Machida H, Shida M, Katahira T, Imanishi T, Hirasawa T, Sato K, Yoshida H, and Mikami M (2020) Comprehensive serum glycopeptide spectra analysis combined with artificial intelligence (CSGSA-AI) to diagnose early-stage ovarian cancer. Cancers 12(9): 2373.[Cancers]
  7. Matsuo K, Tanabe K, Hayashi M, Ikeda M, Yasaka M, Machida H, Shida M, Sato K, Yoshida H, Hirasawa T, Imanishi T, and Mikami M (2020) Utility of comprehensive serum glycopeptide spectra analysis (CSGSA) for the detection of early stage epithelial ovarian cancer. Cancers 12(9): 2374. [Cancers]
  8. Ueda MT, 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. Web PDF
  9. Nakagawa, S.* and Miyazawa, T*. (2020) Genome evolution of SARS-CoV-2 and its virological characteristics. Inflammation and Regeneration, 40: 17. Web PDF
  10. Kryukov K, Ueda MT, 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. [GigaScience] [PubMed]
  11. Oka A*, Takagi A, Komiyama E, Mano S, Hosomichi K, Suzuki S, Motosugi N, Hatanaka T, Kimura M, Takahashi Ueda M, Nakagawa S, Miura H, Ohtsuka M, Haida Y, Tanaka M, Komiyama T, Otomo A, Hadano S, Mabuchi T, Beck S, Inoko H, Ikeda S.* (2020) Alopecia areata susceptibility variant identified by MHC risk haplotype sequencing reproduces symptomatic patched hair loss in mice. EBioMedicine 57: 102810.
  12. 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. PDF
  13. Hashimoto S, Nakajima F, Imanishi T, Kawai Y, Kato K, Kimura T, Miyata S, Takanashi M, Nishio M, Tokunaga K, and Satake M (2020) Implications of HLA diversity among regions for bone marrow donor searches in Japan. HLA 96: 24-42. [HLA] [PubMed]
  14. 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. [DDT] [PubMed]
  15. 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. [PubMed]
  16. Asogawa M, Ohno A, Nakagawa S, Ochiai E, Katahira Y, Sudo M, Osawa M, Sugisawa M, and Imanishi T (2020) Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study. Journal of Human Genetics 65(1):21-24. [PubMed] [J Hum Genet]
  17. 宮沢孝幸、中川草 (2020) 新型コロナウイルスSARS-CoV-2の比較ウイルス学と比較ゲノム解析実験医学 38 (8): 1338-1347. [Web] [大学広報]
  18. 中川草 (2020) 内在性ウイルス配列のデータベースを活用したバイオインフォマティクス解析 医学のあゆみ Vol. 273 No.12, p. 1149 – 1153. 2020.
  19. 中川草 (2020) 大量シークエンス解析によって明らかになるウイルスの素顔 〜新型コロナウイルスを含めて〜 ウイルス Vol. 70 No.1 p45 -48, 2020.
  20. 大槻海人、中川草、今川和彦 (2020) 胎盤の進化や多様性に関与するレトロトランスポゾン Journal of Mammalian Ova Research 37(2): 95-106, 2020.
  21. 大野歩、中川草、Kirill Kryukov、今西規（2020）ナノポアDNAシークエンサーを用いた迅速な細菌同定法 臨床化学 49(4):265-270. [目次]

2019

  1. Kryukov K, Ueda MT, Nakagawa S, and Imanishi T  (2019) Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences. Bioinformatics 35(19): 3826–3828 [PubMed] [Bioinformatics]
  2. Tanaka H, Matsuo Y, Nakagawa S, Nishi K, Okamoto A, Kai S, Iwai T, Tabata Y, Tajima T, Komatsu Y, Satoh M, Kryukov K, Imanishi T, and Hirota K (2019)
    Application of the MinION™ portable DNA sequencer in clinical microbiology evaluation: a case report. JA Clinical Reports 5:24 [PubMed]
  3. Hayashi M, Matsuo K, Tanabe K, Ikeda M, Miyazawa M, Yasaka M, Machida H, Shida M, Imanishi T, Grubbs BH, Hirasawa T, and Mikami M (2019) Comprehensive Serum Glycopeptide Spectra Analysis (CSGSA): A potential new tool for early detection of ovarian cancer. Cancers 11(5): 591. [PubMed] [Cancers]
  4. Mukai Y, Tomita Y, Kryukov K, Nakagawa S, Ozawa M, Matsui T, Tomonaga K, Imanishi T, Kawaoka Y, Watanabe T, and Horie M (2019)
    Identification of a distinct lineage of aviadenovirus from crane feces.Virus Genes 55(6): 815-824. [PubMed] [Virus Genes]
  5. Nakagawa S, Inoue S, Kryukov K, Yamagishi J, Ohno A, Hayashida K, Nakazwe R, Kalumbi M, Mwenya D, Asami N, Sugimoto C, Mutengo MM, and Imanishi T (2019) Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia. Clinical & Translational Immunology 8(11):e01087. [PubMed] [PDF]
  6. 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 (2019) Molecular characterization of feline paramyxovirus in Japanese cat populations. Archives of Virology 1-6. [PubMed] [Web]
  7. Kryukov K, Ueda MT, Imanishi T, and Nakagawa S (2019) Systematic survey of non-retroviral virus-like elements in eukaryotic genomes. Virus Research 262: 30-36. [PubMed] [Virus Research]
  8. 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(3): 548-557. [PubMed] [FEBS Open Bio]

2018

  1. 中川草、三橋里美、Kryukov Kirill、今西規（2018）迅速な細菌種の組成解析、実験医学 36(1): 32-37.
  2. 三橋里美、中川草、上田真保子、今西規、Martin C Frith、三橋弘明（2018）リピート数が関与する疾患の診断に向けてーサブテロメア領域のD4Z4マクロサテライトリピートを読む、実験医学 36(1): 44-48.
  3. 中川草、今西規（2018）ナノポアシーケンサーを活用した感染症細菌叢ゲノムの迅速解析、バイオサイエンスとインダストリー 76(3): 234-235.
  4. 今西規、中川草（2018）新しいゲノム解析システムによる細菌感染症診断、医学のあゆみ 267(4): 299-300.
  5. 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.[Web] [PDF]
  6. Watanabe N, Kryukov K, Nakagawa S, Takeuchi JS, 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. [PubMed] [PLoS One]
  7.  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. [Web] [PDF]
  8. . 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.  [Web] PDF
  9.  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.  [Web] [PDF]

2017

  1. Imanishi T (2017) Protein-coding and non-coding RNA genes. Evolution of the Human Genome I: The Genome and Genes, 93-116.[Web]
  2. Ueda, M.T.*, Nakagawa, S. (2017)Transcription Factor Genes Evolution of the Human Genome I: The Genome and Genes, 241-263. [Web]
  3. 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. [Web] [PDF]
  4. Horio Y†, Shiraishi Y†, Watanabe N, Inoue S, Imanishi T, and Asano K (2017) Empyema associated with Campylobacter curvus infection. Respirology Case Reports 5: e00234. [Web]
  5. Mitsuhashi S†, Kryukov K†, Nakagawa S†, Takeuchi JS, 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. [PubMed] [Sci Rep]
  6. 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: 148-159. [Web] [PDF]
  7.  Imakawa, K.* and Nakagawa, S. (2017) The Phylogeny of Placental Evolution Through Dynamic Integrations of Retrotransposons. Progress in Molecular Biology and  Translational Science, 145: 89-109. [PubMed] [Web]

2016

  1. Kryukov K and Imanishi T* (2016) Human contamination in public genome assemblies. PLoS One 11(9): e0162424. Web PDF
  2. Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, Chakraborty R, Gojobori T, and Imanishi T (2016) Selection pressure on human STR loci and its relevance in repeat expansion disease. Molecular Genetics and Genomics, 291(5):1851-69. [Web] [PDF]
  3. 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), baw087. Web PDF
  4. 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. Web PDF
  5. 宮沢孝幸、下出紗弓、中川草 (2016) RD-114物語：ネコの移動の歴史を探るレトロウイルスウイルス 66 (1): 21-30. Web PDF
  6. 今川和彦、中川草、草間和哉 (2016) 胎盤と内在性レトロウイルス ウイルス 66 (1):1-10. Web PDF

2015

  1. 宮沢孝幸、中川草 (2015) レトロウイルスの起源と進化, 実験医学増刊 33 (17) :117-126. Web
  2. 坂口翔一、小出りえ、中川草、宮沢孝幸 (2015) 猫モルビリウイルス研究の最前線 Felis 7: 110-116. 2015. Web
  3. Imakawa, K.*, Nakagawa, S. and Miyazawa, T.(2015) Baton pass hypothesis: Successive incorporation of unconserved endogenous retroviral genes for placentation during mammalian evolution. Genes to Cells, 20, 771-788. Web PDF.
  4. Miyaho RN, Nakagawa S*, Hashimoto-Gotoh A,Nakaya Y, Shimode S, Sakaguchi S, Yoshikawa R, Takahashi MU and Miyazawa, T* (2015) Susceptibility of domestic animals to a pseudotype virus bearing RD-114 virus envelope protein. Gene, 567(2): 189-195. Web PDF
  5. Kawamura M, Watanabe S, Odahara Y, Nakagawa S, Endo Y, Tsujimoto H and Nishigaki K* (2015) Genetic diversity in the feline leukemia virus gag gene. Virus Research, 204: 74-81. Web PDF
  6. Yoshikawa R, Okamoto M, Sakaguchi S, Nakagawa S, Miura T, Hirai H and Miyazawa T* (2015) Simian Retrovirus 4 Induces Lethal Acute Thrombocytopenia in Japanese Macaques. Journal of Virology Journal of Virology 89: 3965-3975. Web PDF
  7. Shimode S, Nakagawa S and Miyazawa T* (2015) Multiple invasions of infectious retrovirus in cat genomes. Scientific Reports 5: 8164. Web PDF

2014

  1. Yamada C, Kondo M, Kishimoto N, Shibata T, Nagai Y, Imanishi T, Oroguchi T, Ishii N, and Nishizaki Y (2014) Association between insulin resistance and plasma amino acid profile in non-diabetic Japanese subjects. Journal of Diabetes Investigation 6(4):408-415. Web PDF
  2. Nagai Y†, Takahashi Y†, and Imanishi T* (2014) VaDE: a manually-curated database of reproducible associations between various traits and human genomic polymorphisms. Nucleic Acids Research, 43(Database issue):D868-D872. Web PDF
  3. Hettiarachchi N, Kryukov K, Sumiyama K, and Saitou N (2014) Lineage specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biology and Evolution 6(9):2527-2542. Web PDF
  4. Yamada C, Kondo M, Oroguchi T, Ebihara A, Shibata T, Nagai Y, Imanishi T, Ishii N, and Nishizaki Y (2014) Subclinical visceral fat accumulation is a risk for lifestyle-related diseases and progression of atherosclerosis in Japanese adults – Results from a study of 94 healthy volunteers -. Health Evaluation and Promotion 41(4):518-523. Web PDF
  5. Yoshikawa R†, Nakagawa S†*, Okamura M and Miyazawa Y*(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. Web PDF
  6. International Glossina Genome Initiative (including Imanishi T.) (2014) Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. Science 344(6182):380-386. Web PDF
  7. Sakaguchi S, Nakagawa S, Yoshikawa R, Kuwahara C, Hagiwara H, Asai K, Kawakami K, Yamamoto Y, Ogawa M and Miyazawa Y* (2014) Genetic diversity of feline morbilliviruses isolated in Japan. Journal of General Virology 95(7):1464-1468. Web PDF
  8. Shimode S†, Nakagawa S†, Yoshikawa R, Shojima T and Miyazawa T*(2014)  Heterogeneity of koala retrovirus isolates. FEBS Letters 588(1):41-46. Web PDF
  9. 坂口翔一、中川草、小川誠、宮沢孝幸 (2014) 尿細管間質性腎炎と関連するネコモルビリウイルス J-VET ’14(8月): 74-79.  Web

2013

  1. Nagai Y and Imanishi T*(2013) RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations. Database (Oxford) (vol 2013):bat073. Web PDF
  2. 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. Web PDF
  3. Takenaka Y, Noda-Ogura A, Imanishi T, Yamaguchi A, Gojobori T, Shigeri Y*(2013) Computational analysis and functional expression of ancestral copepod luciferase. Gene 528(2):201-5. Web PDF
  4. 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. Web PDF
  5. 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. Web PDF
      毎日新聞（2013年7月6日朝刊）で紹介されました
  6. Nakagawa S†, Gisselbrecht SS†, Rogers JM†, Hartl DL* and Bulyk ML*(2013) DNA binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci USA 110(30):12349-12354. Web PDF
      Science誌(August 2, 2013)のEditors’ Choiceで紹介されました Web PDF
      東海大学医学部のホームページで紹介されました
  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. Web PDF
  8. 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. Web PDF
  9. Imanishi T*, Nagai Y, Habara T, Yamasaki C, Takeda J, Mikami S, Bando Y, Tojo H, Nishimura T(2013) Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics. J Proteome Res12(1):62-66. Web PDF
  10. Takeda J, Yamasaki C, Murakami K, Nagai Y, Sera M, Hara Y, Obi N, Habara T, Gojobori T, Imanishi T*(2013) H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Res 41(Database issue):D915-D919. Web PDF