Publications

 (†: equal contribution, *: corresponding author）

2020

  1. Yoriyuki Konno†, Izumi Kimura†, Keiya Uriu, Masaya Fukushi, Takashi Irie, Yoshio Koyanagi, Daniel Sauter, Robert J. Gifford, USFQ-COVID19 consortium, So Nakagawa, Kei Sato*. (2020)
    SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant.
    Cell Reports accepted.
  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.
  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.
    PMID: 32782283 DOI: 10.1038/s41598-020-70442-y 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.
  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 (in press).
  9. Nakagawa, S.* and Miyazawa, T*. (2020) Genome evolution of SARS-CoV-2 and its virological characteristics. Inflammation and Regeneration, in press.
  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.https://www.biorxiv.org/content/10.1101/644781v1 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]

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. 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]
  2. 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]
  3.  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]
  4. . 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
  5.  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), 2016: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

2015

  1. 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 (Review).Web PDF.
  2. 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
  3.  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
  4.  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
  5.  Shimode S, Nakagawa S and Miyazawa T* (2015) Multiple invasions of infectious retrovirus in cat genomes. Scientific Reports 5: 8164. Web PD

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

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
  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
      Introduced in Editors’ Choice in Science Web PDF
  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