Welcome to Biomedical Informatics Laboratory
Genome analysis


 (†: equal contribution, *: corresponding author)


  1. 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) Application of the MinION™ portable DNA sequencer in clinical microbiology evaluation: a case report. JA Clinical Reports, 5:24. Web PDF
  2. Kryukov K*, Ueda MT, Nakagawa S, and Imanishi T (2019) Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences. Bioinformatics, in press. Web PDF
  3. 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. Web PDF
  4. 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. Web PDF
  5. 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. Web PDF


  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, 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. Web PDF
  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: 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 Virology99(2): 181-186Web PDF


  1. Tenno M, Shiroguchi K, Muroi S, Kawakami E, Koseki K, Kryukov K, Imanishi T, Ginhoux F, and Taniuchi I (2017) Cbfβ2-deficiency preserves Langerhans cell precursors by lack of selective TGFβ receptor signaling. The Journal of Experimental Medicine 214: 2933. Web PDF
  2. Ogawa T, Kryukov K, Imanishi T, and Shiroguchi K (2017) The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules. Scientific Reports 7: 13576. Web PDF
  3. Mitsuhashi,S.*, Nakagawa, S., Ueda M.T., Imanishi, T., Frith M. C., and Mitsuhashi, H. Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy. Scientific Reports, 7: 14789. Web PDF
  4. 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. Web PDF
  5. 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 PDF
  6. Mitsuhashi,S.†, Kryukov, K.†, Nakagawa, S., Takeuchi, J.S., Shiraishi, Y., Asano, K. and Imanishi, T.* A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions. Scientific Reports,7: 5657. Web PDF
  7. 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): 3922-3931Web PDF
  8. 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 Web PDF
  9. 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
  10. 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. Web PDF


  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


  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 Research204: 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 PDF


  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):408-15. 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):D868-72. 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):2527-42. 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*. Construction of an infectious clone of simian foamy virus of Japanese macaque (SFVjm) and phylogenetic analyses of SFVjm isolates. Gene 2014 548(1):149-54. Web PDF
  6. International Glossina Genome Initiative (including Imanishi T). Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. Science 2014 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*. Genetic diversity of feline morbilliviruses isolated in Japan. Journal of General Virology 2014 95(7):1464-1468. Web PDF
  8. Shimode S†, Nakagawa S†, Yoshikawa R, Shojima T and Miyazawa T*. Heterogeneity of koala retrovirus isolates. FEBS Letters 2014 588(1):41-46 Web PDF


  1. Nagai Y and Imanishi T*. RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations. Database (Oxford). 2013 Oct 23;2013(0):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*. Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese Black cattle during peri-implantation period. PLoS ONE 2013 8(11), e80427. Web PDF
  3. Takenaka Y, Noda-Ogura A, Imanishi T, Yamaguchi A, Gojobori T, Shigeri Y*.

    Computational analysis and functional expression of ancestral copepod luciferase. Gene. 2013 Oct 10;528(2):201-5. Web PDF

  4. Nakaya Y, Koshi K, Nakagawa S, Hashizume K and Miyazawa T*. Fematrin-1 is involved in fetomaternal cell-to-cell fusion in Bovinae placenta and contributed to diversity of ruminant placentation. Journal of Virology 2013 87(19):10563-72. Web PDF
  5. Shojima T, Yoshikawa R, Hoshino S, Shimode S, Nakagawa S, Ohata T, Nakaoka R and Miyazawa T*. Identification of a Novel Subgroup of Koala Retrovirus from Koalas in Japanese Zoos. Journal of Virology 2013 87(17):9943-9948. Web PDF
  6. Nakagawa S†, Gisselbrecht SS†, Rogers JM†, Hartl DL* and Bulyk ML*. DNA binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci USA. 2013 110(30):12349-12354. Web PDF
      Introduced in Editors’ Choice in Science August 2, 2013. Web PDF
  7. Watanabe S, Kawamura M, Anai Y, Ochi H, Odahara Y, Nakagawa S, Endo Y, Tsujimoto H and Nishigaki K*. Phylogenetic and Structural Diversity in the Feline Leukemia Virus Env Gene. PLoS ONE 2013 8(4): e61009. Web PDF
  8. Nakagawa S, Bai H, Sakurai T, Nakaya Y, Konno T, Miyazawa T, Gojobori T and Imakawa K*. Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation. Genome Biology and Evolution 2013 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.

    Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics. J Proteome Res. 2013 Jan 4;12(1):62-6. Web PDF

  10. Takeda J, Yamasaki C, Murakami K, Nagai Y, Sera M, Hara Y, Obi N, Habara T, Gojobori T, Imanishi T*. H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Res. 2013 Jan;41(Database issue):D915-9. Web PDF