Welcome to Biomedical Informatics Laboratory
Genome analysis


 (†: equal contribution, *: corresponding author)


  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. J. Biol. Chem. in press.
  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, in press. Web PDF
  5. Kryukov, K., Ueda, M.T., Imanishi, T. and Nakagawa, S.* (2018) Systematic survey of non-retroviral virus-like elements in eukaryotic genomes. Virus Research, in press. Web PDF
  6. 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