Welcome to Biomedical Informatics Laboratory
Genome analysis


 (†: equal contribution, *: corresponding author)


  1. 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
  2. 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. BioRxiv Web PDF
  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, gkx124. doi: 10.1093/nar/gkx124.  Web PDF.
  4. 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
  5. 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 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 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