原著論文

• 42. Matsumoto Y, Yik-Lok Chung C, Isobe S, Sakamoto M, Lin X, Chan TF, Hirakawa H, Ishihara G, Lam HM, Nakayama S, Sasamoto S, Tanizawa Y, Watanabe A, Watanabe K, Yagura M, Niimura Y, Nakamura Y. (2024) Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats. J Adv Res, in press. DOI: 10.1016/j.jare.2024.10.023（宮崎大学プレスリリース｜アニコム損害保険株式会社プレスリリース））
• 41. Niimura Y, Biswa BB, Kishida T, Toyoda A, Fujiwara K, Ito M, Touhara K, Inoue-Murayama M, Jenkins SH, Adenyo C, Kayang BB, Koide T. (2024) Synchronized expansion and contraction of olfactory, vomeronasal, and taste receptor gene families in hystricomorph rodents. Mol Biol Evol 41: msae071. DOI: 10.1093/molbev/msae071（宮崎大学プレスリリース｜日本経済新聞 4月28日）
• 40. Sato-Akuhara N, Trimmer C, Keller A, Niimura Y, Shirasu M, Mainland JD, Touhara K. (2023) Genetic variation in the human olfactory receptor OR5AN1 associates with the perception of musks. Chem Senses 48: bjac037. DOI: 10.1093/chemse/bjac037（東京大学プレスリリース）
• 39. Morinaga S, Nagata K, Ihara S, Yumita T, Niimura Y, Sato K, Touhara K (2022) Structural model for ligand binding and channel opening of an insect gustatory receptor. J Biol Chem, 298: 102573. DOI: 10.1016/j.jbc.2022.102573
• 38. Akhtar MS, Ashino R, Oota H, Ishida H, Niimura Y, Touhara K, Melin AD, Kawamura S (2022) Genetic variation of olfactory receptor gene family in a Japanese population. Anthropol Sci, 130: 93-106. DOI: 10.1537/ase.211024
• 37. Niimura Y, Tsunoda M, Kato S, Murata K, Yanagawa T, Suzuki S, Touhara K (2021) Origin and evolution of the gene family of proteinaceous pheromones, the exocrine gland-secreting peptides, in rodents. Mol Biol Evol, 38: 634-649.（PDF｜Website｜東京大学プレスリリース｜UTokyo Press Release）
• 36. Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, del Campo J, Hernandez SC, Fiore AD, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E, Martin MP, Niimura Y, Perry GH, Valverde CS, Tang J, Warren WC, de Magalhães JP, Kawamura S, Marquès-Bonet T, Krawetz R, Melin AD (2021) The evolution of ecological flexibility, large brains, and long lives: capuchin monkey genomics revealed with fecalFACS. Proc Natl Acad Sci USA, 118: e2010632118. (Website)
• 35. Nikaido M, Kondo S, Zhang Z, Wu J, Nishihara H, Niimura Y, Suzuki S, Touhara K, Suzuki Y, Noguchi H, Minakuchi Y, Toyoda A, Fujiyama A, Sugano S, Yoneda M, Kai C (2020) Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera. DNA Res 27: dsaa021.（Website｜東京工業大学プレスリリース）
• 34. Ijichi C, Wakabayashi H, Sugiyama S, Ihara Y, Nogi Y, Nagashima A, Ihara S, Niimura Y, Shimizu Y, Kondo K, Touhara K (2019) Metabolism of odorant molecules in human nasal/oral cavity affects the odorant perception. Chem Senses 44: 465–481. (Website）
• 33. Niimura Y, Matsui A, Touhara K (2018) Acceleration of olfactory receptor gene loss in primate evolution: Possible link to anatomical change in sensory systems and dietary transition. Mol Biol Evol 35: 1437–1450.（PDF｜Website｜東京大学プレスリリース｜JSTプレスリリース｜UTokyo Research｜朝日新聞 4月11日夕刊）
• 32. Ota S, Mogushi K, Hirai A, Niimura Y, Tanaka H (2018) Improvements in diabetic patients’ outcomes in a clinical decision support system. Eur J Biomed Inform 14: 29–36.
• 31. Iwata T, Niimura Y, Kobayashi C, Shirakawa D, Suzuki H, Enomoto T, Touhara K, Yoshihara Y, Hirota J (2017) A long-range cis-regulatory element for class I odorant receptor genes. Nat Comm 8: 885. (PDF | 東京工業大学プレスリリース）
• 30. Nakagawa S, Niimura Y, Gojobori T (2017) Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes. Nucleic Acids Res 45: 3922–3931. (PDF）
• 29. Sato-Akuhara N, Horio N, Kato-Namba A, Yoshikawa K, Niimura Y, Ihara S, Shirasu M, Touhara K (2016) Ligand specificity and evolution of mammalian musk odor receptors: Effect of single receptor deletion on odor detection. J Neurosci 36: 4482–4491. (PDF | UTokyoResearch | 東京大学プレスリリース)
• 28. Watanabe K, Tanaka H, Takahashi K, Niimura Y, Watanabe K, Kurihara Y (2016) NIRS-Based Language Learning BCI System. IEEE Sens J 16: 2726–2734.
• 27. Watanabe K, Niimura Y, Kurihara Y, Watanabe K (2015) Temporal changes in NIRS outputs in prefrontal regions when listening to languages. Artif Life Robotics 20: 183–189.
• 26. Niimura Y, Matsui A, Touhara K (2014) Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals. Genome Res 24: 1485–1496. (PDF | Website)
  Corrigendum (2015) 25: 926. (PDF | Website)
  – Thankfully, this paper was introdced in many medias in many languages, including:
  Japanese: 毎日新聞（7月23日夕刊）| 東京新聞（7月23日夕刊）| 日経産業新聞（7月23日朝刊）| 産経新聞（7月28日朝刊）| Newton 11月号 | 東京大学プレスリリース | UTokyoResearch | サイエンスポータル | TBSテレビ「ひるおび！」（7月24日）| TBSテレビ「いっぷく！」（7月24日）| 日本テレビ「スッキリ！」（7月28日）
  English: | Genome Reserach Press Release | Washington Post (July 23) | National Geographic (This site got >46,000 likes on FB!) | Discovery Channel | Livescience
• 25. Niimura Y (2013) Identification of chemosensory receptor genes from vertebrate genomes. Methods Mol Biol 1068: 95–105. (PDF | Website)
• 24. Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, et al. (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet 45: 701–706. (PDF)
  – This paper got the cover of Nature Genetics!
• 23. Niimura Y (2013) Identification of olfactory receptor genes from mammalian genome sequences. Methods Mol Biol 1003: 39–49. (PDF | Website)
• 22. Matsumae H, Hamada M, Fujie M, Niimura Y, Tanaka H, Kawashima T (2013) A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis. Gene 519: 82–90. (PDF)
• 21. Johnson TA, Niimura Y, Tanaka H, Nakamura Y, Tsunoda T (2011) hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets. Genome Biol 12: R21. (PDF)
• 20. Hase T, Niimura Y, Tanaka H (2010) Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes. BMC Evol Biol 10: 358. (PDF)
  – Top 1 BMC Evolutionary Biology: Most viewed articles in past 30 days
• 19. Nakagawa S, Niimura Y, Miura K, Gojobori T (2010) Dynamic evolution of translation initiation mechanisms in prokaryotes. Proc Natl Acad Sci USA 107: 6382–6387. (PDF)
• 18. Matsui A, Go Y, Niimura Y (2010) Degeneration of olfactory receptor gene repertories in primates: No direct link to full trichromatic vision. Mol Biol Evol 27: 1192–1200. (PDF)
• 17. Niimura Y (2009) On the origin and evolution of vertebrate olfactory receptor genes: Comparative genome analysis among 23 chordate species. Genome Biol Evol 1: 34–44. (PDF)
  – Top 3 full-text HTML downloaded article in Genome Biology and Evolution during 2009
• 16. Go Y, Niimura Y (2008) Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Mol Biol Evol 25: 1897–1907. (PDF)
• 15. Hase T, Niimura Y, Kaminuma T, Tanaka H (2008) Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network. PLoS ONE 27: e1667. (PDF)
• 14. Nakagawa S, Niimura Y, Gojobori T, Tanaka H, Miura K (2008) Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res 36: 861–871. (PDF)
• 13. Genome Information Integration Project and H-Invitational 2 Consortium. Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, ..., Niimura Y, et al. (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 36: D793–799. (PDF)
• 12. Niimura Y, Nei M (2007) Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS ONE 2: e708. (PDF)
• 11. Niimura Y, Nei M (2005) From The Cover: Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci USA 102: 6039–6044. (PDF)
  – This paper was introduced in Editor's Choice in Science! (PDF)
• 10. International Rice Genome Sequencing Project. Annotation and Analysis: Iwama H, Gojobori T, Itoh T, Niimura Y, Fujii Y, et al. (2005) The map-based sequence of the rice genome. Nature 436: 793–800. (PDF)
• 9. Niimura Y, Nei M (2005) Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 346: 13–21. (PDF)
• 8. Niimura Y, Nei M (2005) Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages. Gene 346: 23–28. (PDF)
• 7. Niimura Y, Nei M (2003) Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci USA 100: 12235–12240. (PDF)
• 6. Niimura Y, Terabe M, Gojobori T, Miura K (2003) Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes. Nucleic Acids Res 31: 5195–5201. (PDF)
• 5. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, et al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312–316. (PDF)
• 4. Niimura Y, Gojobori T (2002) In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence. Proc Natl Acad Sci USA 99: 797–802. (PDF)
• 3. Homma R, Kimoto T, Niimura Y, Krivosheev A, Hara T, Ohta Y, Kawato S (2000) Real-time fluorescence analysis on molecular mechanisms for regulation of cytochrome P450scc activity upon steroidogenic stimulation in adrenocortical cells. J Inorg Biochem 82: 171–180.
• 2. Sato Y, Niimura Y, Yura Y, Go M (1999) Module-intron correlation and intron sliding in family F/10 xylanase genes. Gene 238: 93–101.
• 1. Homma R, Kouyama T, Yamada M, Niimura Y, Krivosheev A, Hara T, Kawato S (1997) Time resolved study of effect of chlorpromazine on mobility of cytochrome P-450 and phospholipids in the inner membrane of adrenocortical mitochondria. J Pharm Biomed Anal 15: 1215–1222.