Research Summary

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

• 1. *Ishigaki K, Lagattuta KA, Luo Y, James EA, Buckner JH, Raychaudhuri S.
  "HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors."
  Nature Genetics. 54(4):393-402 (2022)
• 2. *Lagattuta KA, Kang JB, Nathan A, Pauken KE, Jonsson AH, Rao DA, Sharpe AH, Ishigaki K (co-corresponding author), Raychaudhuri S.
  "Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate."
  Nature Immunology. 23(3):446-457 (2022)
• 3. *Nathan A, Asgari S, Ishigaki K, Valencia C, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price AL, Lecca L, Murray MB, Moody DB, Raychaudhuri S.
  "Single-cell eQTL models reveal dynamic T cell state dependence of disease loci."
  Nature. 606(7912):120-128 (2022)
• 4. *Ota M, Nagafuchi Y, Hatano H, Ishigaki K, Terao C, Takeshima Y, Yanaoka H, Kobayashi S, Okubo M, Shirai H, Sugimori Y, Maeda J, Nakano M, Yamada S, Yoshida R, Tsuchiya H, Tsuchida Y, Akizuki S, Yoshifuji H, Ohmura K, Mimori T, Yoshida K, Kurosaka D, Okada M, Setoguchi K, Kaneko H, Ban N, Yabuki N, Matsuki K, Mutoh H, Oyama S, Okazaki M, Tsunoda H, Iwasaki Y, Sumitomo S, Shoda H, Kochi Y, Okada Y, Yamamoto K, Okamura T, Fujio K.
  "Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases."
  Cell. 27;184(11):3006-3021.e17 (2021)
• 5. Ishigaki K, Akiyama M, Kanai M, Takahashi A, Kawakami E, Sugishita H, Sakaue S, Matoba N, Low SK, Okada Y, Terao C, Amariuta T, Gazal S, Kochi Y, Horikoshi M, Suzuki K, Ito K, Koyama S, Ozaki K, Niida S, Sakata Y, Sakata Y, Kohno T, Shiraishi K, Momozawa Y, Hirata M, Matsuda K, Ikeda M, Iwata N, Ikegawa S, Kou I, Tanaka T, Nakagawa H, Suzuki A, Hirota T, Tamari M, Chayama K, Miki D, Mori M, Nagayama S, Daigo Y, Miki Y, Katagiri T, Ogawa O, Obara W, Ito H, Yoshida T, Imoto I, Takahashi T, Tanikawa C, Suzuki T, Sinozaki N, Minami S, Yamaguchi H, Asai S, Takahashi Y, Yamaji K, Takahashi K, Fujioka T, Takata R, Yanai H, Masumoto A, Koretsune Y, Kutsumi H, Higashiyama M, Murayama S, Minegishi N, Suzuki K, Tanno K, Shimizu A, Yamaji T, Iwasaki M, Sawada N, Uemura H, Tanaka K, Naito M, Sasaki M, Wakai K, Tsugane S, Yamamoto M, Yamamoto K, Murakami Y, Nakamura Y, Raychaudhuri S, Inazawa J, Yamauchi T, Kadowaki T, Kubo M, Kamatani Y.
  "Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases."
  Nature Genetics. 52(7): 669-679 (2020)
• 6. Terao C, Suzuki A, Momozawa Y, Akiyama M, Ishigaki K, Yamamoto K, Matsuda K, Murakami Y, McCarroll SA, Kubo M, Loh PR, Kamatani Y.
  "Chromosomal alterations among age-related haematopoietic clones in Japan."
  Nature. 584(7819): 130-135 (2020)
• 7. *Amariuta T, Ishigaki K (co-first author), Sugishita H, Ohta T, Koido M, Dey KK, Matsuda K, Murakami Y, Price AL, Kawakami E, Terao C, Raychaudhuri S.
  "Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements."
  Nature Genetics. 52(12): 1346-1354 (2020)
• 8. Akiyama M, Ishigaki K, Sakaue S, Momozawa Y, Horikoshi M, Hirata M, Matsuda K, Ikegawa S, Takahashi A, Kanai M, Suzuki S, Matsui D, Naito M, Yamaji T, Iwasaki M, Sawada N, Tanno K, Sasaki M, Hozawa A, Minegishi N, Wakai K, Tsugane S, Shimizu A, Yamamoto M, Okada Y, Murakami Y, Kubo M, Kamatani Y.
  "Characterizing rare and low-frequency height-associated variants in the Japanese population."
  Nature Communications. 27;10(1): 4393 (2019)
• 9. Ishigaki K, Kochi Y, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Yamaguchi K, Nagafuchi Y, Nakachi S, Kato R, Sakurai K, Shoda H, Ikari K, Taniguchi A, Yamanaka H, Miya F, Tsunoda T, Okada Y, Momozawa Y, Kamatani Y, Yamada R, Kubo M, Fujio K, Yamamoto K.
  "Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis."
  Nature Genetics. 49(7):1120-1125 (2017)
• 10. *Ishigaki K, Shoda H, Kochi Y, Yasui T, Kadono Y, Tanaka S, Fujio K, Yamamoto K.
  "Quantitative and qualitative characterization of expanded CD4+ T cell clones in rheumatoid arthritis patients."
  Scientific Reports. 6;5:12937 (2015)

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