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RIKEN Center for Sustainable Resource Science Molecular Ligand Target Research Team

Team Leader: Charles Boone (Ph.D.)

Research Summary

Charles  Boone(Ph.D.)

Small molecular ligands with unique activities must have the specific target molecules that exist in their cells or organisms. Identification of the target molecules is critical for elucidating the mode of action of the molecular ligands and for drug development. However, drug target identification has been difficult in general, because the mode of interactions between the molecular ligands and their targets is not uniform. Our team aims at developing innovative techniques based on global analysis of yeast genetic interactions, which leads to quick and accurate detection of the ligand-target interactions.

Main Research Fields

  • Biology

Related Research Fields

  • Medicine, Dentistry & Pharmacy


  • Chemical Genomics
  • Target Identification
  • Yeast

Selected Publications

  • 1.Zhou FL, Li SC, Zhu Y, Guo WJ, Shao LJ, Nelson J, Simpkins S, Yang DH, Liu Q, Yashiroda Y, Xu JB, Fan YY, Yue JM, Yoshida M, Xia T, Myers CL, Boone C, Wang MW.:
    "Integrating yeast chemical genomics and mammalian cell pathway analysis."
    Acta Pharmacol Sin. doi: 10.1038/s41401-019-0231-y. (2019)
  • 2.Scott W. Simpkins, Raamesh Deshpande, Justin Nelson, Sheena C. Li, Jeff S. Piotrowski, Henry Neil Ward, Yoko Yashiroda, Hiroyuki Osada, Minoru Yoshida, Charles Boone & Chad L. Myers.:
    "Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments."
    Nat. Protoc. 14, 415-440 (2019)
  • 3.Scott W. Simpkins, Justin Nelson, Raamesh Deshpande, Sheena C. Li, Jeff S. Piotrowski, Erin H. Wilson, Abraham A. Gebre, Hamid Safizadeh, Reika Okamoto, Mami Yoshimura, Michael Costanzo, Yoko Yashiroda, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L. Myers.:
    "Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions."
    PLoS Comput. Biol. 14, e1006532 (2018)
  • 4.Nelson J, Simpkins SW, Safizadeh H, Li SC, Piotrowski JS, Hirano H, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL.:
    "MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action."
    Bioinformatics. 2018 Apr 1;34(7):1251-1252. doi: 10.1093/bioinformatics/btx732.
  • 5.Piotrowski, J. S., Li, S. C., Deshpande, R., Simpkins, S. W., Nelson, J., Yashiroda, Y., Barber, J. M., Safizadeh, H., Wilson, E., Okada, H., Gebre, A. A., Kubo, K., Torres, N. P., LeBlanc, M. A., Andrusiak, K., Okamoto, R., Yoshimura, M., van Leeuwen, J., Shirahige, K., Baryshnikova, A., Brown, G. W., Hirano, H., Costanzo, M., Andrews, B., Ohya, Y., Osada, H., Yoshida, M., Myers, C. L., and Boone, C.:
    "Functional annotation of chemical libraries across diverse biological processes."
    Nature Chemical Biology, DOI: 10.1038/nchembio.2436, 2017.
  • 6.Costanzo, M., VanderSluis, B., Koch, EN., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, SD., Pelechano, V., Styles, EB., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, ZY., Kuzmin, E., Nelson, J., Piotrowski, JS., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, CF., Li, SC., Li, Z., Usaj, MM., Okada, H., Pascoe, N., San Luis, BJ., Sharifpoor, S., Shuteriqi, E., Simpkins, SW., Snider, J., Suresh, HG., Tan, Y., Zhu, H,. Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, OG., Stagljar, I., Xia, T., Ohya, Y., Gingras, AC., Raught, B., Boutros, M., Steinmetz, LM., Moore, CL., Rosebrock, AP., Caudy, AA., Myers, CL., Andrews, B., and Boone, C.:
    "A global genetic interaction network maps a wiring diagram of cellular function."
    Science, 353: aaf1420, 2016.
  • 7.Dickinson, Q., Bottoms, S., Hinchman, L., McIlwain, S., Li, S., Myers, CL., Boone, C., Coon, JJ., Hebert, A., Sato, TK., Landick, R., and Piotrowski JS.:
    "Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain."
    Microb. Cell Fact., 15: 17, 2016.
  • 8.Serate, J., Xie, D., Pohlmann, E., Donald, C Jr., Shabani, M., Hinchman, L, Higbee, A., Mcgee, M., La Reau, A., Klinger, GE., Li, S., Myers, CL., Boone, C., Bates, DM., Cavalier, D., Eilert, D., Oates, LG., Sanford, G., Sato, TK., Dale, B., Landick, R., Piotrowski, J., Ong, RG., and Zhang, Y.:
    "Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation."
    Biotechnol. Biofuels, 8: 180, 2015.
  • 9.Piotrowski, JS., Okada, H., Lu, F., Li, SC., Hinchman, L., Ranjan, A., Smith, DL., Higbee, AJ., Ulbrich, A., Coon, JJ., Deshpande, R., Bukhman, YV., McIlwain, S., Ong, IM., Myers, CL., Boone, C., Landick, R., Ralph, J., Kabbage, M., and Ohya Y.:
    "Plant-derived antifungal agent poacic acid targets β-1,3-glucan."
    Proc. Natl. Acad. Sci. USA, 112: E1490-1497, 2015.
  • 10.Piotrowski, JS., Simpkins, SW., Li, SC., Deshpande, R., McIlwain, SJ., Ong, IM., Myers, CL., Boone, C., and Andersen, RJ.:
    "Chemical genomic profiling via barcode sequencing to predict compound mode of action."
    Methods Mol. Biol., 1263: 299-318, 2015.

Recent Research Results

Related Links

Lab Members

Principal investigator

Charles Boone
Team Leader

Core members

Yoko Yashiroda
Deputy Team Leader
Lien Thi Kim Pham
Postdoctoral Researcher
Yumi Kawamura
Technical Staff I
Mami Yoshimura
Technical Staff I
Hiromi Kimura
Technical Staff II

Contact Information

N202 Sustainable Resource Science Building,
2-1 Hirosawa,
Wako, Saitama
351-0198, Japan

Email: charlieboone [at] riken.jp