Research Summary

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.

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  Oct. 6, 2017
  A smarter way to screen molecular libraries

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