Dr. Xuenan Mi successfully defended her thesis on “Data Driven Peptide Drug Discovery and Design” in December, 2024. Xuenan was a graduate student in Center for Biophysics and Quantitative Biology. She joined Shukla group in Fall 2019. Xuenan collaborated with Prof. Wilfred van der donk and Doug Mitchell in the Department of Chemistry to develop computational models of RIPPs natural products. For excellence in graduate research, Xuenan received the CCG graduate student excellence award from ACS Division of Computers in Chemistry. Xuenan will join Johnson & Johnson as a senior scientist. To learn more about her thesis work, you can read some of her published research articles included below.
Xuenan Mi, Susanna E. Barrett, Douglas A. Mitchell and Diwakar Shukla*, LassoESM: A tailored language model for enhanced lasso peptide property prediction. Nature Communications, In review, 2024. Available on bioRxiv, doi: 10.1101/2024.10.25.620295
Krishna K. Narayanan, Austin T. Weigle, Lingyun Xu, Xuenan Mi, Li-Qing Chen, Erik Procko and Diwakar Shukla*. Sequence to function constraints for plant SWEET transporter using deep mutational scanning. bioRxiv, 2024. doi: 10.1101/2024.06.28.601307
Joseph D. Clark, Xuenan Mi, Douglas A. Mitchell and Diwakar Shukla*, Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning. Digital Discovery, Volume 4, Issue 2, Pages 343-354, 2025.
Song Yin#, Xuenan Mi# and Diwakar Shukla*, Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction, RSC Chemical Biology, Volume 5, Pages 401-417, 2024. # denotes co-first author
Xuenan Mi, Emily K. Desormeaux, Tung T. Le, Wilfred A. van der Donk and Diwakar Shukla*, Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical Science, Volume 14, Pages 6904-6914, 2023.
Xuenan Mi and Diwakar Shukla*, Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning, Journal of Physical Chemistry B, Volume 126, Issue 7, Pages 1492–1503, 2022.
Corina N D’Alessandro-Gabazza, Taro Yasuma, Tetsu Kobayashi, Masaaki Toda, Ahmed M Abdel-Hamid, Hajime Fujimoto, Osamu Hataji, Hiroki Nakahara, Atsuro Takeshita, Kota Nishihama, Tomohito Okano, Haruko Saiki, Yuko Okano, Atsushi Tomaru, Valeria Fridman D’Alessandro, Miyako Shiraishi, Akira Mizoguchi, Ryoichi Ono, Junpei Ohtsuka, Masayuki Fukumura, Tetsuya Nosaka, Xuenan Mi, Diwakar Shukla, Kensuke Kataoka, Yasuhiro Kondoh, Masaki Hirose, Toru Arai, Yoshikazu Inoue, Yutaka Yano,
Roderick I Mackie, Isaac Cann, Esteban C Gabazza. Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis, Nature Communications, Volume 13, Issue 1, Article number 1558, 2022.