Additional Campus Affiliations
Professor, Chemical and Biomolecular Engineering
James W. Westwater Scholar, Chemical and Biomolecular Engineering
Affiliate, Chemistry
Professor, Bioengineering
Professor, National Center for Supercomputing Applications (NCSA)
Professor, Center for Digital Agriculture, National Center for Supercomputing Applications (NCSA)
Affiliate, Carl R. Woese Institute for Genomic Biology
Recent Publications
Barrett, S. E., Yin, S., Jordan, P., Brunson, J. K., Gordon-Nunez, J., Costa Machado da Cruz, G., Rosario, C., Okada, B. K., Anderson, K., Pires, T. A., Wang, R., Shukla, D., Burk, M. J., & Mitchell, D. A. (2025). Substrate interactions guide cyclase engineering and lasso peptide diversification. Nature chemical biology, 21(3), 412-419. https://doi.org/10.1038/s41589-024-01727-w
Chan, M. C., Alfawaz, Y., Paul, A., & Shukla, D. (2025). Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicA. Biophysical journal, 124(2), 379-392. https://doi.org/10.1016/j.bpj.2024.12.013
Cui, H., Su, Y., Dean, T. J., Yu, T., Zhang, Z., Peng, J., Shukla, D., & Zhao, H. (2025). Enzyme specificity prediction using cross attention graph neural networks. Nature, 647(8090), 639-647. https://doi.org/10.1038/s41586-025-09697-2
Long, S. P., Wang, Y., Carmo-Silva, E., Cavanagh, A. P., Jonikas, M. C., Kromdijk, J., Long, B. M., Marshall-Colon, A., Shukla, D., Wilson, R. H., Zhu, X. G., & Ainsworth, E. A. (2025). Feeding from the sun—Successes and prospects in bioengineering photosynthesis for food security. Cell, 188(24), 6700-6719. https://doi.org/10.1016/j.cell.2025.10.033
Mi, X., Barrett, S. E., Mitchell, D. A., & Shukla, D. (2025). LassoESM a tailored language model for enhanced lasso peptide property prediction. Nature communications, 16(1), Article 8545. https://doi.org/10.1038/s41467-025-63412-3