Discovery of Novel DNA Cytosine Deaminase Activities Enables a Nondestructive Single-Enzyme Methylation Sequencing Method for Base Resolution High-Coverage Methylome Mapping of Cell-Free and Ultra-Low Input DNA. Romualdas V*, Johnson SR*, Yan B, Dai N., Bourkia BM, Chen M., Corrêa IR, Yigit E., and Sun Z. (2023) bioRxiv. DOI: https://doi.org/10.1101/2023.06.29.547047.

Sensitive Remote Homology Search by Local Alignment of Small Positional Embeddings from Protein Language Models. Johnson SR*, Peshwa M, and Sun Z* (2023) eLife. PMID: 38488154. DOI: 10.7554/eLife.91415.3.

Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment. Yan B, Wang D, Vaisvila R, Sun Z*, Ettwiller L*. (2022) Genome Res. PMID: 36332968. DOI: 10.1101/gr.277080.122.

Computational Scoring and Experimental Evaluation of Enzymes Generated by Neural Networks Johnson, S. R., Fu, X., Viknander, S., Goldin, C., Monaco, S., Zelezniak, A., Yang, K. K. (2023) Nature Biotechnology. 2023.2003.2004.531015, PMID: 38653796. DOI: 10.1038/s41587-024-02275-3.

Chemical capping improves template switching and enhances sequencing of small RNAs. Wulf, M.G., Maguire, S., Dai, N., Blondel, A., Posfai, D., Krishnan, K., Sun, Z., Guan, S., Corrêa, I.R. Jr. (2021) Nucl. Acids Res.. gkab861. PMID: 34581823. DOI: 10.1093/nar/gkab861.