Johnson, Sean R.

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. (2025) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 99

Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme

Vaisvila, R., Johnson, S. R., Yan, B., Dai, N., Bourkia, B. M., Chen, M., Corrêa, I. R., Yigit, E., & Sun, Z. (2024) · Molecular Cell

Epigenetics and DNA MethylationDNA and Nucleic Acid Chemistry

Cited by 32

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

Vaisvila, R., Johnson, S. R., Yan, B., Dai, N., Bourkia, B. M., Chen, M., Corrêa, I. R., Yigit, E., & Sun, Z. (2023) · Molecular Cell

Epigenetics and DNA MethylationDNA and Nucleic Acid Chemistry

Cited by 32

Sensitive remote homology search by local alignment of small positional embeddings from protein language models

Johnson, S. R., Peshwa, M., & Sun, Z. (2024) · eLife

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 17

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Johnson, S. R., Weigele, P. R., Fomenkov, A., Ge, A., Vincze, A., Eaglesham, J. B., Roberts, R. J., & Sun, Z. (2025) · Nucleic Acids Research

Genomics and Phylogenetic StudiesCRISPR and Genetic Engineering

Cited by 10

Sensitive remote homology search by local alignment of small positional embeddings from protein language models

Johnson, S. R., Peshwa, M., & Sun, Z. (2024) · eLife

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 2

Sensitive remote homology search by local alignment of small positional embeddings from protein language models

Johnson, S. R., Peshwa, M., & Sun, Z. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 0