Ingraham, John B.

Mutation effects predicted from sequence co-variation

Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017) · Nature Biotechnology

Genomics and Rare DiseasesEvolution and Genetic Dynamics

Cited by 775

Deep generative models of genetic variation capture the effects of mutations

Riesselman, A. J., Ingraham, J. B., & Marks, D. S. (2018) · Nature Methods

Genomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Cited by 601

Illuminating protein space with a programmable generative model

Ingraham, J. B., Baranov, M., Costello, Z., Barber, K. W., Wang, W., Ismail, A., Frappier, V., Lord, D. M., Ng-Thow-Hing, C., Van Vlack, E. R., et al. (2023) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 444

3D RNA and Functional Interactions from Evolutionary Couplings

Weinreb, C., Riesselman, A. J., Ingraham, J. B., Gross, T., Sander, C., & Marks, D. S. (2016) · Cell

RNA and protein synthesis mechanismsProtein Structure and Dynamics

Cited by 159

Illuminating protein space with a programmable generative model

Ingraham, J., Baranov, M., Costello, Z., Frappier, V., Ismail, A., Tie, S., Wang, W., Xue, V., Obermeyer, F., Beam, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 83

Simultaneous enhancement of multiple functional properties using evolution-informed protein design

Fram, B., Truebridge, I., Su, Y., Riesselman, A. J., Ingraham, J. B., Passera, A., Napier, E., Thadani, N. N., Lim, S., Roberts, K., et al. (2023) · Nature Communications

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 34

Simultaneous enhancement of multiple functional properties using evolution-informed protein design

Fram, B., Su, Y., Truebridge, I., Riesselman, A. J., Ingraham, J. B., Passera, A., Napier, E., Thadani, N. N., Lim, S., Roberts, K., et al. (2024) · Nature Communications

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 34