The causes of evolvability and their evolution

JL Payne, A Wagner - Nature Reviews Genetics, 2019 - nature.com
Evolvability is the ability of a biological system to produce phenotypic variation that is both
heritable and adaptive. It has long been the subject of anecdotal observations and …

Evolutionary pathways and trajectories in antibiotic resistance

F Baquero, JL Martinez, V F. Lanza… - Clinical Microbiology …, 2021 - Am Soc Microbiol
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have
provided a wealth of information, but knowledge regarding “what happened” has precluded …

Language models enable zero-shot prediction of the effects of mutations on protein function

J Meier, R Rao, R Verkuil, J Liu… - Advances in neural …, 2021 - proceedings.neurips.cc
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function …

Efficient evolution of human antibodies from general protein language models

BL Hie, VR Shanker, D Xu, TUJ Bruun… - Nature …, 2024 - nature.com
Natural evolution must explore a vast landscape of possible sequences for desirable yet
rare mutations, suggesting that learning from natural evolutionary strategies could guide …

Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval

P Notin, M Dias, J Frazer… - International …, 2022 - proceedings.mlr.press
The ability to accurately model the fitness landscape of protein sequences is critical to a
wide range of applications, from quantifying the effects of human variants on disease …

Drivers and impacts of the most extreme marine heatwave events

A Sen Gupta, M Thomsen, JA Benthuysen… - Scientific reports, 2020 - nature.com
Prolonged high-temperature extreme events in the ocean, marine heatwaves, can have
severe and long-lasting impacts on marine ecosystems, fisheries and associated services …

State-of-the-art estimation of protein model accuracy using AlphaFold

JP Roney, S Ovchinnikov - Physical Review Letters, 2022 - APS
The problem of predicting a protein's 3D structure from its primary amino acid sequence is a
longstanding challenge in structural biology. Recently, approaches like alphafold have …

Proteingym: Large-scale benchmarks for protein fitness prediction and design

P Notin, A Kollasch, D Ritter… - Advances in …, 2024 - proceedings.neurips.cc
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …

Low-N protein engineering with data-efficient deep learning

S Biswas, G Khimulya, EC Alley, KM Esvelt… - Nature …, 2021 - nature.com
Protein engineering has enormous academic and industrial potential. However, it is limited
by the lack of experimental assays that are consistent with the design goal and sufficiently …

Unsupervised evolution of protein and antibody complexes with a structure-informed language model

VR Shanker, TUJ Bruun, BL Hie, PS Kim - Science, 2024 - science.org
Large language models trained on sequence information alone can learn high-level
principles of protein design. However, beyond sequence, the three-dimensional structures of …