Scalable functional assays for the interpretation of human genetic variation
Scalable sequence–function studies have enabled the systematic analysis and cataloging of
hundreds of thousands of coding and noncoding genetic variants in the human genome …
hundreds of thousands of coding and noncoding genetic variants in the human genome …
Multiplexed assays of variant effects contribute to a growing genotype–phenotype atlas
Given the constantly improving cost and speed of genome sequencing, it is reasonable to
expect that personal genomes will soon be known for many millions of humans. This stands …
expect that personal genomes will soon be known for many millions of humans. This stands …
Language models enable zero-shot prediction of the effects of mutations on protein function
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function …
understanding and designing proteins. Since evolution encodes information about function …
Proteingym: Large-scale benchmarks for protein fitness prediction and design
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 …
understanding genetic disease to designing novel proteins to address our most pressing …
Deep generative models of genetic variation capture the effects of mutations
The functions of proteins and RNAs are defined by the collective interactions of many
residues, and yet most statistical models of biological sequences consider sites nearly …
residues, and yet most statistical models of biological sequences consider sites nearly …
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …
Protein language-model embeddings for fast, accurate, and alignment-free protein structure prediction
Advanced protein structure prediction requires evolutionary information from multiple
sequence alignments (MSAs) from evolutionary couplings that are not always available …
sequence alignments (MSAs) from evolutionary couplings that are not always available …
Inferring protein 3D structure from deep mutation scans
We describe an experimental method of three-dimensional (3D) structure determination that
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …
Scientific utopia III: Crowdsourcing science
EL Uhlmann, CR Ebersole… - Perspectives on …, 2019 - journals.sagepub.com
Most scientific research is conducted by small teams of investigators who together formulate
hypotheses, collect data, conduct analyses, and report novel findings. These teams operate …
hypotheses, collect data, conduct analyses, and report novel findings. These teams operate …
A statistical framework for analyzing deep mutational scanning data
AF Rubin, H Gelman, N Lucas, SM Bajjalieh… - Genome biology, 2017 - Springer
Deep mutational scanning is a widely used method for multiplex measurement of functional
consequences of protein variants. We developed a new deep mutational scanning statistical …
consequences of protein variants. We developed a new deep mutational scanning statistical …