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Learning sequence, structure, and function representations of proteins with language models Open
The sequence-structure-function relationships that ultimately generate the diversity of extant observed proteins is complex, as proteins bridge the gap between multiple informational and physical scales involved in nearly all cellular proc…
Automated Protein Function Description for Novel Class Discovery Open
Knowledge of protein function is necessary for understanding biological systems, but the discovery of new sequences from high-throughput sequencing technologies far outpaces their functional characterization. Beyond the problem of assignin…
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity Open
Motivation Transferring knowledge between species is challenging: different species contain distinct proteomes and cellular architectures, which cause their proteins to carry out different functions via different interaction networks. Many…
NetQuilt: Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity Open
Transferring knowledge between species is challenging: different species contain distinct proteomes and cellular architectures, which cause their proteins to carry out different functions via different interaction networks. Many approaches…
View article: The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens Open
The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAF…
deepNF: deep network fusion for protein function prediction Open
Motivation The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provides a rich source of information for infer…
deepNF: Deep network fusion for protein function prediction Open
The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provide a rich source of information for inferring functio…