Article

A Suite of Foundation Models Captures the Contextual Interplay Between Codons

2024-10-13

Abstract excerpt

In the canonical genetic code, many amino acids are assigned more than one codon. Work by us and others has shown that the choice of these synonymous codon is not random, and carries regulatory and functional consequences. Existing protein foundation models ignore this context-dependent role of coding sequence in shaping the protein landscape of the cell. To address this gap, we introduce cdsFM, a suite of codon-r...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: be72211a-bf46-5532-ab0d-1d5fdaaa4c80
DOI: 10.1101/2024.10.10.617568

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

A Suite of Foundation Models Captures the Contextual Interplay Between CodonsDOI 10.1101/2024.10.10.617568Read

Coupling codon and protein constraints decouples drivers of variant pathogenicitySemantic proximity Read

1 CodonBERT and ESM-2 Embedding Spaces Share an Evolutionarily Con-served Paired Geometry Encoding Synonymous Codon InformationSemantic proximity Read

Genetic variation shapes human mRNA translation and disease riskSemantic proximity Read

The codon frustration index as a new metric for mRNA stability, translation efficiency, and rates of protein synthesisSemantic proximity Read

Fine-tuning protein language models on human spatial constraint improves variant effect prediction by reducing wild-type sequence biasSemantic proximity Read

Mapping the Inter- and Intra-genic Codon Usage Landscape in <i>Homo sapiens</i>Semantic proximity Read

COUSIN (COdon Usage Similarity INdex): A normalized measure of Codon Usage PreferencesSemantic proximity Read

Deep learning modeling of ribosome profiling reveals regulatory underpinnings of translatome and interprets disease variantsSemantic proximity Read

Benchmarking DNA Foundation Models for zero-shot variant effect prediction: the role of context, training, and architectureSemantic proximity Read

Benchmarking DNA Foundation Models for zero-shot variant effect prediction: the role of context, training, and architectureSemantic proximity Read

Species-specific codon context rules unveil non-neutrality effects of synonymous mutations.Semantic proximity Read

Protein Language Model Predicts Mutation Pathogenicity and Clinical PrognosisSemantic proximity Read