Deciphering the impact of genomic variation on function

Code of Conduct Committee (alphabetical by last name … - Nature, 2024 - nature.com
Our genomes influence nearly every aspect of human biology—from molecular and cellular
functions to phenotypes in health and disease. Studying the differences in DNA sequence …

Genomic language models: opportunities and challenges

G Benegas, C Ye, C Albors, JC Li, YS Song - Trends in Genetics, 2025 - cell.com
Large language models (LLMs) are having transformative impacts across a wide range of
scientific fields, particularly in the biomedical sciences. Just as the goal of natural language …

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

J Linder, D Srivastava, H Yuan, V Agarwal, DR Kelley - Nature Genetics, 2025 - nature.com
Sequence-based machine-learning models trained on genomics data improve genetic
variant interpretation by providing functional predictions describing their impact on the cis …

The expanding diagnostic toolbox for rare genetic diseases

KD Kernohan, KM Boycott - Nature Reviews Genetics, 2024 - nature.com
Genomic technologies, such as targeted, exome and short-read genome sequencing
approaches, have revolutionized the care of patients with rare genetic diseases. However …

SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions

LM Blaabjerg, N Jonsson, W Boomsma, A Stein… - Nature …, 2024 - nature.com
The ability to predict how amino acid changes affect proteins has a wide range of
applications including in disease variant classification and protein engineering. Many …

Will variants of uncertain significance still exist in 2030?

DM Fowler, HL Rehm - The American Journal of Human Genetics, 2024 - cell.com
Summary In 2020, the National Human Genome Research Institute (NHGRI) made ten" bold
predictions," including that" the clinical relevance of all encountered genomic variants will be …

Advancing variant effect prediction using protein language models

BJ Livesey, JA Marsh - Nature Genetics, 2023 - nature.com
Advancing variant effect prediction using protein language models | Nature Genetics Skip to main
content Thank you for visiting nature.com. You are using a browser version with limited support …

Predicting pathogenic protein variants

JA Marsh, SA Teichmann - Science, 2023 - science.org
Many of the genetic mutations that cause disease in humans occur in protein-coding
regions. Although the capacity to sequence DNA and identify these variants has …

Randomizing the human genome by engineering recombination between repeat elements

J Koeppel, R Ferreira, T Vanderstichele, LM Riedmayr… - Science, 2025 - science.org
We lack tools to edit DNA sequences at scales necessary to study 99% of the human
genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert …

Site-saturation mutagenesis of 500 human protein domains

A Beltran, X Jiang, Y Shen, B Lehner - Nature, 2025 - nature.com
Missense variants that change the amino acid sequences of proteins cause one-third of
human genetic diseases. Tens of millions of missense variants exist in the current human …