ArticleGenome biology2024
Species-aware DNA language models capture regulatory elements and their evolution.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 42 citations in OpenAlex.
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- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- The DNA dialect: a comprehensive guide to pretrained genomic language models.Molecular systems biology · 2026Review
- Short-Context Regulatory DNA Language Models with Motif-Discovery Regularization.bioRxiv : the preprint server for biology · 2026Article
- New insights into neurodevelopmental disorders by whole genome sequencing of 100 families from Italy.NPJ genomic medicine · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- A comprehensive survey of genome language models in bioinformatics.Briefings in bioinformatics · 2026Review
- Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.Genetics · 2026Article
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- multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data.bioRxiv : the preprint server for biology · 2025Article
- Pangenome-Informed Language Models for Synthetic Genome Sequence Generation.bioRxiv : the preprint server for biology · 2025Article
- The Constrained Disorder Principle: A Paradigm Shift for Accurate Interactome Mapping and Information Analysis in Complex Biological Systems.Bioengineering (Basel, Switzerland) · 2025Review
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Nucleotide dependency analysis of genomic language models detects functional elements.Nature genetics · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- Investigating the performance of foundation models on human 3'UTR sequences.Nucleic acids research · 2025Article
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- In silico prediction of variant effects: promises and limitations for precision plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
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6 authors at 3 institutions in 1 country.
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Abstract
backgroundThe rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution.
resultsHere, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA language models capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA language models reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery.
conclusionsCollectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.