ArticleBioinformatics (Oxford, England)2021
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 585 papers, 1 of them a synthesis that pooled it.
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Who cites it
585 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Astronomical spectra as language: Order-agnostic foundation model for low-SNR reconstruction and stellar parameter prediction.iScience · 2026Article
- Small Activating RNAs: A Curated Database and an Overview of Rational Design Principles.Molecules (Basel, Switzerland) · 2026Review
- GLM-Prior: a genomic language model for transferable sequence-derived priors in gene regulatory network inference.Nature communications · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
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- A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.Scientific reports · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Unveiling the terra cognita of sequence spaces using Cartesian projection of asymmetric distances.NAR genomics and bioinformatics · 2026Article
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- VeloHARMO: a deep learning framework for mRNA coding sequence generation and design via translation velocity harmonization.Briefings in bioinformatics · 2026Article
- Balanced DNA interpolation improves learning of genetic distance-informed embeddings in plants.PLoS computational biology · 2026Article
- AI-assisted phage formulation delivered via injectable hydrogels for localized control of implant-associated infections.Bioactive materials · 2026Article
- iEnhancer-Flow: Integrating Transformer-Based Sequence Learning with DNA Shape Insights for Robust Enhancer Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
525 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationDeciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios.
resultsTo address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks. AVAILABILITY AND IMPLEMENTATION: The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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.