ArticleNature genetics2022
A sequence-based global map of regulatory activity for deciphering human genetics.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers, 1 of them a synthesis that pooled it.
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Who cites it
190 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Hypothyroidism and rheumatoid arthritis: a two-sample Mendelian randomization study.Frontiers in endocrinology · 2023Pooled it
- Leveraging genomic deep learning models for the prediction of noncoding variant effects.Nature genetics · 2026Review
- Spatiotemporal AI-based modeling of gene regulation and variant effects in the developing human brain using Seal.Nature neuroscience · 2026Article
- DeCTCF: Decoding CTCF binding sequences by leveraging predicted epigenomic features.PLoS computational biology · 2026Article
- Mechanisms underlying disease-causing variants in promoters and enhancers.Nature genetics · 2026Review
- HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions.PLoS computational biology · 2026Article
- GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles.Nucleic acids research · 2026Article
- From conservation scores to language models: a feature engineering perspective on machine learning for genetic variant interpretation.Briefings in bioinformatics · 2026Review
- A token-pruning framework enables efficient representation of the human genome for RNA modification analysis.Bioinformatics (Oxford, England) · 2026Article
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- A chromatin-structure-guided framework for predictive and interpretable regulatory genomics.Briefings in bioinformatics · 2026Article
- Decoding common and rare noncoding variant effects across cellular and developmental contexts.Nature genetics · 2026Article
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
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- Decoding sequence determinants of gene expression in diverse cellular and disease states.Nature methods · 2026Article
- Multiple instance fine-mapping: Predicting causal regulatory variants with a deep sequence model.PLoS genetics · 2026Article
- PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.Nature communications · 2026Article
- Massively parallel reporter assay-informed modeling improves prediction of context-specific enhancer-gene regulatory interactions.Nucleic acids research · 2026Article
130 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Epigenomic profiling has enabled large-scale identification of regulatory elements, yet we still lack a systematic mapping from any sequence or variant to regulatory activities. We address this challenge with Sei, a framework for integrating human genetics data with sequence information to discover the regulatory basis of traits and diseases. Sei learns a vocabulary of regulatory activities, called sequence classes, using a deep learning model that predicts 21,907 chromatin profiles across >1,300 cell lines and tissues. Sequence classes provide a global classification and quantification of sequence and variant effects based on diverse regulatory activities, such as cell type-specific enhancer functions. These predictions are supported by tissue-specific expression, expression quantitative trait loci and evolutionary constraint data. Furthermore, sequence classes enable characterization of the tissue-specific, regulatory architecture of complex traits and generate mechanistic hypotheses for individual regulatory pathogenic mutations. We provide Sei as a resource to elucidate the regulatory basis of human health and disease.
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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.