ArticleNature genetics2021
Base-resolution models of transcription-factor binding reveal soft motif syntax.
Article in Nature genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 403 papers.
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Who cites it
403 citing papers in PubMed.
- SpliceDetector: A Splice Sites Detection Method Based on Biology Attention and Ensemble Module.Interdisciplinary sciences, computational life sciences · 2026Article
- Tangermeme: a toolkit for understanding cis-regulatory logic using deep learning models.Nature methods · 2026Article
- Mechanisms underlying disease-causing variants in promoters and enhancers.Nature genetics · 2026Review
- Flexible use of conserved motifs constrains genome access in cell type evolution.Nature ecology & evolution · 2026Article
- AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026Article
- dubTAGs enable on-demand stabilization for tunable and reversible control of endogenous protein levels.bioRxiv : the preprint server for biology · 2026Article
- Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.Nature genetics · 2026Article
- Cis- and trans-regulatory factors contributing to divergent activity of the TDH3 promoter in Saccharomyces yeast.Molecular biology and evolution · 2026Article
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.Nucleic acids research · 2026Article
- Using Deep Learning Models of Gene Regulation to Guide Drug Prioritization.Pharmaceuticals (Basel, Switzerland) · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding.Nucleic acids research · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- A systematic benchmarking framework and dual-view optimization strategy for single-cell DNA methylation imputation.Briefings in bioinformatics · 2026Article
- Functional motif detection via in silico ablation using AlphaGenome.Briefings in bioinformatics · 2026Article
- Unlocking the Regulatory Genome: Interpreting the Clinical Impact of Noncoding Variants in Genetic Cardiomyopathies.Circulation. Genomic and precision medicine · 2026Review
- Evolution of CTCF binding sites in the human genome.Molecular biology and evolution · 2026Article
343 more citing papers are in PubMed but not listed here.
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11 authors.
Funding
Abstract
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution chromatin immunoprecipitation (ChIP)-nexus binding profiles of pluripotency TFs. We develop interpretation tools to learn predictive motif representations and identify soft syntax rules for cooperative TF binding interactions. Strikingly, Nanog preferentially binds with helical periodicity, and TFs often cooperate in a directional manner, which we validate using clustered regularly interspaced short palindromic repeat (CRISPR)-induced point mutations. Our model represents a powerful general approach to uncover the motifs and syntax of cis-regulatory sequences in genomics data.
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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 Socratic graph.