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README.md

@@ -9,13 +9,13 @@ tags:
   - colon
   - hg38
 ---
-# ENCODE ChromBPNet Atlas
-As part of the ENCODE 4 Project, we trained ChromBPNet models on 1,512 ENCODE DNAse-seq and ATAC-seq across 408 biosamples. Here, we provide all models for open-source use.
+# ENCODE GRAMMAR: ChromBPNet collection
+**ENCODE GRAMMAR (Genomic Regulatory Atlas of sequence Models, Motifs, Annotations and Rules)**: As part of the ENCODE 4 Project, we trained ChromBPNet models on 1,512 ENCODE DNAse-seq and ATAC-seq across 408 unique biosamples. Here, we provide all models for open, unrestricted use.
 
 For more information about the models, see:
-- Main ENCODE 4 Paper
-- [A unified lexicon of predictive DNA sequence motifs from ENCODE transcription factor binding and chromatin accessibility assays](https://doi.org/10.5281/zenodo.17123347) (Deshpande et al., Zenodo 2025)
-- [ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants](https://doi.org/10.1101/2024.12.25.630221) (Pampari et al., bioRxiv 2024)
+- **ENCODE GRAMMAR**: [A unified lexicon of predictive DNA sequence motifs from ENCODE transcription factor binding and chromatin accessibility assays](https://doi.org/10.5281/zenodo.17123347) (Yun et al., _Zenodo_ 2026)
+- **ENCODE 4**: [The Encyclopedia of DNA Elements](https://www.biorxiv.org/content/10.64898/2026.07.06.731365v1) (The ENCODE Project Consortium, _bioRxiv_ 2026)
+- **ChromBPNet**: [ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants](https://doi.org/10.1101/2024.12.25.630221) (Pampari et al., _bioRxiv_ 2024)
 
 ## ChromBPNet model: DNASE in colonic mucosa (ENCSR576UAF)
 - Model: ChromBPNet
@@ -117,4 +117,4 @@ predictions = softmax(outputs["logits_profile_predictions"]) * (np.exp(outputs["
 # License & citation
 External data users may freely download, analyze and publish results based on any ENCODE data without restrictions.
 
-Released under the [ENCODE data-use policy](https://www.encodeproject.org/about/data-use-policy/). Please cite the ENCODE Project Consortium and the model software: [ChromBPNet](https://github.com/kundajelab/chrombpnet) (Pampari et al., bioRxiv 2024).
+Released under the [ENCODE data-use policy](https://www.encodeproject.org/about/data-use-policy/). Please cite the ENCODE Project Consortium and the model software: [ChromBPNet](https://github.com/kundajelab/chrombpnet) (Pampari et al., _bioRxiv_ 2024).