Update README.md

README.md

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----
-license: afl-3.0
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+---
+license: mit
+tags:
+- neuroscience
+- genomics
+- dna
+- sequence-modeling
+- basal-ganglia
+- spinal-cord
+- astrocyte
+- regulatory-genomics
+pretty_name: DNA Sequence Modeling for BG Cell Atlas Package
+---
+
+# DNA Sequence Modeling for the Basal Ganglia Cell Atlas Package
+
+This repository contains DNA-sequence modeling resources associated with the basal ganglia (BG) cell atlas package. It serves as a centralized entry point for sequence-based regulatory analyses across multiple companion studies.
+
+## What this repository is
+
+This repository is a landing page and resource hub for DNA-sequence modeling analyses associated with the basal ganglia cell atlas package.
+
+## What this repository is not
+
+This repository is not intended to duplicate the full analysis pipelines of the companion studies. Instead, it provides a centralized entry point for sequence-modeling-related resources, outputs, and links.
+
+## Overview
+
+Across these studies, sequence-based modeling is used to investigate cis-regulatory logic underlying cell type specialization. These analyses complement multiomic profiling (snRNA-seq, snATAC-seq, spatial transcriptomics, methylation, and chromatin conformation) by providing a sequence-level perspective on candidate enhancers and regulatory programs.
+
+## Associated studies
+
+### 1. Basal ganglia consensus taxonomy  
+**Johansen, Fu et al., 2025**
+
+This study establishes a consensus basal ganglia taxonomy by integrating HMBA single-nucleus RNA-seq data from human, macaque, marmoset, and previously published mouse datasets. The resulting framework provides a standardized naming system for basal ganglia cell types, enabling cross-species comparison, community-wide adoption, and downstream tool development.
+
+### 2. Cross-species spinal cord atlas  
+**Schmitz, Johansen et al., 2026**
+
+This study presents a unified cross-species atlas integrating single-nucleus multiomic profiling and spatial transcriptomics across human, macaque, and mouse. In addition to defining a conserved cell type hierarchy, it links molecular identities to anatomical organization and cis-regulatory programs, including sequence-based modeling of enhancer logic.
+
+### 3. Human BG astrocyte subgroup study  
+**Fu et al., 2026**
+
+This study identifies three major astrocyte subgroups in the human basal ganglia and characterizes their spatial, molecular, and regulatory specialization. Sequence-based modeling is used to evaluate subgroup-associated regulatory elements and candidate enhancer programs.
+
+## Repository contents
+
+Depending on the final organization, this repository include:
+- model configuration files  
+- input sequence sets (candidate regulatory regions)  
+- cell type-enriched regions  
+- model predictions and scoring outputs  
+- motif and enhancer-level summaries  
+- example loci used in the manuscript  
+
+## Conceptual workflow
+
+1. Define candidate regulatory regions from multiomic data  
+2. Extract DNA sequences for modeling  
+3. Train or apply sequence-based models  
+4. Score sequences for regulatory activity  
+5. Interpret subgroup- or cell type-specific regulatory patterns  
+
+## Links
+
+- Basal ganglia consensus taxonomy paper: [add link]  
+- Spinal cord consensus atlas paper: [add link]  
+- Basal ganglia astrocyte study: [add link]  
+- Multiomic track viewer (SCMDAP): [add link]  
+- Project GitHub repository: [add link]  
+
+## Citation
+
+Please cite the relevant companion manuscripts when using these resources.
+
+@article{BG_PACKAGE,
+  title   = {Cross-species consensus atlas of the primate basal ganglia},
+  author  = {Johansen, Nelson and Fu, Yuanyuan and others},
+  journal = {bioRxiv},
+  year    = {2025}
+}
+
+@article{BG_PACKAGE,
+  title   = {A consensus spinal cord cell type atlas across mouse, macaque, and human},
+  author  = {Schmitz, Matthew and Johansen, Nelson and others},
+  journal = {bioRxiv},
+  year    = {2026}
+}
+
+@article{BG_PACKAGE,
+  title   = {Circuit-dependent specialization of human basal ganglia astrocytes},
+  author  = {Fu, Yuanyuan and others},
+  journal = {bioRxiv},
+  year    = {2025}
+}