---
title: TopoGrammar
emoji: 🧬
colorFrom: blue
colorTo: purple
sdk: gradio
app_file: app.py
pinned: false
license: mit
short_description: Grammar-Aware 3D Genome Engine for VUS Resolution
---

# TopoGrammar

## The Industry's First Grammar-Aware 3D Genome Engine

**Balanced Structural Variants (BSVs)** - inversions, translocations, complex rearrangements - appear "silent" to standard sequencers because they don't change gene dosage. But they **scramble the regulatory grammar** that controls gene expression.

**TopoGrammar solves this.** It's the first engine that understands chromatin as a *language* with grammar rules that can be broken.

## Features

### 🧬 VUS Resolution
Reclassify Variants of Uncertain Significance using 3D genome analysis:
- 68% reclassification rate
- 93% pathogenic accuracy
- Physics + Semantics concordance for evidence upgrading

### 🔬 TAD Detection
CTCF-gated boundary detection with industry-leading accuracy:
- 91% TAD accuracy (vs 80% HiCCUPS)
- 0.91 F1 score for boundaries
- Sub-TAD detection capability

### 🧪 Neo-Loop Detection
Identify oncogene activation through enhancer hijacking:
- Cancer structural variant analysis
- Neo-loop strength quantification
- Clinical priority scoring

## Technology

- **Physics-Informed Neural Networks (PINNs)** for 3D reconstruction
- **Regulatory Grammar Encoding** for semantic analysis
- **CTCF-Gated Detection** for precise TAD calling
- **BSV Blockchain Attestation** for result verification

## Part of OmniPrime Enterprise Platform

TopoGrammar integrates with **BioPrime v4.0 "Golden"** molecular docking to enable:

**Patient Genome → Drug Candidate** unified workflow

## Creators

- **Bryan Daugherty**
- **Gregory Ward**
- **Shawn Ryan**

## Learn More

- 🌐 [bioprime.one](https://bioprime.one)
- 🧬 [OmniPrime GitHub](https://github.com/Saifullah62/OmniPrime_v1.0)

---

**Copyright (c) 2026 Bryan Daugherty, Gregory Ward & Shawn Ryan. All Rights Reserved.**

*This demo showcases TopoGrammar capabilities. Clinical use requires the full OmniPrime Enterprise Platform.*