# Establishment of Active Chromatin Domains

> **NIH NIH R35** · BROWN UNIVERSITY · 2021 · $74,191

## Abstract

RESEARCH SUMMARY:
Understanding the mechanisms which drive coordinate gene activation will provide critical
biological insights into development and disease. This supplement aims to enable AI/ML
methods to integrate diverse datasets to help achieve that goal. Specifically, we plan
to computationally model the spatiotemporal regulation of genes in Drosophila by combining
ChIP-Seq, Hi-C/ Micro-C, and mRNA-Seq datasets. Moreover, we will obtaining and model
single-cell measurements (scRNA-Seq and scATAC-Seq) across early embryonic developmental
stages when domains of coordinate gene activation are established. Therefore, we propose three
tasks to produce AI/ML-ready datasets for the community. (1) Development of robust
preprocessing pipelines for easy access and input to graph-based neural networks for integrating
datasets. (2) Application of sub-graph selection methods to extract informative interactions from
large and noisy graphs generated from chromatin capture technologies. (3) Integrating single-cell
measurements and providing these combinations for data modeling and analysis purposes. The
proposed methods will assist the goals of accurately capturing the underlying biological
information when using various machine learning approaches. Furthermore, we will provide
processed datasets and scripts to the community to enable methodological innovations. Dr.
Larschan will collaborate with machine learning expert Dr. Singh and we have collaborated on
several projects based on the proposed topic with joint students and publications. This
supplement will be essential to allowing us to continue collaborating and generating new
methods and data sets which will provide key insight into coordinate gene activation.

## Key facts

- **NIH application ID:** 10410617
- **Project number:** 3R35GM126994-04S2
- **Recipient organization:** BROWN UNIVERSITY
- **Principal Investigator:** Erica Nicole Larschan
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $74,191
- **Award type:** 3
- **Project period:** 2018-04-01 → 2023-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10410617

## Citation

> US National Institutes of Health, RePORTER application 10410617, Establishment of Active Chromatin Domains (3R35GM126994-04S2). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10410617. Licensed CC0.

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