Ovcharenko Group Wiki

Group Meetings

Wednesdays at 10:00am, the 6th floor conference room

Papers to present:

Borzoi (https://www.biorxiv.org/content/10.1101/2023.08.30.555582v1.full.pdf)
"Increased enhancer–promoter interactions during developmental enhancer activation in mammals" Nature Genetics. Kvon Lab
"Range extender mediates long-distance enhancer activity" https://www.nature.com/articles/s41586-025-09221-6 Nature. Kvon Lab https://www.nature.com/articles/s41467-024-55513-2
UniversalEPI: Harnessing Attention Mechanisms to Decode Chromatin Interactions in Rare and Unexplored Cell Types
https://www.biorxiv.org/content/10.1101/2024.11.22.624813v1
Evaluation of deep learning approaches for high-resolution chromatin accessibility prediction from genomic sequence
https://www.biorxiv.org/content/10.1101/2025.03.01.641000v1.abstract
Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing
https://www.nature.com/articles/s41592-024-02511-3#Sec19
SHAP: https://shap.readthedocs.io/en/latest/
"Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions"
https://www.biorxiv.org/content/10.1101/2025.04.21.649048v1.full
"Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs"
https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1.full

Project discussions (Monday meetings)

• Monday, 9:00 am - Xiaoqin
• Monday, 9:30 am - Jaya
• Monday, 10:00 am - Di
• Monday, 10:30 am - Gaetano

Group Members

• Di Huang
• Xiaoqin Huang
• Sanjarbek Hudaiberdiev
• Gaetano Manzo
• Jaya Srivastava
• Ivan Ovcharenko