Group Meetings
Wednesdays at 10:00am, the 6th floor conference room
| Presentation date | Progress Report | Journal Club | |
|---|---|---|---|
| 2026 | |||
| March | |||
| 4/8 | Di | "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 | |
| 4/29 | Xiaoqin | "Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs" https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1.full | |
| 5/20 | Jaya | "Range extender mediates long-distance enhancer activity" https://www.nature.com/articles/s41586-025-09221-6 |
Papers to present:
"Uncovering the whole genome silencers of human cells via Ss-STARR-seq" (https://www.nature.com/articles/s41467-025-55852-8)
"An expanded registry of candidate cis-regulatory elements" (https://www.nature.com/articles/s41586-025-09909-9)
"A plasma proteomics-based candidate biomarker panel predictive of amyotrophic lateral sclerosis" (https://www.nature.com/articles/s41591-025-03890-6)
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
"Functional dissection of complex trait variants at single-nucleotide resolution"
https://www.nature.com/articles/s41586-026-10121-6
Project discussions (Monday meetings)
- Monday, 9:00 am - Xiaoqin
- Monday, 9:30 am - Jaya
- Monday, 10:00 am - Di
- Monday, 10:30 am - Gaetano
Acknowledgement (included in publications)
This research was supported [in part] by the Intramural Research Program of the National Institutes of Health (NIH). The contributions of the NIH author(s) are considered Works of the United States Government. The findings and conclusions presented in this paper are those of the author(s) and do not necessarily reflect the views of the NIH or the U.S. Department of Health and Human Services.
Group Members