Group Meetings

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

 Presentation datePresenterProgress ReportJournal Club
2026   
April   
 4/15Di "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
 4/29Xiaoqin "Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs" https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1.full
June   
 6/3Jaya "Range extender mediates long-distance enhancer activity" https://www.nature.com/articles/s41586-025-09221-6
 6/10Xiaoqin "Uncovering the whole genome silencers of human cells via Ss-STARR-seq" (https://www.nature.com/articles/s41467-025-55852-8)
 6/24Gaetano "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)
July   
 7/2Jaya "Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling" (https://www.biorxiv.org/content/10.1101/2025.02.20.639398v3)
 7/15Yash, Shivang, and Vayunprogress reports 
 7/22Gaetano "Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry" (https://www.nature.com/articles/s41467-025-64631-4)"
 7/29Yash, Shivang, and Vayunposter presentations 



Papers to present:
"Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers" (https://www.biorxiv.org/content/10.64898/2026.06.25.734173v1)
"Decoding common and rare noncoding variant effects across cellular and developmental contexts" (https://www.nature.com/articles/s41588-026-02619-6)
"Gene regulatory landscape dissected by single-cell four-omics sequencing" (https://www.nature.com/articles/s41586-026-10322-z)
"Linking GWAS risk genes to transcriptional features of major depressive disorder via in vivo Perturb-seq" (https://www.nature.com/articles/s41588-026-02638-3)
"Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry" (https://www.nature.com/articles/s41467-025-64631-4)
"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)
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
"Functional dissection of complex trait variants at single-nucleotide resolution"
https://www.nature.com/articles/s41586-026-10121-6
"Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation"
https://link.springer.com/article/10.1186/s13073-021-00857-3
"Gigabase-scale deletion scanning of the human genome"
https://www.biorxiv.org/content/10.64898/2026.05.29.728882v1.full


Project discussions (Monday meetings) [STARTING SEPTEMBER 7]

  • Monday, 9:30 am - Stas
  • Monday, 10:00 am - Di
  • Monday, 10:30 am - Alexandra
  • Monday, 11:00 am - Jaya


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