Group Meetings
Wednesdays at 10:00am, the 6th floor conference room
| Presentation date | Progress Report | Journal Club | |
|---|---|---|---|
| 2024 | |||
| November | |||
| 11/20 | - | Sanjar | |
| December | |||
| 12/11 | - | Jaya: An encyclopedia of enhancer-gene regulatory interactions in the human genome, https://pubmed.ncbi.nlm.nih.gov/38014075/ | |
| 12/18 | Xiaoqin | Di: Machine-guided design of cell-type-targeting cis-regulatory elements, https://www.nature.com/articles/s41586-024-08070-z | |
| 2025 | |||
| January | |||
| 1/15 | - | Gaetano: DegCre, https://www.biorxiv.org/content/10.1101/2023.10.04.560923v1 | |
| 1/22 | Sanjar | - | |
| February | |||
| 2/5 | - | Jaya: CRISPRi TF knockouts (https://academic.oup.com/nar/article/48/D1/D93/5584524, "More than 200 gene expression profiles for TF knockdown or knockout are provided by ENCODE, involving 145 human TFs from four cell lines (14)") | |
| 2/12 | - | Xiaoqin: Massively parallel characterization of transcriptional regulatory elements, https://www.nature.com/articles/s41586-024-08430-9 | |
| 2/19 | Di | - | |
| March | |||
| 3/5 | - | Gaetano: DeepLift, https://arxiv.org/abs/1704.02685 | |
| 3/19 | Xiaoqin | - | |
| 3/26 | - | Jaya: TF-Modisco, https://arxiv.org/pdf/1811.00416 | |
| April | |||
| 4/2 | - | Sanjar:ADASTRA, https://www.nature.com/articles/s41467-021-23007-0 | |
| 4/9 | - | Gaetano: DeepSHAP (https://arxiv.org/pdf/1705.07874.pdf, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9349278/pdf/41467_2022_Article_31384.pdf) | |
| 4/16 | - | Xiaoqin: Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed (https://www.medrxiv.org/content/10.1101/2025.02.19.25322561v1) | |
| May | |||
| 5/7 | - | Gaetano: TAP-Seq (https://pubmed.ncbi.nlm.nih.gov/32483332/) | |
| 5/14 | - | Jaya: Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens, https://pubmed.ncbi.nlm.nih.gov/38308274/ | |
| 5/21 | - | Sanjar: ChromBPNet https://www.biorxiv.org/content/10.1101/2024.12.25.630221v2.full | |
| 5/28 | - | Xiaoqin: FLARE https://www.biorxiv.org/content/10.1101/2025.02.18.638922v2.full |
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
UDACHA-Statistical framework for calling allelic imbalance in high-throughput sequencing data
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
SHAP: https://shap.readthedocs.io/en/latest/
!!Project discussions (Monday meetings)
- Monday, 9:00 am - Sanjar
- Monday, 9:30 am - Di
- Monday, 10:00 am - Jaya
- Monday, 10:30 am - Gaetano
- Monday, 11:00 am - Xiaoqin
!!Group Members
Zoom link: https://nih.zoomgov.com/j/1604809536