Sana Badri

Identification of new therapeutic targets in CRLF2-overexpressing B-ALL through discovery of2 TF-gene regulatory interactions.

The paper identifies new therapeutic targets in CRLF2-overexpressing B-ALL by analyzing TF-gene regulatory interactions using network inference and experimental validation.

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

The paper investigates the distinct and combined roles of CTCF and CTCFL in chromosome organization and transcription by analyzing their binding sites and functional domains.

EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation

EpiMethylTag combines ATAC-seq or ChIP-seq with bisulfite conversion to simultaneously assess chromatin accessibility/TF binding and DNA methylation.

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

The paper shows NSD2 overexpression alters chromatin structure and gene expression by affecting CTCF and H3K27ac in specific chromatin domains.

Dissection of purified LINE-1 reveals distinct nuclear and cytoplasmic intermediates

The paper identifies distinct nuclear and cytoplasmic intermediates of LINE-1 retrotransposition using mass spectrometry and affinity purification.

The interdependent nature of multi-loci associations can be revealed by 4C-Seq

The paper introduces a method to identify multi-loci chromatin interactions using 4C-seq data and demonstrates its application to Tcrb and Igk enhancer interactions.

4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

This paper introduces 4C-ker, a method that improves the reproducibility of identifying genome-wide interactions from 4C-Seq data by accounting for signal biases and varying resolution.