Xuhua Chen

Inducible Calling Cards: Developing Mouse Reagents for Experimentally Controlled Transposon Insertion in vivo.

This paper develops inducible Calling Cards in mice to control transposon insertion timing in vivo, showing varying efficacy and developmental impacts based on the transcription factor used.

MYT1L deficiency impairs excitatory neuron trajectory during cortical development

This study examines the role of MYT1L in neuronal development by analyzing gene expression in wild-type and MYT1L-deficient mice, finding disruptions in excitatory neuron proportions and gene expression.

Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues

Calling Cards records protein-DNA interactions over time using transposons, enabling analysis of historical molecular states through sequencing.

Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes

This paper introduces barcoded self-reporting transposon calling cards to efficiently measure transcription factor binding and gene expression in bulk populations, demonstrating their use in vitro and in vivo.

Brd4-bound enhancers drive cell intrinsic sex differences in glioblastoma

This study identifies sex differences in glioblastoma driven by Brd4-bound enhancers, showing opposing responses to BET inhibitors in male and female tumor cells.

Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

This paper introduces self-reporting transposons (SRTs) and the scCC assay to simultaneously capture gene expression and TF binding in single cells, demonstrating their use in cultured cells and mouse cortex.

MAPPING TRANSCRIPTION FACTOR NETWORKS BY COMPARING TF BINDING LOCATIONS TO TF PERTURBATION RESPONSES

The paper improves transcription factor network mapping by combining dual threshold optimization, NetProphet 2.0, and new methods for binding and response data.

A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

The paper introduces FLEX Calling Cards, a method to map transcription factor-DNA interactions in specific cell types within heterogeneous tissues using viral delivery and transposon insertion.