Alexandra Bradu

Genome-wide single-cell perturbation screens with VIPerturb-seq

VIPerturb-seq enables genome-wide CRISPR perturbation screens using probe-based detection, improving throughput and efficiency for single-cell analysis.

Systematic identification of seed-driven off-target effects in Perturb-seq experiments

The paper identifies off-target effects in CRISPRi Perturb-seq experiments by analyzing transcriptional similarity between on-target and off-target guide effects.

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting

This paper introduces RNA fingerprinting, a method to map transcriptional responses to perturbations using reference dictionaries, showing accurate single-cell assignments and broad biological applications.

Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators

The paper presents an iterative framework to identify mTOR signaling regulators using multimodal single-cell data and validates novel regulators through experimental testing.

Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens

The paper uses Perturb-seq to systematically identify signaling regulator targets across multiple cell lines and contexts, introducing Mixscale to improve analysis and infer pathway activation changes.

Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells

Phospho-seq integrates phosphorylated protein profiling with scATAC-seq and scRNA-seq to study cell signaling and gene regulation in single cells.

Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet

The paper analyzes gene expression in Drosophila sechellia fed noni fruit to identify genetic mechanisms underlying toxin resistance and diet specialization.