Pratiksha I. Thakore

Perturb-ME combines CRISPR screening and single-cell profiling to identify regulatory modules governing gene programs in melanoma.

The paper designs Müller glia-specific cis-regulatory elements using deep learning and validates their function in vivo.

This study uses dynamic caging to link live-cell behavior with transcriptional responses across perturbations, revealing new insights into immune and inflammatory gene regulation.

PerturbView enables highly multiplexed optical pooled screens in primary cells and tissues by improving barcode amplification, revealing regulators of NFκB signaling and enabling spatial transcriptomics integration.

The paper uses Perturb-seq to systematically study 1,130 E3 ligases and their roles in inflammatory responses in dendritic cells, revealing co-functional modules and genetic interactions.

The paper benchmarks a new low-cost sequencing by synthesis method for scRNA-seq, showing comparable results to existing technologies and enabling cost-effective large-scale applications.

The paper introduces Compass, an algorithm that uses single-cell RNA-Seq and flux balance analysis to characterize metabolic states in Th17 cells, revealing a metabolic switch and novel anti-inflammatory regulators.

The paper uses Perturb-CITE-Seq to identify novel immune evasion mechanisms in cancer by analyzing multi-modal single-cell data from patient-derived models.

The paper uses Perturb-seq to assess the phenotypic impact of somatic variants in cancer, revealing a continuum of gain-of-function KRAS variants.

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.