Arjun Raj

The paper shows that transcriptional bursting in gene networks can produce rare coordinated high expression states in cancer cells, which are linked to drug resistance.

The paper identifies rare cell states in melanoma that contribute to drug resistance by analyzing single-cell gene expression and signaling dynamics.

This paper introduces LADL, a light-activated system to dynamically control chromatin looping, showing it can redirect enhancer-promoter interactions and alter gene expression within four hours.

The paper uses allele-specific RNA imaging to show that allelic imbalances in tissues can result from transcriptional bursting and low mRNA abundance.

The paper develops a framework to link Pol II ChIP-seq and single-cell data to transcriptional step rates, showing burst initiation and pause release are key regulated steps, while polymerase binding is not.

Quantius provides a crowd-based image annotation platform that achieves high-fidelity human annotation at 105 clicks per hour, matching deep learning performance while reducing time and cost.

The paper introduces DESCEND, a method to deconvolve true gene expression distributions from noisy scRNA-seq data, improving estimates of dispersion and burstiness while adjusting for covariates.

SAVER improves gene expression estimates in scRNA-seq by imputing zeros and enhancing low/moderate expression genes, improving downstream analysis accuracy.

This paper introduces clampFISH, a method for detecting RNA with high-gain signal amplification, enabling single-cell and single-molecule resolution using fluorescent probes.

This paper compares single cell RNA sequencing and single molecule RNA FISH for rare cell analysis, finding that higher transcriptome complexity per cell improves accuracy for small gene sets.

The paper develops an RNA FISH method to visualize adenosine-to-inosine editing in single cells and finds no correlation with nuclear localization or paraspeckle association.

The paper re-examines HIV LTR mRNA and protein expression data, finding that noise scales inversely with mean expression, supporting the inverse correlation between noise and mean.

The paper tracks Pol II occupancy genome-wide during mitosis-G1 transition and finds a transcriptional spike at the mitosis-G1 transition that exceeds later G1 levels.