Jonathan D. Fischer

Robust and Adaptive Non-Parametric Tests for Detecting General Distributional Shifts in Gene Expression

This paper introduces QRscore, a non-parametric test for detecting distributional shifts in gene expression, showing it outperforms existing methods in detecting variance and mean shifts.

RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and initiates a novel mRNA decay pathway

The paper shows that RNA-controlled shuttling of Xrn1 and its decay factors regulates mRNA synthesis and decay, revealing a novel nuclear-initiated cytoplasmic decay pathway.

Robust and annotation-free analysis of alternative splicing across diverse cell types in mice

The paper analyzes alternative splicing across diverse mouse cell types using two large-scale single-cell datasets, identifying novel isoforms and splicing regulation patterns.

A likelihood-based deconvolution of bulk gene expression data using single-cell references

This paper introduces RNA-Sieve, a likelihood-based method to deconvolve bulk RNA-seq data using single-cell references, providing accurate cell type proportion estimates and confidence intervals.

Numerous post-translational modifications of RNA polymerase II subunit Rpb4 link transcription to post-transcriptional mechanisms

The paper identifies over 100 post-translational modifications of Rpb4/7 that regulate mRNA lifecycle stages by modulating interactions with key regulators.

Cytoplasmic mRNA decay factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast

The paper shows Xrn1, a decay factor, modulates RNA polymerase II processivity in yeast genes, affecting transcription initiation, elongation, and termination.

Three-way clustering of multi-tissue multi-individual gene expression data using constrained tensor decomposition

The paper introduces MultiCluster, a tensor decomposition method for analyzing multi-tissue gene expression data, showing improved accuracy and speed over existing methods.