Matthew D. Simon

The paper introduces a method to infer isoform-level kinetics of nonsense-mediated mRNA decay using short-read NR-seq data, revealing variability in NMD efficiency and decay rates of transcripts with and without PTCs.

The paper identifies Kacme as a histone modification marking accessible chromatin that resists compaction, particularly at regulatory regions and insulator elements.

This study identifies TRMT61B as an m1A methyltransferase active on cytosolic mRNAs and shows context-dependent effects of m1A on translation and ribosome recruitment.

RNAdecayCafe provides a uniformly processed atlas of RNA half-life estimates across 11 human cell lines, revealing RNA stability's role in gene expression.

The paper introduces EZbakR and fastq2EZbakR tools to enhance NR-seq data analysis by supporting multi-label modeling, improved variance accounting, and flexible statistical comparisons.

This study shows that the RBM15-MKL1 fusion protein drives leukemia through m6A methylation and WNT pathway activation, with METTL3 inhibition reducing tumor growth.

This paper identifies a new function of MYOD as a transcriptional repressor through E-box-independent chromatin binding, revealing a mechanism to repress gene expression and maintain cell identity during myogenesis.

The paper develops CoSTseq to study nascent RNA base pairing in yeast, revealing rapid folding dynamics and helicase roles in ribosome biogenesis.

This study identifies ELOF1 as a critical factor for somatic hypermutation and class switch recombination by facilitating RNAPII pausing and AID targeting.

The paper develops bakR, a Bayesian method to compare RNA kinetic parameters across conditions using NR-seq data, validated on simulated and real datasets.

The paper shows hyperosmotic stress causes transcriptional repression but still leads to downstream-of-gene (DoG) transcripts, with Pol II interactome changes and Integrator complex disruption involved.

A genome-wide CRISPR screen with SARS-CoV-2 recovers ACE2 and Cathepsin L and nominates SWI/SNF, TGF-beta signalling and HMGB1 as pro-viral; pathway inhibitors blocked virus-induced death.

The paper shows antisense lncRNA transcription is required for stochastic Protocadherin promoter choice in neurons.