Jeremy R. B. Newman

Manipulation of alternative splicing of IKZF1 elicits distinct gene regulatory responses in T cells

The paper investigates how alternative splicing of IKZF1 affects gene regulation in T cells, finding significant changes in gene expression and chromatin accessibility.

Multi-omics profiling reveals ethylene signalling as a key pathway underlying both genetic and epigenetic responses to low-dose ionizing radiation in Arabidopsis

This study uses multi-omics profiling to show that low-dose ionizing radiation in Arabidopsis triggers genetic and epigenetic responses mediated by the ethylene signaling pathway.

Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes

The paper identifies shifts in isoform usage in Tregs associated with Type 1 Diabetes by comparing gene expression between cases and controls.

Ozone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content

The paper examines how gene regulation, not gene content, contributes to maize genotypes' sensitivity to ozone stress by analyzing gene expression across diverse inbred lines.

Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele specific expression (BASE)

The paper introduces BASE, a Bayesian pipeline for analyzing allelic imbalance to identify cis regulatory variation, showing it validates ~75% of predicted differences between non-tester alleles.

tappAS: A comprehensive computational framework for the analysis of the functional impact of differential splicing

The paper introduces tappAS, a framework for analyzing the functional impact of differential splicing, showing AltTP plays a major role in neural development by altering protein function and regulation.

Experimental design for large scale omic studies

The paper discusses experimental design for large-scale omic studies, emphasizing the importance of balancing omics batches and accounting for experimental factors to improve statistical power.