Sarah Rennie

This study benchmarks two demultiplexing tools for direct RNA sequencing using IVT spike-ins and species identity, showing their performance differences and the need for calibration.

The paper shows PUMILIO and m6A-YTHDF proteins share mRNA targets and have opposing roles in plant organogenesis.

The paper identifies candidate m6A modification sites on HPV18 early transcripts in HeLa cells using RNA sequencing and perturbation experiments.

The paper introduces DeepCompARE, an in silico ablation framework to analyze TF cooperativity, finding most TF motifs are independent with defined synergy and redundancy effects.

The paper shows ALBA proteins interact with YTHDF proteins to facilitate m6A reading in Arabidopsis, expanding the understanding of m6A regulatory mechanisms in plants.

The paper identifies transcription factor expression as the main factor driving variability in gene co-activity domains using human expression data.

The paper examines how promoter sequence and transcription start site architecture influence expression variability and genetic variant effects in human genes.

hyperTRIBER is an R package for detecting differential RNA editing, showing high statistical power in analyzing low-expression and low-editing proportion scenarios.

The paper identifies overlapping mRNA targets of ECT2 and ECT3 using HyperTRIBE and shows they regulate target mRNA abundance, not alternative polyadenylation.

The paper identifies ECT2 binding sites in Arabidopsis m6A-containing mRNAs using iCLIP and HyperTRIBE, revealing sequence preferences and competition with other RNA-binding proteins.

The paper analyzes transcription start sites in D. melanogaster, revealing widespread divergent transcription and relationships between core promoter strength, enhancer potential, and expression levels.

The paper decomposes transcriptional activity to identify how much is influenced by chromatin architecture and cell-specific regulatory interactions across 76 human cell types.