Michael J. Guertin

The paper introduces a model to analyze RNA polymerase occupancy data, revealing that most paused polymerases terminate quickly and classifying factors by their regulatory roles in transcription.

This study shows ZNF143 regulates nuclear-encoded mitochondrial genes and is essential for development, without affecting chromatin looping or CTCF interactions.

This study investigates ZNF143's role in transcription by showing it activates and represses genes through promoter binding and interference with RNA Polymerase initiation.

This study identifies TRPS1 as a regulator of ER binding and gene expression in luminal breast cancer, showing its role in chromatin accessibility and tumor progression.

The paper identifies Twist2 as a key regulatory node in adipogenesis using kinetic networks derived from ATAC-seq and PRO-seq data.

The paper deconstructs a PRO-seq data processing pipeline, evaluates quality control metrics, and provides a framework for adapting to different protocols.

The paper develops a rule ensemble machine learning method to correct Tn5 transposase sequence bias in ATAC-seq data, improving the interpretation of chromatin accessibility.

The paper identifies distinct structural domains in the MUNC lncRNA that regulate different promyogenic genes through cis and trans mechanisms.

SELMA estimates intrinsic cleavage biases in bulk and single-cell chromatin accessibility data, improving analysis accuracy and cell clustering in single-cell ATAC-seq.

The paper introduces PEPPRO, a workflow for processing nascent RNA profiling data, providing standardized output and quality assessments.

The paper introduces an R package to infer primary transcript annotations from run-on data, improving sensitivity in detecting differentially expressed transcripts and RNA polymerase pause indices.

The paper improves the auxin-inducible degron system to enable rapid, specific protein depletion while preserving native protein levels and patterns.

The paper quantifies Hsf1 binding and transcription in yeast under basal and heat shock conditions, revealing a continuum of Hsf1 occupancy and activity across the genome.

The paper introduces a novel normalization strategy for ChIP-seq to measure absolute fold-change in ER binding, validated using fulvestrant treatment and other experimental conditions.

BART predicts functional transcription factors regulating a gene set or associated with a genomic profile using existing ChIP-seq data.

The paper introduces seqOutBias to correct enzymatic sequence bias in sequencing data, improving the identification of molecular signatures from protein/DNA interactions.