B. Franklin Pugh

The paper uses a multi-modal platform to profile single-cell stress responses in human cell lines, finding a shared stress response program with cell-specific magnitude variations.

ScriptManager v1.0 provides a unified framework for reproducible and scalable analysis of genomics and epigenomics data across diverse assays.

SETIA infers causal gene regulatory networks that reproduce transcriptional profiles as stable attractors using molecular priors and validates them on yeast RNA-seq data.

The paper introduces a high-resolution method using TMP to map torsional stress in yeast chromatin, revealing its role in transcription and 3D genome organization.

The paper identifies Fpt1 as a chromatin-associated regulator that promotes RNA Polymerase III eviction from tRNA genes in response to nutrient changes in yeast.

GenoPipe identifies the genotype of origin in genomic datasets by analyzing unique markers to validate and correct experimental errors.

The paper investigates how sequence preferences and chromatin environments influence Fox TF binding using neural networks and mouse stem cells.

PEGR is a web-based platform that manages epigenomic and genomic research projects, ensuring reproducibility across experimental and computational workflows.

STENCIL is a web templating engine that organizes, visualizes, and shares life science datasets, enabling interactive and customizable data dissemination.

This study investigates how Ssl2/TFIIH influences transcription start site scanning by RNA Polymerase II in yeast, identifying alleles that alter TSS selection and scanning processivity.

The paper compares ChEC-seq data for SAGA, TFIID, and Mediator in yeast and finds high similarity to negative controls, suggesting limited utility for studying broad gene specificity.

The paper presents a computational framework to align and quantify ChIP-exo crosslinking patterns, enabling inference of spatial organization within protein-DNA complexes.

The paper investigates promoter scanning by Pol II in yeast, showing that it occurs across all promoters and is influenced by Pol II activity and promoter architecture.

This study shows the INO80 complex helps RNA Polymerase II move past stalled positions, aiding non-coding RNA termination in yeast.

The paper introduces ChExMix, a method to detect and classify distinct protein-DNA binding subtypes in ChIP-exo data using probabilistic modeling of tag distributions and DNA motifs.