Daniel R. Larson

This study uses OptoTet to manipulate TAD boundaries and shows that boundary pairing enhances gene activity for ERRFI1 but not MYC.

The paper shows that cell size affects mRNA concentrations, driving proteome changes through transcriptional regulation.

This study introduces a kinetic model that integrates scRNA-seq and imaging data to simulate gene transcription dynamics and identifies conserved quantities and improved models for transcription factor mechanisms.

The paper identifies sequence features associated with recursive splicing and develops a classifier to detect these features.

The paper investigates the relationship between TAD boundaries and gene activity using single-cell imaging, finding they are largely uncoupled.

This study shows that transcriptional specificity is achieved through kinetic proofreading, where promoters discriminate specific TF interactions based on dwell time rather than occupancy.

The paper introduces LEAR, a post-processing method to reduce localization errors in multi-loci microscopy, revealing new insights into enhancer biology and chromatin organization.

This study identifies acetylation of the Integrator complex as a key determinant of gene-specific transcriptional bursting patterns through high-throughput imaging screens.

This study identifies U2AF's role in regulating mitochondrial function by controlling translation and localization of nuclear-encoded mitochondrial mRNAs, with implications for disease.

The paper applies a kinetic proofreading model to elucidate how transient U2AF binding leads to high fidelity splice site selection.

HiTIPS provides a flexible, open-source platform for high-throughput image analysis in cell biology, supporting customization and integration of new algorithms for tasks like segmentation, tracking, and quantification.

The paper shows that post-transcriptional PAS cleavage of p53 pre-mRNA allows it to escape DNA damage inhibition, and identifies other DDR-related pre-mRNAs with similar mechanisms.

The paper shows that transcriptional regulation in yeast is cyclic and irreversible, violating thermodynamic equilibrium.

This study uses single-molecule imaging to show that Gal4 dwell time determines transcriptional burst size in yeast, with nucleosomes reducing dwell time and affecting transcriptional bursting kinetics.