Manu

The paper profiles gene expression during myeloid differentiation at high temporal resolution, revealing cascading waves of gene regulation that remodel cellular physiology in a characteristic sequence.

This study investigates how DNA accessibility and transcription factor occupancy influence enhancer activity during macrophage-neutrophil differentiation, showing that TF binding, not total accessibility, drives enhancer upregulation.

LucFlow measures Luciferase reporter expression in single cells with higher accuracy than bulk methods by excluding dead cells.

The paper uses data-driven dynamical modeling to predict gene regulatory network dynamics during hematopoietic differentiation, finding that neutrophil differentiation is driven by C/EBP and Gfi1 rather than the Gata1-PU.1 switch.

This paper introduces FIGR, a classification-based method for inferring gene regulatory networks, showing it is significantly faster than traditional optimization methods.

The paper introduces a regression-based normalization method for Luciferase reporter data, showing it outperforms ratiometric normalization, especially at low transfection efficiency.

The paper experimentally tests thermodynamic models to decode the cis-regulatory logic of Cebpa enhancers and silencers in myeloid and red-blood cell lineages, revealing dominant repression mechanisms and redundant regulatory architectures.