Michael R. Stadler

Machine Learning Method for Optimizing Coding Sequences in Mammalian Cells

The paper develops a machine learning method to optimize coding sequences for improved protein expression in mammalian cells by analyzing synonymous codon effects.

Localization of the pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression

This study shows that the pioneer factor GAF localizes to subnuclear foci through binding to GA-satellite repeats, which is necessary for forming heterochromatin and silencing satellite repeat expression.

Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos

This study uses single-nucleus RNA-sequencing to analyze gene expression differences in Drosophila embryos, revealing spatially distinct clusters and differential expression in specific regions.

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

This study shows that transcription factors like Zelda and Bicoid form dynamic, transient hubs in Drosophila embryos that interact with active transcription sites.

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

The paper maps chromatin contacts in Drosophila embryos to show that insulator boundaries align with polytene interbands and TADs.

Dense Bicoid Hubs Accentuate Binding along the Morphogen Gradient

The paper uses live imaging in Drosophila embryos to show that Bicoid binds DNA with a rapid off-rate and forms localized hubs that enable concentration-sensitive regulation.

A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps

The paper identifies insulator elements in Drosophila embryos as boundaries between topologically associated domains (TADs) and links them to low density polytene interbands.