William E. Allen

Few-shot regulatory sequence design with a genomic language model

This paper demonstrates that a genomic language model can generate functional regulatory DNA sequences using few examples, showing improved performance in cell-type-specific gene expression and neuronal labeling.

MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue

The paper introduces an imaging-based pooled screening method to identify genetic perturbations and their effects on cell states and neighboring cells in intact tissues.

High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer

PEtracer maps cell state and lineage dynamics in vivo with high spatial resolution using prime editing and multimodal imaging.

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

The paper develops a platform combining imaging and sequencing to study genetic perturbations in mouse liver, identifying regulators of hepatocyte zonation and liver unfolded protein response.

Mapping the cellular and molecular organization of mouse cerebral aging by single-cell transcriptome imaging

This study maps age-related changes in mouse brain cellular and molecular organization using spatial transcriptomics, revealing significant shifts in non-neuronal cells and glial activation patterns.

Cerebellar nuclei evolved by repeatedly duplicating a conserved cell type set

The paper identifies a conserved cell type set in cerebellar nuclei across species and shows how it was duplicated to form new regions, with a shift in dominance in humans.

Differential encoding in prefrontal cortex projection neuron classes across cognitive tasks

The paper examines how transcriptomic types of mouse prefrontal cortex projection neurons relate to axonal projections and encoding properties across cognitive tasks, finding redundant but quantitatively biased task signal encoding.

Temporal Evolution of Cortical Ensembles Promoting Remote Memory Retrieval

The paper uses TRAP2 to study how prefrontal cortex neurons involved in memory retrieval change over time and support remote memory.