David Garfield

Deep learning design and in vivo validation of Müller glia-specific cis-regulatory elements

The paper designs Müller glia-specific cis-regulatory elements using deep learning and validates their function in vivo.

scEPS integrates genetic and single-cell disease atlas data to provide granular mechanistic insights into complex human diseases

scEPS integrates GWAS and single-cell data to identify disease-associated cell neighborhoods by testing gene expression variance explained in disease contexts.

Decoding sequence determinants of gene expression in diverse cellular and disease states

The paper introduces Decima, a model that predicts cell type- and condition-specific gene expression from DNA sequence using single-cell RNA sequencing data.

Maladaptive inflammatory signaling in old mice impairs colonic regeneration by promoting a sustained fetal-like epithelial state

This study identifies how aging impairs colonic regeneration in mice by promoting a fetal-like epithelial state through sustained IFNγ signaling.

NINTEDANIB AND PIRFENIDONE AFFECT GROWTH AND DIFFERENTIATION OF HUMAN ALVEOLAR TYPE 2 CELLS

This study investigates how pirfenidone and nintedanib affect the growth and differentiation of human alveolar type 2 cells in organoid cultures, revealing differences in their impact on surfactant protein C expression and cell identity.

regLM: Designing realistic regulatory DNA with autoregressive language models

This paper introduces regLM, a framework using autoregressive language models to design synthetic regulatory DNA elements with desired properties, showing they match biological features of validated CREs.

Selective Filopodia Adhesion Ensures Robust Cell Matching in the Drosophila Heart

The paper investigates how selective filopodia adhesion mediated by adhesion molecules ensures robust cell matching in Drosophila heart development.