Andrew G. Xue

Computational design of a versatile, zero-radius proximity labeling enzyme

This paper designs a new proximity labeling enzyme, FlexID, using computational methods to improve spatial precision and versatility for mapping protein interactions and proteomes.

Subcellular transcriptome sequencing with single cell APEX-seq identifies regulators of cell-cell interactions

This paper introduces scAPEX-seq, a method to map subcellular transcriptomes, and identifies CTSW as a regulator of CAR T cell function in tumor co-cultures.

Computational design of conformation-biasing mutations to alter protein functions

Contrastive scoring of protein variants across alternative backbone structures with inverse folding models (Conformational Biasing) predicts mutations that shift conformational equilibria and tune effector binding, catalysis, and labeling specificity.

Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics

The paper introduces ExBarSeq, a method for high-resolution multiplexing of barcodes and synaptic proteins in neurons, demonstrating its application in mouse brain tissue.

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.