Amy E. Herr

Same-cell mapping of epigenetic regulatory state to functional proteomic output

Proteo-Seq links chromatin accessibility and proteomic output in the same cell, revealing new protein-defined states in breast cancer cells.

Arrayed hydrogels pair whole-cell imaging with single-cell mass spectrometry proteomics

This paper introduces a platform called ProteoParcel that combines whole-cell imaging with single-cell mass spectrometry proteomics for breast cancer cells.

AutoBlot: deterministic single-cell western blotting reveals proteomic diversity in rare cell populations

AutoBlot enables deterministic single-cell western blotting, revealing proteomic diversity in rare cell populations with high occupancy and resolution.

Aiptasia larvae are phenotypically validated as a model of coral bleaching using high-throughput machine-learning image analysis

This paper validates Aiptasia larvae as a coral bleaching model and introduces SYMPHONY, an ML pipeline that efficiently identifies algal localization in larvae under heat stress.

Deterministic DNA barcoding using vacuum-driven loading of free oligonucleotides to microwell arrays

This paper introduces a deterministic DNA barcoding method using vacuum-driven microfluidics to load oligonucleotides into microwells, achieving uniform barcoding with reduced reagent use and cross-contamination.

Single-cell Organelle Extraction with Cellular Indexing

The paper introduces VacTrap, a microfluidic device that isolates and spatially indexes single nuclei from mammalian cells with high efficiency, enabling single-cell multiomics applications.

EpiBlot: Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems

EpiBlot maps chromatin accessibility and proteoform expression in HER2-expressing breast cancer cells, revealing distinct epigenetic and protein responses to therapies.

Paired Analyses of Nuclear Protein Targets and Genomic DNA by Single-Cell Western Blot and Single-Cell PCR

The paper introduces SplitBlot, a microfluidic single-cell assay that pairs genomic DNA analysis with nucleo-cytoplasmic protein measurements from the same cell.

Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms

This paper develops a single-cell western blot method integrated with differential detergent fractionation to detect CK8 proteoforms while preserving nuclear integrity in breast cancer cells.

Electromigration of Charged Analytes Through Immiscible Fluids in Multiphasic Electrophoresis

This study investigates how an interleaving oil layer affects the electrotransfer of charged analytes into a hydrogel, showing increased peak skew and dispersion due to oil viscosity and phase mobility mismatch.

Single-embryo and single-blastomere immunoblotting reports protein expression heterogeneity in early-stage preimplantation embryos

This study develops a microfluidic immunoblot to measure protein expression in single embryos and blastomeres, revealing heterogeneity in DICER-1 isoforms and other proteins during preimplantation development.