Philip Burnham

Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation

The paper shows intestinal epithelial zonation arises from self-organization via local cell-cell communication, not external cues or intrinsic programs.

Multiscale Spatial Mapping of Microbial Communities for Biotherapeutic Development

The paper introduces HiPR-Map, a spectral imaging technology for high-phylogenetic-resolution spatial mapping of microbial communities, and applies it to analyze an LBP in the murine gut.

Cell-free DNA Profiling Informs Major Complications of Hematopoietic Cell Transplantation

This study demonstrates that cell-free DNA analysis can detect multiple post-transplant complications in HCT recipients through methylation, metagenomic, and genomic profiling.

Separating the signal from the noise in metagenomic cell-free DNA sequencing

The paper introduces LBBC, a tool to reduce noise in metagenomic cfDNA sequencing, improving detection of urinary tract infection while minimizing false positives.

A cell-free DNA metagenomic sequencing assay that integrates the damage response to infection

This paper introduces a cell-free DNA metagenomic sequencing assay that integrates host damage response to infection, showing it can accurately capture microbial composition and tissue damage in urinary tract infections.

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

This paper introduces DART-seq, a method that enables multiplexed amplicon sequencing and transcriptome profiling in single cells, applied to study viral transcripts and B cell immune repertoires.

Structure and diversity of urinary cell-free DNA informative of host-pathogen interactions in human urinary tract infection

This study uses urinary cell-free DNA to monitor host and pathogen dynamics in urinary tract infections, revealing insights into microbiome composition, antimicrobial susceptibility, and kidney injury.

Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

This study uses single-stranded DNA library preparation to analyze cfDNA in lung transplant patients, revealing increased mitochondrial and microbial cfDNA and donor-specific mitochondrial cfDNA fragments.