Alexandre Pellan Cheng

Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus

This paper develops SMART-PTA for single-cell whole-genome and transcriptome sequencing, revealing clonal evolution in aged human esophageal tissue over 70 years.

Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules

This paper introduces ppmSeq, a sequencing technology that improves accuracy and efficiency in detecting SNVs by sequencing both DNA strands, showing superior performance in clinical applications like ctDNA detection.

Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

This paper introduces MRD-EDGE, a machine learning platform for ultrasensitive ctDNA detection in plasma WGS, showing improved sensitivity and broader applicability for MRD monitoring.

Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring

This study applies low-cost whole genome sequencing to detect circulating tumor DNA at high sensitivity in plasma samples, achieving error rates as low as 10^-7 and enabling cancer monitoring without matched tumor sequencing.

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination

The paper introduces Coffee-seq, a metagenomic DNA sequencing method that reduces environmental contamination, and applies it to detect infections and microbial signatures in clinical samples.

Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity

This study uses cell-free DNA methylation profiling in plasma to identify organ-specific injury and predict COVID-19 severity in hospitalized patients.

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.