Jessica Chen

Standalone nanopore sequencing for foodborne pathogen surveillance: a large-scale evaluation and quality control framework

This paper evaluates standalone Oxford Nanopore sequencing for foodborne pathogen surveillance, showing it can achieve high accuracy with quality control tools like alpaqa.

Predicting and Controlling Collective Fate in Multicellular Systems

The paper develops a framework to predict and control collective fate in multicellular systems by identifying a control regime where a single guide cell can redirect tissue-level organization.

Neptune: A Bioinformatics Tool for Rapid Discovery of Genomic Variation in Bacterial Populations

Neptune identifies differentially abundant genomic loci in bacterial populations using k-mer matching and probabilistic models, showing sensitivity and specificity on simulated and real data.