Yimeng Kong

This study evaluates gene embeddings from large language models and finds that functional descriptions yield high-quality, biologically meaningful representations.

The paper introduces ICE, a framework for detecting senescent cells using weak single-cell markers, improving detection accuracy from 56% to 98% in pancreatic cells.

This paper introduces modFDR, a framework to assess nanopore sequencing for DNA modification detection, showing it reliably detects abundant modifications but has high false positives for rare ones.

mEnrich-seq selectively sequences specific bacterial taxa from microbiome samples by using methylation-sensitive restriction enzymes to enrich target DNA while depleting background microbiota.