Yu Fan

This study identifies epigenetic phase variation in the gut microbiome, showing it enhances bacterial adaptation through gene regulation and bet-hedging strategies.

The paper assesses low-biomass microbiome detection in tissues using long-read sequencing, finding that genuine microbiome signals are limited to tissues with natural microbial exposure.

The paper develops an integrative sequencing strategy to catalog NRXN1 isoforms across human brain tissues and hiPSC organoids, revealing cell-type-specific splicing patterns and therapeutic potential of ASO targeting.

This study introduces LongTrack, a long-read metagenomics framework for precise strain tracking in FMT, revealing genomic changes in engrafted bacteria over time.

This study investigates the phenotypic complexities of rare heterozygous NRXN1 deletions, showing cell-type-specific synaptic effects through LOF and GOF mechanisms, highlighting the need for precision medicine strategies.

MethylQUEEN is a DNA methylation foundation model that captures epigenetic information and enables tissue-of-origin tracing and disease detection through methylation patterns.

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.

The paper analyzes fecal metagenomic data from NSCLC patients to identify Akkermansia phylogroups associated with response to PD-1 blockade, finding AmIa linked to better outcomes.

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