Feiqiao Brian Yu

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

This study shows that gut microbiome recovery after antibiotics is path-dependent, shaped by ecological and evolutionary dynamics including strain sweeps, genetic changes, and phage activity.

The paper identifies coordinated variation between immune systems and microbiomes in healthy humans, linking it to tonic interferon states.

The paper develops a method to detect invertons in gut microbiome metagenomic data and finds associations between inverton dynamics and intestinal colonization and surface adhesion.

The paper analyzes metagenomic and metatranscriptomic data from hot spring microbial mats to show diel gene expression patterns in key taxa.

This paper introduces rhea, a reference-free method for detecting structural variants in microbiomes using long-read coassembly graphs, showing improved performance over existing methods in simulated and real metagenomic data.

The paper characterizes the microbial community of Auka vents, revealing high diversity, novel metabolic traits, and evidence of long-distance species transfer and thermophilic evolution.

The paper introduces CytoTRACE, a method using transcriptional diversity to predict differentiation states from scRNA-seq data, outperforming existing methods and identifying stem cells and tumor-related genes.

The paper identifies IgnaviCas9, a hyperthermophilic Cas9 from an unculturable Ignavibacterium, which functions at higher temperatures than existing Cas9 variants and is applied in RNA-seq library preparation.

PhaMers identifies 103 novel phage sequences from Yellowstone hot spring metagenomes using tetranucleotide frequency analysis and compares results with VirSorter.

The paper uses single-cell RNA-seq to study stress response heterogeneity in yeast, finding regulatory variation and decoupled transcription-factor activation.