Yi‐Yan Yang

This study identifies phenotype-cloud transitions as an organizational feature of cancer progression and therapeutic adaptation, showing how tumours reorganize phenotypic states during progression and treatment.

The paper investigates how viral anti-defense systems vary with genomic traits, host immunity, and environmental stress across microbial ecosystems.

This study determines the structure of Bap1 bound to VPS and shows how it facilitates biofilm adhesion and VPS organization through a conserved β-propeller interaction.

The study identifies oral microbial signatures associated with IBD and PSC and their potential translocation to the gut, supported by external validation.

This paper introduces VIP2B, a method to extract viral features from bulk metagenomes, showing that viral data improves disease diagnosis and reveals distinct gut virome community states.

The paper investigates how a Vibrio cholerae peptide binds lipids through a β-hairpin conformation, contributing to biofilm adhesion and host colonization.

The paper introduces MultiCAST, a high-throughput CRISPR-associated transposon system for bacterial gene disruption, enabling rapid and scalable genetic screens using amplicon sequencing.

PHILM, a deep learning framework, predicts phage-host interactions from metagenomic data with higher accuracy than traditional methods, identifying more interactions and capturing microbial succession patterns.

This study analyzes the distribution, diversity, and evolution of biofilm matrix clusters and proteins across Vibrio species, revealing structural and evolutionary patterns of key genes.

The paper develops SpikeHunter, a deep learning model to identify tailspike proteins from prophages, revealing associations between these proteins and bacterial serotypes.

The paper identifies two host-derived insertions in SARS-CoV-2 genomes using RNA sequencing and GISAID data, showing integration of human rRNA fragments into viral genomes.

The paper identifies transcriptional regulatory sequences in coronaviruses and finds recombination hotspots are more frequently co-located with TRS-B sites.