Yu Zhao

CENO is a long-context generative model for genomic sequence understanding and design, showing improved variant prediction and regulatory sequence generation across species.

The paper introduces an improved plasmid toolkit to streamline the mSwAP-In method for large-scale genome writing in mammalian cells.

This study introduces a humanized mouse model of XDP with SVA_F insertion in TAF1, revealing myelin loss and oligodendrocyte dysfunction as key pathogenic features.

The paper genomically rewrote a mouse Taf1 allele with a human XDP patient-derived TAF1 allele, revealing that intronic SVA retrotransposons reduce TAF1 levels and cause neurodegeneration.

The paper introduces an automated workflow for high-throughput assembly of large DNA libraries using yeast-based methods, achieving high success rates in assembling diverse DNA constructs.

This paper synthesizes the largest eukaryotic yeast chromosome, synIV, and investigates how its 3D structure affects gene regulation and transcription.

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

The paper uses CRISPR D-BUGS and chromosome swapping to identify and resolve genetic interactions in synthetic chromosomes, revealing unexpected links between transcription, inositol metabolism, and tRNA abundance.

The paper synthesizes a shorter yeast chromosome and studies its fusion with other chromosomes, revealing new 3D structural interactions and Red1 binding patterns.

The paper constructs a synthetic yeast chromosome XI and demonstrates how non-coding DNA modifications affect cell fitness, enabling on-demand extrachromosomal circular DNA formation.

This paper introduces CREEPY, a method for efficiently editing large episomal DNA constructs in yeast, demonstrating its application to a mouse Sox2-harboring episome.

This study uses synthetic genome rearrangement to show that chromatin organization influences the frequency and spatial distribution of genome structural variations in yeast.

This study engineers the biosynthesis of the polyketide bikaverin in yeast by enhancing enzyme expression and using enzyme fusion to increase yield.

The paper uses single-cell RNA-sequencing to identify lung progenitor cell populations in COVID-19 patients and demonstrates their role in alveolar repair.