Zhiyi Sun

The paper introduces a high-resolution single-molecule chromatin accessibility mapping method to quantify transcription factor occupancy and co-accessibility in human cell lines.

Domainator identifies proteins involved in antiviral systems by clustering and analyzing domain-based gene neighborhoods and integrating a protein language model.

The paper demonstrates that positional embeddings from protein language models can improve sensitivity in homology detection without sacrificing search speed.

The paper discovers novel DNA cytosine deaminases and develops a nondestructive single-enzyme methylation sequencing method for high-coverage methylome mapping of low-input DNA.

The paper introduces Induro-tRNAseq, a method using a high-processivity reverse transcriptase to profile tRNA modifications, revealing novel proline codon modifications in humans.

Methyl-SNP-seq captures both methylation and sequence information from single DNA molecules, enabling analysis of allele-specific methylation and methyltransferase specificity.

EM-seq detects DNA methylation at single base resolution using less DNA than bisulfite sequencing, showing improved accuracy and reliability.

This paper introduces LR-EM-seq, an enzymatic deamination method for long-range methylation profiling of 5-mC and 5-hmC, achieving better-defined DMRs over 5 kb.

The paper introduces UniNicE-seq, a method for high-resolution accessible chromatin profiling in formaldehyde-fixed and FFPE tissues without optimization steps.