Silin Zhong

MusTer improves single-cell sequencing by reducing doublets, enhancing signal-to-noise ratio, and improving cell clustering in maize leaf ATAC-seq.

The paper constructs a single-cell chromatin accessibility atlas in rice and compares it across grass species to study the evolution of cell-type-specific cis-regulatory elements.

The paper analyzes chromatin accessibility in 214 maize inbred lines using ATAC-seq, identifies variation in accessible chromatin regions, and links them to gene expression and complex traits.

This study uses single-cell ATAC-seq to analyze cis-regulatory elements in C4 photosynthesis across grass species, revealing cell-type-specific chromatin accessibility patterns and evolutionary dynamics.

This study introduces a combinatorial indexing strategy for single-cell epigenomic profiling in plants, demonstrating its effectiveness in analyzing chromatin accessibility in Arabidopsis root cells.

This study uses ChIP-seq to map TF binding in maize leaves, reconstructs a regulatory network covering 77% of expressed genes, and shows its conserved evolution across species.

This paper evaluates machine learning algorithms for predicting gene functions without relying on homology, finding random forest provides the most accurate results, particularly in Biological Process GO terms.

The paper analyzes Hi-C data from multiple plant tissues to show tissue-specific chromatin dynamics and their association with gene expression and epigenetic features.

The fruitENCODE project identifies three evolutionary origins of regulatory circuits governing climacteric fruit ripening through comparative genomics and epigenetics.