Jixian Zhai

The paper identifies a conserved PPR gene cluster in Arabidopsis that generates siRNAs and contributes to plant immunity through sequence diversification.

Unimeth improves DNA methylation detection from nanopore reads across species and modification types by using a transformer framework with multi-phase training.

The paper presents a low-cost lab-made spatial transcriptomics chip that enables isoform-resolved analysis using a dual-platform sequencing workflow, identifying novel splicing events in tomato-pepper grafts and mouse embryos.

The paper introduces SPARP-seq, a method combining poly(A) assessment and ribosome profiling to show poly(A) tail shortening is a hallmark of active translation in human cells.

DeepSME enables private DNA-based communication by decrypting heavily modified DNA using nanopore sequencing and deep learning, achieving high precision and recall.

The paper introduces a nanopore-based codec system, Composite Hedges Nanopores (CHN), capable of handling high indel and substitution error rates for real-time DNA data readout.

MCIBox is a toolkit for analyzing single-molecule chromatin interactions and identifying micro-domains through visualization and clustering algorithms.

The paper creates an atlas of plant full-length RNA poly(A) tail lengths, revealing tissue-specific and evolutionarily conserved patterns.

The paper introduces Pore-C, a long-read sequencing method for capturing multi-way chromatin interactions and DNA methylation in Arabidopsis.

sRNAanno provides a comprehensive database of uniformly-annotated small RNAs in 138 plant species, including miRNAs, phasiRNAs, and hc-siRNAs, along with a visualization tool for NGS sRNA data.

This study develops a protoplasting-free method for single-nucleus RNA profiling in plants using long-read sequencing to improve cell type identification through isoform information.

The paper introduces a database to access and explore 20,000+ Arabidopsis RNA-seq libraries for gene expression analysis.