Dijun Chen

This study investigates how integrating the DD genome into tetraploid wheat enhances its adaptability by altering gene transcription, chromatin structure, and metabolome.

This study identifies tissue-resident lymphocytes as drivers of age-associated emphysema by impairing alveolar regeneration and shows IL-7R inhibition can reverse lung damage.

GenNA generates nucleotide sequences using natural-language annotations, showing improved performance in semantic and species context alignment without explicit biological rule supervision.

This study uses deep learning to predict histone modifications across plant species, showing improved cross-species performance with family-level models.

CellReasoner is a lightweight LLM for cell type annotation that uses reasoning to map gene expression to labels with zero- and few-shot generalization.

iSeq is a tool for retrieving public sequencing data from multiple databases, supporting various accession formats and enabling parallel downloads and metadata retrieval.

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.

The paper maps rice chromatin accessibility across 23 tissues, identifies regulatory elements, and uses deep learning to model regulatory dynamics, revealing new functions and insights into complex trait regulation.

This study integrates single-cell transcriptomic data from Arabidopsis to identify cell types, developmental trajectories, and gene regulatory networks involved in root-shoot differentiation.

cisDynet is a platform for analyzing chromatin accessibility data, integrating preprocessing, downstream analysis, and visualization to uncover gene regulatory networks and GWAS variant associations.

This study creates a single-cell regulomic and transcriptomic map of cynomolgus monkeys, revealing cell-type similarities to humans over mice.

ChIP-Hub provides a web-based platform integrating and visualizing reanalyzed ChIP-seq data from over 40 plant species to explore plant regulomes.