Bioinformatics resources developed and maintained
A universal genomic search engine covering 500+ horticultural crops. HSE provides querying of genes, functional annotations, protein domains, homologs, and related functional information. Integrated tools include BLAST, Batch Query, Enrichment Analysis, and Synteny Viewer.
Wang et al., Horticulture Research, 2024
A program for genome-wide prediction and classification of plant transcription factors (TFs), transcriptional regulators (TRs), and protein kinases (PKs). Widely adopted with 1,114+ citations.
Zheng et al., Molecular Plant, 2016
An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Performs reference-guided assembly and de novo assembly using Velvet with automated parameter optimization.
Zheng et al., Virology, 2017
A standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs. Employs an iterative assembly strategy using MIRA and CAP3 with automated error corrections of mis-assemblies.
Zheng et al., BMC Bioinformatics, 2011
The cucurbit genomics database, hosting 34 reference genomes from 27 cucurbit species across 10 genera. Features include genotype and expression modules, synteny analysis (595 pair-wise comparisons), BLAST, and genome browser.
Zheng et al., Nucleic Acids Research, 2019; Yu et al., NAR, 2023
A central portal for spinach genomics, providing the reference genome, functional annotations, RNA-Seq expression profiles, genetic variants from 120 accessions, SpinachCyc pathway database, BLAST, and genome browser.
Collins, Zhao, Jiao, Xu et al., Database, 2019
A comprehensive resource for kiwifruit genomics, integrating genome sequences, gene annotations, biochemical pathways, RNA-Seq profiles, and comparative genomics tools (JBrowse, BLAST, Synteny Viewer, differential expression). Developed with Anhui Agricultural University.
Yue, Liu, Tang et al., Horticulture Research, 2020
The first cross-species pangenome platform for Actinidia. Integrates 55 genome assemblies from 12 species, 1,071 transcriptomes, multi-omics data, with tools including JBrowse, BLAST, GO/KEGG enrichment, SV detection, and CRISPR design.
Li, Li, Wang, Liu et al., Plant Communications, 2025
A comprehensive database for chestnut genomics, integrating genomic data for 8 Castanea species/varieties, 213 RNA-Seq samples, 330 resequencing samples, with BLAST, Batch Query, GO/KEGG Enrichment, Synteny Viewer, and genome browser.
Fan et al., Scientific Data, 2025
A call for submission of information about genome-edited plant mutants. A centralized resource for CRISPR/Cas-based genome editing in plants, cataloging gene modifications across model and economically significant plant species.
Zheng, Zhang, Martin, Fei, Molecular Plant, 2019
A database for genomics and genetics of radish (Raphanus spp.), providing genome and transcriptome resources for cultivated and wild radish accessions.
Shen, Sun, Huang, Zheng et al., Plant and Cell Physiology, 2013
A repository for storage and retrieval of phased secondary small interfering RNAs in plants. Collects sequences, originating genes, and expression patterns of these regulatory RNA molecules involved in the RNA interference pathway.
Zheng, Wang, Wu, Ding, Fei, BMC Biology, 2015