Our Services

BioKDE (Biomedical Knowledge Discovery Engine) is a powerful Galaxy instance for integrative genomics data analysis, providing a platform for scientists to cope with the big data challenges in biomedical field.

Below is a list of services we currently offer:


RNA-seq, integrative differential gene expression analysis (iDGEA)

We perform several analyses including gene level DGEA, gene set enrichment analysis, GO term enrichment analysis, pathway analysis and network based analysis.

Precision medicine, biomarker discovery

Machine learning and deep learning methods will be used to discovery biomarkers for diagnosis and patient stratification.

DNA methylation

  • A DNA methylation pipeline is available on our BioKDE platform.

Chip-seq, DNS-seq, nucleosome occupancy, and other epigenomic data

An efficient segmentation algorithm has been developed recently by our scientists and showed superior performance than existing methods for peak calling and segmentation.

DNS-seq data

Nucleosome occupancy data

DNA replication timing data

A proprietary method was developed for cell type identification using DNA replication timing data.

Text mining, information extraction, knowledge discovery

We have developed innovative text mining methods to extract bio-entity relationship information and build knowledge base for automatic hypothesis generation and knowledge discovery.