ZhangLab

Welcome to Plant Bioinformatics and Functional Epigenomics Group.

We are particularly interested in addressing key biological questions via integration of multi-omics data.

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Softwares and Databases

We have developed some softwares and databases, please click following links to learn more.

CARMO is a web-based platform providing comprehensive annotations for multi-omics data, including transcriptomic data sets, epi-genomic modification sites, SNPs from genome re-sequencing, and the large gene lists derived from these omics studies. Well-organized results, as well as multiple tools for interactive visualization, are available through a user-friendly web interface.

Go to CARMO

ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed. Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.

Go to MAnorm

(Under Constuction) With the accumulation of ChIP-seq data across different cell types, an effective and accurate method are essential to unravel the relationship between regulator binding and epigenetic modifications in different cell types. We present an integrative computational toolkit, MAmotif, to infer cell type specific regulators.

Go to Motif-Scan

Cooperation Groups

We have some cooperation groups, please click following links to learn more.

Laboratory of Regulatory and Systems Genomics, PICB

Laboratory of Plant Stem Cells and Regeneration, SIPPE