Bo Zhang, PhD

Research interests

Our research interest focuses on understanding the connection between cell fate determination and regulatory mechanisms of enhancer elements, which are short cis-acting DNA sequences that can perform regulatory functions to adjust gene transcription in a fine-tuned fashion.

Various transcription factors and epigenetic regulatory mechanisms can control the activation of enhancers during embryonic development and regulate the expression of tissue-specific genes, independent of orientation and over various distances.

We develop bioinformatics tools to analyze high-throughput sequencing data and discover epigenetic changes associated with the activation and silencing of enhancer regulatory elements during embryonic development and carcinogenesis. We construct gene regulatory models to integrate genetic variants, epigenetic modifications and enhancer activation to explain the gene expression regulation in normal and cancer cell fate determination.

Education

Research Assistant Professor: 2015 – present Washington University School of Medicine in St. Louis, Saint Louis, MO, US

Postdoctoral training: 2011 – 2015 Washington University School of Medicine in St. Louis, Saint Louis, MO, US

Ph.D. in bioinformatics: 2005 – 2010 Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

B.S. in Biotechnology: 2000-2004 Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region, China

Selected publications

EC Nelson, A Agrawal, AC Heath, R Bogdan, R Sherva, B Zhang, et al. Evidence of CNIH3 involvement in opioid dependence. Molecular psychiatry. 2015

X Zhou, D Li, B Zhang, et al. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nature biotechnology. 2015

HJ Lee, RF Lowdon, B Maricque, B Zhang, et al. Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nature communications. 2015

Integrative analysis of 111 reference human epigenomes. Nature. 2015

Lowdon RF, Zhang B, et al. Regulatory Network Decoded from Epigenomes of Surface Ectoderm-Derived Cell Types. Nature Communication. 2014.

B Zhang^, X Xing^, J Li^, et al. Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. BMC Genomics. 2014. ^ Equal contribution.

Nagarajan RP^, Zhang B^, et al. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res .2014. ^ Equal contribution

D Li, B Zhang, et al. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2014

Zhang B^, Zhou Y^, Lin N^, Lowdon RF^, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 2013. ^ Equal contribution

Xie M^, Hong C^, Zhang B^, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 2013. ^ Equal contribution

B Chen^, B Zhang^, et al. Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells. Int.J of Cell Biology. 2012. ^ Equal contribution

B Zhang^, B Chen^, et al. Estimating developmental states of tumors and normal tissues using a linear time-ordered model. BMC bioinformatics 2011. ^ Equal contribution

B Zhang^, B Chen^, T Wu^, et al. Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns. PloS one. 2011

Y Tan, B Zhang, et al. Transcriptional inhibition of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC molecular biology.  2009