Rochester, Minnesota




Changes of epigenetic marks have been implicated in the initiation and progression of various cancers. Such epigenetic alterations involve the changes of histone modifications, nucleosome remodeling, DNA methylation and non-coding RNAs expression, rather than the changes of DNA sequence itself. Dr. Yan's research focuses on the characterization of possible epigenetic aberrations associated with human cancers, in particular with breast cancer. He is trying to integrate multiple types of large-scale genomic and epigenomic data generated from next-generation sequencing technologies, including SNPs, ChIP-Seq, DNase-Seq, RNA-Seq, miRNA-seq and Hi-C. His main goal is to understand which of the identified changes in DNA sequence might have led to the epigenetic misregulation in human cancers.

Focus areas:

  • Systematic analysis of chromatin immunoprecipitation sequencing (ChIP-Seq) data to generate genome-wide mapping of transcription factors binding sites, histone modifications and key chromatin regulators. These epigenetic marks are known to be involved in the development of human diseases including cancer.
  • Integrated analysis of human disease-associated single nucleotide or structural variations with gene expression, genome-wide epigenomic profiles and long-range chromatin interactions
  • Development of algorithms for analyzing genome-wide epigenomic data

Significance to patient care

This research effort will result in the construction of comprehensive epigenomic landscapes, and the identification of the associations with collections of genetic variants and gene transcripts for a particular disease. Integration of these data with clinical information will greatly contribute to our understanding of how the alterations of chromatin states and their interplay disrupt the transcriptional regulation network, ultimately leading to cancer development. Therefore, the accumulation of such knowledge will be vital to the discovery of biomarkers for cancer diagnosis and to the development of effective treatment strategies.


See my publications


Administrative Appointment

  1. Senior Associate Consultant I-Research, Division of Biomedical Statistics and Informatics, Department of Health Sciences Research

Academic Rank

  1. Associate Professor of Biomedical Informatics


  1. PhD - Genetics Chinese Academy of Agricultural Sciences
  2. MS - Quantitative Genetics and Biostatistics Nanjing Agricultural University
  3. BS - Crop science Hunan Agricultural University

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