27465-Wan, Jun

Jun Wan, PhD, MS

Assistant Professor of Medical & Molecular Genetics

HS 5013

Indianapolis, IN 46202
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Dr. Jun Wan is an assistant professor (tenure-track) in the Department of Medical and Molecular Genetics, Indiana University School of Medicine. He is director of Collaborative Core for Cancer Bioinformatics (C3B) shared by NIC-comprehensive cancer center, Indiana University Simon Comprehensive Cancer Center (IUSCCC), and Purdue University Center for Cancer Research (PUCCR). Dr. Wan got his Ph.D. degree in Physics from Queen's University, Kingston Ontario, Canada, followed by postdoctoral training in bioinformatics at Johns Hopkins University School of Medicine. Prior to moving to Indiana University, Dr. Wan was a research faculty at Johns Hopkins University. He has authored or co-authored over 80 research papers published in peer-reviewed journals, such as Cell, Nature Nanotechnology, JCI, Genome Biology, Molecular Cell, Nature Communications, PNAS, eLife, Nucleic Acids Research, and Bioinformatics among others.

Key Publications

S Hu*, J Wan* (co-first author), Y Su*, Q Song, Y Zeng, HN Nguyen, J Shin, E Cox, HS Rho, C Woodard, S Xia, S Liu, H Lu, G Ming, H Wade, H Song, J Qian, H Zhu (2013) DNA methylation presents distinct binding sites for human transcription factors. eLife 2013 (2), e00726. PMC3762332 (highlighted by the Insight paper “Making the most of methylation” eLife 2013 (2), e01387.

J Wan, Y Su, Q Song, B Tung, O Oyinlade, S Liu, M Ying, G Ming, H Song, J Qian, H Zhu, S Xia (2017) Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration. eLife 2017/5/29, e20068. PMC5466421.

X Huang, B Guo, S Liu, J Wan, H Broxmeyer (2018) Neutralizing negative epigenetic regulation by HDAC5 enhances human haematopoietic stem cell homing and engraftment. Nature Communications 9 (1), 2741. PMC6048146

O Oyinlade, S Wei, K Kammers, S Liu, S Wang, D Ma, Z Huang, J Qian, H Zhu, J Wan (co-corresponding author), S Xia (2018) Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter-enhancer interactions. Epigenetics 13 (7), 751. PMC6224223.

J Xu, Y Liu, Y Li, H Wang, S Stewart, K Van der Jeught, P Agarwal, Y Zhang, S Liu, G Zhao, J Wan, X Lu, X He (2019) Precise targeting of POLR2A as a therapeutic strategy for human triple negative breast cancer. Nature Nanotechnology 14 (4), 388. PMC6449187.

J Liu, S Liu, H Gao, L Han, X Chu, Y Sheng, W Shou, Y Wang, Y Liu, J Wan†(co-corresponding author), L Yang† (2020) Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells. Genome Biology (accepted for publication).

E Beketova, S Fang, J Owens, S Liu, X Chen, Q Zhang, A Asberry, X Deng, J Malola, J Huang, C Li, R Pili, B Elzey, T Ratliff, J Wan†(co-corresponding author), CD Hu† (2020) Protein arginine methyltransferase 5 promotes androgen receptor transcription in a pICln-dependent manner in castration-resistant prostate cancer. Cancer Research (Accepted for publication).

S Fang, K Li, JK Shen, S Liu, J LIu, L Yang, CD Hu, J Wan (2020) GESS: A database of Global Evaluation of SARS-CoV-2/hCoV-19 Sequences. Nucleic Acids Research (Accepted for publication).

Titles & Appointments

  • Assistant Professor of Medical & Molecular Genetics
  • Adjunct Assistant Professor, School of Informatics and Computing
  • Director of Collaborative Core for Cancer Bioinformatics (C3B) shared by NCI-comprehensive cancer center, Indiana University Simon Caner Center, and Purdue University Center for Cancer Research
  • Education
    2011 POSTDOC Johns Hopkins University School of Medicine
    2006 PhD Queen's University
    2001 MS Fudan University
    1991 BS Shanghai Jiao Tong University
  • Research

    Current research interests in Dr. Jun Wan's lab cover broad topics of bioinformatics and computational systems biology, particularly focused on (1) deciphering genetic and epigenetic codes, (2) exploring master regulators and their interactions for gene reprogramming, (3) understanding dynamics of gene regulatory networks, (4) investigating interactions between small molecules and proteins/DNA/RNA, and (5) using machine learning to predict gene regulation and model binding activities of small molecules. Since 2007, Dr. Wan has been conducting studies in gene regulatory mechanisms from multiple dimensions, including transcription factor regulation, DNA methylation, alternative splicing, microRNA regulation, whole-genome nucleosome organization, histone modifications, and chromatin organizations. His lab also works on public domain data to integrate a wide variety of ‘-omics’ data sets to achieve comprehensive patterns of gene regulatory networks, while developing diverse cutting edge analyses on high-throughput data and next generation sequencing (NGS) data, such as RNA-Seq, scRNA-seq, ChIP-Seq, ATAC-seq, scATAC-seq, Whole Genome Bisulfite Sequencing (WGBS), Whole genome/exome sequencing, and CRISPR/Cas9 among others. More detailed can be found on his website: https://wanbioinfo.github.io/Wan-bioinfo/index.html.

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