Jun Wan, PhD
Associate Professor of Medical & Molecular Genetics
Adjunct Associate Professor, School of Informatics and Computing
Director of Collaborative Core for Cancer Bioinformatics (C3B) shared by NCI-comprehensive cancer center, Indiana University Simon Comprehensive Caner Center, and Purdue University Center for Cancer Research
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HS 5013
MMGE
Indianapolis, IN 46202 - PubMed:
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Bio
Dr. Jun Wan is tenured Associate Professor and Principal Investigator (PI) in bioinformatics and computational biology at the Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA. He directs the Collaborative Core for Cancer Bioinformatics (C3B) shared by two NIH/NCI-designated cancer centers in Indiana, Indiana University Simon Comprehensive Cancer Center (IUSCCC) and Purdue University Insititue of Cancer Research (PUCCR).
Jun received his bachelor’s degree in physics from Shanghai Jiaotong University and master’s degree in physics from Fudan University in China. After obtaining his PhD degree in physics at Queen’s University, Kingston, Ontario Canada in 2006, Dr. Wan switched his research field from physics to bioinformatics during the postdoctoral training at Johns Hopkins University School of Medicine, Baltimore, Maryland USA. At the end of 2016, Dr. Wan moved to Indiana University School of Medicine as a tenure-track Assistant Professor and independent PI. He was then promoted in 2022 to Associate Professor with tenure.
Dr. Jun Wan has broad research interests in bioinformatics and computational systems biology, with core motivation of understanding functional alterations of gene regulatory network from the perspectives of epigenetics, transcription, and translation, including but not limited to transcription factor regulation, DNA methylation, alternative splicing, microRNA regulation, histone modifications, genome-wide chromatin organizations, and crosstalk among these functional elements. His lab also employs data mining and deep learning methods to decipher genetic and epigenetic codes, dissect master regulators for gene programming to understand dynamics of gene regulatory networks, and investigate interactions between small molecules and proteins/DNA/RNA by incorporating a wide variety of ‘-omics’ datasets from the public domains to explore comprehensive patterns of gene regulatory networks.
Jun has published over 120 peer-reviewed papers and is well recognized as an expert in computational biology and bioinformatics. He has demonstrated a longstanding record of successful collaborations with over 100 research groups from different universities and institutes. His own research and collaborative projects with other PIs have been supported by multiple grants funded by NIH, DoD, and other societies/foundations in USA.
In 2023, Dr. Wan was awarded as Showalter Scholar selected by Ralph W. and Grace M. Showalter Research Trust and Indiana University School of Medicine.
Key Publications
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.
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 21 (1), 169.
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 80 (22), 4904.
S Fang, K Li, JK Shen, S Liu, J LIu, L Yang, CD Hu, J Wan (2021) GESS: A database of Global Evaluation of SARS-CoV-2/hCoV-19 Sequences. Nucleic Acids Research D1, D706.
S Fang, S Liu, J Shen, AZ Lu, AKY Wang, Y Zhang, K Li, J Liu, L Yang, CD Hu, J Wan (2021) Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association. Journal of Medical Virology (selected as cover image) 93 (12), 6525.
Y Chen, S Fang, Q Ding, R Jiang, J He, Q Wang, Y Jin, X Huang, S Liu, ML Capitano, T Trinh, Y Teng, Q Meng, J Wan† (co-corresponding author), HE Broxmeyer†, B Guo† (2021) ADGRG1 enriches for functional human hematopoietic stem cells following ex vivo expansion-induced mitochondrial oxidative stress. Journal of Clincal Investigation 131 (20), e148329.
| Year | Degree | Institution |
|---|---|---|
| 2011 | POSTDOC | Johns Hopkins University School of Medicine |
| 2006 | PhD | Queen's University |
| 2001 | MS | Fudan University |
| 1991 | BS | Shanghai Jiao Tong University |
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 regulating gene expression, (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 and ATAC-seq at both bulk and single cell level, 10X Multiome, Spatial transcriptomics, ChIP-Seq, CUT&RUN, 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/Lab.