Jun Wan, PhD

Assistant professor

Director of collaborator core of cancer bioinformatics (C3B) shared by Indiana University Simon Cancer Center and Purdue University Center for Cancer Research

C3B website:

CCBB Website:

  • B.A. 1991, Applied Physics, Shanghai Jiaotong University, Shanghai China
  • M.A. 2001, Condensed Matter Physics, Fudan University, Shanghai China
  • Ph.D. 2006, Computational Physics, Queen’s University, Kingston ON Canada
  • Postdoctoral fellowship 2011, Bioinformatics, Johns Hopkins University School of Medicine, Baltimore MD USA
  • Research Associate (Faculty position) 2016, Bioinformatics, Johns Hopkins University School of Medicine, Baltimore MD USA

Dr. Jun Wan’s research interests are in the area of bioinformatics and computational biology. Dr. Wan’s lab currently focuses on regulation of gene expression from transcription to translation, especially effects of epigenetic modifications and genetic mutations, in addition to gene network studies, including protein-DNA interactions, microRNA-gene network, etc. In the meantime, Dr. Wan leads a cancer bioinformatics core to collaborate with multiple investigators at each level. The core conducts large-scale bioinformatics analyses on different cancer researches, while generating and integrating diverse omics data to support grant applications and paper publications.


Selected Publications

  1. DR Kolson, J Wan, J Wu, M Dehoff, AN Brandebura, J Qian, PH Mathers, GA Spirou (2016) Temporal Patterns of Gene Expression During Calyx of Held Development. Developmental neurobiology 76, 166-189.
  2. Y Zeng, B Yao, J Shin, L Lin, N Kim, Q Song, S Liu, Y Su, JU Guo, L Huang, J Wan, H Wu, J Qian, X Cheng, H Zhu, G Ming, P Jin, H Song (2016) Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Molecular Cell 61, 153-160.
  3. J Wan, VF Oliver, G Wang, H Zhu, DJ Zack, SL Merbs, J Qian (2015) Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC genomics 16 (1), 49.
  4. R Li, G Liao, RS Nirujogi, SM Pinto, PG Shaw, T Huang, J Wan, J Qian, H Gowda, X Wu, D Lv, K Zhang, SS Manda, A Pandey, SD Hayward (2015) Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling. PLoS Pathogens 11, e1005346.
  5. J Maruotti, SR Sripathi, K Bharti, J Fuller, KJ Wahlin, V Ranganathan, VM Sluch, CA Berlinicke, J Davis, C Kim, L Zhao, J Wan, J Qian, B Corneo, S Temple, R Dubey, BZ Olenyuk, I Bhutto, GA Lutty, DJ Zack (2015) Small molecule-directed, efficient generation of retinal pigment epithelium from human pluripotent stem cells. PNAS (Proceedings of the National Academy of Sciences) 112, 10950-10955.
  6. G Elachouri, I Lee-Rivera, E Clerin, M Argentini, R Fridlich, F Blond, V Ferracane, Y Yang, W Raffelsberger, J Wan, J Bennett, J-A Sahel, DJ Zack, Thierry Leveillard (2015) Thioredoxin rod-derived cone viability factor protects against photooxidative retinal damage. Free Radical Biology and Medicine 81, 22-29.
  7. T Masuda, X Zhang, C Berlinicke, J Wan, A Yerrabelli, EA Conner, S Kjellstrom, R Bush, SS Thorgeirsson, A Swaroop, S Chen, DJ Zack (2014) The Transcription Factor GTF2IRD1 Regulates the Topology and Function of Photoreceptors by Modulating Photoreceptor Gene Expression across the Retina. The Journal of Neuroscience 34, 15356-15368.
  8. T Masuda*, Karl Wahlin*, J Wan* (co-first author), J Hu, J Maruotti, X Yang, J Iacovelli, N Wolkow, R Kist, JL. Dunaief, J Qian, DJ. Zack, N Esumi (2014) Transcription Factor SOX9 Plays a Key Role in the Regulation of Visual Cycle Gene Expression in the Retinal Pigment Epithelium. The Journal of Biological Chemistry 34 (46), 15356-15368.
  9. M Cano, L Wang, J Wan, BP Barnett, K Ebrahimi, J Qian, JT Handa (2014) Oxidative Stress Induces Mitochondrial Dysfunction and a Protective Unfolded Protein Response in RPE cells. Free Radical Biology and Medicine 69, 1-14.
  10. 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. (Highlighted by Insight paper “Making the most of methylation” eLife 2013 (2), e01387)
  11. J Wan, VF Oliver, H Zhu, D Zack, J Qian, SL Merbs (2013) Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. Nucleic Acids Research 41 (18), 8503-8514.
  12. CL Woodard, CR Goodwin, J Wan, S Xia, R Newman, J Hu, J Zhang, SD Hayward, J Qian, J Laterra, H Zhu (2013) Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One 8 (9), e72671.
  13. VF Oliver, J Wan, S Agarwal, DJ Zack, J Qian, SL Merbs (2013) A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples. Epigenetics & Chromatin 6 (1), 1-11.
  14. C Woodard, M Shamay, G Liao, J Zhu, AN Ng, R Li, R Newman, HS Rho, J Hu, J Wan, J Qian, H Zhu, SD Hayward (2012) Phosphorylation of the Chromatin Binding Domain of KSHV LANA. PLoS Pathogens 8 (10), e1002972.
  15. YR Ren, R Chaerkady, S Hu, J Wan, J Qian, H Zhu, A Pandey, S Kern (2012) Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. Journal of Proteome Research 11 (11), 5301-5310.
  16. RP Kandpal, HK Rajasimha, MJ Brooks, J Nellissery, J Wan, J Qian, TS Kern, A Swaroop (2012) Transcriptome Analysis Using Next Generation Sequencing Reveals Molecular Signatures of Diabetic Retinopathy and Efficacy of Candidate Drugs. Molecular Vision 18, 1123-1146.
  17. SL Merbs, MA Khan, L Hackler, VF Oliver, J Wan, J Qian, DJ Zack (2012) Cell-Specific DNA Methylation Patterns of Retina-specific Genes. PLoS One 7, e32602.
  18. D Zheng*, J Wan* (co-first author), Y Cho*, L Wang, CJ Chiou, S Pai, C Woodard, J Zhu, G Liao, O Martinez-Maza, J Qian, H Zhu, GS Hayward, RF Ambinder, SD Hayward (2011) Comparison of Humeral Immune Responses to Epstein-Barr Virus and Kaposi’s Sarcoma Associated Herpesvirus Using a Viral Proteome Microarray. Journal of Infectious Diseases 204, 1683-1691.
  19. J Wan, T Masuda, L Hackler, K Torres, S Merbs, D Zack, J Qian (2011) Dynamic Usage of Alternative Splicing Exons During Mouse Retina Development. Nucleic Acids Research 39, 7920-7930.
  20. L Hacker*, J Wan* (co-first author), A Swaroop, J Qian, D Zack (2010) MicroRNA profile of the developing mouse retina. Investigative Ophthalmology & Visual Science 51, 1823-1831.
  21. J Hu, J Wan, L Hackler, D Zack, J Qian (2010) Computational analysis of tissue specific gene networks: application to murine retinal functional studies. Bioinformatics 26, 2289-2297.
  22. J Wan, J Lin, D Zack, J Qian (2009) Relating periodicity of nucleosome organization and gene regulation. Bioinformatics 25, 1782-1788.
  23. Y Lin, J Lu, J Zhang, W Walter, W Dang, J Wan, S Tao, J Qian, Y Zhao, JD Boeke, SL Berger, H Zhu (2009) Protein Acetylation Microarray Reveals that NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis. Cell 136, 1073-1084.

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