About Me

I am an HHMI Predoctoral Research Fellow at the University of Chicago, currently pursuing my Ph.D. degree under the mentorship of Prof. Chuan He in the Chemistry Department. My graduate work studies DNA and RNA epigenetics, specifically the chemical modifications on nucleic acid bases and the regulatory roles of these marks. My current research focuses on reversible RNA methylation (m6A), a re-discovered modification that has been recently revealed to carry crucial regulatory functions in mRNA. I am investigating the impacts of m6A in diverse biological systems, such as animal early development and infectious diseases.

Contact Details

Boxuan Zhao
GCIS E307, 929 E 57th St
Chicago, IL 60637 US



The University of Chicago

Ph.D. in Chemistry August 2017

M.S. in Chemistry October 2013

Peking University

B.S. in Chemistry June 2012


He Group at the University of Chicago

HHMI Predoctoral Student Research Fellow and Graduate Student Researcher September 2012 - Present

Boxuan joined Prof. Chuan He’s group to continue his work at the interface of chemistry and biology. During his first year, he completed and published the work of constructing a quinone biosensor with labmate while satisfying all the coursework requirements and TA responsibilities. Starting from his second year passing candidacy, Boxuan turned his focus to the study of DNA and RNA epigenetics, specifically the investigation of chemical modifications on nucleic acid bases and the regulatory roles of these marks. He developed the first high-throughput single-base resolution sequencing methods for detecting 5fC and 5caC modifications in DNA with coworkers, and studied reversible RNA methylation (m6A) with crucial regulatory functions in mRNA. He primarily focused on the investigation of a class of RNA binding proteins that specifically recognized m6A, termed ‘m6A readers’, and jointly characterized and demonstrated the function of the first discovered translation-promoting m6A reader, YTHDF1. He then dived into the investigation of biological functions of m6A, including discovering the impact of m6A during early embryogenesis of zebrafish, revealing the distribution and effects of m6A in many virus species and viral infection. For his final year of graduate study, Boxuan plans to continue studying the functions of m6A in different biological systems and explore the crosstalk between m6A regulatory mechanism with other known pathways, in hopes of providing a clearer picture of the wide-spread biological impacts of m6A and contributing to the proceeding of the research field of RNA.

Chen Group at Peking University

Undergraduate Researcher January 2009 - August 2012

Boxuan started as an independent undergraduate researcher during his first year in college under the mentorship of Prof. Peng Chen, focusing on the development of biosensors for small molecules in living cells via protein engineering. His first project was to construct a genetically encoded biosensor for organic hydroperoxide (OHP) in living cells, an elusive form of reactive oxygen species that may cause severe cellular damages. Utilizing a naturally occurring OHP-sensory bacterial protein OhrR, Boxuan inserted a sensitive fluorescent protein at the predicted conformational switching region of OhrR and developed an OHP selective biosensor that changes fluorescence signal upon detecting the presence of OHP. He continues to work on the biological applications of OHP sensors and later demonstrated their functions at subcellular precision, providing the field with a useful tool for OHP detection.

Peking iGEM Team

Subgroup Leader January 2010 - January 2012

Boxuan joined the research team of International Genetically Engineered Machine competition (iGEM) at Peking University and was actively engaged in the study of synthetic biology with a team of undergraduate researchers under the supervision of Prof. Qi Ouyang at the Center for Quantitative Biology. Working towards the goal of developing a biological solution for heavy metal purification, he led the subgroup of heavy metal bacterial absorbent and together with team members won second place at 2010’s iGEM Jamboree at MIT.


Sicong Zhang, Boxuan Simen Zhao, Aidong Zhou, Kangyu Lin, Yaohui Chen, Keping Xie, Oliver Bögler, Sadhan Majumder, Zhike Lu, Chuan He, and Suyun Huang. The m6A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-Like Cells by Sustaining FOXM1 Expression and Cell Proliferation Programing, Cancer Cell, 2017, 31(4), 591-606.

Boxuan Simen Zhao*, Xiao Wang*, Alana C. Beadell*, Zhike Lu, Hailing Shi, Robert K. Ho, and Chuan He, m6A-dependent maternal mRNA clearance facilitates maternal-to-zygotic transition in zebrafish, Nature, 2017, 542 (7642), 475-478.

Lijia Ma, Boxuan Simen Zhao, Kai Chen, Amber Thomas, Jigyasa H. Tuteja, Xin He, Chuan He, and Kevin P. White, Evolution of transcript modification by N6-methyladenosine in primates, Genome Res., 2017, 27 (3), 385-392.

Hailing Shi, Xiao Wang, Zhike Lu, Boxuan Simen Zhao, Honghui Ma, Phillip Hsu, Chang Liu, and Chuan He. YTHDF3 facilitates translation and decay of the N6-methyladenosine-modified RNA, Cell Res.,2017, 27 (3), 315-328.

Boxuan Simen Zhao, Ian A. Roundtree, and Chuan He. Post-transcriptional gene regulation by the messenger RNA modification marks, Nat. Rev. Mol. Cell Biol., 2017, 18, 31-42.

Gianluigi Lichinchi*, Boxuan Simen Zhao*, Yinga Wu, Zhike Lu, Yue Qin, Chuan He, and Tariq M. Rana. Dynamics of Human and Viral RNA Methylation during ZIKA Virus Infection, Cell Host Microbe, advanced publication, http://dx.doi.org/10.1016/j.chom.2016.10.002.

Nagaraja Tirumuru*, Boxuan Simen Zhao*, Zhike Lu, Chuan He, and Li Wu, YTHDF Proteins Bind to N6-methyladenosines of HIV-1 RNA and Regulate Viral Infection, Elife., 2016, 5:e15528.

Osama Zahid, Boxuan Simen Zhao, Chuan He, and Adam Hall, Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores, Sci. Rep., 2016, 6:29565.

Kai Chen, Boxuan Simen Zhao, and Chuan He, Nucleic Acid Modifications in Regulation of Gene Expression, Cell Chem. Biol., 2016, 23(1), pp. 74-85.

Xiao Wang*, Boxuan Simen Zhao*, Ian A. Roundtree, Zhike Lu, Dali Han, Honghui Ma, Xiaocheng Weng, Kai Chen, Hailing Shi, and Chuan He. N6-methyladenosine Modulates Messenger RNA Translation Efficiency, Cell, 2015, 161(6), pp. 1388–1399.

Boxuan Simen Zhao and Chuan He, Fate by RNA Methylation: m6A Steers Stem Cell Pluripotency, Genome Biol., 2015, 16, pp. 43.

Xingyu Lu, Boxuan Simen Zhao, and Chuan He, TET Family Proteins: Oxidation Activity, Interacting Molecules, and Functions in Diseases, Chem. Rev., 2015, 115 (6), pp. 2225–2239.

Xingyu Lu*, Dali Han*, Boxuan Simen Zhao*, Chun-Xiao Song, Li-Sheng Zhang, Louis C Doré, and Chuan He, Base-Resolution Maps of 5-Formylcytosine and 5-Carboxylcytosine Reveal Genome-Wide DNA Demethylation Dynamics, Cell Res., 2015, 25, pp. 386–389.

Boxuan Simen Zhao, and Chuan He, Pseudouridine in a New Era of RNA Modifications, Cell Res., 2015, 25, pp. 153–154.

Gary C. Hon, Chun-Xiao Song, Tingting Du, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Chia-an Yen, Zhen Ye, Shi-Qing Mao, Bang-An Wang, Samantha Kuan, Lee E. Edsall, Boxuan Simen Zhao, Guoliang Xu, Chuan He, and Bing Ren, 5mc Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming During Differentiation. Mol. Cell, 2014, 56(2), pp. 286-297.

Ziyang Hao, Hubin Lou, Rongfeng Zhu, Jiuhe Zhu, Dianmu Zhang, Boxuan Simen Zhao, Shizhe Zeng, Xing Chen, Jefferson Chan, Chuan He, and Peng R. Chen, The Multiple Antibiotic Resistance Regulator MarR is a Copper Sensor in Escherichia coli, Nat. Chem. Biol., 2014, 10, pp. 21-28.

Boxuan Simen Zhao, Gong Zhang, Shizhe Zeng, Chuan He, and Peng R. Chen, Probing Subcellular Organic Hydroperoxide Formation via a Genetically Encoded Ratiometric and Reversible Fluorescent Indicator, Integr. Biol., 2013, 5(12), pp. 1485-1489.

Quanjiang Ji*, Boxuan Simen Zhao*, and Chuan He, A Highly Sensitive Fluorescent Reporter for Ratiometric Monitoring of Cellular Quinones, Chem. Comm. 2013, 49(73), pp. 8027-8029.

Jing Wang, Jason Karpus, Boxuan Simen Zhao, Zheng Luo, Peng R. Chen, and Chuan He, A Selective Fluorescent Probe for Carbon Monoxide Imaging in Living Cells, Angew. Chem. Int. Ed., 2012, 51 (38), pp. 9652–9656.

Boxuan Simen Zhao, Yujie Liang, Yanqun Song, Chunhong Zheng, Ziyang Hao, and Peng R. Chen, A Highly Selective Fluorescent Probe for Visualization of Organic Hydroperoxides in Living Cells, J. Am. Chem. Soc., 2010, 132(48), pp. 17065–17067.

(*co-authors contributed equally)

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