Jianrong Wang

● LAB WEBSITE
https://wangjr03.github.io/

● PROFESSIONAL EXPERIENCE
2024.08-Present: Associate Chair, Department of CMSE, MSU 
2023.06-Present: Associate Professor, Department of CMSE & Department of BME, MSU

2017.01-2023.06: Assistant Professor, Department of Computational Mathematics, Science and Engineering (CMSE), MSU

2016.03-2016.12: Postdoctoral Associate, Stanford University
2012-2016: Postdoctoral Associate, MIT
2007-2012: Ph.D., Georgia Institute of Technology.
2003-2007: B.S., Tsinghua University


● RESEARCH INTERESTS
Computational Biology, Machine Learning, Bioinformatics and Systems Biology
1.	Probabilistic modeling of long-range 3D enhancer-gene networks in diverse cellular contexts.
2.	Network-based functional annotation of non-coding genetic variants associated with human diseases.
3.	Statistical and machine learning methods for multi-omics integration.



● AWARDS
08/2025: CMSE Faculty Excellence Award
03/2021: Withrow Teaching Excellence Award
07/2020: NSF CAREER Award	


● SELECTED PUBLICATIONS
1. Hao Wang, Jiaxin Yang, Yu Zhang*, Jianliang Qian*, and Jianrong Wang*. Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution. 2025 Nature Communications 16: 3435. 

2. Sikta Das Adhikari, Nina Steele, Brian Theisen, Jianrong Wang* and Yuehua Cui*. SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection. 2025 Nucleic Acids Research 53(18): gkaf936.

3. Emma L. Bush, Brigette Berke-Reynolds, Kaitlyn M. Hutchins, Xinrui Yu, Jorge Colon-Rosado, FuJung Chang, John Curran, Jiaxin Yang, Liangliang Sun, Jianrong Wang* and Yu Zhang*. CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire. 2025 Nature Communications, Accepted. 

4.  Sikta Das Adhikari, Yuehua Cui*, and Jianrong Wang*. BayesKAT: Bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases. 2024 Briefings in Bioinformatics 25(3):bbae182.

5.	Anissia Ait Saada, Wenying Guo, Alex Costa, Jiaxin Yang, Jianrong Wang, Kirill Lobachev. Widely-spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions. 2023 Nucleic Acids Research 51(8):3722-3734.

6.	Hao Wang, Jiaxin Yang, Yu Zhang, Jianliang Qian and Jianrong Wang. Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO. 2022 Nature Communications 13(1):2645. 

7.	Hao Wang, Binbin Huang and Jianrong Wang. Predict long-range enhancer regulation based on protein-protein interactions between transcription factors. 2021 Nucleic Acids Research, 49(18): 10347-10368. 

8.	Sambit Roy, Binbin Huang, Niharika Sinha, Jianrong Wang and Aritro Sen. Androgens Regulate Ovarian Gene Expression by Balancing Ezh2-Jmjd3 Mediated H3K27me3 Dynamics. 2021 PLoS Genetics 17(3): e1009483. 

9.	Yan Liu, Yuzhao Gao, Ruiling Fang, Hongyan Cao, Jian Sa, Jianrong Wang, Hongqi Liu, Tong Wang and Yuehua Cui. Identifying complex gene-gene interactions: a mixed kernel omnibus testing approach. 2021 Briefings in Bioinformatics 22(6):bbab305. 

10.	Hao Wang, Jiaxin Yang, Yu Zhang and Jianrong Wang. Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. 2020 Methods S1046-2023(20)30225-5. 

11.	Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis and Guo-Cheng Yuan. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. 2017 Nature Communications 8:15011. 

12.	Hao Wang, Jiaxin Yang, and Jianrong Wang. Leverage large-scale biological networks to decipher the genetic basis of human diseases using machine learning. 2020 Methods in Molecular Biology 2190:229-248.

13. Jianrong Wang, Cristina Vicente-Garcia, Davide Seruggia, Eduardo Molto, Ana Fernandez-Minan, Ana Neto, Elbert Lee, Jose Luis Gomez-Skarmeta, Lluis Montoliu, Victoria V. Lunyak and I. King Jordan. MIR retrotransposon sequences provide insulators to the human genome. 2015 Proc Natl Acad Sci USA 112(32):E4428-4437. 

14.	Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. 2015 Nature 518:317-330. 

15.	Jianrong Wang, Victoria V. Lunyak and I. King Jordan. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. 2013 Bioinformatics 29(4):492-493.

16.	Daudi Jjingo, Jianrong Wang, Andrew B. Conley, Victoria V. Lunyak and I. King Jordan. Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome. 2013 Bioinformatics 29(24):3109-3112. 

17.	Jianrong Wang, Victoria V. Lunyak and I. King Jordan. Chromatin signature discovery via histone modification profile alignments. 2012 Nucleic Acids Research 40(21):10642-10656. 

18.	Jianrong Wang, Victoria V. Lunyak and I. King Jordan. Genome-wide prediction and analysis of human chromatin boundary elements. 2012 Nucleic Acids Research 40(2):511-529, (Cover Story). 

19.	Jianrong Wang, Glenn J. Geesman, Sirkka Liisa Hostikka, Michelle Atallah, Benjamin Blackwell et al. Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal. 2011 Cell Cycle 10(17):3016-3030. 

20.	Jianrong Wang, Ahsan Huda, Victoria V. Lunyak and I. King Jordan. A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags. 2010 Bioinformatics 26(20):2501-2508. 



● STUDENT AWARDS
David Chau: Croucher Scholarship (08/2025)
Xinrui Yu: Ginther Research Fellowship (01/2025)
Xinrui Yu: Selected talk at MCBIOS (03/2024)
Sikta Das Adhikari: Selected talk at JSM (08/2024)
Wenjie Qi: Academic Achievement Withrow Fellowship Award, MSU (07/2022)
Sikta Das Adhikari: NSF NRT-IMPACTS Fellowship (05/2021)
Jiaxin Yang: NSF NRT-IMPACTS Fellowship (05/2020)
Hao Wang: NSF NRT-IMPACTS Fellowship (05/2019)
Hao Wang: Honorable Mention of Fitch H. Beach Award, MSU (03/2019)
Binbin Huang: NSF NRT-IMPACTS Fellowship (02/2019)
Hao Wang: First Place of DewGood Award for Public Service, MSU (03/2018)


● LAB MEMBERS
Xinrui Yu (co-advise):  Ph.D. in CMSE
Haoyi Lyu: Ph.D. in CMSE
Hongru Zhao: Ph.D. in CMSE
David Chau (co-advise): Ph.D. in CMSE
Xinrui Zhong: Ph.D. in CMSE
Adam Elfawal: Software Developer
Kristina Malkowski: Software Developer
Alexis Bliesener: Software Developer
Zoie Tsoi: Software Developer
Abigail Parisot: Software Developer


● LAB ALUMNI
Pronoy Kanti Mondal
Postdoc (2022-2024)
Now: Postdoctoral Scientist
Department of Biostatistics
Johns Hopkins University

Jiwoong Kim	
Postdoc (2020 – 2022)
Now: Assistant Professor
Department of Mathematics and Statistics
University of South Florida

Binod Manandhar	
Postdoc (2019 – 2020)	
Now: Assistant Professor
Department of Mathematical Sciences
Clark Atlanta University

Binbin Huang	
Ph.D. in CMSE (01/2017 – 12/2021)	
Now: Senior Bioinformatics Scientist @ LabCorp

Hao Wang	
Ph.D. in CMSE (08/2017 – 06/2022)	
Now: Research Scientist @ Meta 

Wenjie Qi	
Ph.D. in BME (08/2017 – 12/2022)	
Now: Lead Bioinformatics Analyst @ St. Jude Children’s Research Hospital.

Jiaxin Yang
Ph.D. in CMSE (08/2019 - 07/2024)	
Now: Research Scientist @ Meta 

Sikta Das Adhikari
Dual Ph.D. in CMSE & Statistics (08/2019 - 07/2024)
Now: Mathematical Statistician @ FDA

Hongjie Ke	
M.S. in CMSE & Statistics (02/2018-01/2019)
Now: Ph.D. student @ University of Maryland

Andre Popovitch
Software Developer (08/2019-08/2022)
Now: Software developer @ Marigold

Alex Deneau
Software Developer (02/2018-09/2020)
Now: Software engineer @ Microsoft