Jianrong Wang

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


● ACTIVE RESEARCH GRANTS
NSF: DMS-2152011
NSF: DBI-1942143
NIH: R01 GM131398
NSF: IOS-2029959
NIH: R01 ES031937
MSU SPG grant


● AWARDS
03/2021: Withrow Teaching Excellence Award
07/2020: NSF CAREER Award	


● SELECTED PUBLICATIONS
1. Hao Wang, Jiaxin Yang, Xinrui Yu, Yu Zhang, Jianliang Qian* and Jianrong Wang*. Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution. 2024 Nature Communications (Accepted)

2.  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 (Accepted)
https://www.biorxiv.org/content/10.11

3.	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.
https://academic.oup.com/nar/article/51/8/3722/7078040

4.	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. 
https://www.nature.com/articles/s41467-022-30270-2

5.	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. 
https://academic.oup.com/nar/article/49/18/10347/6376026

6.	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. 
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009483

7.	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. 
https://academic.oup.com/bib/article-abstract/22/6/bbab305/6346804?redirectedFrom=fulltext

8.	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. 
https://www.sciencedirect.com/science/article/pii/S1046202320302255

9.	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. 
https://www.nature.com/articles/ncomms15011

10.	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. https://pubmed.ncbi.nlm.nih.gov/32804369/

11. 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. 
https://pubmed.ncbi.nlm.nih.gov/26216945/

12.	Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. 2015 Nature 518:317-330. https://www.nature.com/articles/nature14248

13.	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. https://academic.oup.com/bioinformatics/article/29/4/492/199191

14.	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. https://pubmed.ncbi.nlm.nih.gov/24085569/

15.	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. https://pubmed.ncbi.nlm.nih.gov/22989711/

16.	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). https://academic.oup.com/nar/article/40/2/511/2409304

17.	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. https://pubmed.ncbi.nlm.nih.gov/21862875/

18.	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. https://pubmed.ncbi.nlm.nih.gov/20871106/



● STUDENT AWARDS
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
Pronoy Kanti Mondal: Postdoctoral Scientist
Xinrui Yu (co-advise):  Ph.D. in CMSE
Haoyi Lyu: Ph.D. in CMSE
Hongru Zhao: Ph.D. in CMSE
Adam Elfawal: Software Developer
Lindsey Yucha: Software Developer
Kristina Malkowski: Software Developer
Alexis Bliesener: Software Developer


● LAB ALUMNI
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 Statistics (08/2017 – 07/2019)	
Now: Ph.D. student @ University of Maryland

Andre Popovitch
Software Developer (08/2020 - 04/2021)
Now: Software developer @ Marigold

Alex Deneau
Software Developer (09/2018 - 04/2020)
Now: Software engineer @ Microsoft