Jianrong Wang
Associate Professor, Department of Computational Mathematics, Science and Engineering
Location: 2507J Engineering Bldg
Phone: 517-432-0370
Email: wangj164@msu.edu
Bio
● PROFESSIONAL EXPERIENCE 2023.06-Present: Associate Professor, MSU, Department of Computational Mathematics, Science and Engineering. 2017.01-2023.06: Assistant Professor, MSU, Department of Computational Mathematics, Science and Engineering. 2016.03-2016.12: Postdoctoral Associate, Stanford University, Department of Genetics. 2012-2016: Postdoctoral Associate, MIT, EECS Department, Computer Science and Artificial Intelligence Laboratory (CSAIL), Broad Institute of MIT and Harvard. 2007-2012: Ph.D. Bioinformatics, Georgia Institute of Technology. 2003-2007: B.S. Control Science and Engineering, Tsinghua University ● RESEARCH INTERESTS Computational Biology, Machine Learning, Bioinformatics and Systems Biology 1. Probabilistic modeling of long-range three-dimensional enhancer-gene networks in diverse cellular contexts. 2. Network-based prediction and functional annotation of non-coding genetic variants associated with human diseases. 3. Machine learning algorithms to predict regulatory elements of gene expression, large-scale chromatin domains, and histone modification signatures based on genomics, epigenomics and transcriptomics data. 4. Statistical and computational methods for efficient design, analysis and interpretation of biological big-data generated from new high-throughput techniques. ● ACTIVE RESEARCH GRANTS NSF: DMS-2152011 NSF: DBI-1942143 NIH: R01 GM131398 NSF: IOS-2029959 NIH: R01 ES031937 ● AWARDS 03/2021: Withrow Teaching Excellence Award 07/2020: NSF CAREER Award ● SELECTED PUBLICATIONS 1. 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 2. 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 3. 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 4. 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 5. 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 6. 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 7. 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 8. 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 9. 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/ 10. 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/ 11. Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. 2015 Nature 518:317-330. https://www.nature.com/articles/nature14248 12. 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 13. 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/ 14. 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/ 15. 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 16. 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/ 17. 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 Tairan Song: NSF NRT-IMPACTS Fellowship (09/2023) 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) Hao Wang: Outstanding Poster Award, MSU (03/2018) ● LAB MEMBERS Pronoy Kanti Mondal: Postdoctoral Scientist Jiaxin Yang: Ph.D. in CMSE Sikta Das Adhikari: Ph.D. in Statistics Tairan Song: Ph.D. in CMSE Xinrui Yu (co-advise): Ph.D. in CMSE Shuyang Zhang: Ph.D. in CMSE Adam Elfawal: Software Developer Kevin Patel: Software Developer Kristina Malkowski: 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 (Facebook) Wenjie Qi Ph.D. in BME (08/2017 – 12/2022) Now: Lead Bioinformatics Analyst @ St. Jude Children’s Research Hospital. 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