Hairong Wei

Contact

hairong@mtu.edu
906-487-1473
Noblet Building 176

ResearchGate

Professor
Editor-in-Chief, Forestry Research
Adjunct Professor, Departments of Computer Science & Mathematics

PhD, Plant Molecular Biology, University of Hawaii at Manoa
MS, Computer Science, University of Chicago
MS, Forest Genetics and Tree Breeding, Beijing Forestry University
BS, Agricultural Sciences, Beijing Forestry University

Links of Interest

Software developed by Wei group
1. SignalPath-Finder (AI）
2. DyGAF (AI)
3. IntegraGRN (AI)
4. JRmGRN
5. Top-down GGM
6. Bottom-up GGM
7. CollaborativeNet
8. TGMI
9. TGPred
10. HB-PLS
11. BWERF

Prospective students and postdocs interested in plant genomics, bioinformatics, and AI/ML are welcome to contact me about developing competitive external fellowship applications, including NSF graduate and postdoctoral fellowships.

Research Interests

Implementation of AI in life science
Bioinformatics tool and software development
Identification of genes regulating complex traits via systems biology approaches
Algorithms for gene network construction;
Genomics of wood formation
Functional genomics.
Genome Assembly and annotation

Recent Publications

Islam MK, Tayengwa, R, Kumar, A, Lv, K., Qi, Y., Busov, V., Coleman D., and Wei H *. 2026. SignalPath-Finder: Identification of TOR signaling downstream targets via pseudo-peak-based ranking and autoencoder optimization. Artificial Intelligence in the Life Science. (https://doi.org/10.1016/j.ailsci.2026.100174)
Mummadi, S. T., Islam, M. K., Busov, V., and Wei, H*. 2025. Gene regulatory network prediction using machine learning, deep learning, and hybrid approaches, Forestry Research. 5: e014.
Islam, Md Khairul, H. Wagh, H. Wei*. 2025. Dynamic Gene Attention Focus (DyGAF): Enhancing biomarker identification through dual-model attention networks. Bioinformatics and Biology Insights 19:1-15.
Wei, Z. and Wei *. 2023. Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation (Review article). Horticulture Research

Cao, X., L. Zhang, M. Zhao, C. He, K. Zhang, S. Liu, Q. Sha* and Wei*. 2023. TGPred: Efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning, and optimization. NAR Genomics and Bioinformatics 5(3):1-13
Li, J., F. Han, T. Yuan, W. Li, Y. Li, H. X. Wu, H. Wei and S. Niu. 2023. The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine. Nature Communication 14, 1947. (JIF =17.7).
Niu, S*., J. Li, W. Bo, W. Yang, A. Zuccolo, S. Giacomello, J. Ma, F. Han, X. Chen, J. Yang, Y. Song,Y. Nie, B. Zhou, P. Wang, Q. Zuo, H. Zhang, J. Wang, L. Wang, Z. Liu, X. Zhang, T. Liu, S. Pei, Z. Li, Y. Hu, Y. Yang, W. Li, J. Lin, Y. Zan, L. Zhou, T. Yuan, W. Li, Y. Li, H. Wei* and Harry X. Wu*. 2022. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 185(1):204-217. (JIF =66.58).
Wang, H., S. Pak, J. Yang, Y. Wu, W. Li, H. Feng, J. Yang, H. Wei * and C. Li *. 2022. Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis. Plant Biotechnology Journal, pp. 1-17
Gao, J., P. Zhang, W. Wu, H. Wei* and W. Zhang*. 2021. Toward an understanding of the detection, and function of R-loops in plants (Review paper).Journal of Experimental Botany 72(18):6110-6122
Lin, G, C. He, J. Zheng, D.H. Koo, H. Le, H. Zheng, T. M. Tamang, J. Lin, Y. Liu, M. Zhao, Y. Hao, F. McFraland, B. Wang, Y. Qin, H. Tang, D.R. McCarty, H. Wei, M.J. Cho, S. Park, H. Kaeppler, S. Kaeppler, N. Springer, Y/ Liu, P.S. Schnable, G. Wang, F. F. White, S. Liu. Chromosome-level genome assembly of a regenerable maize Inbred line A188. Genome Biology 22, 175 (2021).
Wu, W., K. Du, X. Kang, and Wei*. 2021. The diverse roles of cytokinins in regulating leaf development (Review paper). Horticulture Research 8:118.
Wu, W., J. Li, Q. Wang, K. Lv, K. Du, W. Zhang, Q. Li, X. Kang* and H. Wei*. 2021. Growth-regulating factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in triploid poplar. 230: 612–628. New Phytologist
Deng, W., K. Zhang, C. He, S. Liu and H. Wei *. 2021. HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression. Forestry Research. 1: 6 doi: 10.48130/FR-2021-0006
Wei, H. 2021. Editorial message, Forestry Research. 1:1 doi: 10.48130/FR-2021-0001
Chen, S., G., Y. Wang, L. Yu, T. Zheng, S. Wang, Z. Yue, J. Jiang, S. Kumari, C. Zheng, H. Tang, J. Li, Y. Li, J. Chen, W. Zhang, H. Kuang, J. Robertson, P. Zhao, H. Li, S. Shu, Y. Yordanov, Ha. Huang, D. Goodstein, Y. Gai, Q. Qi, J. Min, C. Xu, S. Wang, G. Qu, A. Paterson, D. Sankoff, H. Wei, Liu, G,C. Yang,. 2021. Genome sequence and evolution of Betula platyphylla. Horticulture Research 8, 37(2021).
Li, Y., H. Wei, J. Yang, L. K. Du, J.Li, Y. Zhang, T. Qiu,Z. Liu, Y. Ren, L. Song, X. Kang. 2020. High quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into the evolution and rubber biosynthesis. Horticulture Research. 7:183
He, C., G. Lin, H. Wei, H. Tang, F. F. White, B. Valent, and S. Liu. 2020. Factorial estimating assembly base errors using k-mr abundance difference (KAD) between short reads and genome assembled sequences. NAR Genomics and Bioinformatics Vol. 2, No. 3: 1-14.
Wei, M., Q. Liu, Z. Wang, J. Yang, W. Li, Y. Chen, H. Lu, J. Nie, B. Liu, K. Lv, X. Mao, S. Chen, J. Sanders, H. Wei * and Chenghao Li*. 2020. PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis. New Phytologist. 228(4): 1369-1385.
Zhang, P., Y. Feng, Wei* and W. Zhang*. 2019. R-loop identification and profiling in plants. Trends in Plant Science 24(10):971-972.
Wei, H. 2019. Construction of a hierarchical gene regulatory network centered around a transcription factor (Review). Briefing in Bioinformatics.
Fang, Y, L. Chen, K. Lin, Y. Feng, P. Zhang, J. Sanders, X. Pan, Y. Wu, X. Wang, Z. Su, C. Chen, H. Wei*, W. Zhang*. 2019. Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice. Genome Research 29(8):1287-1297 (IF =10.1)
Deng, W., K. Zhang, S. Liu, P. Zhao and S. Xu and H. Wei*. 2018. JRmGRN: Joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions. Bioinformatics 34(20):3470-3478. (IF=7.3)
Peng, T., M. Qiao, H. Liu, S. Teotia, Y. Zhao, D. Zhao, L. Shi, B. Le, K. Rogers, C. Gunasekara, H. Duan, Y. Gu, L. Tian, Z. Zhang, F. Meng, L. Huang, Q. Chen, Z. Wang, J. Tang, X. Tang, H. Wei*, X. Chen*, Q. Zhao* and G. Tang*. 2018. A resource for inactivation of microRNAs using short tandem target mimic technology in model and crop plants. Molecular Plant 11(11):1400-1417 (IF=8.8).
Gunasekara, C, K. Zhang, W. Deng, L. Brown and H. Wei*. 2018. TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction. Nucleic Acids Res Res. 46(11):e67. (IF=11.53)
Kumari, S., W. Deng, C. Gunasekara, V. Chiang, H.S. Chen, H. Ma, X. Davis, and H. Wei*. 2016. Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. BMC Bioinformatics 2016, 17:132
Yang, C and H. Wei*. 2014, Designing microarray and RNA-seq experiments for greater systems biology discovery in modern plant genomics. Molecular Plant 8, 196–206. (IF=8.8)
Wei, H. Y. Yordan, T. Georgieva, X. Li, V. Busov. 2013. Nitrogen deprivation promotes Populus root growth via global transcriptomic reprogramming and activation of hierarchical genetic networks. New Phytologist 200 (2), 483-97 (IF=6.5)
Wei, H., P. F. Kuan, S. Tian, C. Yang, J. Nie, S. Sengupta, V. Ruotti, G. Jonsdottir, S. Keles, J. Thomson and R. Stewart. 2008. A study of the relationships between oligonucleotide properties and hybridization intensities in NimbleGen platform. Nucleic Acids Res, Vol. 36, No. 9:2926-2938.
Kumari, S., J. Nie,, H.S. Chen, R. Stewart, H. Ma, X. Li, M. Lu, W.M. Taylor, and H. Wei. 2012. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery. PLos ONE 7(11): e50411
Nie, J., R. Stewart, F. Ruan, J. Thomson, H. Zhang, X. Cui and H. Wei. 2011. TF-cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). BMC Systems Biology, 5:53
Cui, X, T. Wang, H.S. Chen, V. Busov and H. Wei. 2010. TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base. BMC Bioinformatics, 11:425
Wei, H, S. Persson, T. Mehta, V. Srinivasasainagendra, L. Chen, G. Page, C. Somerville, A. Loraine. 2006. Transcriptional coordination of the metabolic network in Arabidopsis thaliana. Plant Physiology 142(2):762-74.

Recent Funding

Genomic surveillance and epidemiology in the Upper Peninsula. $4,370,000. DMHHS. Caryn Heldt, Dukka, KC, and Hairong Wei. Oct 1, 2021- July 31, 2023.
ECA-PGR: Under the Hood: The Genetic Components of Maize Regeneration. Plant Genome Program, NSF Award No.(FAIN): 174109. $2,500,000. Sanzhen Liu, Frank White, Sunghun Park, Myeong-Je Cho and Hairong Wei. July 1, 2018 ~ June 30, 2022.
Inactivation of microRNAs in Crop Plants Using Short Tandem Target Mimic (STTM) Technology. Award Number:1340001; Principal Investigator:Guiliang Tang; Co-Principal Investigator:Xuemei Chen, Wenbo Ma, Harold Trick, Hairong Wei; $2,499,979.00. IOS NSF. 06/01/2014 ~ 0/31/2017;
Collaborative Research: ABI Innovation: Plant Genotype-Phenotype (G2P) Association Discovery via Integrative Genome-scale Biological Network & Genome-wide Association Analysis. Hairong Wei, Advances in Bioinformatics, NSF. $384,351.00, July 1, 2015 ~ June 30, 2018

Research Projects

Identifying genes controlling complex traits via gene network construction and decomposition
Bioinformatics tool and software development
Genome assembly and annotation
A system biology approach to elucidate root development in poplar un low nitrogen

Teaching Experience

FW5510 - Experimental Design, Spring 2018

FW4099 - Programming Skills for Bioinformatics, Fall 2009, 2011, 2013, 2015 and 2017

FW5082 - Gene Expression Data Analysis, Fall 2010, 2012 and 2018

CS2321 - Data Structure in Java, Spring 2011

FW5510 - Informative graphics with R, Spring 2012

BMB6030 - Advanced Molecular Biology Lab, Spring 2013, 2014 and 2015

FW3320 - Fundamental of Genetics, Spring 2013

FW3200 - Forest Biometrics and Data Analysis, Spring 2014，2015 and 2016