Hairong Wei

"We are doing excellent job in describing how an individual gene functions, but not how life functions. Systems biology is to fill this gap."

Contact

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

ResearchGate

Professor
Editor-in-Chief, Forestry Research (ForRes): https://www.maxapress.com/journal/forres
Affiliated Professor, Department of Computer Science & Department of Mathematics

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

Software developed by Wei group

(click the above link to downlaod)

1. JRmGRN
2. Top-down GGM
3. Bottom-up GGM
4. CollaborativeNet
5. TGMI
6. TGPred
7. HB-PLS
8. BWERF
9. SPLS
10.TF-finder

Research Interests

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

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 https://doi.org/10.1093/nargab/lqad083
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). https://doi.org/10.1038/s41467-023-37684-6
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). https://www.cell.com/cell/pdf/S0092-8674(21)01428-8.pdf
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). https://doi.org/1186/s13059-021-02396-x
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 https://doi.org/10.1111/nph.17179

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 https://doi.org/10.1038/s41438-020-00406-w

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. https://doi.org/10.1093/nargab/lqaa075

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. https://doi.org/10.1111/nph.16778

Wei, H. 2019. Construction of a hierarchical gene regulatory network centered around a transcription factor (Review). Briefing in Bioinformatics. DOI:https://doi.org/10.1093/bib/bbx152.

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) https://www.genome.org/cgi/doi/10.1101/gr.246009.118

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) https://doi.org/10.1093/bioinformatics/bty354.

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). https://doi.org/10.1016/j.molp.2018.09.003

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) https://doi.org/10.1093/nar/gky210

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 https://doi.org/10.1186/s12859-016-0981-1

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) https://doi.org/10.1016/j.molp.2014.11.012

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) https://doi.org/10.1111/nph.12375

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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511551/

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 https://doi.org/10.1186/1752-0509-5-53

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 https://doi.org/10.1186/1471-2105-11-425

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