- Editor-in-Chief, Forestry Research (ForRes): http://www.maxapress.com/journal/forres
- Affiliated Professor, Mathematical Sciences & Computer Science
- 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
Research interests and areas
My research is focused on the following areas:
(1) Identification of important and essential genes that govern various biological processes and complex traits using systems biology approaches. We achieve such a goal through a combined computational and experimental approach: (a) Designing biological experiments to yield information-enriched gene expression data sets. (b) Develop algorithms and software pipelines for constructing collaborative gene networks, hub-centered gene regulatory networks (GRNs) and multilayered hierarchical gene regulatory networks (ML-hGRN). (c) Experimental validation using ChIP-seq and DAP-seq technologies.
(2) Elucidation of the molecular mechanisms underlying leaf development in polyploid poplar.
(3) Gene networks that control adventitious root development, and root development under low nitrogen.
(4) Genome sequencing and assembly.
Links of Interest
Areas of Expertise
- Identification of genes regulating complex traits via systems biology approaches
- Gene expression data analysis
- Gene network construction and decomposition
- Developing software for mining large-scale biological data
- Genomics of wood formation
- 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 https://doi.org/10.1093/jxb/erab280. (JIF =5.9).
- 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 (JIF =10.8).
- Wu, W., K. Du, X. Kang*, and Wei*. 2021. The diverse roles of cytokinins in regulating leaf development (Review paper). Horticulture Research 8:118 (JIF =5.4).
- 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. New Phytologist (in press) (JIF =8.5)
- Wei, H. 2021. Editorial message, Forestry Research. (in press)
- 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). (JIF =5.4).
- 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 (JIF =5.4) 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. (IF =8.5) 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. (IF =9.3). 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) http://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
- 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
- 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
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