- Affiliated Professor, Mathematical Sciences
- Affiliated Professor, 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
1) 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 ( In press) ( IF =10.1 )
Zheng, J., C. He, Y. Qin, G. Lin, D. Park, M. Sun, J. Li, X. Lu, C. Zhang, C. Zhang, D. D Bade, CT “Eddy” Yeh, E. Zeng, H. Wei, P. S. Schnable, G. Wang, S. Liu. 2018. Co-expression analysis aids in the identification of new genes in the epicuticular wax pathway. Plant Journal ( In press)
- 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. 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 ( In press )
- 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. 46(11):e67.
Wei, H. 2017. Construction of a hierarchical gene regulatory network centered around a transcription factor (Review). Briefing in Bioinformatics. DOI:10.1093/bib/bbx152. (IF =6.7).
- Gunasekara, C. A. Subramanian, Avvari, R. K., B. Li, Chen, S. and H. Wei. 2016. ExactSearch: A web-based plant motif search tool (http://sys.bio.mtu.edu/motif/index.php). Plant Methods 12:26 Read More
- 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 Read More
- Dash, M, Y. Yordan, S. Kumari, T. Georgieva, H. Wei and V. Busov. 2015. A system biology approach identifies new regulators of poplar root development under low nitrogen. Plant Journal, 84(2):335-346 Read More
- 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. Read More
- Lin, Y.C.*, Li, W., Sun, Y.H., Kumari, S., Wei, H., Li, Q.Z., Tunlaya-Anukit, S., Sederoff, R.R., and Chiang, V.L. (2013). SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell. 25(11):4324-41. Read More
- 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 Read More
- Lu, S., Li, Q., Wei, H., Chang, M.J., Anukit, S.T., Kim, H., Liu, J., Song, J., Sun, Y.H., Yuan, L., Yeh, T.F., Peszlen, I., Ralph, J. Sederoff, R.R., Chiang, V.L. 2013. Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proc Natl Acad Sci USA 110 (26) 10848-10853 Read More
- Li, J. H. Wei, T. Liu and P. Zhao. 2013. GPLEXUS: Enable genome-scale gene regulatory network analysis for plants through ultrafast mutual information computing and filtering. Nucleic Acids Research. (online now: 10.1093/nar/gkt983) Read More
- 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 Read More
- 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 Read More
- 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 Read More
- Ming, R., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J. Saw, P. Senin, W. Wang, S. Salzberg, X. Wang, E. Lyons, D. Rice, M. Riley, R. Skelton, J. Murray, C. Chen, M. Eustice, E. Tong, H. Albert, R. E. Paull, M.-L. Wang, Y. Zhu, M. Schatz, N. Nagarajan, R. Agbayani, P. Guan, A. Blas, J. Wang, J.-K. Na, T. Michael, E. V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, H. Tang, J. E. Bowers, J. Suzuki, S. Tripathi, K. Neupane, H. Wei, R. Singh, B. Irikura, N. Jiang, W. Zhang, K. Wall, G. Presting, A. Gschwend, Y. Li, A. Windsor, R. N. Pérez, M. J. Torres, F. A. Feltus, B. Porter, M. Paidi, M.-C. Luo, L. Liu, D. Christopher, P. H. Moore, T. Sugimura, C. dePamphilis, J. Jiang, M. Schuler, T. Mitchell-Olds, D. Shippen, J. Palmer, M. R. Freeling, A. H. Paterson, D. Gonsalves, L. Wang and M. Alam. 2008. The genome sequence of transgenic papaya, Carica papaya. Nature, Vol. 452, No. 7190:991-996 Read More
- 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 Research, Vol. 36, No. 9:2926-2938 Read More
- Pan, P., S. Tian, J. Nie, C. Yang, V. Ruotti, H. Wei, G. Jonsdottir, R. Stewart, and J. Thomson. 2007. Whole genome analysis of Histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell, Vol. 1, No 3:299~312. Read More
- 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. Read More
- Persson, S., H. Wei, J. Milne, G. Page, C. Somerville. 2005. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA, 102: 8633-8638. (Faculty 1000 evaluation) Read More
- Wei, H., Y. Kaznessis. 2005. Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination. Biotechnology and Bioengineering. Vol. 89, No1: 53-77 Read More
- Albert, H and H. Wei. Sugarcane Ubi9 gene promoter and methods of use thereof. 2004, U.S. Patent No. 6706948
- 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