Hairong Wei

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."


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  • Associate Professor, SFRES
  • Affiliated Associate Professor, Mathematical Sciences
  • Affiliated Associate 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

Yes, we can.

I am exploring the possibility of identifying genes regulating biological traits via systems biology approaches. We achieve this goal through combinatorial approaches: (1) Designing very efficient biological experiments to yield information-enriched gene expression data sets. (2) Performing gene reduction to identify major regulators controlling traits via complex data analysis. (3) Construction of local regulatory networks controlling a trait. We have developed the algorithms and software pipelines for accurately identifying transcription factors controlling a trait with 50-100 % accuracy. I am in general interested in identifying genes regulating the following traits: (1) Wood productivity and quality. (2) Resistance to disease and pest. (3) Biomass production. However, identification of genes regulating any of agriculturally important traits interests me.

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

Recent Publications

  • Gunasekara, C. A. Subramanian, Avvari, R. K., B. Li, Chen, S. and H. Wei. 2016. ExactSearch: A web-based plant motif search tool ( 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 

Recent Funding

  • 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

  • A system biology approach to elucidate root development in Populus

Teaching Experience

  • CS2321: Data Structure and Java. Spring 2011
  • FW5802: Gene Expression Data Analysis. Fall 2010
  • FW4099: Bioinformatics Programming & Skills. Fall 2009