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."

Contact

 

Assistant Professor, School of Forest Resources and Environmental Science

Department of Computer Science (Adjunct)

Department of Mathematics (Adjunct)

  • 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.

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

Recent Publications

  • 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 (accepted) 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 master 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. (Accepted)
  • 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
  • Ma. H., Houttler, C., H. Wei, M. Recroad III, J. Yao. 2012. Characterization of the rainbow trout oocyte microRNA transcriptome (Oncorhynchus mykiss). PLoS ONE 7(6): e39649. 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

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