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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

Assistant Professor, School of Forest Resources and Environmental Science

Adjunct Assistant 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.

Links of Interest

Open Graduate Positions

Areas of Expertise

Identification of genes regulating 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

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
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
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
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

Co-PI: USDA-DOE: A Systems Biology Approach to Elucidate Regulation of Root Development in Populus, $900,000, from 2009 to 2012

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

Department

Undergraduate

Graduate

Facilities

Research

Resources For . . .