Zhangjun Fei
Research Summary
The development of high throughput technologies has given rise to a wealth of information at system level including genome, transcriptome, proteome and metabolome. However, it remains a major challenge to digest the massive amounts of information and use it in an intelligent and comprehensive manner. To address this question, Dr. Fei’s group has focused on developing computational tools and resources to analyze and integrate large scale "omics" datasets", which help researchers to understand how genes work together to comprise functioning cells and organisms.
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Publications
- Mueller L, Lankhorst RK, Tanksley SD, Giovannoni JJ, White R, Vrebalov J, Fei Z, et al. 2009. A Snapshot of the Emerging Tomato Genome Sequence. The Plant Genome 2: 78-92
- Joung J-G, Fei Z. 2009. Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information. BMC Bioinformatics 10: (Suppl 1):S34
- Mathieu S, Dal Cin V, Fei Z, Li H, Bliss P, Taylor M, Klee H, Tieman D. 2009. Flavor compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. J. Exp. Bot 60: 325-337
- Joung J-G, Fei Z. 2009. Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. Bioinformatics 25: 387-393
- Wechter P, Levi A, Harris K, Davis A, Fei Z, Katzir N, Giovannoni J, Salman-Minkov A, Hernandez A, Thimmapuram J, Tadmor Y, Portnoy V, Trebitsh T. 2008. Gene expression in developing watermelon fruit. BMC Genomics 9: 275
- Liu S, Xu L, Xu Y, Yang Q, Fei Z, Chen H, Huang S. 2008. Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.). Theor. Appl. Genet 117: 927-933
- Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, Martino-Catt S, Bricker B, Yu G, Du L, Sobral BW. 2008. Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes. PLoS ONE 3(5): e2193
- Zimmer S, Fei Z, Stern D. 2008. Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features. Genetics 179: 125-136
- Wang XP,, Wang Y, Fei Z. 2008. Identification and characterization of resistance gene analogues from wild Chinese Vitis species. J. Hortic. Sci. Biotech 83: 345-350
- Itaya A, Bundschuh R, Archual A, Joung J, Fei Z, Dai X, Zhao P, Tang Y, Nelson R, and Ding B. 2008. Small RNAs in tomato fruit and leaf development. BBA - Gene Regulatory Mechanisms 1779: 99-107
- Djavani, M.M., O.R. Crasta, J.C. Zapata, Z. Fei, O. Folkerts, B. Sobral, M. Swindells, J.. Bryant, H. Davis, C.D. Pauza, I.S. Lukashevich, R. Hammamieh, M. Jett, M.S. Salvato. 2007. Early blood profiles of virus infection in a monkey model for Lassa Fever. J. Virol. 81: 7960-7973
- Ouyang, B., T. Yang, H. Li, L. Zhang, Y. Zhang, J. Zhang, Z. Fei, Z. Ye. 2007. Identification of salt stress regulated genes in tomato seedlings by suppression subtracted hybridization and microarray analysis . Journal of Experimental Botany 58: 507-520
- Dan, Y, Fei Z, and Rothan, C. 2007. MicroTom – A New Model System for Plant Genomics. Genes, Genomes and Genomics 1: 167-179
- Gilchrist, C., E. Houpt, N. Trapaidze, Z. Fei, O. Crasta, A. Asgharpour, C. Evans, C. Martino-Catt, D. Baba, S. Stroup, S. Hamano, G. Ehrenkaufer, O. Okada, U. Singh, T. Nozaki, B. Mann, W. Petri Jr.. 2006. Impact of intestinal colonization and invasion on the E. histolytica transcriptome. Mol Biochem Parasitol 147: 163-176
- Fei, Z., X. Tang, R. Alba, J. Giovannoni. 2006. Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. Nucleic Acids Research 34: D766
- Alba, R., P. Payton, Z. Fei, R. McQuinn, P. Debbie, G. B. Martin, S. D. Tanksley, J. J. Giovannoni. 2005. Transcriptome and Selected Metabolite Analysis Reveal Multiple Points of Ethylene Control During Tomato Fruit Development. Plant Cell 17(11): 2954-2965
- Fei, Z., X. Tang, R. Alba, J. White, C. Ronning, G. Martin, S. Tanksley, J. Giovannoni. 2004. Comprehensive EST Analysis of Tomato and Comparative Genomics of Fruit Ripening. The Plant Journal 40(1): 47-59
- Alba, R., Z. Fei, P. Payton, Y. L. Liu, S. Moore, P. Debbie, J. Gordon, J. Rose, G. Martin, S. Tanksley, M. Bouzayen, M. Jahn, J. Giovannoni. 2004. ESTs, cDNA Microarrays, and Gene Expression Profiling: Tools for Dissecting Plant Physiology and Development. The Plant Journal 39: 697-714
Lab Members
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Je-Gun Joung
Lei Zhao
Shaogui Guo
Yi Zheng
Mingyun Huang