Boyce Thompson Institute for Plant Research
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Zhangjun Fei

Zhangjun Fei
Zhangjun Fei
Associate Professor
Office/Lab: 227
zf25@cornell.edu
Office: 607 254 3234
Lab:

Lab Web Page

Research Summary

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 andresources 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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Selected Publications

Selected Publications

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Chen, Y.R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J. and Fei, Z. 2012. A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods 8: 41

Gao, M., Niu, J., Zhao, S.P., Jiao, C., Xu, W.R., Fei, Z.J. and Wang, X.P. 2012. Characterization of erysiphe necator-responsive genes in Chinese wild Vitis quinquangularis.. Int J Mol Sci 13: 11497-11519

Gao, M., Wang, Q., Wan, R., Fei, Z.J. and Wang, X.P. 2012. Identification of genes differentially expressed in grapevine associated with resistance to Elsinoe ampelina through suppressive subtraction hybridization.. Plant Physiol Bioch 58: 253-268

Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B.K., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L.A., Zhao, H., He, H., Zhang, Y., Zhang, Z., Huang, S., Tan, T., Pang, E., Lin, K., Hu, Q., Kuang, H., Ni, P., Wang, B., Liu, J., Kou, Q., Hou, W., Zou, X., Jiang, J., Gong, G., Klee, K., Schoof, H., Huang, Y., Hu, X., Dong, S., Liang, D., Wang, J., Wu, K., Xia, Y., Zhao, X., Zheng, Z., Xing, M., Liang, X., Huang, B., Lv, T., Wang, J., Yin, Y., Yi, H., Li, R., Wu, M., Levi, A., Zhang, X., Giovannoni, J.J., Wang, J., Li, Y., Fei, Z. and Xu, Y. 2012. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45: 51-58

Huang, S.X., Gao, Y.F., Liu, J.K., Peng, X.L., Niu, X.L., Fei, Z.J., Cao, S.Q. and Liu, Y.S. 2012. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Molecular Genetics and Genomics 287: 495-513

Lee, J.M., Joung, J.G., McQuinn, R., Chung, M.Y., Fei, Z., Tieman, D., Klee, H. and Giovannoni, J. 2012. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. The Plant journal : for cell and molecular biology 70: 191-204

Levi, A., Thies, J.A., Wechter, W.P., Harrison, H.F., Simmons, A.M., Reddy, U.K., Nimmakayala, P. and Fei, Z. 2012. High frequency oligonucleotides: targeting active gene (HFO-TAG) markers revealed wide genetic diversity among Citrullus spp. accessions useful for enhancing disease or pest resistance in watermelon cultivars. Genetic Resources and Crop Evolution 0: 1-14

Li, R.G., Gao, S., Hernandez, A.G., Wechter, W.P., Fei, Z.J. and Ling, K.S. 2012. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One 0: 7

Lopez-Casado, G., Covey, P.A., Bedinger, P.A., Mueller, L.A., Thannhauser, T.W., Zhang, S., Fei, Z.J., Giovannoni, J.J. and Rose, J.K.C. 2012. Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case. Proteomics 12: 761-774

Ouyang, B., Fei, Z.J., Joung, J.G., Kolenovsky, A., Koh, C.S., Nowak, J., Caplan, A., Keller, W.A., Cui, Y.H., Cutler, A.J. and Tsang, E.W.T. 2012. Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1) . Plant Molecular Biology 79: 315-331

Zhang, Y.C., Gao, M., Singer, S.D., Fei, Z.J., Wang, H. and Wang, X.P. 2012. Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape. PLoS One 7: e44465

Zhang, Y.C., Mao, L.Y., Wang, H., Brocker, C., Yin, X.J., Vasiliou, V., Fei, Z.J. and Wang, X.P. 2012. Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily. PLoS One 7: e32153

Zhou, X., Fei, Z., Thannhauser, T.W. and Li, L. 2011. Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis). Bmc Plant Biol 11: 169

Zhou, X.J., Mcquinn, R., Fei, Z.J., Wolters, A.M.A., Van Eck, J., Brown, C., Giovannoni, J.J. and Li, L. 2011. Regulatory control of high levels of carotenoid accumulation in potato tubers. Environ 34: 1020-1030

Zhong, S., Joung, J.G., Zheng, Y., Chen, Y.R., Liu, B., Shao, Y., Xiang, J.Z., Fei , Z. and Giovannoni, J.J. 2011. High-throughput Illumina strand-specific RNA sequencing library preparation. Cold Spring Harb Protoc 2011: 940-949

Sorensen, I., Pettolino, F.A., Bacic, A., Ralph, J., Lu, F.C., O'Neill, M.A., Fei, Z.Z., Rose, J.K.C., Domozych, D.S. and Willats, W.G.T. 2011. The charophycean green algae provide insights into the early origins of plant cell walls. Plant J 68: 201-211

Zheng, Y., Zhao, L., Gao, J. and Fei, Z. 2011. iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12: 453

Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., Arvidsson, S., van der Merwe, M.J., Riano-Pachon, D.M., Mueller-Roeber, B., Fei, Z., Nesi, A.N., Giovannoni, J.J. and Fernie, A.R. 2011. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68: 999-1013

Osorio, S., Alba, R., Damasceno, C.M.B., Lopez-Casado, G., Lohse, M., Zanor, M.I., Tohge, T., Usadel, B., Rose, J.K.C., Fei, Z.J., Giovannoni, J.J. and Fernie, A.R. 2011. Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157: 405-425

Lu, G.Y., Guo, S.G., Zhang, H.Y., Geng, L.H., Song, F.M., Fei, Z.J. and Xu, Y. 2011. Transcriptional profiling of watermelon during its incompatible interaction with Fusarium oxysporum f. sp niveum. Eur J Plant Pathol 131: 585-601

Li, Z., Zhang, Z.H., Yan, P.C., Huang, S.W., Fei, Z.J. and Lin, K. 2011. RNA-Seq improves annotation of protein-coding genes in the cucumber genome.. Bmc Genomics 12: 540

Guo, S.G., Liu, J.A., Zheng, Y., Huang, M.Y., Zhang, H.Y., Gong, G.Y., He, H.J., Ren, Y., Zhong, S.L., Fei, Z.J. and Xu, Y. 2011. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. Bmc Genomics 12: 454

Fei, Z. and Liu, Y. 2011. Genomic and functional genomic resources of melon. In Genetics, Genomics and Breeding of Cucurbits (Wang, Y.-H., Behera, T.K. and Kole, C. eds. 0: Science Publishers, pp. 286-308

Fei, Z., Joung, J.G., Tang, X., Zheng, Y., Huang, M., Lee, J.M., McQuinn, R., Tieman, D.M., Alba, R., Klee, H.J. and Giovannoni, J.J. 2011. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 39: D1156-1163

Dai, N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G.F., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z.J., Giovannoni, J., Burger, Y. , Katzir, N. and Schaffer, A.A. 2011. Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 76: 1-18

Clepet, C., Joobeur, T., Zheng, Y., Jublot, D., Huang, M.Y., Truniger, V., Boualem, A., Hernandez-Gonzalez, M.E., Dolcet-Sanjuan, R., Portnoy, V., Mascarell-Creus, A., Cano-Delgado, A.I., Katzir, N., Bendahmane, A., Giovannoni, J.J., Aranda, M.A., Garcia-Mas, J. and Fei, Z.J. 2011. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. Bmc Genomics 12: 252

Levi, A., Wechter, W.P., Harris, K.R., Davis, A.R. and Fei, Z.J. 2010. High-frequency oligonucleotides in watermelon expressed sequenced tag-unigenes are useful in producing polymorphic polymerase chain reaction markers among watermelon genotypes. Journal of the American Society for Horticultural Science 135: 369-378

Joshi, V., Joung, J.G., Fei, Z. and Jander, G. 2010. Interdependence of threonine, methionine and isoleucine metabolism in plants: accumulation and transcriptional regulation under abiotic stress. Amino Acids 39: 933-947

Harel-Beja, R., Tzuri, G., Portnoy, V., Lotan-Pompan, M., Lev, S., Cohen, S., Dai, N., Yeselson, L., Meir, A., Libhaber, S.E., Avisar, E., Melame, T., van Koert, P., Verbakel, H., Hofstede, R., Volpin, H., Oliver, M., Fougedoire, A., Stalh, C., Fauve, J., Copes, B., Fei, Z., Giovannoni, J., Ori, N., Lewinsohn, E., Sherman, A., Burger, J., Tadmor, Y., Schaffer, A.A. and Katzir, N. 2010. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theoretical and Applied Genetics 121: 511-533

Guo, S.G., Zheng, Y., Joung, J.G., Liu, S.Q., Zhang, Z.H., Crasta, O.R., Sobral, B.W., Xu, Y., Huang, S.W. and Fei, Z.J. 2010. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11: 384

Gong, P.J., Zhang, J.H., Li, H.X., Yang, C.X., Zhang, C.J., Zhang, X.H., Khurram, Z., Zhang, Y.Y., Wang, T.T., Fei, Z.J. and Ye, Z.B. 2010. Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. Journal of Experimental Botany 61: 3563-3575

Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavini, S., Costa, G., Fei, Z.J. and Giovannoni, J. 2010. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biology 10: 229

Rhee, J.K., Joung, J.G., Chang, J.H., Fei, Z. and Zhang, B.T. 2009. Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis. Bmc Genomics 10: Suppl 3, S29

Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A., Menda, N., Tecle, I.Y., Bombarely, A., Stack, S., Royer, S.M., Chang, S.-B., Shearer, L.A., Kim, B.D., Jo, S.-H., Hur, C.-G., Choi, D., Li, C.-B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G.B., Bishop, G.J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I.A., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M.W.E.J., van Ham, R.C.H.J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M.A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M.L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jcker, A., Bruggmann, R., Spannagl, M., Mayer, K.X.F., Guig, R., Camara, F., Rombauts, S., Fawcett, J.A., Van de Peer, Y., Knapp, S., Zamir, D. and Stiekema, W. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome 2: 78-92

Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni , J.J. and Fei, Z. 2009. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol 151: 1758-1768

Joung, J.G. and Fei, Z. 2009. Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. Bioinformatics 25: 387-393

Joung, J.G. and Fei, Z.J. 2009. Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information. BMC Bioinformatics 10: Suppl 1, S34

Mathieu, S., Cin, V.D., Fei, Z.J., Li, H., Bliss, P., Taylor, M.G., Klee, H.J. and Tieman, D.M. 2009. Flavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. J Exp Bot 60: 325-337

Huang, S.W., Li, R.Q., Zhang, Z.H., Li, L., Gu, X.F., Fan, W., Lucas, W.J., Wang, X.W., Xie, B.Y., Ni, P.X., Ren, Y.Y., Zhu, H.M., Li, J., Lin, K., Jin, W.W., Fei, Z.J., Li, G.C., Staub, J., Kilian, A., van der Vossen, E.A.G., Wu, Y., Guo, J., He, J., Jia, Z.Q., Ren, Y., Tian, G., Lu, Y., Ruan, J., Qian, W.B., Wang, M.W., Huang, Q.F., Li, B., Xuan, Z.L., Cao, J.J., Asan, Wu, Z.G., Zhang, J.B., Cai, Q.L., Bai, Y.Q., Zhao, B.W., Han, Y.H., Li, Y., Li, X.F., Wang, S.H., Shi, Q.X., Liu, S.Q., Cho, W.K., Kim, J.Y., Xu, Y., Heller-Uszynska, K., Miao, H., Cheng, Z.C., Zhang, S.P., Wu, J., Yang, Y.H., Kang, H.X., Li, M., Liang, H.Q., Ren, X.L., Shi, Z.B., Wen, M., Jian, M., Yang, H.L., Zhang, G.J., Yang, Z.T., Chen, R., Liu, S.F., Li, J.W., Ma, L.J., Liu, H., Zhou, Y., Zhao, J., Fang, X.D., Li, G.Q., Fang, L., Li, Y.R., Liu, D.Y., Zheng, H.K., Zhang, Y., Qin, N., Li, Z., Yang, G.H., Yang, S., Bolund, L., Kristiansen, K., Zheng, H.C., Li, S.C., Zhang, X.Q., Yang, H.M., Wang, J., Sun, R.F., Zhang, B.X., Jiang, S.Z., Wang, J., Du, Y.C. and Li, S.G. 2009. The genome of the cucumber, Cucumis sativus L. Nat Genet 41: 1275-U1229

Dal Cin, V., Kevany, B., Fei, Z.J. and Klee, H.J. 2009. Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions. Theor Appl Genet 119: 1183-1192

Wang, X.P., Wang, Y.J. and Fei, Z.J. 2008. Identification and characterisation of resistance gene analogues from wild Chinese Vitis species. J Hortic Sci Biotech 83: 345-350

Liu, S.Q., Xu, L., Jia, Z.Q., Xu, Y., Yang, Q., Fei, Z.J., Lu, X.Y., Chen, H.M. and Huang, S.W. 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

Itaya, A., Bundschuh, R., Archual, A.J., Joung, J.G., Fei, Z.J., Dai, X.B., Zhao, P.X., Tang, Y.H., Nelson, R.S. and Ding, B.A. 2008. Small RNAs in tomato fruit and leaf development. Bba-Gene Regul Mech 1779: 99-107

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 . Genes, Genomes and Genomics 1: 167-179

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

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

Features

Features

How are massive plant genomics data organized and interpreted?

feature released -2008

Consider that just one tomato plant contains about 35,000 genes that express thousands of different proteins. Then consider how many different plants are currently under study, and it’s easy to understand the enormity of the data generated in all of biological research.

Organizing that data and making it accessible for further research is an area called bioinformatics. The interface between biology, statistics and computer science, bioinformatics develops computational tools and resources that organize massive amounts of data into usable sets so that the knowledge contained in them can be retrieved, analyzed and applied in biological research. Zhangjun Fei’s laboratory at BTI develops both the databases and the interfaces needed to help scientists understand how genes work together and how they form functioning cells and organisms. He also has developed analytical and data-mining tools that allow scientists to efficiently extract biological information from the database for use in their research.

Fei has collaborated with the Giovannoni laboratory at BTI to develop databases that contain information on the expression of more than 10,000 tomato genes, as well as profiles of tomato fruit nutrition and flavor-related metabolites, during different developmental stages, upon various stresses, and in different genetic backgrounds. As a part of International Cucurbit Genomics Initiative (ICuGI), the Fei lab has also developed a database, along with its corresponding interface and tools, for the organization of all the genomics information gathered to date on the cucurbit family of plants,which includes melon,watermelon, cucumber and pumpkin, among others.

Work in Fei’s laboratory is providing tools and resources that organize genomics information about an organism into a form scientists can easily use to analyze and visualize the data they’ve gathered.

Lab Members

Lab Members

Linyong Mao
Linyong Mao
Postdoc
Office/Lab: 231
lm585@cornell.edu
Office: 607 254 1267
Lab:
Honghe Sun
Honghe Sun
Visiting Scholar
Office/Lab: 229/203
hs738@cornell.edu
Office: 607 254 2334
Lab:
Wenbo Chen
Wenbo Chen
Post Doc
Office/Lab: 229
wc529@cornell.edu
Office:
Lab:
Jeong Seob Kim
Jeong Seob Kim
Visiting Scholar
Office/Lab:
jk2365@cornell.edu
Office:
Lab:
Yi Zheng
Yi Zheng
Postdoc
Office/Lab: 229
yz357@cornell.edu
Office: 607 254 2334
Lab:
Chen Jiao
Chen Jiao
Visiting Scholar
Office/Lab: 229
cj334@cornell.edu
Office: 607 254 2334
Lab:
Naibin Duan
Naibin Duan
Visiting Scholar
Office/Lab: 231
duannaibin@gmail.com
Office: 607 254 1267
Lab:
Chen  Xu
Chen Xu
Visiting Scholar
Office/Lab: 231
cx58@cornell.edu
Office: 607-254-1267
Lab:

PGRP

Plant Genome Research Program

Research ProjectFunctional genomics of fruit flavor and nutrition pathways

Participating Interns

2011 – Interns
2009 – Interns
2008 – Interns
2007 – Interns