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Research Overview

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.

Publications

  • Identification of multiple salicylic acid-binding proteins using two high throughput screens 2015

    Manohar, M., Tian, M., Moreau, M., Park, S-W., Choi, H.W., Fei, Z., Friso, G., Asif, M., Manosalva, P., von Dahl, C.C., Shi, K., Ma, S., Dinesh-Kumar, S.P., O'Doherty, I., Schroeder, F.C., van Wijk, K.J., and Klessig, D.F.
    Front. Plant Sci. 5,  777
    Full text...
  • Transcriptome responses of the host, Trichoplusia ni, to infection by the baculovirus, Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV) 2014

    Chen, Y. R., Zhong, S., Fei, Z., Gao, S., Zhang, S., Li, Z., Wang, P., and Blissard, G.W.
    J. Virol. 88,  13781-13797
    Full text...
  • Complete Genome Sequence of a Novel Genotype of Squash Mosaic Virus Infecting Squash in Spain 2015

    Li, R., Gao, S., Berendsen, S., Fei, Z., and Ling, K-S.
    Genome Announc. 3(1),  e01583-14
    Full text...
  • A Zinc Finger Protein Regulates Flowering Time and Abiotic Stress Tolerance in Chrysanthemum by Modulating Gibberellin Biosynthesis 2014

    Yang, Y., Ma, C., Xu, Y., Wei, Q., Imtiaz, M., Lan, H., Gao, S., Cheng, L., Wang, M., Fei, Z., Hong, B., and Gao, J.
    The Plant Cell tpc.114.124867,  tpc.114.124867
    Full text...
  • Interdependence of threonine, methionine and isoleucine metabolism in plants: accumulation and transcriptional regulation under abiotic stress 2010

    Joshi, V., Joung, J.G., Fei, Z. and Jander, G.
    Amino Acids 39,  933-947
    Full text...
  • Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf 2015

    Li, N., Chen, Y-R., Ding, Z., Li, P., Wu Y., Zhang, A., Yu, S., Giovannoni, J.J., Fei, Z., Zhang, W., Xiang, J.Z., Xu, C., Liu, B., and Zhong, S.
    Scientific Reports 5,  Article number: 8015
    Full text...
  • Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca × V. vinifera) cv. Kyoho flowers 2015

    Cheng, C., Jiao, C., Singer, S.D., Gao, M., Xu, X., Zhou, Y., Li, Z., Fei, Z., Wang, Y., and Wang, X
    BMC Genomics 16,  128
    Full text...
  • Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis).

    Zhang, J., Yuan, H., Fei, Z., Pogson, B.J., Zhang, L., and L., Li.
    Planta DOI 10.1007/s00425-015-2262-z
    Full text...
  • Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits 2015

    Freilich, S., Lev, S., Gonda, I., Reuveni, E., Portnoy, V., Oren, E., Lohse, M., Galpaz, N., Bar, E., Tzuri, G., Wissotsky, G., Meir, A., Burger, J., Tadmor, Y., Schaffer, A., Fei, Z., Giovannoni, J., Lewinsohn, E., and Katzir, N.
    BMC Plant Biology 15,  71
    Full text...
  • A “golden” SNP in CmOr governs fruit flesh color of melon (Cucumis melo) 2015

    Tzuri, G., Zhou, X., Chayut, N., Yuan, H., Portnoy, V., Meir, A., Sa'ar, U., Baumkoler, F., Mazourek, M., Lewinsohn, E., Fei, Z., Schaffer, A.A., Li, L., Burger, J., Katzir, N., and Tadmor, Y.
    Plant J. Accepted Article, DOI: 10.1111/tpj.12814
    Full text...
  • Blocking the Q -binding site of photosystem II by tenuazonic acid, a non-host-specific toxin of Alternaria alternata, activates singlet oxygen-mediated and EXECUTER-dependent signalling in Arabidopsis 2015

    Chen, S., Kim, C., Lee, J.M., Lee, H.A., Fei, Z., Wang, L., and Apel, K.
    Plant Cell Environ.
    Full text...
  • The PH gene determines fruit acidity and contributes to the evolution of sweet melons 2014

    Cohen, S., Itkin, M., Yeselson, Y., Tzuri, G., Portnoy, V., Harel-Baja, R., Lev, S., Sa'ar, U., Davidovitz-Rikanati, R., Baranes, N., Bar, E., Wolf, D., Petreikov, M., Shen, S., Ben-Dor, S., Rogachev, I., Aharoni, A., Ast, T., Schuldiner, M., Belausov, E., Eshed, R., Ophir, R., Sherman, A., Frei, B., Neuhaus, H.E., Xu, Y., Fei, Z., Giovannoni, J., Lewinsohn, E., Tadmor, Y., Paris, H.S., Katzir, N., Burger, Y., and Schaffer, A.A.
    Nature Communications 5,  4026
    Full text...
  • Evolutionary and expression analyses of basic zipper transcription factors in the highly homozygous model grape PN40024 (Vitis vinifera L.) 2014

    Gao, M., Zhang, H.J., Guo, C.L., Cheng, C.X., Guo, R.R., Mao, L.Y., Fei, Z.J., and Wang, X.P
    Plant Molecular Biology Reporter 32,  1085-1102
    Full text...
  • The genome of the stress-tolerant wild tomato species Solanum pennellii 2014

    Bolger, A., Scossa, F., Bolger, M.E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sorensen, I., Lichtenstein, G., Fich, E.A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S.A., Schijlen, E., Jimenez-Gomez, J.M., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L.R., Maloof, J.N., Sinha, N., van Ham, R.C., Lankhorst, R.K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J.K., Zamir, D., Carrari, F., Giovannoni, J.J., Weigel, D., Usadel, B., and Fernie, A.R.
    Nature Genetics 46,  1034-1038
    Full text...
  • Draft genome of the kiwifruit Actinidia chinensis 2013

    Huang, S., Ding, J., Deng, D., Tang, W., Sun, H., Liu, D., Zhang, L., Niu, X., Zhang, X., Meng, M., Yu, J., Liu, J., Han, Y., Shi, W., Zhang, D., Cao, S., Wei, Z., Cui, Y., Xia, Y., Zeng, H., Bao, K., Lin, L., Min, Y., Zhang, H., Miao, M., Tang, X., Zhu, Y., Sui, Y., Li, G., Sun, H., Yue, J., Sun, J., Liu, F., Zhou, L., Lei, L., Zheng, X., Liu, M., Huang, L., Song, J., Xu, C., Li, J., Ye, K., Zhong, S., Lu, B-R., He, G., Xiao, F., Wang, H-L., Zheng, H., Fei, Z., and Liu, Y.
    Nature Communications 4,  2640
    Full text...
  • Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening 2013

    Zhong, S., Fei, Z., Chen, Y.R., Zheng, Y., Huang, M., Vrebalov, J., McQuinn, R., Gapper, N., Liu, B., Xiang, J., Shao, Y., and Giovannoni, J.J.
    Nature Biotechnology 31,  154-159
    Full text...
  • The tomato genome sequence provides insights into fleshy fruit evolution 2012

    The Tomato Genome Consortium
    Nature 485,  635-641
    Full text...
  • The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions 2012

    Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L., 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., Wang, J., Li, Y., Fei, Z., and Xu, Y.
    Nature Genetics 45,  51-58
    Full text...
  • Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins 2014

    Pombo, M.A., Zheng, Y., Fernandez-Pozo, N., Dunham, V., Fei, Z., and Martin, G.B.
    Genome Biology 15,  492
    Full text...
  • Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity 2013

    Rosli, H. G., Zheng, Y., Pombo, M. A., Zhong, S., Bombarely, A., Fei, Z., Collmer, A., and Martin, G.B.
    Genome Biology 14,  R139
    Full text...
  • Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions 2013

    Castandet, B., Hotto, A.M., Fei, Z., and Stern, D.B.
    FEBS Lett. 587,  3096-3101
    Full text...
  • Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case 2012

    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.
    Proteomics 12,  761-774
    Full text...
  • Antagonistic Basic Helix-Loop-Helix/bZIP Transcription Factors Form Transcriptional Modules That Integrate Light and Reactive Oxygen Species Signaling in Arabidopsis 2013

    Chen, D.Q., Xu, G., Tang, W.J., Jing, Y.J., Ji, Q., Fei, Z.J. and Lin, R.C.
    Plant Cell 25,  1657-1673
    Full text...
  • The Transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells 2013

    Chen, Y.R., Zhong, S., Fei, Z., Hashimoto, Y., Xiang, J.Z., Zhang, S., and Blissard, G.W.
    J. Virol. 87,  6391-6405
    Full text...
  • Catabolism of L-methionine in the formation of sulfur and other volatiles in melon (Cucumis melo L.) fruit 2013

    Gonda, I., Lev, S., Bar, E., Sikron, N., Portnoy, V., Davidovich-Rikanati, R., Burger, J., Schaffer, A.A., Tadmor, Y., Giovannonni, J.J., Huang, M.Y., Fei, Z.J., Katzir, N., Fait, A., and Lewinsohn, E.
    Plant J. 74,  458-472
    Full text...
  • A snapshot of the emerging tomato genome sequence 2009

    The Tomato Genome Consortium
    The Plant Genome 2,  78-92
    Full text...
  • Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit 2013

    Grassi, S., Piro, G., Lee, J.M., Zheng, Y., Fei, Z., Dalessandro, G., Giovannoni, J.J., and Lenucci, M.S.
    BMC Genomics 14,  781
    Full text...
  • Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape 2013

    Hou, H.M., Li, J., Gao, M., Singer, S.D., Wang, H., Mao, L.Y., Fei, Z.J., and Wang, X.P.
    PLoS ONE 8,  e59358
    Full text...
  • Genome-wide identification and analysis of the SBP-box family genes in apple (Malus x domestica Borkh.) 2013

    Li, J., Hou, H.M., Li, X.Q., Xiang, J., Yin, X.J., Gao, H., Zheng, Y., Bassett, C.L., and Wang, X.P.
    Plant Physiol. Bioch. 70,  100-114
    Full text...
  • Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus x domestica Borkh.) 2013

    Li, X.Q., Guo, R.R., Li, J., Singer, S.D., Zhang, Y.C., Yin, X.J., Zheng, Y., Fan, C.H., and Wang, X.P.
    Plant Physiol. Bioch. 71,  268-282
    Full text...
  • Catalyzing plant science research with RNA-seq. 2013

    Martin, L.B.B., Fei, Z.J., Giovannoni, J.J., and Rose, J.K.C.
    Frontiers in Plant Science 4,  66
    Full text...
  • Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum 2013

    Melo, J.O., Lana, U.G.P., Pineros, M.A., Alves, V.M.C., Guimaraes, C.T., Liu, J.P., Zheng, Y., Zhong, S.L., Fei, Z.J., Maron, L.G., Schaffert, R.E., Kochian, L.V., and Magalhaes, J.V .
    Plant J. 73,  276-288
    Full text...
  • Integrative Analysis of miRNA and mRNA Profiles in Response to Ethylene in Rose Petals during Flower Opening 2013

    Pei, H.X., Ma, N., Chen, J.W., Zheng, Y., Tian, J., Li, J., Zhang, S., Fei, Z.J., and Gao, J.P.
    PLoS ONE 8,  e64290
    Full text...
  • An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals 2013

    Pei, H.X., Ma, N., Tian, J., Luo, J., Chen, J.W., Li, J., Zheng, Y., Chen, X., Fei, Z.J., and Gao, J.P.
    Plant Physiol. 163,  775-791
    Full text...
  • A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity 2013

    Qi, J.J., Liu, X., Shen, D., Miao, H., Xie, B. Y., Li, X. X., Zeng, P., Wang, S. H., Shang, Y., Gu, X. F., Du, Y. C., Li, Y., Lin, T., Yuan, J. H., Yang, X. Y., Chen, J. F., Chen, H. M., Xiong, X. Y., Huang, K., Fei, Z. J., Mao, L. Y., Tian, L., Stadler, T., Renner, S. S., Kamoun, S., Lucas, W. J., Zhang, Z. H., and Huang, S. W.
    Nature Genetics 45,  1510–1515
    Full text...
  • RadishBase: A database for genomics and genetics of radish 2013

    Shen, D., Sun, H.H., Huang, M.Y., Zheng, Y., Li, X.X., and Fei, Z.J.
    Plant Cell Physiol. 54,  e3
    Full text...
  • Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.) 2013

    Shen, D., Sun, H.H., Huang, M.Y., Zheng, Y., Qiu, Y., Li, X.X., and Fei, Z.J.
    BMC Genomics 14,  721
    Full text...
  • Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development 2013

    Wang, Y.Q., Yang, Y., Fei, Z.J., Yuan, H., Fish, T., Thannhauser, T.W., Mazourek, M., Kochian, L.V., Wang, X.W., and Li, L.
    Journal of Experimental Botany 64,  949-961
    Full text...
  • Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress 2013

    Xu, Y.J., Gao, S., Yang, Y.J., Huang, M.Y., Cheng, L.N., Wei, Q., Fei, Z.J., Gao, J.P., and Hong, B.
    BMC Genomics 14,  662
    Full text...
  • A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters 2012

    Chen, Y.R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J., and Fei, Z.
    Plant Methods 8,  41
    Full text...
  • Characterization of erysiphe necator-responsive genes in Chinese wild Vitis quinquangularis 2012

    Gao, M., Niu, J., Zhao, S.P., Jiao, C., Xu, W.R., Fei, Z.J., and Wang, X.P
    Int. J. Mol. Sci. 13,  11497-1151
    Full text...
  • Identification of genes differentially expressed in grapevine associated with resistance to Elsinoe ampelina through suppressive subtraction hybridization 2012

    Gao, M., Wang, Q., Wan, R., Fei, Z.J., and Wang, X.P.
    Plant Physiol. Bioch. 58,  253-268
    Full text...
  • Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum 2012

    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.
    Molecular Genetics and Genomics 287,  495-513
    Full text...
  • 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. 2012

    Lee, J.M., Joung, J.G., McQuinn, R., Chung, M.Y., Fei, Z., Tieman, D., Klee, H., and Giovannoni, J.
    The Plant J. 70,  191-204
    Full text...
  • 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 2012

    Levi, A., Thies, J.A., Wechter, W.P., Harrison, H.F., Simmons, A.M., Reddy, U.K., Nimmakayala, P., and Fei, Z.
    Genetic Resources and Crop Evolution 1-14
    Full text...
  • Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation 2012

    Li, R.G., Gao, S., Hernandez, A.G., Wechter, W.P., Fei, Z.J., and Ling, K.S.
    PLoS ONE 7
    Full text...
  • Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1) 2012

    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.
    Plant Mol. Biol. 79,  315-331
    Full text...
  • Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape 2012

    Zhang, Y.C., Gao, M., Singer, S.D., Fei, Z.J., Wang, H., and Wang, X.P
    PLoS ONE 7,  e44465
    Full text...
  • Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily 2012

    Zhang, Y.C., Mao, L.Y., Wang, H., Brocker, C., Yin, X.J., Vasiliou, V., Fei, Z.J., and Wang, X.P.
    PLoS ONE 7,  e32153
    Full text...
  • Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis) 2011

    Zhou, X., Fei, Z., Thannhauser, T.W., and Li, L.
    BMC Plant Biol. 11,  169
    Full text...
  • Regulatory control of high levels of carotenoid accumulation in potato tubers 2011

    Zhou, X.J., Mcquinn, R., Fei, Z.J., Wolters, A.M.A., Van Eck, J., Brown, C., Giovannoni, J.J., and Li, L .
    Environ. 34,  1020-1030
    Full text...
  • High-throughput Illumina strand-specific RNA sequencing library preparation 2011

    Zhong, S., Joung, J.G., Zheng, Y., Chen, Y.R., Liu, B., Shao, Y., Xiang, J.Z., Fei , Z., and Giovannoni, J.J.
    Cold Spring Harb. Protoc. 2011,  940-949
    Full text...
  • The charophycean green algae provide insights into the early origins of plant cell walls 2011

    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.
    Plant J. 68,  201-211
    Full text...
  • iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences 2011

    Zheng, Y., Zhao, L., Gao, J., and Fei, Z.
    BMC Bioinformatics 12,  453
    Full text...
  • Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development 2011

    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.
    Plant J. 68,  999-1013
    Full text...
  • 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 2011

    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.
    Plant Physiol. 157,  405-425
    Full text...
  • Transcriptional profiling of watermelon during its incompatible interaction with Fusarium oxysporum f. sp niveum 2011

    Lu, G.Y., Guo, S.G., Zhang, H.Y., Geng, L.H., Song, F.M., Fei, Z.J., and Xu, Y.
    Eur. J. Plant Pathol. 131,  585-601
    Full text...
  • RNA-Seq improves annotation of protein-coding genes in the cucumber genome 2011

    Li, Z., Zhang, Z.H., Yan, P.C., Huang, S.W., Fei, Z.J., and Lin, K.
    BMC Genomics 12,  540
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  • Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles 2011

    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.
    BMC Genomics 12,  454
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  • Genomic and functional genomic resources of melon 2011

    Fei, Z., and Liu, Y.
    Genetics, Genomics and Breeding of Cucurbits (Wang, Y.-H., Behera, T.K. and Kole, C. eds.). Science Publishers,  286-308
    Full text...
  • Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. 2011

    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.
    Nucleic Acids Res. 39,  D1156-1163
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  • Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation 2011

    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.
    Plant Mol. Biol. 76,  1-18
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  • Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon 2011

    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.
    BMC Genomics 12,  252
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  • High-frequency oligonucleotides in watermelon expressed sequenced tag-unigenes are useful in producing polymorphic polymerase chain reaction markers among watermelon genotypes. 2010

    Levi, A., Wechter, W.P., Harris, K.R., Davis, A.R., and Fei, Z.J.
    Journal of the American Society for Horticultural Science 135,  369-378
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  • A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes 2010

    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.
    Theoretical and Applied Genetics 121,  511-533
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  • Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types 2010

    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.
    BMC Genomics 11,  384
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  • Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato 2010

    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.
    Journal of Experimental Botany 61,  3563-3575
    Full text...
  • Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening 2010

    Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavini, S., Costa, G., Fei, Z.J., and Giovannoni, J.
    BMC Plant Biol. 10,  229
    Full text...
  • Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis 2009

    Rhee, J.K., Joung, J.G., Chang, J.H., Fei, Z., and Zhang, B.T.
    BMC Genomics 10,  S3-S29
    Full text...
  • Plant MetGenMAP: an integrative analysis system for plant systems biology 2009

    Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni , J.J., and Fei, Z.
    Plant Physiol. 151,  1758-1768
    Full text...
  • Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model 2009

    Joung, J.G., and Fei, Z.
    Bioinformatics 25,  387-393
    Full text...
  • Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information 2009

    Joung, J.G., and Fei, Z.J.
    BMC Bioinformatics 10,  Suppl 1, S34
    Full text...
  • lavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. 2009

    Mathieu, S., Cin, V.D., Fei, Z.J., Li, H., Bliss, P., Taylor, M.G., Klee, H.J., and Tieman, D.M.
    Journal of Experimental Botany 60,  325-337
    Full text...
  • The genome of the cucumber, Cucumis sativus L 2009

    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.
    Nature Genetics 41,  1275-U1229
    Full text...
  • Identification and characterisation of resistance gene analogues from wild Chinese Vitis species 2008

    Wang, X.P., Wang, Y.J., and Fei, Z.J.
    J. Hortic. Sci. Biotech. 83,  345-350
    Full text...
  • Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions. 2009

    Dal Cin, V., Kevany, B., Fei, Z.J., and Klee, H.J.
    Theor. Appl. Genet. 119,  1183-1192
    Full text...
  • Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.) 2008

    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.
    Theor. Appl. Genet. 117,  927-933
    Full text...
  • Small RNAs in tomato fruit and leaf development 2008

    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.
    B.B.A.-Gene Regul. Mech. 1779,  99-107
    Full text...
  • Identification of salt stress regulated genes in tomato seedlings by suppression subtracted hybridization and microarray analysis 2007

    Ouyang, B., Yang, T., Li, H., Zhang, L., Zhang, Y., Zhang, J., Fei, Z., and Ye, Z.
    Journal of Experimental Botany 58,  507-520
    Full text...
  • MicroTom 2007

    Dan, Y., Fei Z., and Rothan, C.
    Genes, Genomes and Genomics 1,  167-179
    Full text...
  • Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. 2006

    Fei, Z., Tang, X., Alba, R., and Giovannoni, J.
    Nucleic Acids Research 34,  D766
    Full text...
  • Impact of intestinal colonization and invasion on the E. histolytica transcriptome 2006

    Gilchrist, C., Houpt, E., Trapaidze, N., Fei, Z., Crasta, O., Asgharpour, A., Evans, C., Martino-Catt, C., Baba, D., Stroup, S., Hamano, S., Ehrenkaufer, G., Okada, O., Singh, U., Nozaki, T., Mann, B., and Petri Jr, W.
    Mol. Biochem. Parasit. 147,  163-176
    Full text...

Intern Projects

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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Interns

Research Utilization

Computational Bioinformatics and Databases

The development of high throughput technologies has given rise to a wealth of genome-wide data, including DNA sequence, transcriptome, proteome, and metabolome data from samples representing environmental, genetic, and evolutionary diversity. It remains a major challenge to digest the massive amounts of data and use them to make hypotheses and predict phenotypes. To address this challenge, 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.

Using next-generation sequencing for crop improvement. The Fei group is using next-generation sequencing (NGS) technologies to investigate genomes, epigenomes and transcriptomes of several economically important crops including tomato, cucurbits, apple, sweetpotato and kiwifruit, and to perform global virus survey of crops such as tomato and sweetpotato. They are developing new computational tools to process and analyze the ultra-large scale data generated by NGS platforms.

Computational tools for omics data analysis. Several computational tools/pipelines have been developed to mine and analyze large scale genomics datasets. Here is a list of tools developed so far:

  • Plant MetGenMAP – a web-based tool for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways.
  • iAssembler – A de novo assembly package for transcriptome sequences generated using 454 or Sanger platforms
  • iTAK – A package to identify and classify plant transcription factors and protein kinases.

Inferring gene regulatory networks. Plant phenotypes are the product of gene expression programs involving the regulated transcription of thousands of genes. A gene regulatory network describes the interaction of transcription factors with their target genes in response to development or environmental perturbations. New algorithms are being developed to infer gene regulatory networks by integrating datasets from different sources, including gene expression data, metabolomics data, promoter sequences, and microRNA information.

Databases. Making genome-scale data available to users is critical for capturing value from large and diverse datasets.

    • Tomato Functional Genomics Database archives publicly available gene expression, metabolite profile and small RNA information. The database also includes a set of query interfaces and computational tools that allow users to mine, analyze, and integrate tomato expression, metabolite and small RNA datasets.
    • Tomato Epigenome Database presents single-base resolution methylomes of tomato.
    • Cucurbit Genomics Database is a web-accessible data resource for genomics and functional genomics analysis of cucurbit species, including cucumber, melon, watermelon, and pumpkin. Currently the database contains the genome and EST sequences, small RNAs, and genetic maps for all cucurbit species.
    • RadishBase is a genomics and genetics database of radish. Currently the database contains radish mitochondrial genome sequences, EST sequences and annotations, biochemical pathways, EST-derived single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, and genetic maps

Collaboration and Consulting Opportunities

Collaborations and Consulting

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