Zhangjun Fei

Associate Professor
Zhangjun Fei
zf25@cornell.edu
Office/Lab: 227
Phone: 607-254-3234
Office/Lab: 227
Email: zf25@cornell.edu
Office Phone: 607-254-3234
Research Areas:    Genomics and Systems
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.

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.

Click the links to return to the Intern FacultyInternship Program,  Apply for an Internship pages on the BTI website.
Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development
2016
Author(s):Pattison, R.J., Csukasi, F., Zheng, Y., Fei, Z., van der Knaap, E., Catala, C
Plant Physiology
10.1104
pp.​15.​00287
View
A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.
2016
Author(s):Worley, J. N., Pombo, M. A., Zheng, Y., Dunham, D. M., Myers, C. R., Fei, Z., Martin, G.
BMC Genomics
10.1186,
s12864-016-2534-4
View
Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca ̗ V. vinifera) cv. Kyoho flowers
2015
Author(s):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
View
A ‰€œgolden‰€ SNP in CmOr governs fruit flesh color of melon (Cucumis melo)
2015
Author(s):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
View
Complete Genome Sequence of a Novel Genotype of Squash Mosaic Virus Infecting Squash in Spain
2015
Author(s):Li, R., Gao, S., Berendsen, S., Fei, Z., and Ling, K-S.
Genome Announc.
3(1)
e01583-14
View
Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca × V. vinifera) cv. Kyoho flowers
2015
Author(s):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
View
A “golden” SNP in CmOr governs fruit flesh color of melon (Cucumis melo)
2015
Author(s):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
View
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
Author(s):Chen, S., Kim, C., Lee, J.M., Lee, H.A., Fei, Z., Wang, L., and Apel, K.
Plant Cell Environ.
Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf
2015
Author(s):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
View
Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits
2015
Author(s):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
View
Identification of multiple salicylic acid-binding proteins using two high throughput screens. Front
2015
Author(s):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.
Plant Sci.
5,
777
View
Identification of multiple salicylic acid-binding proteins using two high throughput screens
2015
Author(s):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
View
Transcriptome responses of the host, Trichoplusia ni, to infection by the baculovirus, Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV)
2014
Author(s):Chen, Y. R., Zhong, S., Fei, Z., Gao, S., Zhang, S., Li, Z., Wang, P., and Blissard, G.W.
J. Virol.
88
13781-13797
View
A Zinc Finger Protein Regulates Flowering Time and Abiotic Stress Tolerance in Chrysanthemum by Modulating Gibberellin Biosynthesis
2014
Author(s):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
View
Evolutionary and expression analyses of basic zipper transcription factors in the highly homozygous model grape PN40024 (Vitis vinifera L.)
2014
Author(s):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
View
The genome of the stress-tolerant wild tomato species Solanum pennellii
2014
Author(s):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
View
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
Author(s):Pombo, M.A., Zheng, Y., Fernandez-Pozo, N., Dunham, V., Fei, Z., and Martin, G.B.
Genome Biology
15,
492
The PH gene determines fruit acidity and contributes to the evolution of sweet melons
2014
Author(s):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
View
The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, 46, 1034-1038
2014
Author(s):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
View
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
Author(s):Pombo, M.A., Zheng, Y., Fernandez-Pozo, N., Dunham, V., Fei, Z., and Martin, G.B.
Genome Biology
15,
492
View
Draft genome of the kiwifruit Actinidia chinensis
2013
Author(s):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
View
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
2013
Author(s):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
View
Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity
2013
Author(s):Rosli, H. G., Zheng, Y., Pombo, M. A., Zhong, S., Bombarely, A., Fei, Z., Collmer, A., and Martin, G.B.
Genome Biology
14,
R139
View
Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions
2013
Author(s):Castandet, B., Hotto, A.M., Fei, Z., and Stern, D.B.
FEBS Lett.
587,
3096-3101
View
Antagonistic Basic Helix-Loop-Helix/bZIP Transcription Factors Form Transcriptional Modules That Integrate Light and Reactive Oxygen Species Signaling in Arabidopsis
2013
Author(s):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
View
The Transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells
2013
Author(s):Chen, Y.R., Zhong, S., Fei, Z., Hashimoto, Y., Xiang, J.Z., Zhang, S., and Blissard, G.W.
J. Virol.
87,
6391-6405
View
Catabolism of L-methionine in the formation of sulfur and other volatiles in melon (Cucumis melo L.) fruit
2013
Author(s):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
View
Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape
2013
Author(s):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
View
Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum
2013
Author(s):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
View
Integrative Analysis of miRNA and mRNA Profiles in Response to Ethylene in Rose Petals during Flower Opening
2013
Author(s):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
View
An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals
2013
Author(s):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
View
A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity
2013
Author(s):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
View
RadishBase: A database for genomics and genetics of radish
2013
Author(s):Shen, D., Sun, H.H., Huang, M.Y., Zheng, Y., Li, X.X., and Fei, Z.J.
Plant Cell Physiol.
54,
e3
View
Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.)
2013
Author(s):Shen, D., Sun, H.H., Huang, M.Y., Zheng, Y., Qiu, Y., Li, X.X., and Fei, Z.J.
BMC Genomics
14,
721
View
Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development
2013
Author(s):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
View
Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress
2013
Author(s):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
View
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology, 31, 154-159
2013
Author(s):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
View
2013. Catabolism of L-methionine in the formation of sulfur and other volatiles in melon (Cucumis melo L.) fruit
2013
Author(s):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
View
Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit
2013
Author(s):Grassi, S., Piro, G., Lee, J.M., Zheng, Y., Fei, Z., Dalessandro, G., Giovannoni, J.J., and Lenucci, M.S.
BMC Genomics
14,
781
View
Catalyzing plant science research with RNA-seq.
2013
Author(s):Martin, L.B.B., Fei, Z.J., Giovannoni, J.J., and Rose, J.K.C.
Frontiers in Plant Science
4,
66
View
Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity.
2013
Author(s):Rosli, H. G., Zheng, Y., Pombo, M. A., Zhong, S., Bombarely, A., Fei, Z., Collmer, A., and Martin, G.B.
Genome Biology
14,
R139
View
Characterization of erysiphe necator-responsive genes in Chinese wild Vitis quinquangularis
2012
Author(s):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
View
Identification of genes differentially expressed in grapevine associated with resistance to Elsinoe ampelina through suppressive subtraction hybridization
2012
Author(s):Gao, M., Wang, Q., Wan, R., Fei, Z.J., and Wang, X.P.
Plant Physiol. Bioch.
58,
253-268
View
Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum
2012
Author(s):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
View
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
Author(s):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
View
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
Author(s):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
View
Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation
2012
Author(s):Li, R.G., Gao, S., Hernandez, A.G., Wechter, W.P., Fei, Z.J., and Ling, K.S.
PLoS ONE
7
View
Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1)
2012
Author(s):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
View
Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape
2012
Author(s):Zhang, Y.C., Gao, M., Singer, S.D., Fei, Z.J., Wang, H., and Wang, X.P
PLoS ONE
7,
e44465
View
Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily
2012
Author(s):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
View
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
2012
Author(s):Chen, Y.R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J., and Fei, Z.
Plant Methods
8,
41
View
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
Author(s):Lee, J.M., Joung, J.G., McQuinn, R., Chung, M.Y., Fei, Z., Tieman, D., Klee, H., and Giovannoni, J.
The Plant Journal
70,
191-204
View
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
2012
Author(s):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
View
Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case
2012
Author(s):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
View
Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis)
2011
Author(s):Zhou, X., Fei, Z., Thannhauser, T.W., and Li, L.
BMC Plant Biol.
11,
169
View
The charophycean green algae provide insights into the early origins of plant cell walls
2011
Author(s):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
View
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
2011
Author(s):Zheng, Y., Zhao, L., Gao, J., and Fei, Z.
BMC Bioinformatics
12,
453
View
Transcriptional profiling of watermelon during its incompatible interaction with Fusarium oxysporum f. sp niveum
2011
Author(s):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
View
RNA-Seq improves annotation of protein-coding genes in the cucumber genome
2011
Author(s):Li, Z., Zhang, Z.H., Yan, P.C., Huang, S.W., Fei, Z.J., and Lin, K.
BMC Genomics
12,
540
View
Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles
2011
Author(s):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
View
Genomic and functional genomic resources of melon
2011
Author(s):Fei, Z., and Liu, Y.
Genetics, Genomics and Breeding of Cucurbits td>
(Wang, Y.-H., Behera, T.K. and Kole, C. eds.). Science Publishers,
286-308
View
Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.
2011
Author(s):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
View
Regulatory control of high levels of carotenoid accumulation in potato tubers
2011
Author(s):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
View
Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development
2011
Author(s):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
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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
Author(s):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
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Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation
2011
Author(s):Matas, A.J., Yeats, T.H., Buda, G.J., Zheng, Y., Chatterjee, S., Tohge, T., Ponnala, L., Adato, A., Aharoni, A., Stark, R., Fernie, A.R., Fei, Z., Giovannoni, J.J., and Rose, J.K.
Plant Cell
23,
3893-3910
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Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
2011
Author(s):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 Research
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
Author(s):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
Author(s):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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Unexpected diversity of chloroplast noncoding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome G3
2011
Author(s):Hotto, A.M., Schmitz, R.J., Fei, Z., Ecker, J.E., and Stern, D.B.
G3 (Bethesda)
1(7),
559–570
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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
Author(s):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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Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
2010
Author(s):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
Author(s):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
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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
Author(s):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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Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
2010
Author(s):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 Biology
10,
229
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Interdependence of threonine, methionine and isoleucine metabolism in plants: accumulation and transcriptional regulation under abiotic stress
2010
Author(s):Joshi, V., Joung, J.G., Fei, Z. and Jander, G.
Amino Acids
39,
933-947
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Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis
2009
Author(s):Rhee, J.K., Joung, J.G., Chang, J.H., Fei, Z., and Zhang, B.T.
BMC Genomics
10,
S3-S29
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Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model
2009
Author(s):Joung, J.G., and Fei, Z.
Bioinformatics
25,
387-393
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Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
2009
Author(s):Joung, J.G., and Fei, Z.J.
BMC Bioinformatics
10,
Suppl 1, S34
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lavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition.
2009
Author(s):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
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The genome of the cucumber, Cucumis sativus L
2009
Author(s):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
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Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions.
2009
Author(s):Dal Cin, V., Kevany, B., Fei, Z.J., and Klee, H.J.
Theor. Appl. Genet.
119,
1183-1192
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Plant MetGenMAP: an integrative analysis system for plant systems biology
2009
Author(s):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
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Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis
2009
Author(s):Marchive, C., Yehudai-Resheff, S., Germain, A., Fei, Z.J., Jiang, X.S., Judkins, J., Wu, H., Fernie, A.R., Fait, A., and Stern, D.B.
Plant Physiology
151,
905-924
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Identification and characterisation of resistance gene analogues from wild Chinese Vitis species
2008
Author(s):Wang, X.P., Wang, Y.J., and Fei, Z.J.
J. Hortic. Sci. Biotech.
83,
345-350
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Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.)
2008
Author(s):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,
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Small RNAs in tomato fruit and leaf development
2008
Author(s):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
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Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features
2008
Author(s):Zimmer, S.L., Fei, Z.J., and Stern, D.B.
Genetics
179,
125-136
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Identification of salt stress regulated genes in tomato seedlings by suppression subtracted hybridization and microarray analysis
2007
Author(s):Ouyang, B., Yang, T., Li, H., Zhang, L., Zhang, Y., Zhang, J., Fei, Z., and Ye, Z.
Journal of Experimental Botany
58,
507-520
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Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools.
2006
Author(s):Fei, Z., Tang, X., Alba, R., and Giovannoni, J.
Nucleic Acids Research
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D766
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Impact of intestinal colonization and invasion on the E. histolytica transcriptome
2006
Author(s):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
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Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. Nucleic Acids Research, 34, D766
2006
Author(s):Fei, Z., Tang, X., Alba, R., and Giovannoni, J.
Nucleic Acids Research
34,
D766
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Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis).
Author(s):Zhang, J., Yuan, H., Fei, Z., Pogson, B.J., Zhang, L., and L., Li.
Planta
DOI 10.1007/s00425-015-2262-z
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