Zhangjun Fei

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
Affiliations: Adjunct Professor / Section of Plant Pathology & Plant-Microbe Biology / School of Integrative Plant Science / Cornell University
Graduate Fields: Plant Pathology & Plant-Microbe Biology; Plant Biology
Research Areas:    Genomics and Systems
Google Scholar ID
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.

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Development of online databases to facilitate data distribution, analysis, mining and integration

Development of computational tools for omics data analysis

  • 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.
  • VirusDetect – An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.

Application of NGS technologies and bioinformatics in crop improvement

During the past several years, significant progresses have been made regarding the DNA sequencing technologies. As a result, several next-generation sequencing (NGS) platforms, such Illumina HiSeq, have received wide applications due to their high throughput and low cost. We are interested in using NGS technologies to investigate genomes, epigenomes and transcriptomes of several economically important crops including tomato, cucurbits, sweetpotato, and fruit tree crops, to facilitate the understanding of the evolution and regulatory networks of important agronomical traits. We are also using NGS technologies to perform large-scale virus survey for crops like sweet potato and tomato, in an effort to understand global virus diversity, distribution and evolution in important food crops.

Inferring gene regulatory networks

Living cells are the product of gene expression programs involving regulated transcription of thousands of genes. How a collection of transcriptional regulatory factors associates with genes during specific biological processes or under specific environmental conditions can be described as a gene regulatory network. We are interested in developing new algorithms to infer gene regulatory networks by integrating datasets from various different sources, including gene expression data, metabolomics data, promoter sequences, and microRNA information.

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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
Horizontally transferred genes as RNA interference targets for aphid and whitefly control
2022.
Feng, H., Chen, W., Hussain, S., Shakir, S., Tzin, V., Adegbayi, F., Ugine, T., Fei, Zhangjun, Jander, Georg
Plant Biotechnol J..
:
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Domestication and selection footprints in Persian walnuts (Juglans regia)
2022.
Luo, X., Zhou, H., Cao, D., Yan, F., Chen, P., Wang, J., Woeste, K., Chen, X., Fei, Zhangjun, An, H., Malvolti, M., Ma, K., Liu, C., Ebrahimi, A., Qiao, C., Ye, H., Li, M., Lu, Z., Xu, J., Cao, S., Zhao, P.
PLoS Genet..
18
:
e1010513
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Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.
2022.
Tu, X., Ren, S., Shen, W., Li, J., Li, Y., Li, C., Li, Y., Zong, Z., Xie, W., Grierson, D., Fei, Zhangjun, Giovannoni, James J., Li, P., Zhong, S.
Nat Commun..
13
:
7632
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CuGenDBv2: an updated database for cucurbit genomics.
2022.
Yu, J., Wu, S., Sun, H., Wang, X., Tang, X., Guo, S., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., McGregor, C., Renner, S.S., Branham, S., Kousik, C., Wechter, W.P., Levi, A., Grumet, R., Zheng, Y., Fei, Zhangjun
Nucleic Acids Res..
:
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Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae
2022.
Zhang, N., Hecht, C., Sun, X., Fei, Zhangjun, Martin, Gregory B.
Plant Physiol..
190
:
1334–1348
View
Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress.
2022.
Nicolas, P., Shinozaki, Y., Powell, A., Philippe, G., Snyder, S.I., Bao, K., Zheng, Y., Xu, Y., Courtney, L., Vrebalov, J., Casteel, C.L., Mueller, Lukas A., Fei, Zhangjun, Giovannoni, James J., Rose, J.K.C., Catalá, Carmen
Plant Physiol..
:
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Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors
2022.
Chen, M., Guo, L., Ramakrishnan, M., Fei, Zhangjun., Vinod, K.K., Ding, Y., Jiao, C., Gao, Z., Zha, R., Wang, C., Gao, Z., Yu, F., Ren, G., Wei, Q.
The Plant Cell.
34
:
3577–3610
View
Cellular differentiation, hormonal gradient, and molecular alternation between the division zone and the elongation zone of bamboo internodes
2022.
Guo, L., Wang, C., Chen, J., Ju, Y., Yu, F., Jiao, C., Fei, Zhangjun, Ding, Y., Wei, Q.
Physiologia Plantarum.
174
:
e13744
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An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion
2022.
Ban, S., El-Sharkawy, I., Zhao, J., Fei, Zhangjun, Xu, K.
The Plant Journal.
111
:
1609–1625
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Genome Sequencing of up to 6,000-Year-Old Citrullus Seeds Reveals Use of a Bitter-Fleshed Species Prior to Watermelon Domestication
2022.
Pérez-Escobar, O.A., Tusso, S., Przelomska, N.A.S., Wu, S., Ryan, P., Nesbitt, M., Silber, M.V., Preick, M., Fei, Zhangjun, Hofreiter, M., Chomicki, G., Renner, S.S.
Molecular Biology and Evolution.
39
:
View
Long-Term Lacticaseibacillus rhamnosus GG Storage at Ambient Temperature in Vegetable Oil: Viability and Functional Assessments
2022.
Davachi, S.M., Dogan, B., Khazdooz, L., Zhang, S., Khojastegi, A., Fei, Zhangjun, Sun, H., Meletharayil, G., Kapoor, R., Simpson, K.W., Abbaspourrad, A.
Journal of Agricultural and Food Chemistry.
70
:
9399–9411
View
Chromosome-scale genome assemblies of wild tomato relatives Solanum habrochaites and Solanum galapagense reveal structural variants associated with stress tolerance and terpene biosynthesis
2022.
Yu, X., Qu, M., Shi, Y., Hao, C., Guo, S., Fei, Zhangjun, Gao, L.
Horticulture Research.
9
:
View
Graph pangenome captures missing heritability and empowers tomato breeding.
2022.
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L., Fang, Y., Wu, K., Zhang, J., Lyu, H., Lin, T., Gao, Q., Saha, S., Mueller, Lukas A., Fei, Zhangjun, Städler, T., Xu, S., Zhang, Z., Speed, D., Huang, S.
Nature.
606
:
527–534
View
Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance
2022.
Cao, K., Peng, Z., Zhao, X., Li, Y., Liu, K., Arus, P., Fang, W., Chen, C., Wang, X., Wu, J., Fei, Zhangjun , Wang, L.
BMC Biology.
20(1)
:
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Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields
2022.
Wang, L., Sun, X., Peng, Y., Chen, K., Wu, S., Guo, Y., Zhang, J., Yang, H., Jin, T., Wu, L., Zhou, X., Liang, B., Zhao, Z., Liu, D., Fei, Zhangjun, Bai, L.
15
:
1045–1058
View
Combined nature and human selections reshaped peach fruit metabolome
2022.
Cao, K., Wang, B., Fang, W., Zhu, G., Chen, C., Wang, X., Li, Y., Wu, J., Tang, T., Fei, Zhangjun, Luo, J., Wang, L.
Genome Biology.
23(1)
:
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Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication
2022.
Qing, Y., Zheng, Y., Mlotshwa, S., Smith, H.N., Wang, X., Zhai, X., van der Knaap, E., Wang, Y., Fei, Zhangjun
The Plant Journal.
110
:
1536–1550
View
The tomato yellow leaf curl virus C4 protein alters the expression of plant developmental genes correlating to leaf upward cupping phenotype in tomato.
2022.
Padmanabhan, C., Zheng, Y., Shamimuzzaman, M., Wilson, J.R., Gilliard, A., Fei, Zhangjun, Ling, K.S.
PLoS One.
17
:
e0257936
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A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity.
2022.
Powell, A.F., Feder, A., Li, J., Schmidt, M.H., Courtney, L., Alseekh, S., Jobson, E.M., Vogel, A., Xu, Y., Lyon, D., Dumschott, K., McHale, M., Sulpice, R., Bao, K., Lal, R., Duhan, A., Hallab, A., Denton, A.K., Bolger, M.E., Fernie, A.R., Hind, S.R., Mueller, Lukas A., Martin, Gregory B., Fei, Zhangjun, Martin, C., Giovannoni, James J., Strickler, S.R., Usadel, B.
Plant J..
110
:
1791–1810
View
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
2022.
Li, H., Wang, S., Chai, S., Yang, Z., Zhang, Q., Xin, H., Xu, Y., Lin, S., Chen, X., Yao, Z., Yang, Q., Fei, Zhangjun, Huang, S., Zhang, Z.
Nature Communications.
13
:
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