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
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.

Lab Members
In the News

  • New CRISPR database to catalyze collaborations

    January 30th, 2019
    Recently developed gene editing tools like CRISPR/Cas enable plant scientists to figure out the functions of myriad plant genes. While these studies could eventually lead to the creation of crops with improved traits like increased disease resistance or higher yield, researchers first need a good way to keep track of the increasingly large amounts of […] Read more »

  • Orange is the new white: New sweetpotato data is something to be thankful for

    November 2nd, 2018
    The genome sequences of I. trifida and I. triloba can be used as robust references to facilitate sweetpotato breeding. The genomic resources developed in this study set the stage for increased rates of genetic gains for key traits such as yield, resistance to disease, and high beta-carotene. Read more »

  • Back to our roots: Insights from genomes of a plant-associated fungus and its bacterial endosymbionts

    October 25th, 2018
    In an article published this month in the journal New Phytologist, researchers at the Boyce Thompson Institute and the National Center for Genome Resources describe the genome sequences (DNA sequences), of the fungus Diversispora epigaea (formerly known as Glomus versiforme) and its endosymbionts – beneficial bacteria that live inside its cells. D. epigaea is a […] Read more »
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.

Internship Program | Projects & Faculty | Apply for an Internship
Interns
Publications
Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency
2018.
Zhang, Z., Zheng, Y., Ham, B., Zhang, S., Fei, Zhangjun, Lucas, W.J.
Journal of Integrative Plant Biology.
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Transcriptomic and functional analysis of cucumber (Cucumis sativus L.) fruit phloem during early development
2018.
Sui, X., Nie, J., Li, X., Scanlon, M.J., Zhang, C., Zheng, Y., Ma, S., Shan, N., Fei, Zhangjun, Turg…
The Plant Journal.
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Global Analysis of Baculovirus Autographa californica Multiple Nucleopolyhedrovirus Gene Expression in the Midgut of the Lepidopteran Host Trichoplusia ni
2018.
Shrestha, A., Bao, K., Chen, Y., Chen, W., Wang, P., Fei, Zhangjun and Blissard, Gary
Journal of Virology.
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Tomato stigma exsertion induced by high temperature is associated with the jasmonate signalling pathway
2018.
Pan, C., Yang, D., Zhao, X., Jiao, C., Yan, Y., Lamin‐Samu, A.T., Wang, Q., Xu, X., Fei, Zhangjun …
Plant, Cell and Environment.
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Global Analysis of Baculovirus Autographa californica Multiple Nucleopolyhedrovirus Gene Expression in the Midgut of the Lepidopteran Host Trichoplusia ni
2018.
Shrestha, A., Bao, K., Chen, Y., Chen, W., Wang, P., Fei, Zhangjun and Blissard, G.W.
Journal of Virology.
92
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Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening
2018.
Lü, P., Yu, S., Zhu, N., Chen, Y., Zhou, B., Pan, Y., Tzeng, D., Fabi, J.P., Argyris, J., Garcia-M…
Nature Plants.
4
:
784–791
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Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement
2018.
Wu, S,, Lau, K.H., Cao, Q., Hamilton, J.P., Sun, H., Zhou, C., Eserman, L., Gemenet, D.C., Olukolu, …
Nature Communications.
9
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Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance
2018.
Lau, K.H., Herrera, M.R., Crisovan, E., Wu, S., Fei, Zhangjun, Khan, M.A., Buell, R.C., Gemenet, D.C…
Plant Direct.
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1–13
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MaMADS2 repression in banana fruits modifies hormone synthesis and signalling pathways prior to climacteric stage
2018.
Yakir, E., Fei, Zhangjun, Sela, N., Xu, Y., Singh, V., Dagar, A., Joshi, J.R., Müller, M., Munné-…
BMC Plant Biology.
18
:
1471–2229
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A high‐quality chromosome‐level genome assembly of a generalist herbivore, Trichoplusia ni
2018.
Chen, W, Yang, X., Tetreau, G., Song, X., Coutu, C. Hegedus, D., Blissard, G., Fei, Zhangjun and Wan…
Molecular Ecology Resources.
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Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death
2018.
Guo, L., Sun, X., Li, Z., Wang, Y., Fei, Zhangjun, Jiao, J., Feng, J., Cui, D., Feng, X., Ding, Y., …
Plant Biotechnology Journal.
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Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato
2018.
Yazdani, M., Sun, Z., Yuan, H., Zeng, S., Thannhauser, T. W., Vrebalov, J., Ma, Q., Xu, Y., Fei, Zha…
Plant Biotechnology Journal.
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Elucidation of the Mechanisms of Long-Distance mRNA Movement in a Nicotiana benthamiana /Tomato Heterograft System
2018.
Xia, C., Zheng, Y., Huang, J., Zhou, X., Li, R., Zha, M., Wang, S., Huang, Z., Lan, H., Turgeon, R.,…
Plant Physiology.
177
:
745–758
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Tecia solanivora infestation increases tuber starch accumulation inPastusa Suprema potatoes
2018.
Kumar, P., Garrido, E., Zhao, K., Zheng, Y., Alseekh, S., Vargas-Ortiz, E., Fernie, A. R., Fei, Zhan…
Journal of Integrative Plant Biology.
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Maternal Inheritance of a Single Somatic Animal Cell Displayed by the Bacteriocyte in the Whitefly Bemisia tabaci
2018.
Luan, J., Sun, X., Fei, Zhangjun, Douglas, Angela E.
Current Biology.
28
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459–465.e3
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The Secretome and N-Glycosylation Profiles of the Charophycean Green Alga, Penium margaritaceum, Resemble Those of Embryophytes
2018.
Ruiz-May, E., Sorensen, Iben, Fei, Zhangjun, Zhang, Sheng, Domozych, D. S., Rose, Jocelyn
Proteomes.
6
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14–14
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Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL
2018.
Branham, S. E., Levi, A., Katawczik, M., Fei, Zhangjun, Wechter, W. P.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
131
:
829–837
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Differential metabolism of L–phenylalanine in the formation of aromatic volatiles in melon (Cucumis melo L.) fruit
2018.
Gonda, I., Davidovich-Rikanati, R., Bar, E., Lev, S., Jhirad, P., Meshulam, Y., Wissotsky, G., Portn…
Phytochemistry.
148
:
122–131
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Deciphering Genetic Factors that Determine Melon Fruit-Quality Traits Using RNA-Seq-Based High-Resolution QTL and eQTL Mapping
2018.
Galpaz, N., Gonda, I., Shem-Tov, D., Barad, O., Tzuri, G., Lev, S., Fei, Zhangjun, Xu, Y., Lombardi,…
The Plant Journal.
94
:
169–191
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High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening
2018.
Shinozaki, Y., Nicolas, P., Fernandez-Pozo, N., Ma, Q., Evanich, D. J., Shi, Y., Xu, Y., Zheng, Y., …
Nature Communications.
9
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