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.

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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.

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 & FacultyApply for an Internship
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
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
:
Comparative transcriptome analysis reveals networks of genes activated in the whitefly, Bemisia tabaci when fed on tomato plants infected with Tomato yellow leaf curl virus
2018.
Hasegawa, D. K., Chen, W., Zheng, Y., Kaur, N., Wintermantel, W. M., Simmons, A. M., Fei, Zhangjun, …
Virology.
513
:
52–64
TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton
2017.
Cox, K. L., Meng, F., Wilkins, K. E., Li, F., Wang, P., Booher, N. J., Carpenter, S. CD, Chen, L. Q.…
Nature Communications.
8
:
15588–15588
The Tomato Kinase Pti1 Contributes to Production of Reactive Oxygen Species in Response to Two Flagellin-Derived Peptides and Promotes Resistance to Pseudomonas syringae Infection
2017.
Schwizer, S., Kraus, C. M., Dunham, D. M., Zheng, Y., Fernandez-Pozo, N., Pombo, M. A., Fei, Zhangju…
Molecular Plant-Microbe Interactions.
30
:
725–738
Next-generation sequencing-based QTL mapping for unravelling causative genes associated with melon fruit quality traits
2017.
Portnoy, V., Gonda, I., Galpaz, N., Tzuri, G., Lev, S., Kenigswald, M., Fei, Zhangjun, Barad, O., Ha…
II INTERNATIONAL SYMPOSIUM ON TOMATO DISEASES.
1151
:
9–16
Molecular and Biological Characterization of Tomato mottle mosaic virus and Development of RT-PCR Detection
2017.
Sui, X., Zheng, Y., Li, R., Padmanabhan, C., Tian, T., Deborah, G. H., Keinath, A. P., Fei, Zhangjun…
Plant Disease.
101
:
704–711
Distinct Mechanisms of the ORANGE Protein in Controlling Carotenoid Flux
2017.
Chayut, N., Yuan, H., Ohali, S., Meir, A., Sa ar, U., Tzuri, G., Zheng, Y., Mazourek, M., Gepstein, …
Plant Physiology.
173
:
376–389
Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes
2017.
Tafolla-Arellano, J. C., Zheng, Y., Sun, H., Jiao, C., Ruiz-May, E., Hernandez-Onate, M. A., Gonzale…
Nature Scientific Reports.
7
:
46163–46163
VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs
2017.
Zheng, Y., Gao, S., Padmanabhan, C., Li, R., Galvez, M., Gutierrez, D., Fuentes, S., Ling, K. S., Kr…
Virology.
500
:
130–138
Loss-of-function mutation of the calcium sensor CBL1 increases aluminum sensitivity in Arabidopsis
2017.
Ligaba-Osena, A., Fei, Zhangjun, Liu, J., Xu, Y., Shaff, J., Lee, S. C., Luan, S., Kudla, J., Kochia…
New Phytologist.
214
:
830–841
Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo
2017.
Wei, Q., Jiao, C., Ding, Y., Gao, S., Guo, L., Chen, M., Hu, P., Xia, S., Ren, G., Fei, Zhangjun
Tree Physiology.
:
1–14
Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant
2017.
Omidvar, V., Mohorianu, I., Dalmay, T., Zheng, Y., Fei, Zhangjun, Pucci, A., Mazzucato, A., Večeřo…
PLOS One.
12
:
e0170715–e0170715
The Tomato Expression Atlas
2017.
Fernandez-Pozo, N., Zheng, Y., Snyder, S. I., Nicolas, P., Shinozaki, Y., Fei, Zhangjun, Catala, Car…
Bioinformatics (Oxford, England).
33
:
2397–2398
Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses
2017.
Niu, X., Sun, Y., Chen, Z., Li, R., Padmanabhan, C., Ruan, J., Kreuze, J. F., Ling, K. S., Fei, Zhan…
Genes (Basel).
8
:
163–163
Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement
2017.
Duan, N., Bai, Y., Sun, H., Wang, N., Ma, Y., Li, M., Wang, X., Jiao, C., Legall, N., Mao, L., Wan, …
Nature Communications.
8
:
Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes
2017.
Sun, H., Wu, S., Zhang, G., Jiao, C., Guo, S., Ren, Y., Zhang, J., Zhang, H., Gong, G., Jia, Z., Zha…
Molecular Plant.
10
:
1293–1306
Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis
2017.
Gapper, N. E., Hertog, M. LATM, Lee, J., Buchanan, D. A., Leisso, R. S., Fei, Zhangjun, Qu, G., Giov…
BMC Plant Biology.
17
:
Decreased sorbitol synthesis leads to abnormal stamen development and reduced pollen tube growth via an MYB transcription factor, MdMYB39L, in apple ( Malus domestica )
2017.
Meng, D., He, M., Bai, Y., Xu, H., Dandekar, A. M., Fei, Zhangjun, Cheng, L.
New Phytologist.
217
:
641–656
Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 during feeding on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes
2017.
Kaur, N., Chen, W., Zheng, Y., Hasegawa, D. K., Ling, K. S., Fei, Zhangjun, Wintermantel, W. M.
BMC Genomics.
18
: