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
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

Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)
2019.
Chen, W., Shakir, S., Bigham, M., Richter, A., Fei, Zhangjun, Jander, Georg
GigaScience.
8
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giz033
The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening
2019.
Wang, A., Chen, D., Ma, Q., Rose, J.K.C., Fei, Zhangjun, Liu, Y., Giovannoni, James J.
Horticulture Research.
6
:
15
Plant Viruses Transmitted in Two Different Modes Produce Differing Effects on Small RNA-Mediated Processes in Their Aphid Vector
2019.
Pinheiro, P.V., Wilson, J.R., Xu, Y., Zheng, Y., Rebelo, A.R., Fattah-Hosseini, S., Kruse, A., Santo…
Phytobiomes.
3
:
71–81
Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts
2019.
Sun, X., Chen, W., Ivanov, S., MacLean, A.M., Wight, H., Ramaraj, T., Mudge, J., Harrison, Maria J.,…
New Phytologist.
221
:
1556–1573
Transcriptional responses of the Trichoplusia ni midgut to oral infection by the baculovirus Autographa californica Multiple Nucleopolyhedrovirus
2019.
Shrestha, A., Bao, K., Chen, W., Wang, P., Fei, Zhangjun, Blissard, Gary W.
Journal of Virology.
:
Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato
2019.
Li, W., Ai, G., Li, C., Liu, G., Chen, W., Wang, B., Wang, W., Lu, Y., Zhang, J., Li, H., Ouyang, B.…
PLOS Genetics.
15
:
Genome-wide identification of genes encoding putative secreted E3 ubiquitin ligases and functional characterization of PbRING1 in the biotrophic protist Plasmodiophora brassicae
2019.
Yu, F., Wang, S., Zhang, W., Tang, J., Wang, H., Yu, L., Zhang, X., Fei, Zhangjun, Li, J.
Current Genetics.
:
1–11
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
2019.
Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D., Burzynski-Chang, E., Fish, T., Stromberg, …
Nature Genetics.
:
1546–1718
Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
2019.
Pombo, M.A., Ramos, R.N., Zheng, Y., Fei, Zhangjun, Martin, Gregory B., Rosli, H.G.
Scientific Reports.
9
:
Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants
2019.
Zheng,Y., Zhang, N., Martin, Gregory B., Fei, Zhangjun
Molecular Plant.
12
:
127–129
Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection
2018.
Gonda, I., Ashrafi, H., Lyon, D.A., Strickler, S.R., Hulse-Kemp, A.M., Ma, Q., Sun, H., Stoffel, K.,…
The Plant Genome.
12
:
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
2018.
Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., …
Nucleic Acids Research.
47
:
D1128–D1136
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, Gary, Fei, Zhangjun, Wa…
Molecular Ecology Resources.
19
:
485–496
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.
:
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.
:
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.
:
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.
:
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
:
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
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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