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.

  • BTI Welcomes Summer Student Interns

  • BTI Scientists Create New Genomic Resource for Improving Tomatoes

    Tomato breeders have traditionally emphasized traits that improve production, like larger fruits and more fruits per plant. As a result, some traits that improved other important qualities, such as flavor and disease resistance, were lost. Researchers from Boyce Thompson Institute and colleagues from partnering institutions have created a pan-genome that captures all of the genetic […] Read more »
  • BTI Promotes Faculty Member Fei

    David Stern, president of the Boyce Thompson Institute (BTI), is delighted to announce that faculty member Zhangjun Fei has been promoted to Full Professor on February 27, 2019. Fei was evaluated on his achievements to date and the potential he possesses. Fei has made a name for himself as one of the world’s foremost experts […] Read more »
  • New CRISPR database to catalyze collaborations

    Recently developed gene editing tools like CRISPR/Cas enable 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 resulting […] Read more »
  • Orange is the new white: New sweetpotato data is something to be thankful for

    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 »

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

A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni
2019.
Chen, W., Yang, X., Tetreau, G., Song, X., Coutu, C., Hegedus, D., Blissard, Gary W., Fei, Zhangjun,…
Molecular Ecology Resources.
19
:
485–496
Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses JO – BMC Genomics
2019.
Zhang, W., Wang, S., Yu, F., Tang, J., Shan, X., Bao, K., Yu, L., Wang, H., Fei, Zhangjun, Li, J.
BMC Genomics.
20
:
Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato
2019.
Piedra-Aguilera, Á., Jiao, C, Luna, A.P., Villanueva, F., Dabad, M., Esteve-Codina, A., Díaz-Pend…
Scientific Reports.
9
:
Genome-wide profiling of piRNAs in the whitefly Bemisia tabaci reveals cluster distribution and association with begomovirus transmission
2019.
Shamimuzzaman, M., Hasegawa, D.K., Chen W., Simmons, A.M., Fei, Zhangjun, Kai-Shu, L.
PLOS One.
:
Identification of the grape basic helix–loop–helix transcription factor family and characterization of expression patterns in response to different stresses
2019.
Wang, L.,Tang, W.,Hu, Y.,Zhang, Y.,Sun, J.,Guo, X.,Lu, H.,Yang, Y.,Fang, C.,Niu, X.,Yue, J.,Fei, Zha…
Plant Growth Regulation.
88
:
19–39
A MYB/bHLH complex regulates tissue‐specific anthocyanin biosynthesis in the inner pericarp of red‐centered kiwifruit Actinidia chinensis cv. Hongyang
2019.
Wang, L.,Tang, W.,Hu, Y.,Zhang, Y.,Sun, J.,Guo, X.,Lu, H.,Yang, Y.,Fang, C.,Niu, X.,Yue, J.,Fei, Zha…
The.
The Plant Journal
:
Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat (Eriobotrya japonica) fruit
2019.
Liu, W., Zhang, J., Jiao, C., Yin, X., Fei, Zhangjun, Wu, Q., Chen, K.
Horticulture Research.
6
:
Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)
2019.
Silva, K.J.P., Singh, J., Bednarek, R., Fei, Zhangjun, Khan, A.
Horticulture Research.
6
:
Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping
2019.
Tang, W., Sun, X., Yue, J., Tang, X., Jiao, C., Yang, Y., Niu, X., Miao, M., Zhang, D., Huang, S., S…
GigaScience.
8
:
Detection and genome characterization of a novel member of the genus Polerovirus from zucchini (Cucurbita pepo) in China
2019.
Peng, B, Kang, B., Wu, H., Liu, L., Liu, L, Fei, Zhangjun, Hong, N., Gu, Q.
Archives of Virology.
:
Rosa hybrida RhERF1 and RhERF4 Mediate Ethylene and Auxin‐Regulated Petal Abscission by Influencing Pectin Degradation
2019.
Gao, Y. ,Liu, Y., Liang, Y., Lu, J., Jiang, C., Fei, Zhangjun, Jiang, C., Ma, C., Gao, J.
The Plant Journal.
:
Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus
2019.
Padmanabhan, C., Ma, Q., Shekasteband, R., Stewart, K.S., Hutton, S.F., Scott, J.W., Fei, Zhangjun, …
Scientific Reports.
9
:
2045–2322
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
:
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

Contact:

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contact@btiscience.org