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.

  • Gene discovery may help peaches tolerate climate stress

    A BTI-led team has identified genes enabling peaches and their wild relatives to tolerate stressful conditions – findings that could help the domesticated peach adapt to climate change. The study, co-led by Boyce Thompson Institute faculty member Zhangjun Fei, examined the genomes of peach’s wild relatives and landraces – varieties that have adapted over a […] Read more »
  • Tomato’s Wild Ancestor Is a Genomic Reservoir for Plant Breeders

    Thousands of years ago, people in the region now known as South America began domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant evolved into S. lycopersicum – the modern cultivated tomato. Although today’s tomatoes are larger and easier to farm compared with their wild ancestor, they also are […] Read more »
  • Silk Road Contains Genomic Resources for Improving Apples

    The fabled Silk Road – the 4,000-mile stretch between China and Western Europe where trade flourished from the second century B.C. to the 14th century A.D. – is responsible for one of our favorite and most valuable fruits: the domesticated apple (Malus domestica). Snack-packing travelers would pick apples at one spot, eat them and toss […] Read more »
  • Congratulations Spring 2020 Graduates!

    We are pleased to announce that six BTI researchers received their degrees from Cornell University this spring. Congratulations to our newest alumni: Jason Hoki, Schroeder lab, PhD in Chemistry & Chemical Biology, Dissertation title: “Development of click-chemistry based enrichment strategies to characterize ligand binding and metabolism” Jennifer Wilson, Heck lab, PhD in Plant Pathology, Thesis […] Read more »
  • Algal genome provides insights into first land plants

    In order to shift from water to land – a transition that still puzzles scientists – plants had to protect themselves from drying out and from ultraviolet (UV) radiation, and they had to develop structures to support themselves without the buoyancy provided by water. Researchers including BTI’s Zhangjun Fei found footprints of all these adaptations in […] 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

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics
2021.
Yue, J., Liu, J., Tang, W., Wu, YQ., Tang, X., Li, W., Yang, Y., Wang, L., Huang, S., Fang, C., Zhao…
Horticulture Research.
7(1)
:
Natural Genetic Diversity in Tomato Flavor Genes
2021.
Pereira, L., Sapkota, M., Alonge, M., Zheng, Y., Zhang, Y., Razifard, H., Taitano, NK., Schatz, MC.,…
Frontiers in Plant Science.
:
A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons
2021.
Renner, SS., Wu, S., Pérez-Escobar, OA., Silber,MV., Fei, Zhangjun, Chomicki, G.
Proceedings of the National Academy of Sciences of the United States of America.
118
:
Unraveling a Genetic Roadmap for Improved Taste in the Domesticated Apple
2021.
Liao, L., Zhang, W., Zhang, B., Fang, T., Wang, X.F., Cai, Y., Ogutu, C., Gao, L., Chen, G., Nie, X.…
Mol Plant.
:
A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons
2021.
Renner, S.S., Wu, S., Perez-Escobar, O.A., Silber, M.V., Fei, Zhangjun, Chomicki, G.
Proc Natl Acad Sci U S A.
:
PIF4 negatively modulates cold tolerance in tomato anthers via temperature-dependent regulation of tapetal cell death
2021.
Pan, C., Yang, D., Zhao, X., Liu, Y., Li, M., Ye, L., Ali, M., Yu, F., Lamin-Samu, A.T., Fei, Zhangj…
Plant Cell.
:
Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification
2021.
Guo, N., Wang, S., Gao, L., Liu, Y., Wang, X., Lai, E., Duan, M., Wang, G., Li, J., Yang, M., Zong, …
BMC Biol..
:
Comparative transcriptome profiling of Chinese wild grapes provides insights into powdery mildew resistance
2021.
Jiao, C., Sun, X., Yan, X., Xu, X., Yan, Q., Gao, M., Fei, Zhangjun, Wang, X.
:
Ethylene-regulated asymmetric growth of the petal base promotes flower opening in rose (Rosa hybrida)
2021.
Cheng, C., Yu, Q., Wang, Y., Wang, H., Dong, Y., Ji, Y., Zhou, X., Li, Y., Jiang, C.Z., Gan, S.S., Z…
Plant Cell..
:
Genomic analyses provide insights into peach local adaptation and responses to climate change
2021.
Li, Y., Cao, K, Li, N., Zhu, G., Fang, Q., Chen, C., Wang, X., Guo, J., Wang, Q., Wang J., Guan, L.,…
Genome Res..
:
Genome-wide association studies provide insights into the genetic determination of fruit traits of pear
2021.
Zhang, M.Y., Cheng, X., Hu, H., Li, J., Xue, Y., Wang, R., Fan, J., Zou, C., Tao, S., Qin, M., Bai, …
:
Transcriptome analysis provides insights into the responses of sweet potato to sweet potato virus disease (SPVD)
2021.
Bednarek, R., David, M., Fuentes, S., Kreuze, J., Fei, Zhangjun
:
Endomembrane architecture and dynamics during secretion of the extracellular matrix of the unicellular charophyte, Penium margaritaceum
2020.
Domozych, D.S., Sun, L., Palacio-Lopez, K., Reed, R., Jeon, S., Li, M., Jiao, C., Sorensen, I., Fei,…
J Exp Bot..
:
Auxin Regulates Sucrose Transport to Repress Petal Abscission in Rose (Rosa hybrida)
2020.
Liang, Y., Jiang, C., Liu, Y., Gao, Y., Lu, J., Aiwaili, P., Fei, Zhangjun, Jiang, C.Z., Hong, B., M…
Plant Cell.
:
The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants
2020.
Jiao, C., Sorensen, I., Sun, X., Sun, H., Behar, H., Alseekh, S., Philippe, G., Lopez, K.P., Sun, L.…
Cell.
:
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening
2020.
Ma, L., Wang, Q., Mu, J., Fu, Z., Wen, C., Zhao, X., Gao, L., Li, J., Shi, K., Wang, Y., Zhang, X., …
Hortic Res..
:
Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
2020.
Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P.S., Saha, S., Zhang, J., Mainiero, S., Str…
Nat Commun.
11
:
5817
GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces
2020.
Rodriguez, M., Scintu, A., Posadinu, C.M., Xu, Y., Nguyen, C.V., Sun, H., Bitocchi, E., Bellucci, E.…
Genes (Basel).
11
:
Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening
2020.
McQuinn, R.P., Gapper, N.E., Gray, A.G., Zhong, S., Takayuki, T., Fei, Zhangjun, Fernie, A.R., Giova…
:
Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations
2020.
Zhou, C., Olukolu, B., Gemenet, D.C., Wu, S., Gruneberg, W., Cao, M.D., Fei, Zhangjun, Zeng, Z.B., G…
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Contact:

Boyce Thompson Institute
533 Tower Rd.
Ithaca, NY 14853
607.254.1234
contact@btiscience.org