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
Affiliations: Adjunct Professor / Section of Plant Pathology & Plant-Microbe Biology / School of Integrative Plant Science / Cornell University
Graduate Fields: Plant Pathology & Plant-Microbe Biology; Plant Biology
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
Graph pangenome captures missing heritability and empowers tomato breeding.
2022.
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L., Fang, Y., Wu, K., Zhang, J., Lyu, H., Lin, T., Gao, Q., Saha, S., Mueller, Lukas A., Fei, Zhangjun, Städler, T., Xu, S., Zhang, Z., Speed, D., Huang, S.
Nature.
606
:
527–534
The tomato yellow leaf curl virus C4 protein alters the expression of plant developmental genes correlating to leaf upward cupping phenotype in tomato.
2022.
Padmanabhan, C., Zheng, Y., Shamimuzzaman, M., Wilson, J.R., Gilliard, A., Fei, Zhangjun, Ling, K.S.
PLoS One.
17
:
e0257936
A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity.
2022.
Powell, A.F., Feder, A., Li, J., Schmidt, M.H., Courtney, L., Alseekh, S., Jobson, E.M., Vogel, A., Xu, Y., Lyon, D., Dumschott, K., McHale, M., Sulpice, R., Bao, K., Lal, R., Duhan, A., Hallab, A., Denton, A.K., Bolger, M.E., Fernie, A.R., Hind, S.R., Mueller, Lukas A., Martin, Gregory B., Fei, Zhangjun, Martin, C., Giovannoni, James J., Strickler, S.R., Usadel, B.
Plant J..
:
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
2022.
Li, H., Wang, S., Chai, S., Yang, Z., Zhang, Q., Xin, H., Xu, Y., Lin, S., Chen, X., Yao, Z., Yang, Q., Fei, Zhangjun, Huang, S., Zhang, Z.
Nature Communications.
13
:
Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits
2021.
Cai, X., Sun, X., Xu, C., Sun, H., Wang, X., Ge, C., Zhang, Z., Wang, Q., Fei, Zhangjun, Jiao, C., Wang, Q.
Nat Commun..
12
:
7246
Interspecific Recombination Between Zucchini Tigre Mosaic Virus and Papaya Ringspot Virus Infecting Cucurbits in China
2021.
Peng, B., Liu, L., Wu, H., Kang, B., Fei, Zhangjun, Gu, Q.
Frontiers in Microbiology.
12
:
Bt Cry1Ac resistance in Trichoplusia ni is conferred by multi-gene mutations
2021.
Ma, X., Shao, E., Chen,W., Cotto-Rivera, R., Yang, W., Kain, W., Fei, Zhangjun, Wang, P.
Insect Biochemistry and Molecular Biology.
140
:
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit
2021.
Wang, R., Xue, Y., Fan, F., Yao, J., Qin, M., Lin, T., Lian, Q., Zhang, M., Li, X., Li, J., Sun, M., Song, B., Zhang, J., Zhao, K., Chen, X., Hu, H., Fei, Zhangjun, Xue, C., Wu, J.
Genome Biology.
22
:
Spelling Changes and Fluorescent Tagging With Prime Editing Vectors for Plants
2021.
Wang, L., Kaya, H. B., Zhang, N., Rai, R., Willmann, M. R., Carpenter, S., Read, A. C., Martin, F., Fei, Zhangjun, Leach, J. E., Martin, Gregory B., & Bogdanove, A. J.
Frontiers in Genome Editing.
3
:
Cellular and molecular characterizations of the irregular internode division zone formation of a slow growing bamboo variant
2021.
Gao, Z., Guo, L., Ramakrishnan, M., Xiang, Y., Jiao, C., Jiang, J., Vinod, K.K., Fei, Zhangjun, Que, F., Ding, Y., Yu, F., Chen, T., Wei, Q.
Tree Physiology.
:
Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato
2021.
Ye, J., Wang, X., Wang, W., Yu, H., Ai, G., Li, C., Sun, P., Wang, X., Li, H., Ouyang, B., Zhang, J., Zhang, Y., Han, H., Giovannoni, James, Fei, Zhangjun, Ye, Z.
Plant Physiology.
186
:
2078–2092
Genetic Resources and Vulnerabilities of Major Cucurbit Crops
2021.
Grumet, R., McCreight, J.D., McGregor, C., Weng, Y., Mazourek, M., Reitsma, K., Labate, J., Davis, A., Fei, Zhangjun
Genes.
12
:
1222
A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening.
2021.
Shi, Y., Vrebalov, J., Zheng, H., Xu, Y., Yin, X., Liu, W., Liu, Z., Sorensen, I., Su, G., Ma, Q., Evanich, D., Rose, J.K.C., Fei, Zhangjun, Van Eck, Joyce, Thannhauser, T., Chen, K., Giovannoni, James J.
Proc Natl Acad Sci.
118
:
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, K., Fei, Zhangjun, Liu, Y., Zheng, Y.
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., Fernie, AR., Wang, Y., Fei, Zhangjun, Caicedo, AL., Tieman, DM., van der Knaap, E.
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., Xu, J., Zhang, Q., Ren, Y., Yu, J., Wang, C., Deng, C.H., Ma, B., Zheng, B., You, C.X., Hu, D.G., Espley, R., Lin-Wang, K., Yao, J.L., Allan, A.C., Khan, A., Korban, S.S., Fei, Zhangjun, Ming, R., Hao, Y.J., Li, L., Han, Y.
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, Zhangjun, Lu, G.
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, M., Han, S., Pei, Y., Borm, T., Sun, H., Miao, L., Liu, D., Yu, F., Zhang, W., Ji, H., Zhu, C., Xu, Y., Bonnema, G., Li, J., Fei, Zhangjun, Liu, F.
BMC Biol..
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