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.

  • 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 »
  • Harvesting Genes to Improve Watermelons

    When many people think of watermelon, they likely think of Citrullus lanatus, the cultivated watermelon with sweet, juicy red fruit enjoyed around the world as a dessert. Indeed, watermelon is one of the world’s most popular fruits, second only to tomato – which many consider a vegetable. But there are six other wild species of […] Read more »
  • 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 »

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

An integrated peach genome structural variation map uncovers genes associated with fruit traits
2020.
Guo, J., Cao, K., Deng, C., Li, Y., Zhu, G., Fang, W., Chen, C., Wang, X., Wu, J., Guan, L., Wu, S.,…
Genome Biol..
21
:
258
QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus
2020.
Branham, S.E., Wechter, W.P., Ling, K., Chanda, B., Massey, L., Zhao, G., Guner, N., Bello, M., Kabe…
Theor Appl Genet..
133
:
677–687
Dietary Fructose Alters the Composition, Localization and Metabolism of Gut Microbiota in Association with Worsening Colitis
2020.
Montrose, D.C., Nishiguchi, R., Basu, S., Staab, H.A., Zhou, X.K., Wang, H., Meng, L., Johncilla, M,…
Cell Mol Gastroenterol Hepatol.
:
Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]
2020.
Gemenet, D.C., Pereira, G.S., De Boeck, B., Wood, J.C., Mollinari, M., Olukolu, B.A., Diaz, F., Mosq…
Theor Appl Genet..
133
:
23–36
Genetic mapping of green curd gene Gr in cauliflower
2020.
Tan, H., Wang, X., Fei, Zhangjun, Li, H., Tadmor, Y., Mazourek, M., Li, L.
Theor Appl Genet..
133
:
353–364
Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics
2020.
Yue, J., Liu, J., Tang, W., Wu, Y.Q., Tang, X., Li, W., Yang, Y., Wang, L., Huang, S., Fang, C., Zha…
Hortic Res..
7
:
Deep Sequencing of Small RNAs in the Whitefly Bemisia tabaci Reveals Novel MicroRNAs Potentially Associated with Begomovirus Acquisition and Transmission
2020.
Hasegawa, D.K., Shamimuzzaman, M., Chen, W., Simmons, A.M., Fei, Zhangjun, Ling, K.S.
Insects..
:
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..
:
Setaria viridis chlorotic and seedling-lethal mutants define critical functions for chloroplast gene expression
2020.
Feiz, L., Strickler, S.R., Van Eck, Joyce, Mao, L., Movahed, N., Taylor, C., Gourabathini, P., Fei, …
Plant J..
:
Rosa Hybrida RhERF1 and RhERF4 Mediate Ethylene- And Auxin-Regulated Petal Abscission by Influencing Pectin Degradation
2020.
Gao, Y., Liu, Y., Liang, Y., Lu, J., Jiang, C., Fei, Zhangjun, Jiang, C.Z., Ma, C., Gao, J.
Plant J..
:
Identification of Conserved Gene-Regulatory Networks That Integrate Environmental Sensing and Growth in the Root Cambium
2020.
Hoang, N.V., Choe, G., Zheng, Y., Fandino, A.C.A., Sung, I., Hur, J., Kamran, M., Park, C., Kim, H.,…
Curr Biol..
:
Localization Shift of a Sugar Transporter Contributes to Phloem Unloading in Sweet Watermelons
2020.
Ren, Y., Sun, H., Zong, M., Guo, S., Ren, Z., Li, M., Zhang, J., Tian, S., Wang, J., Yu, Y., Gong, G…
New Phytol..
:
The Penium Margaritaceum Genome: Hallmarks of the Origins of Land Plants
2020.
Jiao, C., Sørensen, I., Xuepeng, S., Sun, H., Hila, B., Alseekh, S., Philippe, G., Lopez, K.P., Sun…
Cell..
:
Genome analysis of plant growth-promoting rhizobacterium Pseudomonas chlororaphis subsp. aurantiaca JD37 and insights from comparasion of genomics with three Pseudomonas strains.
2020.
Zhang, L., Chen, W., Jiang, Q., Fei, Zhangjun, Xiao, M.
Microbiol Res..
:
Citrullus lanatus.
2020.
Guo, S., Sun, H., Xu, Y., Fei, Zhangjun
Trends Genet..
:
A MYB/bHLH complex regulates tissue-specific anthocyanin biosynthesis in the inner pericarp of red-centered kiwifruit Actinidia chinensis cv. Hongyang.
2020.
Wang, L., Tang, W., Hu, Y., Zhang, Y., Sun, J., Guo, X., Lu, H., Yang, Y., Fang, C., Niu, X., Yue, J…
Plant J..
:
A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’.
2020.
Yang, Y., Cuenca, J., Wang, N., Liang, Z., Sun, H., Gutierrez, B., Xi, X., Arro, J., Wang, Y., Fan, …
Hortic Res..
7
:
Genome-wide identification of genes encoding putative secreted E3 ubiquitin ligases and functional characterization of PbRING1 in the biotrophic protist Plasmodiophora brassicae.
2020.
Yu, F., Wang, S., Zhang, W., Tang, J., Wang, H., Yu, L., Zhang, X., Fei, Zhangjun, Li, J.
Curr Genet..
:
Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi.
2020.
Watts-Williams, S.J., Emmett, B.D., Levesque-Tramblay, V., MacLean, A.M., Sun, X. Satterlee, J.W., F…
Plant Cell Environ..
:
Chromosome-level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood).
2020.
Xie, W., He, C., Fei, Zhangjun, Zhang, Y.
Mol Ecol Resour..
:
 

Contact:

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