Zhangjun Fei

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. pmc A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.)
    Aurora Diaz
    Instituto de Biologia Molecular y Celular de Plantas, Universidad Politecnica de Valencia Consejo Superior de Investigaciones Cientificas, Ciudad Politécnica de la Innovación C Ingeniero Fausto Elio s n, Valencia, Spain
    BMC Plant Biol 11:111. 2011
  2. pmc Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
    Fabrizio Costa
    Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
    BMC Plant Biol 10:229. 2010
  3. pmc RNA-Seq improves annotation of protein-coding genes in the cucumber genome
    Zhen Li
    College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875, China
    BMC Genomics 12:540. 2011
  4. pmc Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles
    Shaogui Guo
    National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
    BMC Genomics 12:454. 2011
  5. pmc Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
    Christian Clepet
    URGV Plant Genomics, Unite de Recherche en Genomique Vegetale, UMR1165 ERL8196 INRA UEVE CNRS 2, rue Gaston Crémieux, 91057 Evry, France
    BMC Genomics 12:252. 2011
  6. pmc Gene expression in developing watermelon fruit
    W Patrick Wechter
    USDA, ARS, US Vegetable Lab, 2700 Savannah Highway, Charleston, SC, USA
    BMC Genomics 9:275. 2008
  7. pmc Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis
    Je Keun Rhee
    Graduate Program in Bioinformatics, Seoul National University, Seoul 151 744, Korea
    BMC Genomics 10:S29. 2009
  8. pmc Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim
    Shaohua Zeng
    Key Laboratory of Pant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
    BMC Genomics 11:94. 2010
  9. pmc Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
    Zhangjun Fei
    Boyce Thompson Institute for Plant Research, Cornell University, USDA Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
    Nucleic Acids Res 39:D1156-63. 2011
  10. pmc iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
    Yi Zheng
    Department of Ornamental Horticulture, China Agricultural University, Beijing 100094, China
    BMC Bioinformatics 12:453. 2011

Collaborators

Detail Information

Publications30

  1. pmc A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.)
    Aurora Diaz
    Instituto de Biologia Molecular y Celular de Plantas, Universidad Politecnica de Valencia Consejo Superior de Investigaciones Cientificas, Ciudad Politécnica de la Innovación C Ingeniero Fausto Elio s n, Valencia, Spain
    BMC Plant Biol 11:111. 2011
    ....
  2. pmc Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
    Fabrizio Costa
    Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
    BMC Plant Biol 10:229. 2010
    ....
  3. pmc RNA-Seq improves annotation of protein-coding genes in the cucumber genome
    Zhen Li
    College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875, China
    BMC Genomics 12:540. 2011
    ..We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set...
  4. pmc Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles
    Shaogui Guo
    National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
    BMC Genomics 12:454. 2011
    ....
  5. pmc Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
    Christian Clepet
    URGV Plant Genomics, Unite de Recherche en Genomique Vegetale, UMR1165 ERL8196 INRA UEVE CNRS 2, rue Gaston Crémieux, 91057 Evry, France
    BMC Genomics 12:252. 2011
    ..It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited...
  6. pmc Gene expression in developing watermelon fruit
    W Patrick Wechter
    USDA, ARS, US Vegetable Lab, 2700 Savannah Highway, Charleston, SC, USA
    BMC Genomics 9:275. 2008
    ....
  7. pmc Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis
    Je Keun Rhee
    Graduate Program in Bioinformatics, Seoul National University, Seoul 151 744, Korea
    BMC Genomics 10:S29. 2009
    ..In the present study, we propose a kernel-based approach to efficiently identify core regulatory elements involved in specific biological processes using gene expression profiles...
  8. pmc Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim
    Shaohua Zeng
    Key Laboratory of Pant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
    BMC Genomics 11:94. 2010
    ..Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum...
  9. pmc Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
    Zhangjun Fei
    Boyce Thompson Institute for Plant Research, Cornell University, USDA Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
    Nucleic Acids Res 39:D1156-63. 2011
    ..The suite of tools and interfaces in TFGD allow intelligent data mining of recently released and continually expanding large-scale tomato functional genomics data sets. TFGD is available at http://ted.bti.cornell.edu...
  10. pmc iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
    Yi Zheng
    Department of Ornamental Horticulture, China Agricultural University, Beijing 100094, China
    BMC Bioinformatics 12:453. 2011
    ..In order to generate more accurate consensus sequences from ESTs, tools are needed to reduce or eliminate errors from de novo assemblies...
  11. doi request reprint Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation
    Je Min Lee
    Boyce Thompson Institute for Plant Research, Tower Rd, Cornell University Campus, Ithaca, NY 14853, USA
    Plant J 70:191-204. 2012
    ..Reduced expression of SlERF6 by RNAi enhanced both carotenoid and ethylene levels during fruit ripening, demonstrating an important role for SlERF6 in ripening, integrating the ethylene and carotenoid synthesis pathways...
  12. doi request reprint Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
    Silin Zhong
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
    Nat Biotechnol 31:154-9. 2013
    ..Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenome...
  13. pmc Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
    Shaogui Guo
    1National Engineering Research Center for Vegetables, Beijing 100097, China
    BMC Genomics 11:384. 2010
    ....
  14. pmc Plant MetGenMAP: an integrative analysis system for plant systems biology
    Je Gun Joung
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
    Plant Physiol 151:1758-68. 2009
    ..Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP...
  15. doi request reprint Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development
    Johannes Rohrmann
    Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D 14476 Potsdam, Germany
    Plant J 68:999-1013. 2011
    ..The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes...
  16. doi request reprint Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case
    Gloria Lopez-Casado
    Department of Plant Biology, Cornell University, Ithaca, NY, USA
    Proteomics 12:761-74. 2012
    ..We conclude that RNA-Seq provides a cost-effective and robust platform for protein identification and will be increasingly valuable to the field of proteomics...
  17. doi request reprint Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions
    Benoît Castandet
    Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 1801, USA
    FEBS Lett 587:3096-101. 2013
    ..These results, together with previously published data, suggest that RNA-Seq represents a unique opportunity to decipher the roles of organellar ribonucleases and deepen our understanding of chloroplast gene expression. ..
  18. pmc Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development
    Yong qiang Wang
    Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
    J Exp Bot 64:949-61. 2013
    ..This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants...
  19. pmc Tomato Expression Database (TED): a suite of data presentation and analysis tools
    Zhangjun Fei
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
    Nucleic Acids Res 34:D766-70. 2006
    ..TED can be accessed at http://ted.bti.cornell.edu...
  20. pmc Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis
    Chloe Marchive
    Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
    Plant Physiol 151:905-24. 2009
    ....
  21. doi request reprint Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model
    Je Gun Joung
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
    Bioinformatics 25:387-93. 2009
    ..Here, we propose a method based on the probabilistic graphical model to identify the regulatory modules of miRNAs and the core regulatory motifs involved in their ability to regulate gene expression...
  22. pmc Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation
    Antonio J Matas
    Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
    Plant Cell 23:3893-910. 2011
    ..Finally, patterns of similar gene expression between tissues led to the characterization of a cuticle on the inner surface of the pericarp, demonstrating the utility of this approach as a platform for biological discovery...
  23. pmc Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
    Je Gun Joung
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
    BMC Bioinformatics 10:S34. 2009
    ..Here we demonstrate that gene expression profiles contain useful information in separating miRNA targets from non-targets...
  24. doi request reprint Interdependence of threonine, methionine and isoleucine metabolism in plants: accumulation and transcriptional regulation under abiotic stress
    Vijay Joshi
    Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
    Amino Acids 39:933-47. 2010
    ..A bioinformatics approach to understanding the transcriptional regulation of the genes involved in amino acid metabolism under abiotic stress is also presented...
  25. ncbi request reprint Comprehensive EST analysis of tomato and comparative genomics of fruit ripening
    Zhangjun Fei
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
    Plant J 40:47-59. 2004
    ....
  26. pmc The transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells
    Yun Ru Chen
    Boyce Thompson Institute at Cornell University, Ithaca, New York, USA
    J Virol 87:6391-405. 2013
    ..Combined, these data provide an emerging global picture of the organization and regulation of AcMNPV transcription through the infection cycle...
  27. pmc Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis)
    Xiangjun Zhou
    Robert W Holley Center for Agriculture and Health, USDA ARS, Cornell University, Ithaca, NY 14853, USA
    BMC Plant Biol 11:169. 2011
    ..Despite extensive studies of this process, the genetic basis and the regulatory control of chloroplast biogenesis and development remain to be elucidated...
  28. ncbi request reprint ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development
    Rob Alba
    Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, USA
    Plant J 39:697-714. 2004
    ....
  29. pmc A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
    Yun Ru Chen
    Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
    Plant Methods 8:41. 2012
    ..abstract:..
  30. pmc Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features
    Sara L Zimmer
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Genetics 179:125-36. 2008
    ....