Xuechun Zhao

Summary

Affiliation: Plant Biology Division
Country: USA

Publications

  1. pmc An RNA-Seq based gene expression atlas of the common bean
    Jamie A O'Rourke
    Department of Agronomy and Plant Genetics, University of Minnesota, St, Paul, MN 55108, USA
    BMC Genomics 15:866. 2014
  2. pmc A new systematic computational approach to predicting target genes of transcription factors
    Xinbin Dai
    Plant Biology Division, The Samuel Robert Noble Foundation, Ardmore, OK 73401, USA
    Nucleic Acids Res 35:4433-40. 2007
  3. pmc pssRNAMiner: a plant short small RNA regulatory cascade analysis server
    Xinbin Dai
    Plant Biology Division, The Samuel Robert Noble Foundation, Ardmore OK 73401, USA
    Nucleic Acids Res 36:W114-8. 2008
  4. pmc psRNATarget: a plant small RNA target analysis server
    Xinbin Dai
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Nucleic Acids Res 39:W155-9. 2011
  5. pmc Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives
    Firoz Ahmed
    Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble Foundation Ardmore, OK, USA
    Front Plant Sci 2:84. 2011
  6. pmc GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data
    Jun Li
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA and School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
    Nucleic Acids Res 42:e32. 2014
  7. pmc LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
    Jun Li
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Nucleic Acids Res 40:D1221-9. 2012
  8. pmc DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis
    Jun Li
    Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Biomed Res Int 2013:856325. 2013
  9. pmc PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool
    Xinbin Dai
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway 73401 Ardmore, OK, USA
    BMC Bioinformatics 14:321. 2013
  10. pmc Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner
    Yan Zhang
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
    Plant Methods 4:19. 2008

Collaborators

Detail Information

Publications20

  1. pmc An RNA-Seq based gene expression atlas of the common bean
    Jamie A O'Rourke
    Department of Agronomy and Plant Genetics, University of Minnesota, St, Paul, MN 55108, USA
    BMC Genomics 15:866. 2014
    ..An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species...
  2. pmc A new systematic computational approach to predicting target genes of transcription factors
    Xinbin Dai
    Plant Biology Division, The Samuel Robert Noble Foundation, Ardmore, OK 73401, USA
    Nucleic Acids Res 35:4433-40. 2007
    ..Using ten-fold cross validations, the area under curve value of the receiver operating characteristic reaches around 0.73...
  3. pmc pssRNAMiner: a plant short small RNA regulatory cascade analysis server
    Xinbin Dai
    Plant Biology Division, The Samuel Robert Noble Foundation, Ardmore OK 73401, USA
    Nucleic Acids Res 36:W114-8. 2008
    ..The pssRNAMiner web server is freely available at http://bioinfo3.noble.org/pssRNAMiner/...
  4. pmc psRNATarget: a plant small RNA target analysis server
    Xinbin Dai
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Nucleic Acids Res 39:W155-9. 2011
    ..The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/...
  5. pmc Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives
    Firoz Ahmed
    Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble Foundation Ardmore, OK, USA
    Front Plant Sci 2:84. 2011
    ..We encourage plant bioinformaticians to turn their attention to this subject to help identify novel mechanisms of gene expression regulation using RNA motifs that have potentially evolved or diverged in plant species...
  6. pmc GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data
    Jun Li
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA and School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
    Nucleic Acids Res 42:e32. 2014
    ..We demonstrate GPLEXUS's capabilities by construing global GANs and analyzing subnetworks related to defense against biotic and abiotic stress, cell cycle growth and division in Arabidopsis thaliana. ..
  7. pmc LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
    Jun Li
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Nucleic Acids Res 40:D1221-9. 2012
    ..Finally, LegumeIP provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny and relative gene expression...
  8. pmc DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis
    Jun Li
    Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Biomed Res Int 2013:856325. 2013
    ..In addition, we integrated the SNBuilder and GeNa algorithms for subnetwork extraction and functional module discovery. DeGNServer is publicly and freely available online. ..
  9. pmc PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool
    Xinbin Dai
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway 73401 Ardmore, OK, USA
    BMC Bioinformatics 14:321. 2013
    ..An understanding of plant gene regulatory mechanisms at a systems level requires the identification of these regulatory elements on a genomic scale...
  10. pmc Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner
    Yan Zhang
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
    Plant Methods 4:19. 2008
    ..The objectives of this study were to develop an integrated approach for microsatellite development and to evaluate the approach for the development of new SSR markers for white clover...
  11. pmc Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots
    Li Tian
    Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
    BMC Plant Biol 9:1. 2009
    ..Genomic and proteomic approaches were applied to identify candidate genes and proteins involved in antimicrobial defense and (heavy) metal uptake and translocation...
  12. pmc Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub)
    Marina Naoumkina
    Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
    BMC Plant Biol 7:62. 2007
    ..To better understand regulation of guar seed development and galactomannan metabolism we created cDNA libraries and a resulting EST dataset from different developmental stages of guar seeds...
  13. pmc A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa
    Amanda K Broz
    Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523 1173, USA
    BMC Plant Biol 7:25. 2007
    ..Limited genetic resources are available for most invasive and weedy species, making it difficult to study molecular and genetic aspects that may be associated with invasion...
  14. pmc Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis
    Yuanhong Han
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    BMC Genomics 12:1-11. 2011
    ..We describe the use of 454 technology and high resolution melting analysis (HRM) for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L.), a species with high economic value but limited genomic resources...
  15. pmc TransportTP: a two-phase classification approach for membrane transporter prediction and characterization
    Haiquan Li
    Plant Biology Division, The Samuel Roberts Noble Foundation, Inc, Ardmore, OK 73401, USA
    BMC Bioinformatics 10:418. 2009
    ..Second, machine learning methods were used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides...
  16. pmc The Medicago truncatula gene expression atlas web server
    Ji He
    Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
    BMC Bioinformatics 10:441. 2009
    ..We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose...
  17. doi request reprint A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
    Haiquan Li
    Bioinformatics Lab, Plant Biology Division, The Samuel Roberts Noble Foundation, Inc, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Bioinformatics 24:1129-36. 2008
    ..To approach this problem, we utilized a nearest neighbor method which seamlessly integrates homologous search and topological analysis into a machine-learning framework...
  18. doi request reprint Computational analysis of miRNA targets in plants: current status and challenges
    Xinbin Dai
    Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
    Brief Bioinform 12:115-21. 2011
    ....
  19. pmc PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
    Ji He
    Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    BMC Bioinformatics 8:53. 2007
    ..Systematically reviewing the results and identifying information of interest remains tedious and time-consuming...
  20. pmc Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages
    M A Rouf Mian
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73402, USA
    BMC Plant Biol 8:27. 2008
    ..The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported...