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Huaqin Xu

Huaqin Xu

4302 UC Davis Genome Center-GBSF
451 Health Sciences Drive
University of California
Davis, California 95616

Phone: (530)754-9127
Fax: (530)752-9658
Email: huaxu@ucdavis.edu

 Lab member: 2005- .
Position Associate Specialist
Education M.S. in Computer Science, 2006. California State University, Sacramento.
Research Summary
  • Develop the web interface and manage the charge_db database of the CHARGE project.
    The main purpose of the web interface of the CHARGE Project is for users to query the data from the charge_db database. Users can visualize the data by functional screening, search and download the data, and input or update the data. This interface is developed by using HTML, PHP, JavaScript, Ajax, and CSS.
    Visit the web interface of the CHARGE project.
    The charge_db database is a relational database in MySQL5 that contains genetic information about the resistance genes of plants and bacterial effectors and the reaction data.

  • Data analysis and visualization of bioinformatics data; processing data for the NCBI submission.
    Write scripts and software to analysis and visualize bioinformatics data by using Perl, Python, R, and other tools.
    Example: Pixelirator
  • Publications

    --- Key Publications ---

  • Lee J, Manning AJ, Wolfgeher D, Jelenska J, Cavanaugh KA, Xu H, Fernandez SM, Michelmore RW, Kron SJ, Greenberg JT. (2015Acetylation of an NB-LRR Plant Immune-Effector Complex Suppresses Immunity. Cell Rep. 2015. Nov 24;13(8):1670-82.     
  • Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, Govindarajulu M, Kozik A, Michelmore RW. (2014Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis. RNA. 2014. Dec;20(12):1987-99.     
  • Truco, M. J., Ashrafi, H., Kozik, A., van Leeuwen, H., Bowers, J., Wo, S. R. C., Stoffel, K., Xu, H., Hill, T., Deynze, A. V., & Michelmore, R. W.  (2013An Ultra High-Density, Transcript-Based, Genetic Map of Lettuce G3: Genes| Genomes| Genetics. 2013.   
  • Wroblewski T, Caldwell KS, Piskurewicz U, Cavanaugh KA, Xu H, Kozik A, Ochoa O, McHale LK, Lahre K, Jelenska J, Castillo JA, Blumenthal D, Vinatzer BA, Greenberg JT and Michelmore RW (2009Comparative large-scale analysis of interactions between several crop species and the effector repertoires from multiple pathovars of Pseudomonas and Ralstonia. Plant Physiology. 2009. 10.1104/pp.109.  
  • Huaqin Xu, Ying Jin. (2008A Framework Supporting XML-based Active Rules for Biological Database Constraint Management.  IJCITP  2008. 3(1): 31-42.  
  • Huaqin Xu, Ying Jin.  (2008BioRL: An XML-based Active Rule Language for Biological Database Constraint Management.  BMEI  2008. (1): 883-887.  
  • Denise Jones, Ying Jin, Huaqin Xu.  (2007An Active Rule-Based Approach for Constraint Management of Biological Data in XML Documents.  BIBM 2007. : 111-116.  
  • Ying Jin, Matthew L. Tescher, Huaqin Xu. (2007Middleware Support to the Specification and Execution of Active Rules for Biological Database Constraint Management.  IRI 2007. : 406-411.  
  • --- Presentations ---

  • Truco MJ, Reyes-Chin-Wo S, Lavelle D, Kozik A, Froenicke L, Xu H, Michelmore RW. (2014Lettuce Genome Assembly, Structure and Annotation. Plant and Animal Genome XXII 2014 Jan. 11-15  
  • Kozik A, Froenicke L, Lavelle D, Truco MJ, Xu H, Reyes-Chin-Wo S, Michelmore RW. (2014Chromosome-Scale Assembly of the Lettuce (Lactuca sativa) Genome Using Genotyping By Shotgun Sequencing (GBSS) Plant and Animal Genome XXII 2014 Jan. 11-15  
  • Dean O. Lavelle, Leah K. McHale, Marilena Christopoulou, María José Truco, Oswaldo E. Ochoa , Jim Cervantes , Jason M. Argyris , Marta Matvienko , Alex Kozik , Huaqin Xu, Kent J. Bradford , RW. Michelmore (2009Candidate Gene Analysis In Lactuca spp. Plant & Animal Genomes XVII Conference 2009 January 10-14, 2009 Town & Country Convention Center San Diego,   
  • Wroblewski, T., Vinatzer, B., Caldwell, K.S., Piskurewicz, U., Cavanaugh, K.A., Jelenska, J., Teitzel, G., McHale, L.K., Xu, H., Kozik, A., Ochoa, O., Williams, L.A., Greenberg, J.T. and Michelmore, R.W. (2007Comparative Large-Scale Analysis of Resistance Gene Evolution.  Plant and Animal Genomes XV Conference, January 13-17, 2007; P76 2007   
  • Wroblewski, T., Caldwell, K., Vinatzer, B., Piskurewicz, U., Cavanaugh, K., Jelenska, J., McHale, L., Xu, H., Kozik, A., Ochoa, O., Williams, L., Greenberg, J. and Michelmore, R. (2007Large-Scale Analysis of Interactions between Several Crop Species and Effector Repertoires from Multiple Bacterial Pathogens.  XIII International Congress on Molecular Plant-Microbe Interacti 2007   
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