Xiaohan Yang

Summary

Affiliation: Oak Ridge National Laboratory
Country: USA

Publications

  1. pmc Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon
    Ludmila Tyler
    USDA ARS Western Regional Research Center, Albany, CA 94710, USA
    BMC Genomics 11:600. 2010
  2. pmc Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom
    Zhanyou Xu
    Department of Plant Pathology and Microbiology, Texas A and M University, College Station, TX, USA
    BMC Bioinformatics 10:S3. 2009
  3. pmc MicroSyn: a user friendly tool for detection of microsynteny in a gene family
    Bin Cai
    College of Horticulture, Nanjing Agricultural University, China
    BMC Bioinformatics 12:79. 2011
  4. pmc Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
    Xiaohan Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Genome Res 21:634-41. 2011
  5. doi request reprint Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics
    Xiaohan Yang
    Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant Sci 181:675-87. 2011
  6. doi request reprint Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes
    Abhijit A Karve
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    New Phytol 196:726-37. 2012
  7. doi request reprint Evolutionary analyses of non-family genes in plants
    Chu Yu Ye
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant J 73:788-97. 2013
  8. doi request reprint Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis
    Chu Yu Ye
    Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant Sci 181:688-95. 2011
  9. doi request reprint Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
    David J Weston
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant Cell Environ 34:1488-506. 2011
  10. doi request reprint Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis, and fitness
    David J Weston
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Mol Plant Microbe Interact 25:765-78. 2012

Collaborators

  • David J Weston
  • Udaya C Kalluri
  • Stan D Wullschleger
  • Dale A Pelletier
  • Jin Gui Chen
  • Gerald A Tuskan
  • Chu Yu Ye
  • Ting Li
  • Timothy J Tschaplinski
  • Abhijit A Karve
  • Bin Cai
  • Ludmila Tyler
  • Zhanyou Xu
  • Hengfu Yin
  • Lee E Gunter
  • Sara S Jawdy
  • Sara M Allen
  • Zong Ming Cheng
  • Jennifer N Bragg
  • John P Vogel
  • Jiajie Wu
  • Jason N Burris
  • Robert W Sykes
  • Ryan D Syrenne
  • Joseph J Bozell
  • Nicole Labbe
  • Max Zong Ming Cheng
  • C Neal Stewart
  • Nathan R Stewart
  • Peng Gao
  • Kristen L Reichel
  • Mark Davis
  • Dandan Zhang
  • Xia Ye
  • Xin Zhou
  • Joshua S Yuan
  • Jun Hu
  • Crissa Doeppke
  • Douglas G Hayes
  • Weibing Shi

Detail Information

Publications12

  1. pmc Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon
    Ludmila Tyler
    USDA ARS Western Regional Research Center, Albany, CA 94710, USA
    BMC Genomics 11:600. 2010
    ..We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families...
  2. pmc Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom
    Zhanyou Xu
    Department of Plant Pathology and Microbiology, Texas A and M University, College Station, TX, USA
    BMC Bioinformatics 10:S3. 2009
    ..Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement...
  3. pmc MicroSyn: a user friendly tool for detection of microsynteny in a gene family
    Bin Cai
    College of Horticulture, Nanjing Agricultural University, China
    BMC Bioinformatics 12:79. 2011
    ..For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes...
  4. pmc Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
    Xiaohan Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Genome Res 21:634-41. 2011
    ..This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available...
  5. doi request reprint Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics
    Xiaohan Yang
    Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant Sci 181:675-87. 2011
    ..Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional characterization in relation to cell wall biosynthesis...
  6. doi request reprint Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes
    Abhijit A Karve
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    New Phytol 196:726-37. 2012
    ....
  7. doi request reprint Evolutionary analyses of non-family genes in plants
    Chu Yu Ye
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant J 73:788-97. 2013
    ..This research highlights the roles that NF genes may play in evolutionary and functional genomics research...
  8. doi request reprint Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis
    Chu Yu Ye
    Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant Sci 181:688-95. 2011
    ..This study provided new insights into the evolution and functional diversification of the GT14/GT14-like family genes...
  9. doi request reprint Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
    David J Weston
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Plant Cell Environ 34:1488-506. 2011
    ..trichocarpa and A. thaliana. These results indicate that although the heat shock response is highly conserved, there is considerable species-specific variation in its regulation...
  10. doi request reprint Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis, and fitness
    David J Weston
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Mol Plant Microbe Interact 25:765-78. 2012
    ..Both strains reduced host plant carbon gain and fitness, yet provided a clear fitness benefit when plants were challenged with the pathogen P. syringae DC3000...
  11. doi request reprint Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus
    Xiaohan Yang
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 6422, USA
    Genomics 93:473-80. 2009
    ..The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research...
  12. pmc The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants
    Xiaohan Yang
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Plant Physiol 148:1189-200. 2008
    ..This study provides insights into the relationship between the structure and composition of the F-box gene family in herbaceous and woody species and their associated developmental and physiological features...