Yijun Sun

Summary

Affiliation: University of Florida
Country: USA

Publications

  1. pmc ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610 3622, USA
    Nucleic Acids Res 37:e76. 2009
  2. pmc A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610 3622, USA
    Brief Bioinform 13:107-21. 2012
  3. pmc Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL 32610 3622, USA
    Nucleic Acids Res 38:e205. 2010
  4. pmc Local-learning-based feature selection for high-dimensional data analysis
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610 3622, USA
    IEEE Trans Pattern Anal Mach Intell 32:1610-26. 2010
  5. pmc Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants
    Volker Mai
    Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
    PLoS ONE 8:e52876. 2013
  6. pmc Optimizing molecular signatures for predicting prostate cancer recurrence
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32009, USA
    Prostate 69:1119-27. 2009
  7. doi The Arabidopsis Mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses
    Xudong Zhang
    Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
    Plant J 75:484-97. 2013
  8. pmc The Arabidopsis elongator complex subunit2 epigenetically regulates plant immune responses
    Yongsheng Wang
    Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
    Plant Cell 25:762-76. 2013
  9. pmc Derivation of molecular signatures for breast cancer recurrence prediction using a two-way validation approach
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
    Breast Cancer Res Treat 119:593-9. 2010
  10. doi Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes
    Melanie J Correll
    Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL 32611, USA
    Planta 238:519-33. 2013

Collaborators

Detail Information

Publications20

  1. pmc ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610 3622, USA
    Nucleic Acids Res 37:e76. 2009
    ..Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html...
  2. pmc A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610 3622, USA
    Brief Bioinform 13:107-21. 2012
    ....
  3. pmc Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL 32610 3622, USA
    Nucleic Acids Res 38:e205. 2010
    ..Our approach provides rigorous statistical tools for sequence-based studies aimed at elucidating associations between known or unknown organisms and a variety of physiological or environmental conditions...
  4. pmc Local-learning-based feature selection for high-dimensional data analysis
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610 3622, USA
    IEEE Trans Pattern Anal Mach Intell 32:1610-26. 2010
    ..Experiments on 11 synthetic and real-world data sets demonstrate the viability of our formulation of the feature-selection problem for supervised learning and the effectiveness of our algorithm...
  5. pmc Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants
    Volker Mai
    Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
    PLoS ONE 8:e52876. 2013
    ..Bifidobacteria counts were lower in cases at all time points. Our results support the hypothesis that a distortion in normal microbiota composition, and not an enrichment of potential pathogens, is associated with LOS in preterm infants...
  6. pmc Optimizing molecular signatures for predicting prostate cancer recurrence
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32009, USA
    Prostate 69:1119-27. 2009
    ..The derivation of molecular signatures indicative of disease status and predictive of subsequent behavior could facilitate the optimal choice of treatment for prostate cancer patients...
  7. doi The Arabidopsis Mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses
    Xudong Zhang
    Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
    Plant J 75:484-97. 2013
    ....
  8. pmc The Arabidopsis elongator complex subunit2 epigenetically regulates plant immune responses
    Yongsheng Wang
    Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
    Plant Cell 25:762-76. 2013
    ..Together, our data demonstrate a new role for Elongator in somatic DNA demethylation/methylation and suggest a function for Elongator-mediated chromatin regulation in pathogen-induced transcriptome reprogramming...
  9. pmc Derivation of molecular signatures for breast cancer recurrence prediction using a two-way validation approach
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
    Breast Cancer Res Treat 119:593-9. 2010
    ..The cross-validation approach revealed CEGP1 and PRAME as major candidates for breast cancer biomarker development...
  10. doi Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes
    Melanie J Correll
    Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL 32611, USA
    Planta 238:519-33. 2013
    ....
  11. pmc M-pick, a modularity-based method for OTU picking of 16S rRNA sequences
    Xiaoyu Wang
    Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
    BMC Bioinformatics 14:43. 2013
    ..Furthermore, existing binning methods usually require a priori decisions regarding binning parameters such as a distance level for defining an OTU...
  12. pmc Improved breast cancer prognosis through the combination of clinical and genetic markers
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
    Bioinformatics 23:30-7. 2007
    ..Given the complexity of breast cancer prognosis, a more practical strategy would be to utilize both clinical and genetic marker information that may be complementary...
  13. pmc ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
    Yunpeng Cai
    Interdisciplinary Center for Biotechnology Research University of Florida, Gainesville, FL 32610, USA
    Nucleic Acids Res 39:e95. 2011
    ..The new algorithm exhibits a quasilinear time and space complexity comparable to greedy heuristic clustering algorithms, while achieving a similar accuracy to the standard hierarchical clustering algorithm...
  14. ncbi Iterative RELIEF for feature weighting: algorithms, theories, and applications
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
    IEEE Trans Pattern Anal Mach Intell 29:1035-51. 2007
    ..The results of large-scale experiments on the UCI and microarray data sets are reported, which demonstrate the effectiveness of the proposed algorithms, and verify the presented theoretical results...
  15. doi The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition
    Drion G Boucias
    Department of Entomology and Nematology, University of Florida, Gainesville, FL 32610 3622, USA
    Mol Ecol 22:1836-53. 2013
    ....
  16. pmc High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems
    Li Yin
    Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 2033 Mowry Road, PO Box 103633, Gainesville, FL 32610 3633, USA
    Retrovirology 9:108. 2012
    ....
  17. pmc Spaceflight transcriptomes: unique responses to a novel environment
    Anna Lisa Paul
    Horticultural Sciences and Genetics Institute, University of Florida, Gainesville, Florida, USA
    Astrobiology 12:40-56. 2012
    ....
  18. pmc Bladder cancer-associated gene expression signatures identified by profiling of exfoliated urothelia
    Charles J Rosser
    Department of Urology, University of Florida College of Medicine, Gainesville, FL 32610, USA
    Cancer Epidemiol Biomarkers Prev 18:444-53. 2009
    ..Further investigation and validation of the cancer-associated profiles may reveal important biomarkers for the noninvasive detection and surveillance of bladder cancer...
  19. pmc The Arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways
    Xudong Zhang
    Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
    Plant Cell 24:4294-309. 2012
    ....
  20. pmc Fecal microbiota in premature infants prior to necrotizing enterocolitis
    Volker Mai
    Department of Microbiology and Cell Sciences and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
    PLoS ONE 6:e20647. 2011
    ..Our observations suggest that abnormal patterns of microbiota and potentially a novel pathogen contribute to the etiology of NEC...