Yuanyuan Xiao

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Prediction of genomewide conserved epitope profiles of HIV-1: classifier choice and peptide representation
    Yuanyuan Xiao
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 4:Article25. 2005
  2. ncbi request reprint Stepwise normalization of two-channel spotted microarrays
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 4:Article4. 2005
  3. pmc Assessment of differential gene expression in human peripheral nerve injury
    Yuanyuan Xiao
    Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
    BMC Genomics 3:28. 2002
  4. ncbi request reprint A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94107, USA
    Bioinformatics 23:1459-67. 2007
  5. pmc Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology
    Terri Rice
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94107, USA
    Neuro Oncol 15:535-41. 2013
  6. pmc Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies
    Kyle M Walsh
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
    Genet Epidemiol 37:222-8. 2013
  7. pmc Identification of yeast transcriptional regulation networks using multivariate random forests
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, California, USA
    PLoS Comput Biol 5:e1000414. 2009
  8. pmc PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia
    Jianqiao Xiao
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
    Int J Cancer 135:1101-9. 2014
  9. ncbi request reprint Identifying differentially expressed genes from microarray experiments via statistic synthesis
    Yee Hwa Yang
    Departments of Medicine, Center for Bioinformatics and Molecular Biostatistics, University of California San Francisco, CA 94143, USA
    Bioinformatics 21:1084-93. 2005
  10. pmc A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network
    Seung Tae Lee
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
    Nucleic Acids Res 40:11339-51. 2012

Collaborators

Detail Information

Publications21

  1. ncbi request reprint Prediction of genomewide conserved epitope profiles of HIV-1: classifier choice and peptide representation
    Yuanyuan Xiao
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 4:Article25. 2005
    ..Once again, amino acid sequence representation was at least as effective as using properties. Assessment of novel epitope predictions awaits experimental verification...
  2. ncbi request reprint Stepwise normalization of two-channel spotted microarrays
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 4:Article4. 2005
    ..In addition, we evaluate the effectiveness of STEPNORM and other commonly used normalization methods utilizing a set of specially constructed splicing arrays...
  3. pmc Assessment of differential gene expression in human peripheral nerve injury
    Yuanyuan Xiao
    Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
    BMC Genomics 3:28. 2002
    ....
  4. ncbi request reprint A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94107, USA
    Bioinformatics 23:1459-67. 2007
    ..Affymetrix SNP arrays, e.g. use multiple sets of short oligonucleotide probes for each known SNP, and require effective statistical methods to combine these probe intensities in order to generate reliable and accurate genotype calls...
  5. pmc Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology
    Terri Rice
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94107, USA
    Neuro Oncol 15:535-41. 2013
    ..Because the inherited variant in 11q23 has been associated with risk of lower grade glioma and not with glioblastomas, we hypothesized that this variant increases susceptibility to IDH-mutated gliomas, but not to IDH-wild-type gliomas...
  6. pmc Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies
    Kyle M Walsh
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
    Genet Epidemiol 37:222-8. 2013
    ..These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes...
  7. pmc Identification of yeast transcriptional regulation networks using multivariate random forests
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, California, USA
    PLoS Comput Biol 5:e1000414. 2009
    ..These include intriguing instances of differing motif dosages and differing combinatorial motif control that promote regulatory specificity in rRNA metabolism under differing physiological processes...
  8. pmc PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia
    Jianqiao Xiao
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
    Int J Cancer 135:1101-9. 2014
    ..Evidence for additional roles for PTPR family member genes is also suggested. This provides a potential therapeutic target for RAS-related leukemias as well as insight into childhood ALL etiology and pathophysiology. ..
  9. ncbi request reprint Identifying differentially expressed genes from microarray experiments via statistic synthesis
    Yee Hwa Yang
    Departments of Medicine, Center for Bioinformatics and Molecular Biostatistics, University of California San Francisco, CA 94143, USA
    Bioinformatics 21:1084-93. 2005
    ..We further evaluate performance on one other microarray study...
  10. pmc A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network
    Seung Tae Lee
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
    Nucleic Acids Res 40:11339-51. 2012
    ....
  11. doi request reprint Clustering with exclusion zones: genomic applications
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, CA 94107, USA
    Biostatistics 12:234-46. 2011
    ..In several instances, dramatic changes to unadjusted inference that does not accommodate exclusions are evidenced...
  12. pmc Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility
    Margaret Wrensch
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
    Nat Genet 41:905-8. 2009
    ..85 x 10(-10). On 20q13.3, rs6010620 intronic to RTEL1 had discovery P = 1.5 x 10(-7), replication P = 0.00035 and combined P = 3.40 x 10(-9). For both SNPs, the direction of association was the same in discovery and replication phases...
  13. pmc Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans
    Helen M Hansen
    Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
    Hum Mol Genet 19:3652-61. 2010
    ..002). The identified regions contain SNPs predicted to affect gene regulation. There are multiple lung cancer risk loci in the 15q25.1 region in African-Americans...
  14. doi request reprint Biological sequence classification utilizing positive and unlabeled data
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94107, USA
    Bioinformatics 24:1198-205. 2008
    ..Traditional two-class classification methods do not effectively handle such data...
  15. pmc Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors
    Laura A Petrillo
    Department of Medicine, University of California, San Francisco, CA 94115, USA
    Breast Cancer Res Treat 135:913-22. 2012
    ..Xenograft tumors' gene expression faithfully resembles that of their parent tumors, yet also demonstrates a shift toward more aggressive molecular features...
  16. pmc SSBP2 variants are associated with survival in glioblastoma patients
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, University of California, San Francisco 185 Berry St, Suite 5700, San Francisco, CA 94107, USA
    Clin Cancer Res 18:3154-62. 2012
    ..Glioblastoma is a devastating, incurable disease with few known prognostic factors. Here, we present the first genome-wide survival and validation study for glioblastoma...
  17. pmc Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, California, United States of America
    PLoS Comput Biol 1:e39. 2005
    ..Our results suggest that the Spt4-Spt5 complex may help coordinate splicing with transcription under conditions that present kinetic challenges to spliceosome assembly or function...
  18. pmc Direct and indirect targets of the E2A-PBX1 leukemia-specific fusion protein
    Christofer Diakos
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America Department of Pediatrics, St Anna Children s Hospital, Medical University of Vienna, Vienna, Austria
    PLoS ONE 9:e87602. 2014
    ..These findings may also provide evidence of potentially attractive therapeutic targets. ..
  19. pmc Analysis of pharmacogenetic traits in two distinct South African populations
    Ogechi Ikediobi
    University of California, San Francisco, School of Pharmacy, Department of Clinical Pharmacy, CA 94143, USA
    Hum Genomics 5:265-82. 2011
    ..Characterising the Xhosa and CMA population frequencies of variant alleles important for drug transport and metabolism can help to establish the clinical relevance of pharmacogenetic testing in these populations...
  20. pmc TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a
    Christofer Diakos
    Laboratory for Molecular Epidemiology, University of California, San Francisco, San Francisco, CA, USA
    Blood 116:4885-93. 2010
    ..In summary our data suggest that TEL-AML1 might exert its antiapoptotic action at least in part by suppressing miRNA-494 and miRNA-320a, lowering their expression causing enhanced survivin expression...
  21. ncbi request reprint Plasticity of gene expression in injured human dorsal root ganglia revealed by GeneChip oligonucleotide microarrays
    Douglas Rabert
    Neurobiology Unit, Roche Bioscience, Palo Alto, CA, USA
    J Clin Neurosci 11:289-99. 2004
    ..This study represents an important step in identifying new genes and molecular mechanisms in human DRG, with potential therapeutic relevance for nerve repair and relief of chronic neuropathic pain...