Yuanxin Xi

Summary

Affiliation: Baylor College of Medicine
Country: USA

Publications

  1. pmc Improved identification of metabolites in complex mixtures using HSQC NMR spectroscopy
    Yuanxin Xi
    Department of Applied Science, University of California, Davis, Davis, CA 95616, USA
    Anal Chim Acta 614:127-33. 2008
  2. pmc BSMAP: whole genome bisulfite sequence MAPping program
    Yuanxin Xi
    Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Bioinformatics 10:232. 2009
  3. pmc Baseline correction for NMR spectroscopic metabolomics data analysis
    Yuanxin Xi
    Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
    BMC Bioinformatics 9:324. 2008
  4. pmc RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
    Yuanxin Xi
    Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Bioinformatics 28:430-2. 2012
  5. pmc DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing
    Kaifu Chen
    Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 23:341-51. 2013
  6. pmc FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis
    Xu Li
    Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Cell Rep 16:487-97. 2016
  7. pmc G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression
    Xi Zhang
    Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    Nat Commun 7:10810. 2016
  8. pmc Plasticity and epigenetic inheritance of centromere-specific histone H3 (CENP-A)-containing nucleosome positioning in the fission yeast
    Jianhui Yao
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 288:19184-96. 2013
  9. pmc Research resource: The estrogen receptor α cistrome defined by DamIP
    Rui Xiao
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Endocrinol 26:349-57. 2012
  10. pmc In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development
    Tiemo J Klisch
    Department of Molecular and Human Genetics, The Howard Hughes Medical Institute, The Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 108:3288-93. 2011

Collaborators

Detail Information

Publications19

  1. pmc Improved identification of metabolites in complex mixtures using HSQC NMR spectroscopy
    Yuanxin Xi
    Department of Applied Science, University of California, Davis, Davis, CA 95616, USA
    Anal Chim Acta 614:127-33. 2008
    ....
  2. pmc BSMAP: whole genome bisulfite sequence MAPping program
    Yuanxin Xi
    Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Bioinformatics 10:232. 2009
    ....
  3. pmc Baseline correction for NMR spectroscopic metabolomics data analysis
    Yuanxin Xi
    Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
    BMC Bioinformatics 9:324. 2008
    ..The parameters are determined automatically by using LOWESS (locally weighted scatterplot smoothing) regression to estimate the noise variance...
  4. pmc RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
    Yuanxin Xi
    Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Bioinformatics 28:430-2. 2012
    ..In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS...
  5. pmc DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing
    Kaifu Chen
    Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 23:341-51. 2013
    ....
  6. pmc FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis
    Xu Li
    Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Cell Rep 16:487-97. 2016
    ..These results indicate that FOXR2 acts with MYC to promote cancer cell proliferation, which is a potential tumor-specific target for therapeutic intervention against MYC-driven cancers. ..
  7. pmc G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression
    Xi Zhang
    Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    Nat Commun 7:10810. 2016
    ..Along with the PHF20/MOF complex, G9a links the crosstalk between ERα methylation and histone acetylation that governs the epigenetic regulation of hormonal gene expression. ..
  8. pmc Plasticity and epigenetic inheritance of centromere-specific histone H3 (CENP-A)-containing nucleosome positioning in the fission yeast
    Jianhui Yao
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 288:19184-96. 2013
    ..Together, our results reveal the plasticity and the epigenetically inheritable nature of centromeric chromatin organization. ..
  9. pmc Research resource: The estrogen receptor α cistrome defined by DamIP
    Rui Xiao
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Endocrinol 26:349-57. 2012
    ....
  10. pmc In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development
    Tiemo J Klisch
    Department of Molecular and Human Genetics, The Howard Hughes Medical Institute, The Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 108:3288-93. 2011
    ..This study expands current thinking about the transcriptional activities driving neuronal differentiation and provides a framework for further neurodevelopmental studies...
  11. pmc ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression
    Hong Wen
    1 Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA 2 Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA 3
    Nature 508:263-8. 2014
    ..Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression. ..
  12. pmc Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
    Yuanxin Xi
    Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 21:718-24. 2011
    ..We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization...
  13. pmc Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes
    Kaifu Chen
    Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
    Nat Genet 47:1149-57. 2015
    ..Thus, the broad H3K4me3 epigenetic signature provides mutation-independent information for the discovery and characterization of new tumor suppressors...
  14. pmc Dnmt3a is essential for hematopoietic stem cell differentiation
    Grant A Challen
    Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
    Nat Genet 44:23-31. 2011
    ..These data establish Dnmt3a as a critical participant in the epigenetic silencing of HSC regulatory genes, thereby enabling efficient differentiation...
  15. pmc LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56
    Abhinav K Jain
    Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Electronic address
    Mol Cell 64:967-981. 2016
    ..In summary, we describe a p53-regulated, pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity...
  16. pmc Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes
    Xu Li
    Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Mol Syst Biol 11:775. 2015
    ....
  17. pmc Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    R Alan Harris
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1097-105. 2010
    ....
  18. pmc Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to ionizing radiation in human cells
    Beom Jun Kim
    Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 285:22784-92. 2010
    ..Thus, SMC3 modifications is a mechanism for genome-wide reinforcement of cohesin binding in response to DNA damage response in human cells and enhanced cohesion is a downstream event of DDR...
  19. pmc A statistical method for the detection of alternative splicing using RNA-seq
    Liguo Wang
    Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
    PLoS ONE 5:e8529. 2010
    ..Our results were also confirmed by real time RT-PCR assay. The MMES metric can be used either in this empirical statistical model or in other more sophisticated classifiers, such as logistic regression...