Yang Xie

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. pmc Statistical methods of background correction for Illumina BeadArray data
    Yang Xie
    Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, USA
    Bioinformatics 25:751-7. 2009
  2. pmc A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data
    Yang Xie
    Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Stat Med 29:489-503. 2010
  3. pmc Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation
    Di Cai
    Division of Translational Research, Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Cancer Res 70:6477-85. 2010
  4. pmc SMAC mimetic (JP1201) sensitizes non-small cell lung cancers to multiple chemotherapy agents in an IAP-dependent but TNF-α-independent manner
    Rachel M Greer
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Cancer Res 71:7640-8. 2011
  5. pmc Knockdown of oncogenic KRAS in non-small cell lung cancers suppresses tumor growth and sensitizes tumor cells to targeted therapy
    Noriaki Sunaga
    Hamon Center for Therapeutic Oncology Research, Simmons Cancer Center, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
    Mol Cancer Ther 10:336-46. 2011
  6. pmc Probe mapping across multiple microarray platforms
    Jeffrey D Allen
    UT Southwestern Medical Center, Dallas, TX 75390, USA
    Brief Bioinform 13:547-54. 2012
  7. pmc Cytoplasmic TRADD confers a worse prognosis in glioblastoma
    Sharmistha Chakraborty
    Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
    Neoplasia 15:888-97. 2013
  8. pmc Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy
    Liang Hao Ding
    Department of Radiation Oncology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
    BMC Genomics 14:372. 2013
  9. pmc Socioeconomic disparities in lung cancer treatment and outcomes persist within a single academic medical center
    Jeffrey T Yorio
    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
    Clin Lung Cancer 13:448-57. 2012
  10. pmc A novel approach to DNA copy number data segmentation
    Siling Wang
    Department of Computer Science and Engineering, Southern Methodist University, Dallas, Texas 75205, USA
    J Bioinform Comput Biol 9:131-48. 2011

Research Grants

Collaborators

Detail Information

Publications44

  1. pmc Statistical methods of background correction for Illumina BeadArray data
    Yang Xie
    Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, USA
    Bioinformatics 25:751-7. 2009
    ..However, the analysis methods for Illumina BeadArrays are far behind those for Affymetrix oligonucleotide arrays, and so need to be improved...
  2. pmc A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data
    Yang Xie
    Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Stat Med 29:489-503. 2010
    ....
  3. pmc Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation
    Di Cai
    Division of Translational Research, Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Cancer Res 70:6477-85. 2010
    ..Taken together, these data suggest that SRC-3 may be an important oncogene and therapeutic target for lung cancer...
  4. pmc SMAC mimetic (JP1201) sensitizes non-small cell lung cancers to multiple chemotherapy agents in an IAP-dependent but TNF-α-independent manner
    Rachel M Greer
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Cancer Res 71:7640-8. 2011
    ....
  5. pmc Knockdown of oncogenic KRAS in non-small cell lung cancers suppresses tumor growth and sensitizes tumor cells to targeted therapy
    Noriaki Sunaga
    Hamon Center for Therapeutic Oncology Research, Simmons Cancer Center, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
    Mol Cancer Ther 10:336-46. 2011
    ..Our findings suggest that targeting oncogenic KRAS by itself will not be sufficient treatment, but may offer possibilities of combining anti-KRAS strategies with other targeted drugs...
  6. pmc Probe mapping across multiple microarray platforms
    Jeffrey D Allen
    UT Southwestern Medical Center, Dallas, TX 75390, USA
    Brief Bioinform 13:547-54. 2012
    ..Information on all three can be found at http://qbrc.swmed.edu/software/probemapper/...
  7. pmc Cytoplasmic TRADD confers a worse prognosis in glioblastoma
    Sharmistha Chakraborty
    Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
    Neoplasia 15:888-97. 2013
    ..Thus, our study suggests that increased expression of cytoplasmic TRADD is both an important biomarker and a key driver of NF-κB activation in GBM and supports an oncogenic role for TRADD in GBM...
  8. pmc Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy
    Liang Hao Ding
    Department of Radiation Oncology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
    BMC Genomics 14:372. 2013
    ....
  9. pmc Socioeconomic disparities in lung cancer treatment and outcomes persist within a single academic medical center
    Jeffrey T Yorio
    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
    Clin Lung Cancer 13:448-57. 2012
    ..To explore whether these differences are secondary to individual or institutional characteristics, we examined treatment selection and outcome in a diverse population treated at a single medical center...
  10. pmc A novel approach to DNA copy number data segmentation
    Siling Wang
    Department of Computer Science and Engineering, Southern Methodist University, Dallas, Texas 75205, USA
    J Bioinform Comput Biol 9:131-48. 2011
    ..Empirical results show that our method achieves better accuracies on average as compared to three previous methods, namely Circular Binary Segmentation, Hidden Markov Model and Ultrasome...
  11. ncbi request reprint Influence of medical comorbidities on the presentation and outcomes of stage I-III non-small-cell lung cancer
    Daniel H Ahn
    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
    Clin Lung Cancer 14:644-50. 2013
    ..To determine whether medical comorbidities account for these observations, we incorporated a validated medical comorbidity index into an analysis of patients diagnosed with stage I to III NSCLC...
  12. pmc Histone deacetylase inhibitor romidepsin enhances anti-tumor effect of erlotinib in non-small cell lung cancer (NSCLC) cell lines
    Wei Zhang
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
    J Thorac Oncol 4:161-6. 2009
    ..In this study, we examined the effects of the histone deacetylase inhibitor, romidepsin, in combination with erlotinib, in NSCLC cell lines and xenografts...
  13. pmc Predictors and impact of second-line chemotherapy for advanced non-small cell lung cancer in the United States: real-world considerations for maintenance therapy
    David E Gerber
    Department of Internal Medicine, Harold C Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
    J Thorac Oncol 6:365-71. 2011
    ..We, therefore, determined the predictors and impact of second-line chemotherapy administration in a contemporary, diverse NSCLC population...
  14. ncbi request reprint Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data
    Yang Xie
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
    Stat Med 26:2258-75. 2007
    ..This method can also be used to incorporate other information, such as gene ontology (GO), to microarray data analysis to detect differentially expressed genes...
  15. pmc Consent timing and experience: modifiable factors that may influence interest in clinical research
    David E Gerber
    University of Texas Southwestern Medical Center, Dallas, TX
    J Oncol Pract 8:91-6. 2012
    ..However, few studies have examined factors related to the consent process. We therefore evaluated the impact of consent timing and experience on markers of patient interest in research...
  16. pmc Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients
    Yang Xie
    Department of Clinical Sciences, Simmons Cancer Center, Internal Medicine, Pharmacology, and Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX, USA
    Clin Cancer Res 17:5705-14. 2011
    ....
  17. ncbi request reprint A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
    Yang Xie
    Division of Biostatistics, School of Public Health, University of Minnesota Minneapolis, MN 55455, USA
    Bioinformatics 21:4280-8. 2005
    ..Second, we propose a simple modification of the standard permutation to yield a better FDR estimator, which can in turn serve as a more fair criterion to evaluate various statistical methods...
  18. pmc Nuclear receptor expression defines a set of prognostic biomarkers for lung cancer
    Yangsik Jeong
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
    PLoS Med 7:e1000378. 2010
    ....
  19. ncbi request reprint Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens
    Rui Zhong
    Quantitative Biomedical Research Center, Dallas, TX, USA Department of Clinical Sciences, Dallas, TX, USA
    Nucleic Acids Res 42:8214-22. 2014
    ..A public-access graphical-user-interface has been constructed to facilitate application of this algorithm. ..
  20. pmc A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small cell lung cancer patients
    Hao Tang
    Quantitative Biomedical Research Center, Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Clin Cancer Res 19:1577-86. 2013
    ..In this study, we aim to develop and validate a functional gene set that predicts the clinical benefits of ACT in NSCLC...
  21. doi request reprint Detection of epigenetic changes using ANOVA with spatially varying coefficients
    Xiao Guanghua
    Division of Biostatistics, Department of Clinical Sciences, The University of Texas Southwestern Medical Center at Dallas, TX 75390, USA
    Stat Appl Genet Mol Biol 12:189-205. 2013
    ..In addition, it can provide biologically meaningful results...
  22. ncbi request reprint A multicenter phase II study of cisplatin, pemetrexed, and bevacizumab in patients with advanced malignant mesothelioma
    Jonathan E Dowell
    Division of Hematology Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390 8852, USA
    Lung Cancer 77:567-71. 2012
    ..We evaluated the addition of bevacizumab to cisplatin and pemetrexed as first-line treatment in patients with advanced, unresectable MM...
  23. pmc Comparing statistical methods for constructing large scale gene networks
    Jeffrey D Allen
    University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
    PLoS ONE 7:e29348. 2012
    ....
  24. pmc Looking beyond surveillance, epidemiology, and end results: patterns of chemotherapy administration for advanced non-small cell lung cancer in a contemporary, diverse population
    Drew W Rasco
    Department of Internal Medicine Hematology Oncology, Harold C Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390 8852, USA
    J Thorac Oncol 5:1529-35. 2010
    ..Therefore, we determined the use of chemotherapy in a contemporary, diverse NSCLC population encompassing all patient ages...
  25. pmc SbacHTS: spatial background noise correction for high-throughput RNAi screening
    Rui Zhong
    Quantitative Biomedical Research Center, Department of Clinical Science, Harold C Simmons Comprehensive Cancer Center and Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Bioinformatics 29:2218-20. 2013
    ..Correcting these position effects can substantially improve measurement accuracy and screening success...
  26. ncbi request reprint Lung cancer diagnostic and treatment intervals in the United States: a health care disparity?
    Jeffrey T Yorio
    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 8852, USA
    J Thorac Oncol 4:1322-30. 2009
    ..We therefore studied the timing of lung cancer diagnosis and treatment at a U.S. medical center providing care to a diverse patient population within two different hospital systems...
  27. pmc Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology
    Liang Hao Ding
    Simmons Comprehensive Cancer Center Genomics Core Facility, Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Nucleic Acids Res 36:e58. 2008
    ..We conclude that MBCB is a robust background correction method that will lead to more precise determination of gene expression and better biological interpretation of Illumina BeadArray data...
  28. pmc Differential methylation of a short CpG-rich sequence within exon 1 of TCF21 gene: a promising cancer biomarker assay
    Narayan Shivapurkar
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Cancer Epidemiol Biomarkers Prev 17:995-1000. 2008
    ..We further showed similar applications with multiple other malignancies. Our assay might have important implications in early detection and surveillance of multiple malignancies...
  29. pmc Using functional signature ontology (FUSION) to identify mechanisms of action for natural products
    Malia B Potts
    1Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Sci Signal 6:ra90. 2013
    ..Thus, this approach may be an effective method for screening new drugs while simultaneously identifying their targets. ..
  30. pmc Detection of candidate tumor driver genes using a fully integrated Bayesian approach
    Jichen Yang
    Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, U S A
    Stat Med 33:1784-800. 2014
    ..Copyright © 2013 John Wiley & Sons, Ltd. ..
  31. doi request reprint Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies
    Tina W Han
    Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390 9152, USA
    Cell 149:768-79. 2012
    ..Phosphorylation of the LC domain of FUS prevented hydrogel retention, offering a conceptual means of dynamic, signal-dependent control of RNA granule assembly...
  32. ncbi request reprint Development of methods for quantitative comparison of pooled shRNAs by mass sequencing
    Hirotoshi Hoshiyama
    Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390 9039, USA
    J Biomol Screen 17:258-65. 2012
    ..These improvements should permit half-hairpin sequencing to analyze either dropout screens or selective pooled shRNA screens of limited stringency to analyze phenotypes not accessible in transient experiments...
  33. pmc Aldehyde dehydrogenase activity selects for lung adenocarcinoma stem cells dependent on notch signaling
    James P Sullivan
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA
    Cancer Res 70:9937-48. 2010
    ..Therapeutic targeting of the Notch pathway reduces this ALDH(+) component, implicating Notch signaling in lung cancer stem cell maintenance...
  34. pmc The receptor interacting protein 1 inhibits p53 induction through NF-kappaB activation and confers a worse prognosis in glioblastoma
    Seongmi Park
    Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 8813, USA
    Cancer Res 69:2809-16. 2009
    ..Importantly, RIP1 levels correlate strongly with mdm2 levels in glioblastoma. Our results show a key interaction between the NF-kappaB and p53 pathways that may have implications for the targeted treatment of glioblastoma...
  35. pmc 27-Hydroxycholesterol promotes cell-autonomous, ER-positive breast cancer growth
    Qian Wu
    Department of Pediatrics, Division of Pulmonary and Vascular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Cell Rep 5:637-45. 2013
    ..Moreover, 27HC is produced by MCF-7 cells, and it stimulates cell-autonomous, ER-dependent, and GDNF-RET-dependent cell proliferation. Thus, 27HC is a locally modulated, nonaromatized ER ligand that promotes ER+ breast tumor growth. ..
  36. pmc Functional group-based linkage analysis of gene expression trait loci
    Na Li
    Division of Biostatistics, University of Minnesota, A460 Mayo Building MMC 303, 420 Delaware Street Southeast, Minneapolis, Minnesota 55126, USA
    BMC Proc 1:S117. 2007
    ..Future research is needed to develop rigorous methods in mapping of genes affecting the expression of a group of transcripts...
  37. pmc Alterations in genes of the EGFR signaling pathway and their relationship to EGFR tyrosine kinase inhibitor sensitivity in lung cancer cell lines
    Jeet Gandhi
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
    PLoS ONE 4:e4576. 2009
    ..Mutations of EGFR (mEGFR) and copy number gains (CNGs) of EGFR (gEGFR) and HER2 (gHER2) have been reported to predict for TKI response. Mutations in KRAS (mKRAS) are associated with primary resistance to TKIs...
  38. pmc Statistical methods for integrating multiple types of high-throughput data
    Yang Xie
    Division of Biostatistics, Department of Clinical Sciences, The Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
    Methods Mol Biol 620:511-29. 2010
    ..Finally, we present some useful public access databases and program code to facilitate the integrative analysis in practice...
  39. pmc Adaptive prediction model in prospective molecular signature-based clinical studies
    Guanghua Xiao
    Authors Affiliations Quantitative Biomedical Research Center, Department of Clinical Sciences Departments of Internal Medicine and Pharmacology Simmons Cancer Center Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas and Department of Biostatistics, School of Public Health, Yale University, New Haven, Connecticut
    Clin Cancer Res 20:531-9. 2014
    ....
  40. pmc A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data
    Tao Wang
    Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
    PLoS ONE 9:e93248. 2014
    ..r-project.org/web/packages/MiClip/index.html), and a public web-based graphical user interface software (http://galaxy.qbrc.org/tool_runner?tool_id=mi_clip) for customized analysis. ..
  41. ncbi request reprint Hereditary lung cancer syndrome targets never smokers with germline EGFR gene T790M mutations
    Adi Gazdar
    Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX Department of Pathology, UT Southwestern Medical Center, Dallas, TX Cancer Genetics, Simmons Cancer Center, UT Southwestern Medical Center, Dallas, TX Department of Clinical Science and McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY Department of Thoracic Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan Department of Radiology, UT Southwestern Medical Center, Dallas, TX Department of Clinical Science and Simmons Cancer Center, UT Southwestern Medical Center, Dallas, TX Department of Cardiovascular and Thoracic Surgery, UT Southwestern Medical Center, Dallas, TX and Department of Medicine and Simmons Cancer Center, UT Southwestern Medical Center, Dallas, TX
    J Thorac Oncol 9:456-63. 2014
    ..The goal of this study was to determine the clinical features and smoking status of lung cancer cases and unaffected family members with this germline mutation and to estimate its incidence and penetrance...
  42. pmc The starvation hormone, fibroblast growth factor-21, extends lifespan in mice
    Yuan Zhang
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
    elife 1:e00065. 2012
    ..These findings raise the possibility that FGF21 can be used to extend lifespan in other species.DOI:http://dx.doi.org/10.7554/eLife.00065.001...
  43. doi request reprint The impact of consenter characteristics and experience on patient interest in clinical research
    Drew W Rasco
    Division of Hematology Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 8852, USA
    Oncologist 14:468-75. 2009
    ..However, the impact of nonphysician research personnel, who often consent patients for studies, is unclear. We therefore evaluated the association between consenter characteristics and subject interest in clinical research...
  44. pmc Cytoglobin, the newest member of the globin family, functions as a tumor suppressor gene
    Narayan Shivapurkar
    Hamon Center for Therapeutic Oncology Research, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Cancer Res 68:7448-56. 2008
    ..Our data constitute the first direct functional evidence for CYGB, the newest member of the globin family, as a tumor suppressor gene...

Research Grants1

  1. Predicting Adjuvant Chemotherapy Response in Lung Cancer
    Yang Xie; Fiscal Year: 2010
    ..The goal of this proposal is to develop a comprehensive prediction model for adjuvant chemotherapy response to assist in the clinical decision of whether an individual lung cancer patient should receive adjuvant chemotherapy or not. ..