Xiaoping Su

Summary

Affiliation: The University of Texas
Country: USA

Publications

  1. pmc PurityEst: estimating purity of human tumor samples using next-generation sequencing data
    Xiaoping Su
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Bioinformatics 28:2265-6. 2012
  2. pmc Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq
    Joseph D Khoury
    Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas, USA
    J Virol 87:8916-26. 2013
  3. pmc Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes
    Anthony R Flores
    Department of Pediatrics and Molecular Virology and Microbiology, MD Anderson Cancer Center, Houston, TX 77030
    Proc Natl Acad Sci U S A 112:6431-6. 2015
  4. pmc Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes
    Xiaoping Su
    Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Oncotarget 5:9864-76. 2014
  5. pmc Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrations
    Yunyun Jiang
    Department of Gynecologic Oncology and Reproductive Medicine, UT MD Anderson Cancer Center, Houston, TX, USA
    Oncotarget 6:39865-76. 2015
  6. pmc VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
    Yunxin Chen
    Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Bioinformatics 29:266-7. 2013
  7. pmc Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma
    Melissa M Singh
    Department of Pediatrics Research, University of Texas MD Anderson Cancer Center, Houston, Texas M M S, B J, J C Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas A V, E R F Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas M B, J C Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas J Z, X S Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas B J, F L Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas A V, E R F, M B, F L, J C
    Neuro Oncol 17:1463-73. 2015
  8. pmc Characterization of the effect of the histidine kinase CovS on response regulator phosphorylation in group A Streptococcus
    Nicola Horstmann
    Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
    Infect Immun 83:1068-77. 2015
  9. pmc Concordance of genomic alterations between primary and recurrent breast cancer
    Funda Meric-Bernstam
    Authors Affiliations Departments of Investigational Cancer Therapeutics, Surgical Oncology, Bioinformatics and Computational Biology, Pathology, Systems Biology, and Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas Foundation Medicine, Cambridge, Massachusetts Albany Medical College, Albany, New York Fundacion para la Investigacion Departments of Hematology Oncology and Pathology, Hospital Clinico Universitario de Valencia and INCLIVA Biomedical Research Institute, Valencia, Spain
    Mol Cancer Ther 13:1382-9. 2014
  10. pmc Genomic heterogeneity of translocation renal cell carcinoma
    Gabriel G Malouf
    Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030 3721, USA
    Clin Cancer Res 19:4673-84. 2013

Collaborators

  • John N Weinstein
  • Funda Meric-Bernstam
  • Jean Philippe Spano
  • Ying Yuan
  • Ying Wang
  • Li Zhang
  • Gordon B Mills
  • Ana M Gonzalez-Angulo
  • Joseph D Khoury
  • Christopher G Wood
  • Federico A Monzon
  • Hui Yao
  • Nicola Horstmann
  • Anthony R Flores
  • Nizar M Tannir
  • Gabriel G Malouf
  • Yunxin Chen
  • Erika Thompson
  • Pranoti Sahasrabhojane
  • Yunyun Jiang
  • Melissa M Singh
  • Samuel A Shelburne
  • Nadim J Ajami
  • Jianping Zhang
  • Miguel Saldaña
  • Erika J Thompson
  • Karen H Lu
  • Immaculada Margarit y Ros
  • Chang Gong Liu
  • Guido Grandi
  • Joseph F Petrosino
  • Michael E Holder
  • Michelle Barton
  • Xiaofeng Zheng
  • Avinashnarayan Venkatarayan
  • Blake Johnson
  • Frederick Lang
  • Elsa R Flores
  • David Khayat
  • Russell Broaddus
  • Rino Rappuoli
  • Allison Mcgeer
  • Nahuel Fittipaldi
  • Sarah Teatero
  • Paul Sumby
  • Carol J Baker
  • Joya Chandra
  • Jessica Galloway-Peña
  • Roberto Rosini
  • Asha S Multani
  • Jerome Couturier
  • Marileila Garcia
  • Dolores Lopez-Terrada
  • Vincent Molinie
  • Maria Picken
  • Sen Pathak
  • Bernard Escudier
  • Philippe Camparo
  • Pheroze Tamboli

Detail Information

Publications10

  1. pmc PurityEst: estimating purity of human tumor samples using next-generation sequencing data
    Xiaoping Su
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Bioinformatics 28:2265-6. 2012
    ..We applied our tool to a whole cancer genome sequencing datasets and demonstrated the accuracy of PurityEst compared with DNA copy number-based estimation...
  2. pmc Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq
    Joseph D Khoury
    Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas, USA
    J Virol 87:8916-26. 2013
    ....
  3. pmc Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes
    Anthony R Flores
    Department of Pediatrics and Molecular Virology and Microbiology, MD Anderson Cancer Center, Houston, TX 77030
    Proc Natl Acad Sci U S A 112:6431-6. 2015
    ..These data reveal that phenotypic diversity among ST-1 GBS is mainly driven by small genetic changes rather than extensive recombination, thereby extending knowledge into how pathogens adapt to humans. ..
  4. pmc Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes
    Xiaoping Su
    Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Oncotarget 5:9864-76. 2014
    ..In summary, our study depicts the first lncRNA subtype classification in breast cancer and provides the framework for future studies to assess the interplay between lncRNAs and the breast cancer epigenome. ..
  5. pmc Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrations
    Yunyun Jiang
    Department of Gynecologic Oncology and Reproductive Medicine, UT MD Anderson Cancer Center, Houston, TX, USA
    Oncotarget 6:39865-76. 2015
    ..However, the landscape of expressed long non-coding RNAs (lncRNA) and their role in charting EEC subgroups and determining clinical aggressiveness remain largely unknown...
  6. pmc VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
    Yunxin Chen
    Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Bioinformatics 29:266-7. 2013
    ..Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue...
  7. pmc Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma
    Melissa M Singh
    Department of Pediatrics Research, University of Texas MD Anderson Cancer Center, Houston, Texas M M S, B J, J C Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas A V, E R F Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas M B, J C Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas J Z, X S Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas B J, F L Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas A V, E R F, M B, F L, J C
    Neuro Oncol 17:1463-73. 2015
    ..We also investigated the changes in transcriptional programing induced by the combination in an effort to understand the induced molecular mechanisms of GBM cell death...
  8. pmc Characterization of the effect of the histidine kinase CovS on response regulator phosphorylation in group A Streptococcus
    Nicola Horstmann
    Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
    Infect Immun 83:1068-77. 2015
    ....
  9. pmc Concordance of genomic alterations between primary and recurrent breast cancer
    Funda Meric-Bernstam
    Authors Affiliations Departments of Investigational Cancer Therapeutics, Surgical Oncology, Bioinformatics and Computational Biology, Pathology, Systems Biology, and Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas Foundation Medicine, Cambridge, Massachusetts Albany Medical College, Albany, New York Fundacion para la Investigacion Departments of Hematology Oncology and Pathology, Hospital Clinico Universitario de Valencia and INCLIVA Biomedical Research Institute, Valencia, Spain
    Mol Cancer Ther 13:1382-9. 2014
    ..Overall there was high concordance between primary and recurrent tumors. Analysis of recurrent tumors before treatment may provide additional insights, as both gains and losses of targets are observed...
  10. pmc Genomic heterogeneity of translocation renal cell carcinoma
    Gabriel G Malouf
    Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030 3721, USA
    Clin Cancer Res 19:4673-84. 2013
    ..Translocation renal cell carcinoma (tRCC) is a rare subtype of kidney cancer involving the TFEB/TFE3 genes. We aimed to investigate the genomic and epigenetic features of this entity...