Affiliation: The University of Texas
- PurityEst: estimating purity of human tumor samples using next-generation sequencing dataXiaoping 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...
- Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-SeqJoseph D Khoury
Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas, USA
J Virol 87:8916-26. 2013....
- Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changesAnthony 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. ..
- Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypesXiaoping 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. ..
- Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrationsYunyun 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...
- VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissueYunxin 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...
- Preclinical activity of combined HDAC and KDM1A inhibition in glioblastomaMelissa 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...
- Characterization of the effect of the histidine kinase CovS on response regulator phosphorylation in group A StreptococcusNicola Horstmann
Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
Infect Immun 83:1068-77. 2015....
- Concordance of genomic alterations between primary and recurrent breast cancerFunda 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...
- Genomic heterogeneity of translocation renal cell carcinomaGabriel 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...