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....
- 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. ..
- 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...
- 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...