Now showing items 1-4 of 4

    • AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses 

      Ochs, Michael F.; Considine, Michael; Parker, Hilary; Wei, Yingying; Xia, Xaio; Cope, Leslie; Fertig, Elana J. (F1000Research, 2015)
      Automated Genomics Analysis (AGA) is an interactive program to analyze high-throughput genomic data sets on a variety of platforms. An easy to use, point and click, guided pipeline is implemented to combine, define, and ...
    • Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC 

      Ochs, Michael F.; Gaykalova, Daria A.; Zizkova, Veronika; Guo, Theresa; Tiscareno, Ilse; Wei, Yingying; Vatapalli, Rajita; Hennessey, Patrick T.; Ahn, Julie; Danilova, Ludmila V.; Khan, Zubair; Bishop, Justin A.; Gutkind, J. Silvio; Koch, Wayne M.; Westra, William H.; Fertig, Elana J.; Califano, Joseph A. (Impact Journals, 2017)
      Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have ...
    • Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery 

      Ochs, Michael F.; Farrar, Jason E.; Considine, Michael; Wei, Yingying; Meshinchi, Soheil; Arceci, Robert J. (Institute of Electrical and Electronics Engineers, 2013)
      Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, ...
    • Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients 

      Gaykalova, Daria A.; Vatapalli, Rajita; Wei, Yingying; Tsai, Hua-Ling; Wang, Hao; Zhang, Chi; Hennessey, Patrick T.; Guo, Theresa; Tan, Marietta; Li, Ryan; Ahn, Julie; Khan, Zubair; Westra, William H.; Bishop, Justin A.; Zaboli, David; Koch, Wayne M.; Khan, Tanbir; Ochs, Michael F.; Califano, Joseph A. (Public Library of Science, 2015)
      Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance ...