Now showing items 1-14 of 14

    • Activation of the NOTCH Pathway in Head and Neck Cancer 

      Ochs, Michael F.; Gaykalova, Daria A.; Sun, Wenyue; Mambo, Elizabeth; Arnaoutakis, Demetri; Liu, Yan; Loyo, Myriam; Agrawal, Nishant; Howard, Jason D.; Li, Ryan; Ahn, Sun Mi; Fertig, Elana J.; Sidransky, David; Houghton, Jeffery; Buddavarapu, Kalyan; Sanford, Tiffany; Choudhary, Ashish; Darden, Will; Adai, Alex; Latham, Gary; Bishop, Justin A.; Sharma, Rajni; Westra, William H.; Hennessey, Patrick T.; Chung, Christine H.; Califano, Joseph A. (American Association for Cancer Research, 2014)
      NOTCH1 mutations have been reported to occur in 10% to 15% of head and neck squamous cell carcinomas (HNSCC). To determine the significance of these mutations, we embarked upon a comprehensive study of NOTCH signaling in ...
    • 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 ...
    • CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network 

      Ochs, Michael F.; Fertig, Elana J.; Ozawa, Hiroyuki; Thakar, Manjusha; Howard, Jason D.; Kagohara, Luciane T.; Krigsfeld, Gabriel; Ranaweera, Ruchira S.; Hughes, Robert M.; Perez, Jimena; Jonaes, Siân; Favorov, Alexander V.; Carey, Jacob L.; Stein-O'Brien, Genevieve L.; Gaykalova, Daria A.; Chung, Christine H. (Impact Journals, 2016)
      Patients with oncogene driven tumors are treated with targeted therapeutics including EGFR inhibitors. Genomic data from The Cancer Genome Atlas (TCGA) demonstrates molecular alterations to EGFR, MAPK, and PI3K pathways ...
    • CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data 

      Fertig, Elana J.; Ding, Jie; Favorov, Alexander V.; Parmigiani, Giovanni; Ochs, Michael F. (Oxford University Press, 2010)
      Coordinated Gene Activity in Pattern Sets (CoGAPS) provides an integrated package for isolating gene expression driven by a biological process, enhancing inference of biological processes from transcriptomic data. CoGAPS ...
    • Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma 

      Ochs, Michael F.; Li, Ryan; Ahn, Sun Mi; Hennessey, Patrick T.; Tan, Marietta; Soudry, Ethan; Gaykalova, Daria A.; Uemura, Mamoru; Brait, Mariana; Shao, Chunbo; Westra, William H.; Bishop, Justin A.; Fertig, Elana J.; Califano, Joseph A. (Public Library of Science, 2014)
      Purpose Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma ...
    • Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma 

      Ochs, Michael F.; Fertig, Elana J.; Ren, Qing; Cheng, Haxia; Hatakeyama, Hiromitsu; Dicker, Adam P.; Rodeck, Ulrich; Considine, Michael; Chung, Christine H. (BioMed Central, 2012)
      Background Aberrant activation of signaling pathways downstream of epidermal growth factor receptor (EGFR) has been hypothesized to be one of the mechanisms of cetuximab (a monoclonal antibody against EGFR) resistance in ...
    • Hybrid modeling of cell signaling and transcriptional reprogramming and its application in C. elegans development 

      Ochs, Michael F.; Danilova, Ludmila V.; Favorov, Alexander V.; Fertig, Elana J. (Frontiers Media, 2011)
      Modeling of signal driven transcriptional reprogramming is critical for understanding of organism development, human disease, and cell biology. Many current modeling techniques discount key features of the biological ...
    • Identifying context-specific transcription factor targets from prior knowledge and gene expression data 

      Fertig, Elana J.; Favorov, Alexander V.; Ochs, Michael F. (Institute of Electrical and Electronics Engineers, 2013)
      Numerous methodologies, assays, and databases presently provide candidate targets of transcription factors (TFs). However, TFs rarely regulate their targets universally. The context of activation of a TF can change the ...
    • 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 ...
    • NF‐κB and stat3 transcription factor signatures differentiate HPV‐positive and HPV‐negative head and neck squamous cell carcinoma 

      Gaykalova, Daria A.; Manola, Judith B.; Ozawa, Hiroyuki; Zizkova, Veronika; Morton, Kathryn; Bishop, Justin A.; Sharma, Rajni; Zhang, Chi; Michailidi, Christina; Considine, Michael; Tan, Marietta; Fertig, Elana J.; Hennessey, Patrick T.; Ahn, Julie; Koch, Wayne M.; Westra, William H.; Khan, Zubair; Chung, Christine H.; Ochs, Michael F.; Califano, Joseph A. (Wiley, 2015)
      Using high-throughput analyses and the TRANSFAC database, we characterized TF signatures of head and neck squamous cell carcinoma (HNSCC) subgroups by inferential analysis of target gene expression, correcting for the ...
    • PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF 

      Ochs, Michael F.; Stein-O'Brien, Genevieve L.; Carey, Jacob L.; Lee, Wai Shing; Considine, Michael; Favorov, Alexander V.; Flam, Emily; Guo, Theresa; Li, Sijia; Marchionni, Luigi; Sherman, Thomas; Sivy, Shawn; Gaykalova, Daria A.; McKay, Ronald D.; Colantuoni, Carlo; Fertig, Elana J. (Oxford University Press, 2017)
      Non-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g. time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF ...
    • Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis 

      Ochs, Michael F.; Fertig, Elana J.; Markovic, Ana; Danilova, Ludmila V.; Gaykalova, Daria A.; Cope, Leslie; Chung, Christine H.; Califano, Joseph A. (Public Library of Science, 2013)
      Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and –negative. Global DNA methylation changes are known to drive oncogene and ...
    • Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer 

      Ochs, Michael F.; Bahman, Asfari; Guo, Theresa; Considine, Michael; Florea, Liliana; Kagohara, Luciane T.; Stein-O'Brien, Genevieve L.; Kelley, Dylan; Flam, Emily; Zambo, Kristina; Ha, Patrick K.; German, Donald; Califano, Joseph A.; Gaykalova, Daria A.; Favorov, Alexander V.; Fertig, Elana J. (Oxford University Press, 2018)
      Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in ...
    • Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination 

      Ochs, Michael F.; Stansfield, John C.; Rusay, Matthew; Shan, Roger; Kelton, Conor; Gaykalova, Daria A.; Fertig, Elana J.; Califano, Joseph A. (Libertas Academica, 2016)
      The goal of this study was to discover a minimally invasive pathway-specific biomarker that is immune to normal cell mRNA contamination for diagnosing head and neck squamous cell carcinoma (HNSCC). Using Elsevier's MedScan ...