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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 ...

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 ...

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 ...

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 ...