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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...