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Michael F. Ochs
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Journal Articles

Abstract 3577: Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer

Bahman Afsari, Theresa Guo, Michael Considine, Dylan Kelley, Emily Flam, Liliana Florea, Patrick Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana J. Fertig
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 3577.
https://doi.org/10.1158/1538-7445.AM2017-3577
Published: 01 July 2017
View articletitled, Abstract 3577: Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer
Journal Articles

Abstract 777: The CoGAPS matrix factorization algorithm infers feedback mechanisms from therapeutic inhibition of EGFR that increases expression of growth factor receptors

Elana J. Fertig, Hiroyuki Ozawa, Manjusha Thakar, Jason Howard, Gabriel Krigsfeld, Alexander V. Favorov, Daria A. Gaykalova, Michael F. Ochs, Christine H. Chung
Journal: Cancer Research
Cancer Res (2016) 76 (14_Supplement): 777.
https://doi.org/10.1158/1538-7445.AM2016-777
Published: 15 July 2016
View articletitled, Abstract 777: The CoGAPS matrix factorization algorithm infers feedback mechanisms from therapeutic inhibition of EGFR that increases expression of growth factor receptors
Journal Articles

Abstract 815: DTX1 is an epigenetically regulated tumor suppressor gene discovered by integrative analysis of epigenetic and transcriptional alterations in HNSCC

Daria A. Gaykalova, Veronika Zizkova, Ilse Tiscareno, Yingying Wei, Rajita Vatapalli, Patrick T. Hennessey, Julie Ahn, Ludmila V. Danilova, Zubair Khan, Justin A. Bishop, Wayne M. Koch, William H. Westra, Michael F. Ochs, Joseph A. Califano
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 815.
https://doi.org/10.1158/1538-7445.AM2015-815
Published: 01 August 2015
View articletitled, Abstract 815: DTX1 is an epigenetically regulated tumor suppressor gene discovered by integrative analysis of epigenetic and transcriptional alterations in HNSCC
Journal Articles

Abstract 3409: Transcription factor signature of head and neck squamous cell carcinoma

Daria A. Gaykalova, Judi Manola, Hiroyuki Ozawa, Kathryn Morton, Justin Bishop, Michael Considine, Rajni Sharma, Chi Zhang, Elana Fertig, Marietta Tan, Patrick Hennessey, Julie Ahn, Wayne Koch, Zubair Khan, Christine H. Chung, Michael F. Ochs, Joseph A. Califano
Journal: Cancer Research
Cancer Res (2014) 74 (19_Supplement): 3409.
https://doi.org/10.1158/1538-7445.AM2014-3409
Published: 01 October 2014
View articletitled, Abstract 3409: Transcription factor signature of head and neck squamous cell carcinoma
Journal Articles

Abstract 5583: Integrative genomic analyses on pediatric acute myeloid leukemia

Daniel H. Wai, Rhonda E. Ries, Michael Considine, David W. Lee, Sun-Mei Liu, Nicole M. O'Connor, Oliver Pepper, Ranjan Bista, Eiman Aleem, David O. Azorsa, Tanja M. Davidsen, Toni Farley, Jaime Guidry-Auvil, Jason E. Farrar, Malcolm A. Smith, Daniela S. Gerhard, MIchael F. Ochs, Spyro Mousses, Soheil Meshinchi, Robert J. Arceci
Journal: Cancer Research
Cancer Res (2014) 74 (19_Supplement): 5583.
https://doi.org/10.1158/1538-7445.AM2014-5583
Published: 01 October 2014
View articletitled, Abstract 5583: Integrative genomic analyses on pediatric acute myeloid leukemia
Journal Articles

Abstract LB-317: Interactive pipeline for reproducible genomics analyses

Michael Considine, Hilary S. Parker, Yingying Wei, Xiao X. Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
Journal: Cancer Research
Cancer Res (2014) 74 (19_Supplement): LB-317.
https://doi.org/10.1158/1538-7445.AM2014-LB-317
Published: 01 October 2014
View articletitled, Abstract LB-317: Interactive pipeline for reproducible genomics analyses
Journal Articles

Activation of the NOTCH Pathway in Head and Neck Cancer

Wenyue Sun, Daria A. Gaykalova, Michael F. Ochs, Elizabeth Mambo, Demetri Arnaoutakis, Yan Liu, Myriam Loyo, Nishant Agrawal, Jason Howard, Ryan Li, Sun Ahn, Elana Fertig, David Sidransky, Jeffery Houghton, Kalyan Buddavarapu, Tiffany Sanford, Ashish Choudhary, Will Darden, Alex Adai, Gary Latham, Justin Bishop, Rajni Sharma, William H. Westra, Patrick Hennessey, Christine H. Chung, Joseph A. Califano
Journal: Cancer Research
Series: Author Choice
Cancer Res (2014) 74 (4): 1091–1104.
https://doi.org/10.1158/0008-5472.CAN-13-1259
Published: 16 February 2014
View articletitled, Activation of the NOTCH Pathway in Head and Neck Cancer
Open the PDF for Activation of the NOTCH Pathway in Head and Neck Cancer in another window
Includes: Supplementary data
Journal Articles

Abstract 2901: An integrated matrix factorization algorithm for DNA methylation and gene expression identi es HNSCC clinical subtypes and GLI1 signaling speci c to HPV-negative HNSCC.

Elana J. Fertig, Ana Markovic, Ludmila V. Danilova, Daria A. Gaykalova, Leslie Cope, Christine H. Chung, Joseph A. Califano, Michael F. Ochs
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 2901.
https://doi.org/10.1158/1538-7445.AM2013-2901
Published: 15 April 2013
View articletitled, Abstract 2901: An integrated matrix factorization algorithm for DNA methylation and gene expression identi es HNSCC clinical subtypes and GLI1 signaling speci c to HPV-negative HNSCC.
Journal Articles

Abstract 3554: Promoter hypermethylation of zinc finger proteins is the novel epigenetic biomarkers of head and neck squamous cell carcinomas.

Daria A. Gaykalova, Rajita Vatapalli, Yingying Wei, Hao Wang, Patrick Hennessey, Ryan Li, Chi Zhang, Marietta Tan, Zubair Khan, William Westra, Tanbir Khan, David Zaboli, Michael F. Ochs, Joseph A. Califano
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 3554.
https://doi.org/10.1158/1538-7445.AM2013-3554
Published: 15 April 2013
View articletitled, Abstract 3554: Promoter hypermethylation of zinc finger proteins is the novel epigenetic biomarkers of head and neck squamous cell carcinomas.
Journal Articles

Abstract 2166: Identification of novel epigenetically silenced genes by a global reactivation screen of prostate cancer

Ilsiya Ibragimova, Inmaculada Ibáñez de Cáceres, Amanda M. Hoffman, Tahseen Al-Saleem, Gary R. Hudes, Michael F. Ochs, Paul Cairns
Journal: Cancer Research
Cancer Res (2010) 70 (8_Supplement): 2166.
https://doi.org/10.1158/1538-7445.AM10-2166
Published: 15 April 2010
View articletitled, Abstract 2166: Identification of novel epigenetically silenced genes by a global reactivation screen of prostate cancer
Journal Articles

Detection of Treatment-Induced Changes in Signaling Pathways in Gastrointestinal Stromal Tumors Using Transcriptomic Data

Michael F. Ochs, Lori Rink, Chi Tarn, Sarah Mburu, Takahiro Taguchi, Burton Eisenberg, Andrew K. Godwin
Journal: Cancer Research
Cancer Res (2009) 69 (23): 9125–9132.
https://doi.org/10.1158/0008-5472.CAN-09-1709
Published: 30 November 2009
View articletitled, Detection of Treatment-Induced Changes in Signaling Pathways in Gastrointestinal Stromal Tumors Using Transcriptomic Data
Open the PDF for Detection of Treatment-Induced Changes in Signaling Pathways in Gastrointestinal Stromal Tumors Using Transcriptomic Data in another window
Includes: Supplementary data